From a.janke at gmail.com  Fri Jun  1 01:02:27 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 1 Jun 2012 15:02:27 +1000
Subject: [MINC-users] default slice min/max in mincreshape?
In-Reply-To: <CABEEk14N6P6ZqJbp7J3zub93VtVtjCWgxE0N+kuj2NHnE8FhFw@mail.gmail.com>
References: <CABEEk14N6P6ZqJbp7J3zub93VtVtjCWgxE0N+kuj2NHnE8FhFw@mail.gmail.com>
Message-ID: <CAG0CB2324SP2KiKVX1XSc5CC3uKYecw6e7UAhnGb2V59ZwXLBw@mail.gmail.com>

Hi Alex,

On 1 June 2012 13:51, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> It's easy to fix by adding -normalize to the mincreshape call; but the
> question I have is: why is the image-max for added, empty slices set
> to 1 (instead of 0 for example)? It seems to me that this may cause
> trouble for all volumes with real values much smaller than 1.

My bet for this one is definitely on a rounding error given you
combination of a very (very) small range and a byte datatype. I'd be
curious to know if the same thing happens if you first convert the
volume to float.


a

From zijdenbos at gmail.com  Fri Jun  1 11:23:02 2012
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 1 Jun 2012 11:23:02 -0400
Subject: [MINC-users] default slice min/max in mincreshape?
In-Reply-To: <CAG0CB2324SP2KiKVX1XSc5CC3uKYecw6e7UAhnGb2V59ZwXLBw@mail.gmail.com>
References: <CABEEk14N6P6ZqJbp7J3zub93VtVtjCWgxE0N+kuj2NHnE8FhFw@mail.gmail.com>
	<CAG0CB2324SP2KiKVX1XSc5CC3uKYecw6e7UAhnGb2V59ZwXLBw@mail.gmail.com>
Message-ID: <CABEEk169dAOTcXZycbi+dx_DPQMqPG2Ay=q4RRgeqKMh0URypw@mail.gmail.com>

On Fri, Jun 1, 2012 at 1:02 AM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Alex,
>
> On 1 June 2012 13:51, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
>> It's easy to fix by adding -normalize to the mincreshape call; but the
>> question I have is: why is the image-max for added, empty slices set
>> to 1 (instead of 0 for example)? It seems to me that this may cause
>> trouble for all volumes with real values much smaller than 1.
>
> My bet for this one is definitely on a rounding error given you
> combination of a very (very) small range and a byte datatype. I'd be
> curious to know if the same thing happens if you first convert the
> volume to float.

Well that works; and in fact it turns out that the byte volume is also
still correct (contains all the data). mincstats for example gives
meaningful output, and a warning:

*** mincstats - reported max (0.00048708) doesn't equal header (1)

so the problem actually (and arguably) may not be with the minc volume
itself, but with some other tools, such as mincblur, that probably
rely on the header-reported max instead of the real (data) max, and as
a result scale the very very small data values into nothingness.
Either way it still seems to me that the fundamental problem is that
mincreshape adds the blank slices with image-max=1, which is much
higher as the image-max(es) before the padding.

-- A

From trash001 at odu.edu  Fri Jun  1 19:31:25 2012
From: trash001 at odu.edu (Tanweer Rashid)
Date: Fri, 1 Jun 2012 19:31:25 -0400
Subject: [MINC-users] cannot open shared object file
Message-ID: <CAE1j2uiSes3G_wXa7PkQRq59aPfAnnsTiLY-RNV9eYMcCJHYkg@mail.gmail.com>

Hi all,

I installed minc2 and bicpl, followed by the Display and register programs,
but when I try to run either Display or register, I get the following error
message, respectively:

Display: error while loading shared libraries: libvolume_io2.so.1: cannot
open shared object file: No such file or directory
register: error while loading shared libraries: libvolume_io2.so.1: cannot
open shared object file: No such file or directory

Any ideas on why I am getting these errors? I am using Ubuntu 12.04 LTS.
I checked and I see that the I already have the libraries libminc2,
libvolume_io2 and libbicpl in the directory /usr/local/lib
The Display and register programs are in /usr/local/bin

Thanks,
-- 
Tanweer Rashid
MSVE Dept.
Old Dominion University

From a.janke at gmail.com  Fri Jun  1 19:35:21 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 2 Jun 2012 09:35:21 +1000
Subject: [MINC-users] cannot open shared object file
In-Reply-To: <CAE1j2uiSes3G_wXa7PkQRq59aPfAnnsTiLY-RNV9eYMcCJHYkg@mail.gmail.com>
References: <CAE1j2uiSes3G_wXa7PkQRq59aPfAnnsTiLY-RNV9eYMcCJHYkg@mail.gmail.com>
Message-ID: <CAG0CB20W_pN60pUYu0LjEWVkkctrm1PukJpr7qU51aB5ZY1ojg@mail.gmail.com>

Hi Tanweer,

On 2 June 2012 09:31, Tanweer Rashid <trash001 at odu.edu> wrote:
> Display: error while loading shared libraries: libvolume_io2.so.1: cannot
> open shared object file: No such file or directory
>
> Any ideas on why I am getting these errors? I am using Ubuntu 12.04 LTS.
> I checked and I see that the I already have the libraries libminc2,
> libvolume_io2 and libbicpl in the directory /usr/local/lib
> The Display and register programs are in /usr/local/bin

Have you added:

   export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib

to your .bashrc?  (and then opened a new terminal window)


a

From peter.neelin at gmail.com  Sun Jun  3 07:45:13 2012
From: peter.neelin at gmail.com (Peter Neelin)
Date: Sun, 3 Jun 2012 07:45:13 -0400
Subject: [MINC-users] default slice min/max in mincreshape?
In-Reply-To: <CABEEk14N6P6ZqJbp7J3zub93VtVtjCWgxE0N+kuj2NHnE8FhFw@mail.gmail.com>
References: <CABEEk14N6P6ZqJbp7J3zub93VtVtjCWgxE0N+kuj2NHnE8FhFw@mail.gmail.com>
Message-ID: <CANcjydZayG9b9oyUizPmDQPCJ49x3xddhk+4OV2TL2H+92aa5A@mail.gmail.com>

On May 31, 2012 11:53 PM, "Alex Zijdenbos" <zijdenbos at gmail.com> wrote:
> however when I call mincreshape on that volume to pad it, i.e., add
> empty slices, the added slices receive a max value of 1; so the
> resulting image shows, after adding 5 slices:

mincreshape is trying to avoid having a range of zero which could
potentially lead to divide by zero situations for less-than-perfect apps
reading the output file. Unfortunately, the arbitrary value that it picks
is too big for your file.

The guilty code is in progs/mincreshape/copy_data.c, function
get_block_min_and_max(). There is a block of code in there that sets
variable default_extreme to 1.0 for the maximum and 0.0 for the minimum.
This could either be changed to a much smaller number (to preserve the
original intention), or mincreshape could scan all of the min and max to
determine a file-specific default min and max (although you probably don't
want to use the global max here - probably 1% of the range or something).
Note that the choice of 0.0 for the min could also be a problem for files
that have are shifted up and have a narrow range.

Anyway, I'll leave it to you guys to figure out how you want to fix this.

Peter
--
Peter Neelin
peter.neelin at gmail.com

From a.janke at gmail.com  Mon Jun  4 02:32:24 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 4 Jun 2012 16:32:24 +1000
Subject: [MINC-users] default slice min/max in mincreshape?
In-Reply-To: <CANcjydZayG9b9oyUizPmDQPCJ49x3xddhk+4OV2TL2H+92aa5A@mail.gmail.com>
References: <CABEEk14N6P6ZqJbp7J3zub93VtVtjCWgxE0N+kuj2NHnE8FhFw@mail.gmail.com>
	<CANcjydZayG9b9oyUizPmDQPCJ49x3xddhk+4OV2TL2H+92aa5A@mail.gmail.com>
Message-ID: <CAG0CB21W7GbXw+cv5qsdWD0TeHJd=kAY_7sO1kZq3NGqnvn9aQ@mail.gmail.com>

Hi Peter (and others),

Thanks for the pointer.

> mincreshape is trying to avoid having a range of zero which could
> potentially lead to divide by zero situations for less-than-perfect apps
> reading the output file. Unfortunately, the arbitrary value that it picks
> is too big for your file.
>
> The guilty code is in progs/mincreshape/copy_data.c, function
> get_block_min_and_max(). There is a block of code in there that sets
> variable default_extreme to 1.0 for the maximum and 0.0 for the minimum.
> This could either be changed to a much smaller number (to preserve the
> original intention), or mincreshape could scan all of the min and max to
> determine a file-specific default min and max (although you probably don't
> want to use the global max here - probably 1% of the range or something).
> Note that the choice of 0.0 for the min could also be a problem for files
> that have are shifted up and have a narrow range.

I don't think the problem is quite as straight forward as the above
(although setting a smaller number will work -- and eventually break
somewhere else). The problem seems to be that nothing is defined at
the start.  If you do this:

(first make a file that will break things)

   mincreshape -dimrange zspace=50,10 /usr/local/bic/share/model.mnc /tmp/10.mnc
   mincmath -mult -const 0.000001 /tmp/10.mnc /tmp/small.mnc

Now reshape:

   mincreshape -dimrange zspace=0,40 /tmp/small.mnc /tmp/out.mnc
   mincheader /tmp/out.mnc

...

 image-min = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ;

 image-max = 1.50176742592221e-11, 1.4706592772461e-11, 1.47731739408916e-11,
    1.29191933176351e-11, 1.38217782687002e-11, 1.35282269390157e-11,
    1.30565671507807e-11, 1.26761793835777e-11, 1.26660561800091e-11,
    1.35031529091316e-11, 1.36272934702302e-11, 1.30031373028565e-11,
    1.26079339468883e-11, 1.29919927604189e-11, 1.28181591844077e-11,
    1.270971845851e-11, 1.27311934672496e-11, 1.36087412976983e-11,
    1.34799824270089e-11, 1.27816067975376e-11, 1.27816067975376e-11,
    1.27816067975376e-11, 1.27816067975376e-11, 1.27816067975376e-11,
    1.27816067975376e-11, 1.27816067975376e-11, 1.27816067975376e-11,
    1.27816067975376e-11, 1.27816067975376e-11, 1.27816067975376e-11,
    1.27816067975376e-11, 1.27816067975376e-11, 1.27816067975376e-11,
    1.27816067975376e-11, 1.27816067975376e-11, 1.27816067975376e-11,
    1.27816067975376e-11, 1.27816067975376e-11, 1.27816067975376e-11,
    1.27816067975376e-11 ;

Things are fine.

Now if you add those same slices on the front:

   mincreshape -dimrange zspace=-10,40 /tmp/small.mnc /tmp/out.mnc
   mincheader /tmp/out.mnc

   ...

 image-max = 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1.50176742592221e-11,
    1.4706592772461e-11, 1.47731739408916e-11, 1.29191933176351e-11,
    1.38217782687002e-11, 1.35282269390157e-11, 1.30565671507807e-11,
    1.26761793835777e-11, 1.26660561800091e-11, 1.35031529091316e-11,
    1.36272934702302e-11, 1.30031373028565e-11, 1.26079339468883e-11,
    1.29919927604189e-11, 1.28181591844077e-11, 1.270971845851e-11,
    1.27311934672496e-11, 1.36087412976983e-11, 1.34799824270089e-11,
    1.27816067975376e-11, 1.27816067975376e-11, 1.27816067975376e-11,
    1.27816067975376e-11, 1.27816067975376e-11, 1.27816067975376e-11,
    1.27816067975376e-11, 1.27816067975376e-11, 1.27816067975376e-11,
    1.27816067975376e-11, 1.27816067975376e-11 ;

Things break.

So to me it's a problem with an unitialised variable. The correct fix
from what I can see it to scan into the volume looking for the first
real block and using the minimum of that. This seems to be what
happens for following data but I haven't looked into things long
enough to figure out how it picks up the value from the last block.


a

From jared.rowley at gmail.com  Tue Jun  5 16:18:42 2012
From: jared.rowley at gmail.com (Jared Rowley)
Date: Tue, 5 Jun 2012 16:18:42 -0400
Subject: [MINC-users] calculating r-squared values
Message-ID: <CACHMmjMad5wA_Cz-kVrQzO9aAMs2g2E6QrAnWT-u33bK2ewLGg@mail.gmail.com>

Hi Minc Users,

I was wondering if anyone knows a way calculate R-squared values on a voxel
level from a linear regression.

I assume there is a way with either glim_image or RMINC however reading
though the documentation I could not find a solution.

Thanks very much,

Jared

From jason at phenogenomics.ca  Wed Jun  6 13:35:10 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Wed, 6 Jun 2012 13:35:10 -0400
Subject: [MINC-users] calculating r-squared values
In-Reply-To: <CACHMmjMad5wA_Cz-kVrQzO9aAMs2g2E6QrAnWT-u33bK2ewLGg@mail.gmail.com>
References: <CACHMmjMad5wA_Cz-kVrQzO9aAMs2g2E6QrAnWT-u33bK2ewLGg@mail.gmail.com>
Message-ID: <505FFB2E-64AD-4383-ADF0-7972F5155FA5@phenogenomics.ca>

This should work, though is going to be slow:

fff <- function(x) { return(summary(lm(x ~ genotype, gf))$r.squared) }

mincApply(filenames, quote(fff(x)))

Note: replace the formula in that function with the appropriate formula for your purposes, and filenames should be a vector of your filenames. Could be worth specifying a mask, as this will run for a few hours.

And I haven't actually tested it, so it might not run at all!

Jason

On 2012-06-05, at 4:18 PM, Jared Rowley wrote:

> Hi Minc Users,
> 
> I was wondering if anyone knows a way calculate R-squared values on a voxel
> level from a linear regression.
> 
> I assume there is a way with either glim_image or RMINC however reading
> though the documentation I could not find a solution.
> 
> Thanks very much,
> 
> Jared
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From Jonathan.Berken at mail.mcgill.ca  Fri Jun  8 11:15:14 2012
From: Jonathan.Berken at mail.mcgill.ca (Jonathan Berken)
Date: Fri, 8 Jun 2012 11:15:14 -0400
Subject: [MINC-users] FDR analysis for cortical thickness
Message-ID: <CAPKhXHYnDx1xkfM=gyzHt0sG9aPkW3Y3RbpqTwB8utaSPK0eoQ@mail.gmail.com>

Hello,

I was wondering if someone who is familiar with FDR analysis for cortical
thickness might be able to help me work out the script.

Thanks!

Jonathan

From jason at phenogenomics.ca  Fri Jun  8 11:19:30 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Fri, 8 Jun 2012 11:19:30 -0400
Subject: [MINC-users] FDR analysis for cortical thickness
In-Reply-To: <CAPKhXHYnDx1xkfM=gyzHt0sG9aPkW3Y3RbpqTwB8utaSPK0eoQ@mail.gmail.com>
References: <CAPKhXHYnDx1xkfM=gyzHt0sG9aPkW3Y3RbpqTwB8utaSPK0eoQ@mail.gmail.com>
Message-ID: <86D83A58-DAD8-4898-8DE8-96AF1E980788@phenogenomics.ca>

There's an implementation in mni.cortical.statistcs and RMINC as well as Keith's matlab surfstats.

The recipe in R:

1) create a vector of p-values
2) qvals <- p.adjust(pvalues, "fdr")

Jason

On 2012-06-08, at 11:15 AM, Jonathan Berken wrote:

> Hello,
> 
> I was wondering if someone who is familiar with FDR analysis for cortical
> thickness might be able to help me work out the script.
> 
> Thanks!
> 
> Jonathan
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From jared.rowley at gmail.com  Fri Jun  8 11:32:10 2012
From: jared.rowley at gmail.com (Jared Rowley)
Date: Fri, 8 Jun 2012 11:32:10 -0400
Subject: [MINC-users] calculating r-squared values
In-Reply-To: <505FFB2E-64AD-4383-ADF0-7972F5155FA5@phenogenomics.ca>
References: <CACHMmjMad5wA_Cz-kVrQzO9aAMs2g2E6QrAnWT-u33bK2ewLGg@mail.gmail.com>
	<505FFB2E-64AD-4383-ADF0-7972F5155FA5@phenogenomics.ca>
Message-ID: <CACHMmjPTtgsgdEvBDGvgggy+mQMCniDuY5vtiHV444_P6wQiWQ@mail.gmail.com>

Hi Jason,

Thanks for the response.

I did the following and got an error do you have any suggestions:

rm(list=ls(all=TRUE))
> library(RMINC)
> gf1 <- read.csv("dti_gd.csv")
> fff <- function(x) { return(summary(lm(FA ~ score, gf1))$r.squared) }
> mincApply(gf1$FA, quote(fff(x)))
Number of volumes: 91
Volume sizes: 193 229 193
In slice
 0 Error in storage.mode(y) <- "double" :
  invalid to change the storage mode of a factor
In addition: Warning message:
In model.response(mf, "numeric") :
  using type="numeric" with a factor response will be ignored

FA is a column of minc files and score is a column of integers I want to
correlate with FA.

Thanks very much,

Jared


On Wed, Jun 6, 2012 at 1:35 PM, Jason Lerch <jason at phenogenomics.ca> wrote:

> This should work, though is going to be slow:
>
> fff <- function(x) { return(summary(lm(x ~ genotype, gf))$r.squared) }
>
> mincApply(filenames, quote(fff(x)))
>
> Note: replace the formula in that function with the appropriate formula
> for your purposes, and filenames should be a vector of your filenames.
> Could be worth specifying a mask, as this will run for a few hours.
>
> And I haven't actually tested it, so it might not run at all!
>
> Jason
>
> On 2012-06-05, at 4:18 PM, Jared Rowley wrote:
>
> > Hi Minc Users,
> >
> > I was wondering if anyone knows a way calculate R-squared values on a
> voxel
> > level from a linear regression.
> >
> > I assume there is a way with either glim_image or RMINC however reading
> > though the documentation I could not find a solution.
> >
> > Thanks very much,
> >
> > Jared
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Jared Rowley
Translational Neuroimaging Laboratory
McGill Centre for Studies in Aging
Douglas Hospital Research Center
McGill University
6825 LaSalle Blvd.
Montreal, QC Canada
H4H 1R3

From francois.hebert007 at gmail.com  Fri Jun  8 11:36:01 2012
From: francois.hebert007 at gmail.com (francois hebert)
Date: Fri, 8 Jun 2012 11:36:01 -0400
Subject: [MINC-users] Maximum intensity projection
Message-ID: <CACGPbDzNPo0EOwNSKGYt7D0BtuF_cPOMG8eNFC03FNK-Ap_M5Q@mail.gmail.com>

Hi All,

I would like to do a Maximum Intensity Projection in each orthogonal axis.
Is there such tool in the minc library?

Regards,

Francois Hebert

From jason at phenogenomics.ca  Fri Jun  8 12:39:28 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Fri, 8 Jun 2012 12:39:28 -0400
Subject: [MINC-users] calculating r-squared values
In-Reply-To: <CACHMmjPTtgsgdEvBDGvgggy+mQMCniDuY5vtiHV444_P6wQiWQ@mail.gmail.com>
References: <CACHMmjMad5wA_Cz-kVrQzO9aAMs2g2E6QrAnWT-u33bK2ewLGg@mail.gmail.com>
Message-ID: <E9AFE82E-4BCD-4625-9412-14A926EA9CF7@phenogenomics.ca>

Try replacing FA with x - mincApply assigns the current voxel to the variable x in its loop. I.e.:

library(RMINC)
gf1 <- read.csv("dti_gd.csv")
fff <- function(x) { return(summary(lm(x ~ score, gf1))$r.squared) }
mincApply(gf1$FA, quote(fff(x)))

Jason

On 2012-06-08, at 11:32 AM, Jared Rowley wrote:

> Hi Jason,
> 
> Thanks for the response.
> 
> I did the following and got an error do you have any suggestions:
> 
> rm(list=ls(all=TRUE))
>> library(RMINC)
>> gf1 <- read.csv("dti_gd.csv")
>> fff <- function(x) { return(summary(lm(FA ~ score, gf1))$r.squared) }
>> mincApply(gf1$FA, quote(fff(x)))
> Number of volumes: 91
> Volume sizes: 193 229 193
> In slice
> 0 Error in storage.mode(y) <- "double" :
>  invalid to change the storage mode of a factor
> In addition: Warning message:
> In model.response(mf, "numeric") :
>  using type="numeric" with a factor response will be ignored
> 
> FA is a column of minc files and score is a column of integers I want to
> correlate with FA.
> 
> Thanks very much,
> 
> Jared
> 
> 
> On Wed, Jun 6, 2012 at 1:35 PM, Jason Lerch <jason at phenogenomics.ca> wrote:
> 
>> This should work, though is going to be slow:
>> 
>> fff <- function(x) { return(summary(lm(x ~ genotype, gf))$r.squared) }
>> 
>> mincApply(filenames, quote(fff(x)))
>> 
>> Note: replace the formula in that function with the appropriate formula
>> for your purposes, and filenames should be a vector of your filenames.
>> Could be worth specifying a mask, as this will run for a few hours.
>> 
>> And I haven't actually tested it, so it might not run at all!
>> 
>> Jason
>> 
>> On 2012-06-05, at 4:18 PM, Jared Rowley wrote:
>> 
>>> Hi Minc Users,
>>> 
>>> I was wondering if anyone knows a way calculate R-squared values on a
>> voxel
>>> level from a linear regression.
>>> 
>>> I assume there is a way with either glim_image or RMINC however reading
>>> though the documentation I could not find a solution.
>>> 
>>> Thanks very much,
>>> 
>>> Jared
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> 
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> 
> 
> 
> 
> -- 
> Jared Rowley
> Translational Neuroimaging Laboratory
> McGill Centre for Studies in Aging
> Douglas Hospital Research Center
> McGill University
> 6825 LaSalle Blvd.
> Montreal, QC Canada
> H4H 1R3
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From jason at phenogenomics.ca  Fri Jun  8 12:47:55 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Fri, 8 Jun 2012 12:47:55 -0400
Subject: [MINC-users] Maximum intensity projection
In-Reply-To: <CACGPbDzNPo0EOwNSKGYt7D0BtuF_cPOMG8eNFC03FNK-Ap_M5Q@mail.gmail.com>
References: <CACGPbDzNPo0EOwNSKGYt7D0BtuF_cPOMG8eNFC03FNK-Ap_M5Q@mail.gmail.com>
Message-ID: <029CFFCF-9BEE-4D0C-B9CA-E2884BDEEBAD@phenogenomics.ca>

This should do what you want, I think. In python:

from pyminc.volumes.factory import *
from numpy import *
import scipy

v = volumeFromFile("filename.mnc")
axis0 = apply_along_axis(max, 0, v.data)
axis1 = apply_along_axis(max, 1, v.data)
axis2 = apply_along_axis(max, 2, v.data)

# if you want to save it as an image:
scipy.misc.imsave('axis0.jpg', axis0)

Jason

On 2012-06-08, at 11:36 AM, francois hebert wrote:

> Hi All,
> 
> I would like to do a Maximum Intensity Projection in each orthogonal axis.
> Is there such tool in the minc library?
> 
> Regards,
> 
> Francois Hebert
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From mishkind at gmail.com  Fri Jun  8 14:00:22 2012
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Fri, 8 Jun 2012 14:00:22 -0400
Subject: [MINC-users] FDR analysis for cortical thickness
In-Reply-To: <86D83A58-DAD8-4898-8DE8-96AF1E980788@phenogenomics.ca>
References: <CAPKhXHYnDx1xkfM=gyzHt0sG9aPkW3Y3RbpqTwB8utaSPK0eoQ@mail.gmail.com>
	<86D83A58-DAD8-4898-8DE8-96AF1E980788@phenogenomics.ca>
Message-ID: <CAB-GmL2iv5BydSbhOBBuP1M=6r_Q-MmHMJBZVp3tFettxSWJig@mail.gmail.com>

Hi Jonathan,

At the risk of depriving you hours of endless fun coding this up
yourself, attached is my implementation using the
mni.cortical.statistics library (which you will need to install).

There is quite a bit of documentation on the bic wiki:
http://wiki.bic.mni.mcgill.ca/index.php/ThicknessStatistics

I'm at wb319 in the bic if you need help.
mishkin

p.s this is how to install the R library (using a bash shell) if you
didn't know:
1. download the mni.cortical.statistics library
2. R CMD INSTALL --library=/path/to/useful/extra/libraries/for/R/
mni.cortical.statistics
3. export R_LIBS=/path/to/useful/extra/libraries/for/R/


On Fri, Jun 8, 2012 at 11:19 AM, Jason Lerch <jason at phenogenomics.ca> wrote:
> There's an implementation in mni.cortical.statistcs and RMINC as well as Keith's matlab surfstats.
>
> The recipe in R:
>
> 1) create a vector of p-values
> 2) qvals <- p.adjust(pvalues, "fdr")
>
> Jason
>
> On 2012-06-08, at 11:15 AM, Jonathan Berken wrote:
>
>> Hello,
>>
>> I was wondering if someone who is familiar with FDR analysis for cortical
>> thickness might be able to help me work out the script.
>>
>> Thanks!
>>
>> Jonathan
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From mishkind at gmail.com  Fri Jun  8 14:35:03 2012
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Fri, 8 Jun 2012 14:35:03 -0400
Subject: [MINC-users] FDR analysis for cortical thickness
In-Reply-To: <CAPKhXHYD9D+OvjhrZ3FD9F6vs_KNkP9jtcioxgEOyWENY9OrQw@mail.gmail.com>
References: <CAPKhXHYnDx1xkfM=gyzHt0sG9aPkW3Y3RbpqTwB8utaSPK0eoQ@mail.gmail.com>
	<86D83A58-DAD8-4898-8DE8-96AF1E980788@phenogenomics.ca>
	<CAB-GmL2iv5BydSbhOBBuP1M=6r_Q-MmHMJBZVp3tFettxSWJig@mail.gmail.com>
	<CAPKhXHYD9D+OvjhrZ3FD9F6vs_KNkP9jtcioxgEOyWENY9OrQw@mail.gmail.com>
Message-ID: <CAB-GmL1iOTiDQHih8xtr9vAX255-8evvugiv6Hia4UQe0K6K=g@mail.gmail.com>

On Fri, Jun 8, 2012 at 2:06 PM, Jonathan Berken
<jonathan.berken at gmail.com> wrote:
> Hi Mishkin,
>
> Thanks so much for your help!
>
> I already have R library and have ran cortical thickness analyses... I am
> just not sure how to run the FDR analysis... I have the script from the
> site, but not sure where to get the t-values from my results to input?

So if you've ran the cortical thickness analyses, then you should have
some t-values for whatever you tested for.

In my example script, my array of t-values comes from here:
vertexstatistics <- mni.vertex.statistics(glimfile, 'y ~ group',
vertex.table=datatable)

vertexstatistics contains a lot of different items, the array of
t-values are here:
vertexstatistics\$tstatistic[,2]

The t-values represent the result of a two-tailed t-test for the test
y ~ group, which usually means you are testing for differences in
cortical thickness (y) in the different groups (ie. francophones vs.
anglophones). What 'y' and 'group' actually mean, depend on what you
put in your glim file, but if you've ran your analysis already then i
have a feeling you know this already.

> Can
> I run the FDR after I do my initial CT regression?

Sorry, but I don't actually know what you mean by initial CT
regression? I use MRI data, and I don't actually look for differences
in cortical thickness but just use the library for other vertex wise
tests that I need. Like Jason said though, the FDR can be calculated
on any array of t-values (or pvalues) that are the output of anything
you are trying to test for.

If you look at the code (in R type: 'library(mni.crotical.statistics)'
then 'mni.compute.FDR') you can see that it actually needs p-values,
but it can compute those from the given t-stats if you give it the
degrees of freedom.

>
> Jonathan
>
> On Fri, Jun 8, 2012 at 2:00 PM, Mishkin Derakhshan <mishkind at gmail.com>
> wrote:
>>
>> Hi Jonathan,
>>
>> At the risk of depriving you hours of endless fun coding this up
>> yourself, attached is my implementation using the
>> mni.cortical.statistics library (which you will need to install).
>>
>> There is quite a bit of documentation on the bic wiki:
>> http://wiki.bic.mni.mcgill.ca/index.php/ThicknessStatistics
>>
>> I'm at wb319 in the bic if you need help.
>> mishkin
>>
>> p.s this is how to install the R library (using a bash shell) if you
>> didn't know:
>> 1. download the mni.cortical.statistics library
>> 2. R CMD INSTALL --library=/path/to/useful/extra/libraries/for/R/
>> mni.cortical.statistics
>> 3. export R_LIBS=/path/to/useful/extra/libraries/for/R/
>>
>>
>> On Fri, Jun 8, 2012 at 11:19 AM, Jason Lerch <jason at phenogenomics.ca>
>> wrote:
>> > There's an implementation in mni.cortical.statistcs and RMINC as well as
>> > Keith's matlab surfstats.
>> >
>> > The recipe in R:
>> >
>> > 1) create a vector of p-values
>> > 2) qvals <- p.adjust(pvalues, "fdr")
>> >
>> > Jason
>> >
>> > On 2012-06-08, at 11:15 AM, Jonathan Berken wrote:
>> >
>> >> Hello,
>> >>
>> >> I was wondering if someone who is familiar with FDR analysis for
>> >> cortical
>> >> thickness might be able to help me work out the script.
>> >>
>> >> Thanks!
>> >>
>> >> Jonathan
>> >> _______________________________________________
>> >> MINC-users at bic.mni.mcgill.ca
>> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >
>> > _______________________________________________
>> > MINC-users at bic.mni.mcgill.ca
>> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>

From jonathan.berken at gmail.com  Fri Jun  8 14:40:04 2012
From: jonathan.berken at gmail.com (Jonathan Berken)
Date: Fri, 8 Jun 2012 14:40:04 -0400
Subject: [MINC-users] FDR analysis for cortical thickness
In-Reply-To: <CAB-GmL1iOTiDQHih8xtr9vAX255-8evvugiv6Hia4UQe0K6K=g@mail.gmail.com>
References: <CAPKhXHYnDx1xkfM=gyzHt0sG9aPkW3Y3RbpqTwB8utaSPK0eoQ@mail.gmail.com>
	<86D83A58-DAD8-4898-8DE8-96AF1E980788@phenogenomics.ca>
	<CAB-GmL2iv5BydSbhOBBuP1M=6r_Q-MmHMJBZVp3tFettxSWJig@mail.gmail.com>
	<CAPKhXHYD9D+OvjhrZ3FD9F6vs_KNkP9jtcioxgEOyWENY9OrQw@mail.gmail.com>
	<CAB-GmL1iOTiDQHih8xtr9vAX255-8evvugiv6Hia4UQe0K6K=g@mail.gmail.com>
Message-ID: <CAPKhXHZNi0CuRiUBVXc7kdOL+9hg9N_NXokNu0pX6PwdkmTz4Q@mail.gmail.com>

How do I open my list of t-values?

On Fri, Jun 8, 2012 at 2:35 PM, Mishkin Derakhshan <mishkind at gmail.com>wrote:

> On Fri, Jun 8, 2012 at 2:06 PM, Jonathan Berken
> <jonathan.berken at gmail.com> wrote:
> > Hi Mishkin,
> >
> > Thanks so much for your help!
> >
> > I already have R library and have ran cortical thickness analyses... I am
> > just not sure how to run the FDR analysis... I have the script from the
> > site, but not sure where to get the t-values from my results to input?
>
> So if you've ran the cortical thickness analyses, then you should have
> some t-values for whatever you tested for.
>
> In my example script, my array of t-values comes from here:
> vertexstatistics <- mni.vertex.statistics(glimfile, 'y ~ group',
> vertex.table=datatable)
>
> vertexstatistics contains a lot of different items, the array of
> t-values are here:
> vertexstatistics\$tstatistic[,2]
>
> The t-values represent the result of a two-tailed t-test for the test
> y ~ group, which usually means you are testing for differences in
> cortical thickness (y) in the different groups (ie. francophones vs.
> anglophones). What 'y' and 'group' actually mean, depend on what you
> put in your glim file, but if you've ran your analysis already then i
> have a feeling you know this already.
>
> > Can
> > I run the FDR after I do my initial CT regression?
>
> Sorry, but I don't actually know what you mean by initial CT
> regression? I use MRI data, and I don't actually look for differences
> in cortical thickness but just use the library for other vertex wise
> tests that I need. Like Jason said though, the FDR can be calculated
> on any array of t-values (or pvalues) that are the output of anything
> you are trying to test for.
>
> If you look at the code (in R type: 'library(mni.crotical.statistics)'
> then 'mni.compute.FDR') you can see that it actually needs p-values,
> but it can compute those from the given t-stats if you give it the
> degrees of freedom.
>
> >
> > Jonathan
> >
> > On Fri, Jun 8, 2012 at 2:00 PM, Mishkin Derakhshan <mishkind at gmail.com>
> > wrote:
> >>
> >> Hi Jonathan,
> >>
> >> At the risk of depriving you hours of endless fun coding this up
> >> yourself, attached is my implementation using the
> >> mni.cortical.statistics library (which you will need to install).
> >>
> >> There is quite a bit of documentation on the bic wiki:
> >> http://wiki.bic.mni.mcgill.ca/index.php/ThicknessStatistics
> >>
> >> I'm at wb319 in the bic if you need help.
> >> mishkin
> >>
> >> p.s this is how to install the R library (using a bash shell) if you
> >> didn't know:
> >> 1. download the mni.cortical.statistics library
> >> 2. R CMD INSTALL --library=/path/to/useful/extra/libraries/for/R/
> >> mni.cortical.statistics
> >> 3. export R_LIBS=/path/to/useful/extra/libraries/for/R/
> >>
> >>
> >> On Fri, Jun 8, 2012 at 11:19 AM, Jason Lerch <jason at phenogenomics.ca>
> >> wrote:
> >> > There's an implementation in mni.cortical.statistcs and RMINC as well
> as
> >> > Keith's matlab surfstats.
> >> >
> >> > The recipe in R:
> >> >
> >> > 1) create a vector of p-values
> >> > 2) qvals <- p.adjust(pvalues, "fdr")
> >> >
> >> > Jason
> >> >
> >> > On 2012-06-08, at 11:15 AM, Jonathan Berken wrote:
> >> >
> >> >> Hello,
> >> >>
> >> >> I was wondering if someone who is familiar with FDR analysis for
> >> >> cortical
> >> >> thickness might be able to help me work out the script.
> >> >>
> >> >> Thanks!
> >> >>
> >> >> Jonathan
> >> >> _______________________________________________
> >> >> MINC-users at bic.mni.mcgill.ca
> >> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >> >
> >> > _______________________________________________
> >> > MINC-users at bic.mni.mcgill.ca
> >> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From francois.hebert007 at gmail.com  Fri Jun  8 17:05:31 2012
From: francois.hebert007 at gmail.com (francois hebert)
Date: Fri, 8 Jun 2012 17:05:31 -0400
Subject: [MINC-users] Maximum intensity projection
In-Reply-To: <029CFFCF-9BEE-4D0C-B9CA-E2884BDEEBAD@phenogenomics.ca>
References: <CACGPbDzNPo0EOwNSKGYt7D0BtuF_cPOMG8eNFC03FNK-Ap_M5Q@mail.gmail.com>
	<029CFFCF-9BEE-4D0C-B9CA-E2884BDEEBAD@phenogenomics.ca>
Message-ID: <CACGPbDyu8AMQ4wGD5E+s1TVC9S7_wdsny1VkA4NdeaiTvrPK-w@mail.gmail.com>

Hello Jason,

It has worked perfectly,
I just want to say that pyminc seems very easy to use.

Thanks a lot

2012/6/8 Jason Lerch <jason at phenogenomics.ca>

> This should do what you want, I think. In python:
>
> from pyminc.volumes.factory import *
> from numpy import *
> import scipy
>
> v = volumeFromFile("filename.mnc")
> axis0 = apply_along_axis(max, 0, v.data)
> axis1 = apply_along_axis(max, 1, v.data)
> axis2 = apply_along_axis(max, 2, v.data)
>
> # if you want to save it as an image:
> scipy.misc.imsave('axis0.jpg', axis0)
>
> Jason
>
> On 2012-06-08, at 11:36 AM, francois hebert wrote:
>
> > Hi All,
> >
> > I would like to do a Maximum Intensity Projection in each orthogonal
> axis.
> > Is there such tool in the minc library?
> >
> > Regards,
> >
> > Francois Hebert
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From kelvin.mok at mcgill.ca  Fri Jun  8 18:01:42 2012
From: kelvin.mok at mcgill.ca (Kelvin Mok)
Date: Fri, 8 Jun 2012 18:01:42 -0400
Subject: [MINC-users] FDR analysis for cortical thickness
In-Reply-To: <CAPKhXHZNi0CuRiUBVXc7kdOL+9hg9N_NXokNu0pX6PwdkmTz4Q@mail.gmail.com>
References: <CAPKhXHYnDx1xkfM=gyzHt0sG9aPkW3Y3RbpqTwB8utaSPK0eoQ@mail.gmail.com>
	<86D83A58-DAD8-4898-8DE8-96AF1E980788@phenogenomics.ca>
	<CAB-GmL2iv5BydSbhOBBuP1M=6r_Q-MmHMJBZVp3tFettxSWJig@mail.gmail.com>
	<CAPKhXHYD9D+OvjhrZ3FD9F6vs_KNkP9jtcioxgEOyWENY9OrQw@mail.gmail.com>
	<CAB-GmL1iOTiDQHih8xtr9vAX255-8evvugiv6Hia4UQe0K6K=g@mail.gmail.com>
	<CAPKhXHZNi0CuRiUBVXc7kdOL+9hg9N_NXokNu0pX6PwdkmTz4Q@mail.gmail.com>
Message-ID: <4FD27646.7010702@mcgill.ca>

Hey Jonathan,

Mishkin mentioned it below, but your t-stats can be loaded with: 
(assuming that you have analyzed your data in your R session, or you 
used --save option)
vs$tstatistic[0,]
(your script uses the variable name "vs" )

This will spit out the variables where we have t-statistics (ie 
Intercept, Variable1, Variable2, Interaction1:2), then you can choose 
the corresponding column:
vs$tstatistic[,1]  (i.e, Intercept)
vs$tstatistic[,2]  (i.e. Variable1)
vs$tstatistic[,3]  (i.e. Variable2)

Since we're already using Jason's stats library, we can send the column 
of t-statistics values directly into his FDR function, mni.compute.FDR.
qvalues<-mni.compute.FDR(*t.stats=vs$tstatistics,column.name=column#*,df=_inputdegoffreedom__,fdr=0.05)

Then, the false discovery rate value would be here:
qvalues$fdr.threshold

We just made an error in your script defining the t.stats variable.

Kelvin


On 2012-06-08, at 2:40 PM, Jonathan Berken wrote:

> How do I open my list of t-values?
>
> On Fri, Jun 8, 2012 at 2:35 PM, Mishkin Derakhshan <mishkind at gmail.com 
> <mailto:mishkind at gmail.com>>wrote:
>
>> On Fri, Jun 8, 2012 at 2:06 PM, Jonathan Berken
>> <jonathan.berken at gmail.com <mailto:jonathan.berken at gmail.com>> wrote:
>>> Hi Mishkin,
>>>
>>> Thanks so much for your help!
>>>
>>> I already have R library and have ran cortical thickness analyses... 
>>> I am
>>> just not sure how to run the FDR analysis... I have the script from the
>>> site, but not sure where to get the t-values from my results to input?
>>
>> So if you've ran the cortical thickness analyses, then you should have
>> some t-values for whatever you tested for.
>>
>> In my example script, my array of t-values comes from here:
>> vertexstatistics <- mni.vertex.statistics(glimfile, 'y ~ group',
>> vertex.table=datatable)
>>
>> vertexstatistics contains a lot of different items, the array of
>> t-values are here:
>> vertexstatistics\$tstatistic[,2]
>>
>> The t-values represent the result of a two-tailed t-test for the test
>> y ~ group, which usually means you are testing for differences in
>> cortical thickness (y) in the different groups (ie. francophones vs.
>> anglophones). What 'y' and 'group' actually mean, depend on what you
>> put in your glim file, but if you've ran your analysis already then i
>> have a feeling you know this already.
>>
>>> Can
>>> I run the FDR after I do my initial CT regression?
>>
>> Sorry, but I don't actually know what you mean by initial CT
>> regression? I use MRI data, and I don't actually look for differences
>> in cortical thickness but just use the library for other vertex wise
>> tests that I need. Like Jason said though, the FDR can be calculated
>> on any array of t-values (or pvalues) that are the output of anything
>> you are trying to test for.
>>
>> If you look at the code (in R type: 'library(mni.crotical.statistics)'
>> then 'mni.compute.FDR') you can see that it actually needs p-values,
>> but it can compute those from the given t-stats if you give it the
>> degrees of freedom.
>>
>>>
>>> Jonathan
>>>
>>> On Fri, Jun 8, 2012 at 2:00 PM, Mishkin Derakhshan 
>>> <mishkind at gmail.com <mailto:mishkind at gmail.com>>
>>> wrote:
>>>>
>>>> Hi Jonathan,
>>>>
>>>> At the risk of depriving you hours of endless fun coding this up
>>>> yourself, attached is my implementation using the
>>>> mni.cortical.statistics library (which you will need to install).
>>>>
>>>> There is quite a bit of documentation on the bic wiki:
>>>> http://wiki.bic.mni.mcgill.ca/index.php/ThicknessStatistics
>>>>
>>>> I'm at wb319 in the bic if you need help.
>>>> mishkin
>>>>
>>>> p.s this is how to install the R library (using a bash shell) if you
>>>> didn't know:
>>>> 1. download the mni.cortical.statistics library
>>>> 2. R CMD INSTALL --library=/path/to/useful/extra/libraries/for/R/
>>>> mni.cortical.statistics
>>>> 3. export R_LIBS=/path/to/useful/extra/libraries/for/R/
>>>>
>>>>
>>>> On Fri, Jun 8, 2012 at 11:19 AM, Jason Lerch 
>>>> <jason at phenogenomics.ca <mailto:jason at phenogenomics.ca>>
>>>> wrote:
>>>>> There's an implementation in mni.cortical.statistcs and RMINC as well
>> as
>>>>> Keith's matlab surfstats.
>>>>>
>>>>> The recipe in R:
>>>>>
>>>>> 1) create a vector of p-values
>>>>> 2) qvals <- p.adjust(pvalues, "fdr")
>>>>>
>>>>> Jason
>>>>>
>>>>> On 2012-06-08, at 11:15 AM, Jonathan Berken wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I was wondering if someone who is familiar with FDR analysis for
>>>>>> cortical
>>>>>> thickness might be able to help me work out the script.
>>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>> Jonathan
>>>>>> _______________________________________________
>>>>>> MINC-users at bic.mni.mcgill.ca <mailto:MINC-users at bic.mni.mcgill.ca>
>>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>>>
>>>>> _______________________________________________
>>>>> MINC-users at bic.mni.mcgill.ca <mailto:MINC-users at bic.mni.mcgill.ca>
>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>>
>>>> _______________________________________________
>>>> MINC-users at bic.mni.mcgill.ca <mailto:MINC-users at bic.mni.mcgill.ca>
>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>>
>>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca <mailto:MINC-users at bic.mni.mcgill.ca>
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca <mailto:MINC-users at bic.mni.mcgill.ca>
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users



From jared.rowley at gmail.com  Mon Jun 11 10:25:12 2012
From: jared.rowley at gmail.com (Jared Rowley)
Date: Mon, 11 Jun 2012 10:25:12 -0400
Subject: [MINC-users] calculating r-squared values
In-Reply-To: <E9AFE82E-4BCD-4625-9412-14A926EA9CF7@phenogenomics.ca>
References: <CACHMmjMad5wA_Cz-kVrQzO9aAMs2g2E6QrAnWT-u33bK2ewLGg@mail.gmail.com>
	<505FFB2E-64AD-4383-ADF0-7972F5155FA5@phenogenomics.ca>
	<CACHMmjPTtgsgdEvBDGvgggy+mQMCniDuY5vtiHV444_P6wQiWQ@mail.gmail.com>
	<E9AFE82E-4BCD-4625-9412-14A926EA9CF7@phenogenomics.ca>
Message-ID: <CACHMmjNp=e7FvQh-xg-4j_-cG0bkeRpyqa6Ur1Ljmzxh0OHN3A@mail.gmail.com>

Hi Jason,

Everything appeared to work however I'm a little unclear how to save the
data now.  (It does take a very long time to run).

Here is my code.  The last line was my attempt to save the data:

gf1 <- read.csv("dti_nvm_gd.csv")
> fff <- function(x) { return(summary(lm(x ~ score, gf1))$r.squared) }
> mincApply(gf1$FA, quote(fff(x)))
Number of volumes: 91
Volume sizes: 193 229 193
In slice
 0  1  2  3  4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20
 21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58
 59  60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77
 78  79  80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96
 97  98  99  100  101  102  103  104  105  106  107  108  109  110  111
 112  113  114  115  116  117  118  119  120  121  122  123  124  125  126
 127  128  129  130  131  132  133  134  135  136  137  138  139  140  141
 142  143  144  145  146  147  148  149  150  151  152  153  154  155  156
 157  158  159  160  161  162  163  164  165  166  167  168  169  170  171
 172  173  174  175  176  177  178  179  180  181  182  183  184  185  186
 187  188  189  190  191  192
Done

> mincWriteVolume(fff,"rsquared_test.mnc", "score")
Error in minc.dimensions.sizes(like.filename) :
  Error opening input file: score.

Thanks again,

Jared


On Fri, Jun 8, 2012 at 12:39 PM, Jason Lerch <jason at phenogenomics.ca> wrote:

> Try replacing FA with x - mincApply assigns the current voxel to the
> variable x in its loop. I.e.:
>
> library(RMINC)
> gf1 <- read.csv("dti_gd.csv")
> fff <- function(x) { return(summary(lm(x ~ score, gf1))$r.squared) }
> mincApply(gf1$FA, quote(fff(x)))
>
> Jason
>
> On 2012-06-08, at 11:32 AM, Jared Rowley wrote:
>
> > Hi Jason,
> >
> > Thanks for the response.
> >
> > I did the following and got an error do you have any suggestions:
> >
> > rm(list=ls(all=TRUE))
> >> library(RMINC)
> >> gf1 <- read.csv("dti_gd.csv")
> >> fff <- function(x) { return(summary(lm(FA ~ score, gf1))$r.squared) }
> >> mincApply(gf1$FA, quote(fff(x)))
> > Number of volumes: 91
> > Volume sizes: 193 229 193
> > In slice
> > 0 Error in storage.mode(y) <- "double" :
> >  invalid to change the storage mode of a factor
> > In addition: Warning message:
> > In model.response(mf, "numeric") :
> >  using type="numeric" with a factor response will be ignored
> >
> > FA is a column of minc files and score is a column of integers I want to
> > correlate with FA.
> >
> > Thanks very much,
> >
> > Jared
> >
> >
> > On Wed, Jun 6, 2012 at 1:35 PM, Jason Lerch <jason at phenogenomics.ca>
> wrote:
> >
> >> This should work, though is going to be slow:
> >>
> >> fff <- function(x) { return(summary(lm(x ~ genotype, gf))$r.squared) }
> >>
> >> mincApply(filenames, quote(fff(x)))
> >>
> >> Note: replace the formula in that function with the appropriate formula
> >> for your purposes, and filenames should be a vector of your filenames.
> >> Could be worth specifying a mask, as this will run for a few hours.
> >>
> >> And I haven't actually tested it, so it might not run at all!
> >>
> >> Jason
> >>
> >> On 2012-06-05, at 4:18 PM, Jared Rowley wrote:
> >>
> >>> Hi Minc Users,
> >>>
> >>> I was wondering if anyone knows a way calculate R-squared values on a
> >> voxel
> >>> level from a linear regression.
> >>>
> >>> I assume there is a way with either glim_image or RMINC however reading
> >>> though the documentation I could not find a solution.
> >>>
> >>> Thanks very much,
> >>>
> >>> Jared
> >>> _______________________________________________
> >>> MINC-users at bic.mni.mcgill.ca
> >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >
> >
> >
> > --
> > Jared Rowley
> > Translational Neuroimaging Laboratory
> > McGill Centre for Studies in Aging
> > Douglas Hospital Research Center
> > McGill University
> > 6825 LaSalle Blvd.
> > Montreal, QC Canada
> > H4H 1R3
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Jared Rowley
Translational Neuroimaging Laboratory
McGill Centre for Studies in Aging
Douglas Hospital Research Center
McGill University
6825 LaSalle Blvd.
Montreal, QC Canada
H4H 1R3

From jason at phenogenomics.ca  Mon Jun 11 11:07:18 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Mon, 11 Jun 2012 11:07:18 -0400
Subject: [MINC-users] calculating r-squared values
In-Reply-To: <CACHMmjNp=e7FvQh-xg-4j_-cG0bkeRpyqa6Ur1Ljmzxh0OHN3A@mail.gmail.com>
References: <CACHMmjMad5wA_Cz-kVrQzO9aAMs2g2E6QrAnWT-u33bK2ewLGg@mail.gmail.com>
Message-ID: <247716CD-CFBC-4883-B16C-748F1D6B5208@phenogenomics.ca>

You have to save your output to a variable:

output <- mincApply(gf1$FA, quote(fff(x)))

and then call mincWriteVolume(output, "filename.mnc")

If you didn't do that, the internal R variable .Last.value would have saved your last computation - though if you did anything else since then (and the mincWriteVolume call might apply, I'm not sure), then you'll have to rerun mincApply and assign its output to some variable.

Jason

On 2012-06-11, at 10:25 AM, Jared Rowley wrote:

> Hi Jason,
> 
> Everything appeared to work however I'm a little unclear how to save the
> data now.  (It does take a very long time to run).
> 
> Here is my code.  The last line was my attempt to save the data:
> 
> gf1 <- read.csv("dti_nvm_gd.csv")
>> fff <- function(x) { return(summary(lm(x ~ score, gf1))$r.squared) }
>> mincApply(gf1$FA, quote(fff(x)))
> Number of volumes: 91
> Volume sizes: 193 229 193
> In slice
> 0  1  2  3  4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20
> 21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39
> 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58
> 59  60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77
> 78  79  80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96
> 97  98  99  100  101  102  103  104  105  106  107  108  109  110  111
> 112  113  114  115  116  117  118  119  120  121  122  123  124  125  126
> 127  128  129  130  131  132  133  134  135  136  137  138  139  140  141
> 142  143  144  145  146  147  148  149  150  151  152  153  154  155  156
> 157  158  159  160  161  162  163  164  165  166  167  168  169  170  171
> 172  173  174  175  176  177  178  179  180  181  182  183  184  185  186
> 187  188  189  190  191  192
> Done
> 
>> mincWriteVolume(fff,"rsquared_test.mnc", "score")
> Error in minc.dimensions.sizes(like.filename) :
>  Error opening input file: score.
> 
> Thanks again,
> 
> Jared
> 
> 
> On Fri, Jun 8, 2012 at 12:39 PM, Jason Lerch <jason at phenogenomics.ca> wrote:
> 
>> Try replacing FA with x - mincApply assigns the current voxel to the
>> variable x in its loop. I.e.:
>> 
>> library(RMINC)
>> gf1 <- read.csv("dti_gd.csv")
>> fff <- function(x) { return(summary(lm(x ~ score, gf1))$r.squared) }
>> mincApply(gf1$FA, quote(fff(x)))
>> 
>> Jason
>> 
>> On 2012-06-08, at 11:32 AM, Jared Rowley wrote:
>> 
>>> Hi Jason,
>>> 
>>> Thanks for the response.
>>> 
>>> I did the following and got an error do you have any suggestions:
>>> 
>>> rm(list=ls(all=TRUE))
>>>> library(RMINC)
>>>> gf1 <- read.csv("dti_gd.csv")
>>>> fff <- function(x) { return(summary(lm(FA ~ score, gf1))$r.squared) }
>>>> mincApply(gf1$FA, quote(fff(x)))
>>> Number of volumes: 91
>>> Volume sizes: 193 229 193
>>> In slice
>>> 0 Error in storage.mode(y) <- "double" :
>>> invalid to change the storage mode of a factor
>>> In addition: Warning message:
>>> In model.response(mf, "numeric") :
>>> using type="numeric" with a factor response will be ignored
>>> 
>>> FA is a column of minc files and score is a column of integers I want to
>>> correlate with FA.
>>> 
>>> Thanks very much,
>>> 
>>> Jared
>>> 
>>> 
>>> On Wed, Jun 6, 2012 at 1:35 PM, Jason Lerch <jason at phenogenomics.ca>
>> wrote:
>>> 
>>>> This should work, though is going to be slow:
>>>> 
>>>> fff <- function(x) { return(summary(lm(x ~ genotype, gf))$r.squared) }
>>>> 
>>>> mincApply(filenames, quote(fff(x)))
>>>> 
>>>> Note: replace the formula in that function with the appropriate formula
>>>> for your purposes, and filenames should be a vector of your filenames.
>>>> Could be worth specifying a mask, as this will run for a few hours.
>>>> 
>>>> And I haven't actually tested it, so it might not run at all!
>>>> 
>>>> Jason
>>>> 
>>>> On 2012-06-05, at 4:18 PM, Jared Rowley wrote:
>>>> 
>>>>> Hi Minc Users,
>>>>> 
>>>>> I was wondering if anyone knows a way calculate R-squared values on a
>>>> voxel
>>>>> level from a linear regression.
>>>>> 
>>>>> I assume there is a way with either glim_image or RMINC however reading
>>>>> though the documentation I could not find a solution.
>>>>> 
>>>>> Thanks very much,
>>>>> 
>>>>> Jared
>>>>> _______________________________________________
>>>>> MINC-users at bic.mni.mcgill.ca
>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>> 
>>>> _______________________________________________
>>>> MINC-users at bic.mni.mcgill.ca
>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> Jared Rowley
>>> Translational Neuroimaging Laboratory
>>> McGill Centre for Studies in Aging
>>> Douglas Hospital Research Center
>>> McGill University
>>> 6825 LaSalle Blvd.
>>> Montreal, QC Canada
>>> H4H 1R3
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> 
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> 
> 
> 
> 
> -- 
> Jared Rowley
> Translational Neuroimaging Laboratory
> McGill Centre for Studies in Aging
> Douglas Hospital Research Center
> McGill University
> 6825 LaSalle Blvd.
> Montreal, QC Canada
> H4H 1R3
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From jared.rowley at gmail.com  Mon Jun 11 11:10:26 2012
From: jared.rowley at gmail.com (Jared Rowley)
Date: Mon, 11 Jun 2012 11:10:26 -0400
Subject: [MINC-users] calculating r-squared values
In-Reply-To: <247716CD-CFBC-4883-B16C-748F1D6B5208@phenogenomics.ca>
References: <CACHMmjMad5wA_Cz-kVrQzO9aAMs2g2E6QrAnWT-u33bK2ewLGg@mail.gmail.com>
	<505FFB2E-64AD-4383-ADF0-7972F5155FA5@phenogenomics.ca>
	<CACHMmjPTtgsgdEvBDGvgggy+mQMCniDuY5vtiHV444_P6wQiWQ@mail.gmail.com>
	<E9AFE82E-4BCD-4625-9412-14A926EA9CF7@phenogenomics.ca>
	<CACHMmjNp=e7FvQh-xg-4j_-cG0bkeRpyqa6Ur1Ljmzxh0OHN3A@mail.gmail.com>
	<247716CD-CFBC-4883-B16C-748F1D6B5208@phenogenomics.ca>
Message-ID: <CACHMmjNJJPfH=kCdQFGwy5HX4bNvDKUkZWhGBkAP2G+3cF8+Pg@mail.gmail.com>

Got it.  That makes sense.

Thanks very much for the help,

Jared

On Mon, Jun 11, 2012 at 11:07 AM, Jason Lerch <jason at phenogenomics.ca>wrote:

> You have to save your output to a variable:
>
> output <- mincApply(gf1$FA, quote(fff(x)))
>
> and then call mincWriteVolume(output, "filename.mnc")
>
> If you didn't do that, the internal R variable .Last.value would have
> saved your last computation - though if you did anything else since then
> (and the mincWriteVolume call might apply, I'm not sure), then you'll have
> to rerun mincApply and assign its output to some variable.
>
> Jason
>
> On 2012-06-11, at 10:25 AM, Jared Rowley wrote:
>
> > Hi Jason,
> >
> > Everything appeared to work however I'm a little unclear how to save the
> > data now.  (It does take a very long time to run).
> >
> > Here is my code.  The last line was my attempt to save the data:
> >
> > gf1 <- read.csv("dti_nvm_gd.csv")
> >> fff <- function(x) { return(summary(lm(x ~ score, gf1))$r.squared) }
> >> mincApply(gf1$FA, quote(fff(x)))
> > Number of volumes: 91
> > Volume sizes: 193 229 193
> > In slice
> > 0  1  2  3  4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20
> > 21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38
>  39
> > 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57
>  58
> > 59  60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76
>  77
> > 78  79  80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95
>  96
> > 97  98  99  100  101  102  103  104  105  106  107  108  109  110  111
> > 112  113  114  115  116  117  118  119  120  121  122  123  124  125  126
> > 127  128  129  130  131  132  133  134  135  136  137  138  139  140  141
> > 142  143  144  145  146  147  148  149  150  151  152  153  154  155  156
> > 157  158  159  160  161  162  163  164  165  166  167  168  169  170  171
> > 172  173  174  175  176  177  178  179  180  181  182  183  184  185  186
> > 187  188  189  190  191  192
> > Done
> >
> >> mincWriteVolume(fff,"rsquared_test.mnc", "score")
> > Error in minc.dimensions.sizes(like.filename) :
> >  Error opening input file: score.
> >
> > Thanks again,
> >
> > Jared
> >
> >
> > On Fri, Jun 8, 2012 at 12:39 PM, Jason Lerch <jason at phenogenomics.ca>
> wrote:
> >
> >> Try replacing FA with x - mincApply assigns the current voxel to the
> >> variable x in its loop. I.e.:
> >>
> >> library(RMINC)
> >> gf1 <- read.csv("dti_gd.csv")
> >> fff <- function(x) { return(summary(lm(x ~ score, gf1))$r.squared) }
> >> mincApply(gf1$FA, quote(fff(x)))
> >>
> >> Jason
> >>
> >> On 2012-06-08, at 11:32 AM, Jared Rowley wrote:
> >>
> >>> Hi Jason,
> >>>
> >>> Thanks for the response.
> >>>
> >>> I did the following and got an error do you have any suggestions:
> >>>
> >>> rm(list=ls(all=TRUE))
> >>>> library(RMINC)
> >>>> gf1 <- read.csv("dti_gd.csv")
> >>>> fff <- function(x) { return(summary(lm(FA ~ score, gf1))$r.squared) }
> >>>> mincApply(gf1$FA, quote(fff(x)))
> >>> Number of volumes: 91
> >>> Volume sizes: 193 229 193
> >>> In slice
> >>> 0 Error in storage.mode(y) <- "double" :
> >>> invalid to change the storage mode of a factor
> >>> In addition: Warning message:
> >>> In model.response(mf, "numeric") :
> >>> using type="numeric" with a factor response will be ignored
> >>>
> >>> FA is a column of minc files and score is a column of integers I want
> to
> >>> correlate with FA.
> >>>
> >>> Thanks very much,
> >>>
> >>> Jared
> >>>
> >>>
> >>> On Wed, Jun 6, 2012 at 1:35 PM, Jason Lerch <jason at phenogenomics.ca>
> >> wrote:
> >>>
> >>>> This should work, though is going to be slow:
> >>>>
> >>>> fff <- function(x) { return(summary(lm(x ~ genotype, gf))$r.squared) }
> >>>>
> >>>> mincApply(filenames, quote(fff(x)))
> >>>>
> >>>> Note: replace the formula in that function with the appropriate
> formula
> >>>> for your purposes, and filenames should be a vector of your filenames.
> >>>> Could be worth specifying a mask, as this will run for a few hours.
> >>>>
> >>>> And I haven't actually tested it, so it might not run at all!
> >>>>
> >>>> Jason
> >>>>
> >>>> On 2012-06-05, at 4:18 PM, Jared Rowley wrote:
> >>>>
> >>>>> Hi Minc Users,
> >>>>>
> >>>>> I was wondering if anyone knows a way calculate R-squared values on a
> >>>> voxel
> >>>>> level from a linear regression.
> >>>>>
> >>>>> I assume there is a way with either glim_image or RMINC however
> reading
> >>>>> though the documentation I could not find a solution.
> >>>>>
> >>>>> Thanks very much,
> >>>>>
> >>>>> Jared
> >>>>> _______________________________________________
> >>>>> MINC-users at bic.mni.mcgill.ca
> >>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>>>
> >>>> _______________________________________________
> >>>> MINC-users at bic.mni.mcgill.ca
> >>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Jared Rowley
> >>> Translational Neuroimaging Laboratory
> >>> McGill Centre for Studies in Aging
> >>> Douglas Hospital Research Center
> >>> McGill University
> >>> 6825 LaSalle Blvd.
> >>> Montreal, QC Canada
> >>> H4H 1R3
> >>> _______________________________________________
> >>> MINC-users at bic.mni.mcgill.ca
> >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >
> >
> >
> > --
> > Jared Rowley
> > Translational Neuroimaging Laboratory
> > McGill Centre for Studies in Aging
> > Douglas Hospital Research Center
> > McGill University
> > 6825 LaSalle Blvd.
> > Montreal, QC Canada
> > H4H 1R3
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Jared Rowley
Translational Neuroimaging Laboratory
McGill Centre for Studies in Aging
Douglas Hospital Research Center
McGill University
6825 LaSalle Blvd.
Montreal, QC Canada
H4H 1R3

From a.janke at gmail.com  Wed Jun 13 22:00:44 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 14 Jun 2012 12:00:44 +1000
Subject: [MINC-users] Maximum intensity projection
In-Reply-To: <CACGPbDzNPo0EOwNSKGYt7D0BtuF_cPOMG8eNFC03FNK-Ap_M5Q@mail.gmail.com>
References: <CACGPbDzNPo0EOwNSKGYt7D0BtuF_cPOMG8eNFC03FNK-Ap_M5Q@mail.gmail.com>
Message-ID: <CAG0CB21QK15eeR_bejhjWPOKmAM7VUaiCz_QCsbqf1sV=ta=Tw@mail.gmail.com>

Hi Francois,

On 9 June 2012 01:36, francois hebert <francois.hebert007 at gmail.com> wrote:
> I would like to do a Maximum Intensity Projection in each orthogonal axis.
> Is there such tool in the minc library?

I know I'm late to party but for the dinosaurs amongst us who don't
always play with the new toys you could do this using the basic MINC
commands like this (via a perl script):

#! /usr/bin/env perl

use warnings "all";

# create tmp dir
$tmpdir = '/tmp/froogle';
&do_cmd('mkdir', '-p', $tmpdir);

# separate all the slices
for ($i=0; $i<100; $i++){
   &do_cmd('mincreshape', '-clobber',
           '-dimrange', "zspace=$i,0",
           $ARGV[0], "$tmpdir/$i-zslice.mnc");
   push(@files, "$tmpdir/$i-zslice.mnc");
   }

&do_cmd('mincmath', '-clobber', '-max', @files, @ARGV[1]);
&do_cmd('rm', '-rf', $tmpdir);

sub do_cmd {
   print STDOUT "@_\n";
   system(@_) == 0 or die;
   }

I will admit that doing this in pyminc is whole lot easier!

a

From ayman.oweida at mail.mcgill.ca  Thu Jun 14 17:15:19 2012
From: ayman.oweida at mail.mcgill.ca (Ayman Oweida)
Date: Thu, 14 Jun 2012 21:15:19 +0000
Subject: [MINC-users] Display bug?
Message-ID: <790582915299864F9DC262BDDC538DF515CF3B@EXMBX2010-2.campus.MCGILL.CA>

Hi,

When I launch Display, I get the 3D volume correctly, but the menu tab doesn't load correctly.  It's either all white or contains a partial load of the 3D volume.

Any insights on fixing this?

Thanks

Ayman Oweida, MSc
PhD Candidate
McGill University
Department of Experimental Medicine

Montreal General Hospital 
1650 Cedar Ave, L5-112
Montreal, QC  H3G 1A4
(514) 934-1934 x. 43019



From peter.neelin at gmail.com  Fri Jun 15 00:56:29 2012
From: peter.neelin at gmail.com (Peter Neelin)
Date: Fri, 15 Jun 2012 00:56:29 -0400
Subject: [MINC-users] Maximum intensity projection
In-Reply-To: <CAG0CB21QK15eeR_bejhjWPOKmAM7VUaiCz_QCsbqf1sV=ta=Tw@mail.gmail.com>
References: <CACGPbDzNPo0EOwNSKGYt7D0BtuF_cPOMG8eNFC03FNK-Ap_M5Q@mail.gmail.com>
	<CAG0CB21QK15eeR_bejhjWPOKmAM7VUaiCz_QCsbqf1sV=ta=Tw@mail.gmail.com>
Message-ID: <CANcjydbofwHBoh-GTNJbC7-S-cNABvdiggWB5Fww8qCA1BkK-Q@mail.gmail.com>

On Jun 13, 2012 10:02 PM, "Andrew Janke" <a.janke at gmail.com> wrote:

> On 9 June 2012 01:36, francois hebert <francois.hebert007 at gmail.com>
wrote:
> > I would like to do a Maximum Intensity Projection in each orthogonal
axis.
> > Is there such tool in the minc library?
>
> I know I'm late to party but for the dinosaurs amongst us who don't
> always play with the new toys you could do this using the basic MINC
> commands like this (via a perl script):
> [fancy perl script deleted]
> &do_cmd('mincmath', '-clobber', '-max', @files, @ARGV[1]);
>
> I will admit that doing this in pyminc is whole lot easier!

Wouldn't a -dimension option to mincmath do the same thing but in one line?
I haven't tested it, so I'm not sure if it will allow accumulating the
maximum over image dimensions (the original question was for all 3
orthogonal projections). If it does not, then a mincreshape to re-order the
dimensions and a mincmath -dimension should do the trick for the other 2
dimensions.

Peter
--
Peter Neelin
peter.neelin at gmail.com

From trash001 at odu.edu  Fri Jun 15 22:51:45 2012
From: trash001 at odu.edu (Tanweer Rashid)
Date: Fri, 15 Jun 2012 22:51:45 -0400
Subject: [MINC-users] Minc installation problem
Message-ID: <CAE1j2uiK-25fELrApYnprwewHY7VfQA9J6WnvxA0i9LCmTAz1g@mail.gmail.com>

Hi, I am getting some errors when I try to build MINC 2.0.18 from source. I
am using Ubuntu 12.04 LTS. I executed ./configure and it seems to work
fine, no errors here. Then when I execute make I get the following errors:

trash001 at MSVEDE09:~/Downloads/minc-2.0.18$ make
make  all-recursive
make[1]: Entering directory `/home/trash001/Downloads/minc-2.0.18'
Making all in .
make[2]: Entering directory `/home/trash001/Downloads/minc-2.0.18'
depbase=`echo libsrc/image_conversion.lo | sed
's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.
-I./libsrc -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib
-I./conversion/Acr_nema -I./libsrc2    -g -O2 -MT
libsrc/image_conversion.lo -MD -MP -MF $depbase.Tpo -c -o
libsrc/image_conversion.lo libsrc/image_conversion.c &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I./libsrc -I./volume_io/Include
-I./volume_io/Include -I./progs/Proglib -I./conversion/Acr_nema -I./libsrc2
-g -O2 -MT libsrc/image_conversion.lo -MD -MP -MF
libsrc/.deps/image_conversion.Tpo -c libsrc/image_conversion.c -o
libsrc/image_conversion.o
libsrc/image_conversion.c: In function ?miicv_create?:
libsrc/image_conversion.c:219:43: error: ?MAX_NC_OPEN? undeclared (first
use in this function)
libsrc/image_conversion.c:219:43: note: each undeclared identifier is
reported only once for each function it appears in
make[2]: *** [libsrc/image_conversion.lo] Error 1
make[2]: Leaving directory `/home/trash001/Downloads/minc-2.0.18'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/trash001/Downloads/minc-2.0.18'
make: *** [all] Error 2
trash001 at MSVEDE09:~/Downloads/minc-2.0.18$


As far as I know, I have installed all the prerequisite packages, but any
suggestions are welcome. Thanks very much.

-- 
Tanweer Rashid
MSVE Dept.
Old Dominion University

From vladimir.fonov at gmail.com  Sat Jun 16 00:27:40 2012
From: vladimir.fonov at gmail.com (Vladimir S. Fonov)
Date: Sat, 16 Jun 2012 12:27:40 +0800
Subject: [MINC-users] Minc installation problem
In-Reply-To: <CAE1j2uiK-25fELrApYnprwewHY7VfQA9J6WnvxA0i9LCmTAz1g@mail.gmail.com>
References: <CAE1j2uiK-25fELrApYnprwewHY7VfQA9J6WnvxA0i9LCmTAz1g@mail.gmail.com>
Message-ID: <4FDC0B3C.5040701@gmail.com>

Hello Tandweer,

try using later version of MINC from https://github.com/BIC-MNI/minc ( I 
suggest release 2.1.12 ( 
https://github.com/BIC-MNI/minc/tarball/release-2.1.12 )

On 16/06/2012 10:51 AM, Tanweer Rashid wrote:
> Hi, I am getting some errors when I try to build MINC 2.0.18 from source. I
> am using Ubuntu 12.04 LTS. I executed ./configure and it seems to work
> fine, no errors here. Then when I execute make I get the following errors:


-- 
Best regards,

  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com

From a.janke at gmail.com  Sun Jun 17 00:08:46 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Sun, 17 Jun 2012 14:08:46 +1000
Subject: [MINC-users] Display bug?
In-Reply-To: <790582915299864F9DC262BDDC538DF515CF3B@EXMBX2010-2.campus.MCGILL.CA>
References: <790582915299864F9DC262BDDC538DF515CF3B@EXMBX2010-2.campus.MCGILL.CA>
Message-ID: <CAG0CB21Gz=cFL5KaL29VkiFKf4ZSHsevB=h9Y_+5HstWkRbOqw@mail.gmail.com>

Hi Ayman,

There have been a few issues with the latest version of freeglut on
various OS's as of late. Unfortunately nothing seems all that
consistent as of yet.  Which version and which OS are you running on?
It'd also help if you could upload a screen shot of this somewhere or
send it to me directly.

ta

a


On 15 June 2012 07:15, Ayman Oweida <ayman.oweida at mail.mcgill.ca> wrote:
> Hi,
>
> When I launch Display, I get the 3D volume correctly, but the menu tab doesn't load correctly. ?It's either all white or contains a partial load of the 3D volume.
>
> Any insights on fixing this?
>
> Thanks
>
> Ayman Oweida, MSc
> PhD Candidate
> McGill University
> Department of Experimental Medicine
>
> Montreal General Hospital
> 1650 Cedar Ave, L5-112
> Montreal, QC ?H3G 1A4
> (514) 934-1934 x. 43019
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From jared.rowley at gmail.com  Sun Jun 17 00:28:43 2012
From: jared.rowley at gmail.com (Jared Rowley)
Date: Sun, 17 Jun 2012 00:28:43 -0400
Subject: [MINC-users] Display bug?
In-Reply-To: <790582915299864F9DC262BDDC538DF515CF3B@EXMBX2010-2.campus.MCGILL.CA>
References: <790582915299864F9DC262BDDC538DF515CF3B@EXMBX2010-2.campus.MCGILL.CA>
Message-ID: <9164249604016312743@unknownmsgid>

Hi,

So this is probably a stupid answer but I get a problem loading the
menu on Display on Mac os x lion sometimes (menu is all white).  I can
solve the problem by enlarging the menu with the mouse and then
shrinking it again.

Jared

On Jun 14, 2012, at 5:16 PM, Ayman Oweida <ayman.oweida at mail.mcgill.ca> wrote:

> Hi,
>
> When I launch Display, I get the 3D volume correctly, but the menu tab doesn't load correctly.  It's either all white or contains a partial load of the 3D volume.
>
> Any insights on fixing this?
>
> Thanks
>
> Ayman Oweida, MSc
> PhD Candidate
> McGill University
> Department of Experimental Medicine
>
> Montreal General Hospital
> 1650 Cedar Ave, L5-112
> Montreal, QC  H3G 1A4
> (514) 934-1934 x. 43019
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From ayman.oweida at mail.mcgill.ca  Mon Jun 18 09:51:04 2012
From: ayman.oweida at mail.mcgill.ca (Ayman Oweida)
Date: Mon, 18 Jun 2012 13:51:04 +0000
Subject: [MINC-users] Display bug?
In-Reply-To: <9164249604016312743@unknownmsgid>
References: <790582915299864F9DC262BDDC538DF515CF3B@EXMBX2010-2.campus.MCGILL.CA>
	<9164249604016312743@unknownmsgid>
Message-ID: <790582915299864F9DC262BDDC538DF515F6D2@EXMBX2010-2.campus.MCGILL.CA>

It solved my problem :)
Now, I feel stupid for not having thought of this solution ;)

Thanks,

Ayman


-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Jared Rowley
Sent: Sunday, June 17, 2012 12:29 AM
To: MINC users mailing list
Subject: Re: [MINC-users] Display bug?

Hi,

So this is probably a stupid answer but I get a problem loading the menu on Display on Mac os x lion sometimes (menu is all white).  I can solve the problem by enlarging the menu with the mouse and then shrinking it again.

Jared

On Jun 14, 2012, at 5:16 PM, Ayman Oweida <ayman.oweida at mail.mcgill.ca> wrote:

> Hi,
>
> When I launch Display, I get the 3D volume correctly, but the menu tab doesn't load correctly.  It's either all white or contains a partial load of the 3D volume.
>
> Any insights on fixing this?
>
> Thanks
>
> Ayman Oweida, MSc
> PhD Candidate
> McGill University
> Department of Experimental Medicine
>
> Montreal General Hospital
> 1650 Cedar Ave, L5-112
> Montreal, QC  H3G 1A4
> (514) 934-1934 x. 43019
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

-----
No virus found in this message.
Checked by AVG - www.avg.com
Version: 2012.0.2180 / Virus Database: 2433/5076 - Release Date: 06/17/12

From ayman.oweida at mail.mcgill.ca  Mon Jun 18 11:23:07 2012
From: ayman.oweida at mail.mcgill.ca (Ayman Oweida)
Date: Mon, 18 Jun 2012 15:23:07 +0000
Subject: [MINC-users] mni_autoreg volume
Message-ID: <790582915299864F9DC262BDDC538DF515F95B@EXMBX2010-2.campus.MCGILL.CA>

Where can I get the MNI reference MR brain volume? I'd like to use it with mni_autoreg.
I tried the link below, but to no avail.
ftp://ftp.bic.mni.mcgill.ca/pub/mni_autoreg/mni_autoreg_model-1.01.tar.gz

I obtained the above link from the page below....is there and updated page?
http://www.bic.mni.mcgill.ca/users/louis/MNI_AUTOREG_home/readme/node3.html


Thanks,
Ayman


From eskild at gmail.com  Mon Jun 18 13:52:06 2012
From: eskild at gmail.com (Simon Eskildsen)
Date: Mon, 18 Jun 2012 19:52:06 +0200
Subject: [MINC-users] mni_autoreg volume
In-Reply-To: <790582915299864F9DC262BDDC538DF515F95B@EXMBX2010-2.campus.MCGILL.CA>
References: <790582915299864F9DC262BDDC538DF515F95B@EXMBX2010-2.campus.MCGILL.CA>
Message-ID: <CAD3v4362QttPLza3K1qAkaCWfZbWeyRXT4tJQsiWezD6ZL1CDA@mail.gmail.com>

Hi Ayman,
You can get the most recent public templates here:
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009

Simon

On Mon, Jun 18, 2012 at 5:23 PM, Ayman Oweida
<ayman.oweida at mail.mcgill.ca> wrote:
> Where can I get the MNI reference MR brain volume? I'd like to use it with mni_autoreg.
> I tried the link below, but to no avail.
> ftp://ftp.bic.mni.mcgill.ca/pub/mni_autoreg/mni_autoreg_model-1.01.tar.gz
>
> I obtained the above link from the page below....is there and updated page?
> http://www.bic.mni.mcgill.ca/users/louis/MNI_AUTOREG_home/readme/node3.html
>
>
> Thanks,
> Ayman
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From andrew at biospective.com  Tue Jun 19 17:58:07 2012
From: andrew at biospective.com (Andrew Wood)
Date: Tue, 19 Jun 2012 17:58:07 -0400
Subject: [MINC-users] Building minc-2.1.12
Message-ID: <CABApf9F1VfsrJcOXVychv4D+xK59Bkh9HbRe=KgCRq15=SunOw@mail.gmail.com>

Hi All,

I downloaded minc-2.1.12.tar.gz from github.com/BIC-MNI/minc/downloads
and I'm trying to build it. It didn't come with a configure script, so
I'm wondering if this might not be an actual release. I generated a
configure script with autotools, but the next failure was missing
"gram.h" in minccalc. Is there somewhere else I should be looking for
the latest release?

Thanks,
Andrew

From a.janke at gmail.com  Tue Jun 19 18:49:57 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 20 Jun 2012 08:49:57 +1000
Subject: [MINC-users] Building minc-2.1.12
In-Reply-To: <CABApf9F1VfsrJcOXVychv4D+xK59Bkh9HbRe=KgCRq15=SunOw@mail.gmail.com>
References: <CABApf9F1VfsrJcOXVychv4D+xK59Bkh9HbRe=KgCRq15=SunOw@mail.gmail.com>
Message-ID: <CAG0CB20SvUv9iiCBmhVNYO_BFYPAFp2Pte-1uiV7ayYxuU9jFw@mail.gmail.com>

Hi Andrew,

> I downloaded minc-2.1.12.tar.gz from github.com/BIC-MNI/minc/downloads
> and I'm trying to build it. It didn't come with a configure script, so
> I'm wondering if this might not be an actual release. I generated a
> configure script with autotools, but the next failure was missing
> "gram.h" in minccalc. Is there somewhere else I should be looking for
> the latest release?

If you are building from github as opposd from a release from
packages.bic.mni.mcigill.ca you will first need to run:

   $ ./autogen.sh

In the base MINC directory. This will generate you a configure script
that you can then run. You can also bild MINC with Cmake if you are
that way inclined.

a

From andrew at biospective.com  Wed Jun 20 10:18:18 2012
From: andrew at biospective.com (Andrew Wood)
Date: Wed, 20 Jun 2012 10:18:18 -0400
Subject: [MINC-users] Building minc-2.1.12
In-Reply-To: <CAG0CB20SvUv9iiCBmhVNYO_BFYPAFp2Pte-1uiV7ayYxuU9jFw@mail.gmail.com>
References: <CABApf9F1VfsrJcOXVychv4D+xK59Bkh9HbRe=KgCRq15=SunOw@mail.gmail.com>
	<CAG0CB20SvUv9iiCBmhVNYO_BFYPAFp2Pte-1uiV7ayYxuU9jFw@mail.gmail.com>
Message-ID: <CABApf9G7dHu7CupBY0Bk=ySbTyV_CHBDHv1M1Cnkn+c36Xo5Jg@mail.gmail.com>

Hi Andrew,

I used autogen.sh to generate a configure script, but the build still
fails in lex.l for minccalc.

lex.l:4:18: error: gram.h: No such file or directory

Thanks,
Andrew

On Tue, Jun 19, 2012 at 6:49 PM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Andrew,
>
>> I downloaded minc-2.1.12.tar.gz from github.com/BIC-MNI/minc/downloads
>> and I'm trying to build it. It didn't come with a configure script, so
>> I'm wondering if this might not be an actual release. I generated a
>> configure script with autotools, but the next failure was missing
>> "gram.h" in minccalc. Is there somewhere else I should be looking for
>> the latest release?
>
> If you are building from github as opposd from a release from
> packages.bic.mni.mcigill.ca you will first need to run:
>
> ? $ ./autogen.sh
>
> In the base MINC directory. This will generate you a configure script
> that you can then run. You can also bild MINC with Cmake if you are
> that way inclined.
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From assemlal at cim.mcgill.ca  Wed Jun 20 10:31:02 2012
From: assemlal at cim.mcgill.ca (Haz-Edine Assemlal)
Date: Wed, 20 Jun 2012 10:31:02 -0400
Subject: [MINC-users] Building minc-2.1.12
In-Reply-To: <CABApf9G7dHu7CupBY0Bk=ySbTyV_CHBDHv1M1Cnkn+c36Xo5Jg@mail.gmail.com>
References: <CABApf9F1VfsrJcOXVychv4D+xK59Bkh9HbRe=KgCRq15=SunOw@mail.gmail.com>
	<CAG0CB20SvUv9iiCBmhVNYO_BFYPAFp2Pte-1uiV7ayYxuU9jFw@mail.gmail.com>
	<CABApf9G7dHu7CupBY0Bk=ySbTyV_CHBDHv1M1Cnkn+c36Xo5Jg@mail.gmail.com>
Message-ID: <1340202662.3318.16.camel@talos>

Hi,

Try with CMake:

1 - go to the root directory of minc
2 - mkdir build && cd build
3 - cmake .. ( or ccmake for a gui)
4 - make && make install

-
Haz-Edine


On Wed, 2012-06-20 at 10:18 -0400, Andrew Wood wrote:
> Hi Andrew,
> 
> I used autogen.sh to generate a configure script, but the build still
> fails in lex.l for minccalc.
> 
> lex.l:4:18: error: gram.h: No such file or directory
> 
> Thanks,
> Andrew
> 
> On Tue, Jun 19, 2012 at 6:49 PM, Andrew Janke <a.janke at gmail.com> wrote:
> > Hi Andrew,
> >
> >> I downloaded minc-2.1.12.tar.gz from github.com/BIC-MNI/minc/downloads
> >> and I'm trying to build it. It didn't come with a configure script, so
> >> I'm wondering if this might not be an actual release. I generated a
> >> configure script with autotools, but the next failure was missing
> >> "gram.h" in minccalc. Is there somewhere else I should be looking for
> >> the latest release?
> >
> > If you are building from github as opposd from a release from
> > packages.bic.mni.mcigill.ca you will first need to run:
> >
> >   $ ./autogen.sh
> >
> > In the base MINC directory. This will generate you a configure script
> > that you can then run. You can also bild MINC with Cmake if you are
> > that way inclined.
> >
> > a
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users



From andrew at biospective.com  Wed Jun 20 13:43:54 2012
From: andrew at biospective.com (Andrew Wood)
Date: Wed, 20 Jun 2012 13:43:54 -0400
Subject: [MINC-users] Building minc-2.1.12
In-Reply-To: <1340202662.3318.16.camel@talos>
References: <CABApf9F1VfsrJcOXVychv4D+xK59Bkh9HbRe=KgCRq15=SunOw@mail.gmail.com>
	<CAG0CB20SvUv9iiCBmhVNYO_BFYPAFp2Pte-1uiV7ayYxuU9jFw@mail.gmail.com>
	<CABApf9G7dHu7CupBY0Bk=ySbTyV_CHBDHv1M1Cnkn+c36Xo5Jg@mail.gmail.com>
	<1340202662.3318.16.camel@talos>
Message-ID: <CABApf9E0dAfjBZXwbtGMaQZdUW7mjzFz2yLHK2r=9RWTHpcYDg@mail.gmail.com>

Hi,

The cmake build was successful. It would be nice to sort out why the
GNU make isn't working, but I can proceed with cmake for now.

If one wants to stay up to date with minc releases, which is the best
location to watch? Is there a difference between versions suitable for
packages.bic.mni.mcigill.ca versus the downloads page at github?

Thanks,
Andrew


On Wed, Jun 20, 2012 at 10:31 AM, Haz-Edine Assemlal
<assemlal at cim.mcgill.ca> wrote:
> Hi,
>
> Try with CMake:
>
> 1 - go to the root directory of minc
> 2 - mkdir build && cd build
> 3 - cmake .. ( or ccmake for a gui)
> 4 - make && make install
>
> -
> Haz-Edine
>
>
> On Wed, 2012-06-20 at 10:18 -0400, Andrew Wood wrote:
>> Hi Andrew,
>>
>> I used autogen.sh to generate a configure script, but the build still
>> fails in lex.l for minccalc.
>>
>> lex.l:4:18: error: gram.h: No such file or directory
>>
>> Thanks,
>> Andrew
>>
>> On Tue, Jun 19, 2012 at 6:49 PM, Andrew Janke <a.janke at gmail.com> wrote:
>> > Hi Andrew,
>> >
>> >> I downloaded minc-2.1.12.tar.gz from github.com/BIC-MNI/minc/downloads
>> >> and I'm trying to build it. It didn't come with a configure script, so
>> >> I'm wondering if this might not be an actual release. I generated a
>> >> configure script with autotools, but the next failure was missing
>> >> "gram.h" in minccalc. Is there somewhere else I should be looking for
>> >> the latest release?
>> >
>> > If you are building from github as opposd from a release from
>> > packages.bic.mni.mcigill.ca you will first need to run:
>> >
>> > ? $ ./autogen.sh
>> >
>> > In the base MINC directory. This will generate you a configure script
>> > that you can then run. You can also bild MINC with Cmake if you are
>> > that way inclined.
>> >
>> > a
>> > _______________________________________________
>> > MINC-users at bic.mni.mcgill.ca
>> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From ayman.oweida at mail.mcgill.ca  Wed Jun 20 13:59:34 2012
From: ayman.oweida at mail.mcgill.ca (Ayman Oweida)
Date: Wed, 20 Jun 2012 17:59:34 +0000
Subject: [MINC-users] installing mni_autoreg
Message-ID: <790582915299864F9DC262BDDC538DF5162069@EXMBX2010-2.campus.MCGILL.CA>


I installed mni_autoreg on osx 10.6.8 and I received the error below when running related commands (mritoself, etc).
Any insight?

Thanks,
Ayman


Can't locate MNI/Startup.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /usr/local//bic/bin/mritoself line 31.
BEGIN failed--compilation aborted at /usr/local//bic/bin/mritoself line 31.



From jason at phenogenomics.ca  Wed Jun 20 14:03:39 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Wed, 20 Jun 2012 14:03:39 -0400
Subject: [MINC-users] installing mni_autoreg
In-Reply-To: <790582915299864F9DC262BDDC538DF5162069@EXMBX2010-2.campus.MCGILL.CA>
References: <790582915299864F9DC262BDDC538DF5162069@EXMBX2010-2.campus.MCGILL.CA>
Message-ID: <FC413AEB-A273-4B10-BBBE-C86314410EFD@phenogenomics.ca>

Install mni_perllib first.

mni_perllib-0.08.tar.gz

Jason

On 2012-06-20, at 1:59 PM, Ayman Oweida wrote:

> 
> I installed mni_autoreg on osx 10.6.8 and I received the error below when running related commands (mritoself, etc).
> Any insight?
> 
> Thanks,
> Ayman
> 
> 
> Can't locate MNI/Startup.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /usr/local//bic/bin/mritoself line 31.
> BEGIN failed--compilation aborted at /usr/local//bic/bin/mritoself line 31.
> 
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From jason at phenogenomics.ca  Wed Jun 20 14:07:53 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Wed, 20 Jun 2012 14:07:53 -0400
Subject: [MINC-users] installing mni_autoreg
In-Reply-To: <FC413AEB-A273-4B10-BBBE-C86314410EFD@phenogenomics.ca>
References: <790582915299864F9DC262BDDC538DF5162069@EXMBX2010-2.campus.MCGILL.CA>
Message-ID: <36FAE925-5BFD-48B6-8173-636FE5A71124@phenogenomics.ca>

Sorry, the link should have been:

http://packages.bic.mni.mcgill.ca/tgz/mni_perllib-0.08.tar.gz

Jason

On 2012-06-20, at 2:03 PM, Jason Lerch wrote:

> Install mni_perllib first.
> 
> mni_perllib-0.08.tar.gz
> 
> Jason
> 
> On 2012-06-20, at 1:59 PM, Ayman Oweida wrote:
> 
>> 
>> I installed mni_autoreg on osx 10.6.8 and I received the error below when running related commands (mritoself, etc).
>> Any insight?
>> 
>> Thanks,
>> Ayman
>> 
>> 
>> Can't locate MNI/Startup.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /usr/local//bic/bin/mritoself line 31.
>> BEGIN failed--compilation aborted at /usr/local//bic/bin/mritoself line 31.
>> 
>> 
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From ayman.oweida at mail.mcgill.ca  Wed Jun 20 17:45:54 2012
From: ayman.oweida at mail.mcgill.ca (Ayman Oweida)
Date: Wed, 20 Jun 2012 21:45:54 +0000
Subject: [MINC-users] installing mni_autoreg
In-Reply-To: <36FAE925-5BFD-48B6-8173-636FE5A71124@phenogenomics.ca>
References: <FC413AEB-A273-4B10-BBBE-C86314410EFD@phenogenomics.ca>
	<36FAE925-5BFD-48B6-8173-636FE5A71124@phenogenomics.ca>
Message-ID: <790582915299864F9DC262BDDC538DF51626E4@EXMBX2010-2.campus.MCGILL.CA>

Thanks Jason.

I followed the instructions for building mni_perl in the readme file, but didn't succeed.
I get the following error upon executing perl Makefile.pl


Makefile.PL: I don't grok the manifypods section, so can't tweak the pod2man args at Makefile.PL line 162.
Writing Makefile for mni_perllib



On 2012-06-20, at 2:07 PM, Jason Lerch wrote:

> Sorry, the link should have been:
> 
> http://packages.bic.mni.mcgill.ca/tgz/mni_perllib-0.08.tar.gz
> 
> Jason
> 
> On 2012-06-20, at 2:03 PM, Jason Lerch wrote:
> 
>> Install mni_perllib first.
>> 
>> mni_perllib-0.08.tar.gz
>> 
>> Jason
>> 
>> On 2012-06-20, at 1:59 PM, Ayman Oweida wrote:
>> 
>>> 
>>> I installed mni_autoreg on osx 10.6.8 and I received the error below when running related commands (mritoself, etc).
>>> Any insight?
>>> 
>>> Thanks,
>>> Ayman
>>> 
>>> 
>>> Can't locate MNI/Startup.pm in @INC (@INC contains: /sw/lib/perl5/5.10.0/darwin-thread-multi-2level /sw/lib/perl5/5.10.0 /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /usr/local//bic/bin/mritoself line 31.
>>> BEGIN failed--compilation aborted at /usr/local//bic/bin/mritoself line 31.
>>> 
>>> 
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> 
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

Ayman Oweida, MSc
PhD Candidate
McGill University
Department of Experimental Medicine

Montreal General Hospital 
1650 Cedar Ave, L5-112
Montreal, QC  H3G 1A4
(514) 934-1934 x. 43019



From a.janke at gmail.com  Wed Jun 20 23:44:18 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 21 Jun 2012 13:44:18 +1000
Subject: [MINC-users] Building minc-2.1.12
In-Reply-To: <CABApf9E0dAfjBZXwbtGMaQZdUW7mjzFz2yLHK2r=9RWTHpcYDg@mail.gmail.com>
References: <CABApf9F1VfsrJcOXVychv4D+xK59Bkh9HbRe=KgCRq15=SunOw@mail.gmail.com>
	<CAG0CB20SvUv9iiCBmhVNYO_BFYPAFp2Pte-1uiV7ayYxuU9jFw@mail.gmail.com>
	<CABApf9G7dHu7CupBY0Bk=ySbTyV_CHBDHv1M1Cnkn+c36Xo5Jg@mail.gmail.com>
	<1340202662.3318.16.camel@talos>
	<CABApf9E0dAfjBZXwbtGMaQZdUW7mjzFz2yLHK2r=9RWTHpcYDg@mail.gmail.com>
Message-ID: <CAG0CB22m6zDO+T_hOKS7Lq8PO2kt-pHq9X_4rUV9m=9RWvMk1g@mail.gmail.com>

Hi Andrew,

On 21 June 2012 03:43, Andrew Wood <andrew at biospective.com> wrote:
> The cmake build was successful. It would be nice to sort out why the
> GNU make isn't working, but I can proceed with cmake for now.

Do you have bison and yacc installed?  The CMake build builds from a
static generated .c file in minccalc instead of from the original .l
and .y files.

> If one wants to stay up to date with minc releases, which is the best
> location to watch? Is there a difference between versions suitable for
> packages.bic.mni.mcigill.ca versus the downloads page at github?

packages.bic.mni.mcigill.ca contains official releases, the github
pages is for development work.


a

From zijdenbos at gmail.com  Wed Jun 20 23:53:42 2012
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Wed, 20 Jun 2012 23:53:42 -0400
Subject: [MINC-users] mincblur with FWHM =?utf-8?Q?<=3D_?=voxel dims
Message-ID: <0A683A0DC4174CFDBCB6651E4B3DF5E3@gmail.com>

I've been wondering for some time what happens when you (minc)blur a volume with a FWHM that is about the same or less than the voxel dimension. Admittedly I am rather rusty on the intricate and practical details of scale space/FFT/convolution/etc, so this may well be showing my ignorance; but hopefully there are people on this list smarter than me who can enlighten me :)  

Empirically, when you reduce the FWHM to below the voxel dimension, the voxel value of the blurred image increases. Moreover, for an image with 1mm isotropic voxels, the FWHM at which the voxel values of the result are about equivalent to those in the source image seems to be around 1.3, give or take. See this image:  
?
mni_icbm_00102_t1_blurs.png (http://cl.ly/2A1m3Y470P0M3S3J2Q0j)

which shows in the top row the original, 1mm isotropic, volume, followed by the result of running mincblur on it with decreasing FWHM from 1.5 to 0.5mm. I used spectral with a fixed range across all rows to bring out the signal difference.

So - is this expected? Surprising? Follows theory or bad behaviour of mincblur? After scribbling a few pages with normal distributions and looking through the mincblur code I still can't quite figure it out. Anybody can explain this to me?

Thanks,

-- Alex

PS In case you are wondering why one would want to do this, the answer is probably: you don't; but  one of the nice things about MINC is that as a user I don't need to care too much about pesky things like voxel dimensions, so let's say you have a script that blurs with a 2mm FWHM and you happen to pass that an image with 4mm voxels, you will end up with a more than 6-fold signal increase that you probably didn't expect (e.g., run a PET image through an MRI registration script). I could also imagine that in certain circumstances it might bite other blurring-dependent analyses (e.g., fMRI, VBM).

From a.janke at gmail.com  Thu Jun 21 02:34:57 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 21 Jun 2012 16:34:57 +1000
Subject: [MINC-users] mincblur with FWHM <= voxel dims
In-Reply-To: <0A683A0DC4174CFDBCB6651E4B3DF5E3@gmail.com>
References: <0A683A0DC4174CFDBCB6651E4B3DF5E3@gmail.com>
Message-ID: <CAG0CB22ToqGK5j3Soj8FEcx+mJ7xw3N+c9qypxNaB+_OuRyvdQ@mail.gmail.com>

On 21 June 2012 13:53, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> Empirically, when you reduce the FWHM to below the voxel dimension, the voxel value of the blurred image increases. Moreover, for an image with 1mm isotropic voxels, the FWHM at which the voxel values of the result are about equivalent to those in the source image seems to be around 1.3, give or take. See this image:
>
> mni_icbm_00102_t1_blurs.png (http://cl.ly/2A1m3Y470P0M3S3J2Q0j)
>
> which shows in the top row the original, 1mm isotropic, volume, followed by the result of running mincblur on it with decreasing FWHM from 1.5 to 0.5mm. I used spectral with a fixed range across all rows to bring out the signal difference.
>
> So - is this expected? Surprising? Follows theory or bad behaviour of mincblur? After scribbling a few pages with normal distributions and looking through the mincblur code I still can't quite figure it out. Anybody can explain this to me?

I'd say expected (given how mincblur works) and I'd also say is the
correct behaviour.  If you think of the blur as fitting a Gaussian to
your noisy peak then as the width of this peak decreases, the height
of it increases to the same given amount of signal.

As for if it should happen when you (or a script) doesn't sanitise
inputs then you probably have an argument that mincblur should give a
warning. I would argue that the script should check the input sampling
though, certainly I remember doing this in a few scripts of mine. I
won't be so bold to say that I do check in all scripts I write though!



a

From a.janke at gmail.com  Thu Jun 21 02:36:45 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 21 Jun 2012 16:36:45 +1000
Subject: [MINC-users] installing mni_autoreg
In-Reply-To: <790582915299864F9DC262BDDC538DF51626E4@EXMBX2010-2.campus.MCGILL.CA>
References: <FC413AEB-A273-4B10-BBBE-C86314410EFD@phenogenomics.ca>
	<36FAE925-5BFD-48B6-8173-636FE5A71124@phenogenomics.ca>
	<790582915299864F9DC262BDDC538DF51626E4@EXMBX2010-2.campus.MCGILL.CA>
Message-ID: <CAG0CB20X+VapLq-gccr=QdGxO65gcjz2mkJYfOavZYbyJPXx8g@mail.gmail.com>

> I followed the instructions for building mni_perl in the readme file, but didn't succeed.
> I get the following error upon executing perl Makefile.pl
>
> Makefile.PL: I don't grok the manifypods section, so can't tweak the pod2man args at Makefile.PL line 162.
> Writing Makefile for mni_perllib

This should only be a warning.  The general process for perl modules is this:

   $ tar zxvf perllib.tgz

   $ cd perllib

   $ perl Makefile.PL

   $ make

   $ make check   # optional

   $ sudo make install


a

From a.janke at gmail.com  Thu Jun 21 08:15:11 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 21 Jun 2012 22:15:11 +1000
Subject: [MINC-users] HDF5-1.8.5 vs HDF5-1.8.5-patch1
In-Reply-To: <CABApf9GHGEo9yevbgdPA8tbMJKfRCKWJcb_Dg-1fQA62XmR5hg@mail.gmail.com>
References: <CABApf9GHGEo9yevbgdPA8tbMJKfRCKWJcb_Dg-1fQA62XmR5hg@mail.gmail.com>
Message-ID: <CAG0CB20OEPCJKB1F8DH7qgeBCYkOFu5tXM4TdJgA-Qi368h37Q@mail.gmail.com>

Hi Andrew,

> I ran into a problem running minc commands on gzipped files (I'm using a
> locally-built MINC 2.1 and HDF5-1.8.5-patch1):
>
> $ mincinfo icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz
> ?(from miexpand_file): Cannot uncompress the file
> mincinfo: Error expanding file
> "icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz"

Thanks for this report. At the time I remember building against this
specific release and hitting the same problem. I haven't found the
cause of the problem but I have yet to see it rear it's head again
with later builds up to 1.8.9 (the current release).

Here's hoping we can tick this one off as "done".

Thanks


a

From ayman.oweida at mail.mcgill.ca  Fri Jun 22 10:39:01 2012
From: ayman.oweida at mail.mcgill.ca (Ayman Oweida)
Date: Fri, 22 Jun 2012 14:39:01 +0000
Subject: [MINC-users] installing mni_autoreg
In-Reply-To: <CAG0CB20X+VapLq-gccr=QdGxO65gcjz2mkJYfOavZYbyJPXx8g@mail.gmail.com>
References: <FC413AEB-A273-4B10-BBBE-C86314410EFD@phenogenomics.ca>
	<36FAE925-5BFD-48B6-8173-636FE5A71124@phenogenomics.ca>
	<790582915299864F9DC262BDDC538DF51626E4@EXMBX2010-2.campus.MCGILL.CA>
	<CAG0CB20X+VapLq-gccr=QdGxO65gcjz2mkJYfOavZYbyJPXx8g@mail.gmail.com>
Message-ID: <790582915299864F9DC262BDDC538DF51699B5@EXMBX2010-1.campus.MCGILL.CA>


So, after running the commands below, I get the following:

Ayman-Oweidas-MacBook-Pro:mni_perllib-0.08 Ayman$ sudo make install
Password:
Manifying blib/man3/MNI::DataDir.3pm
Not a HASH reference at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 557.
make: *** [pure_site_install] Error 2

Your help is appreciated.

-Ayman


On 2012-06-21, at 2:36 AM, Andrew Janke wrote:

>> I followed the instructions for building mni_perl in the readme file, but didn't succeed.
>> I get the following error upon executing perl Makefile.pl
>> 
>> Makefile.PL: I don't grok the manifypods section, so can't tweak the pod2man args at Makefile.PL line 162.
>> Writing Makefile for mni_perllib
> 
> This should only be a warning.  The general process for perl modules is this:
> 
>   $ tar zxvf perllib.tgz
> 
>   $ cd perllib
> 
>   $ perl Makefile.PL
> 
>   $ make
> 
>   $ make check   # optional
> 
>   $ sudo make install
> 
> 
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From jon.pipitone at utoronto.ca  Fri Jun 22 11:27:55 2012
From: jon.pipitone at utoronto.ca (jon pipitone)
Date: Fri, 22 Jun 2012 11:27:55 -0400
Subject: [MINC-users] mincresample MINC 2.0 compression
Message-ID: <CAKS_Keoe9GOJYs0xBxFO2ZDJn9kYScP8yj2BVR=HFS=g0u01bQ@mail.gmail.com>

Hey all,

I'm currently doing some processing work in which I need to take care of
the storage space I'm consuming, so I'd like to keep my minc volumes
compressed where possible.  I see that mincconvert has the option to
compress a volume in 2.0 format, but is there any way to *produce* a
compressed volume as the output of mincresample and friends?  The help for
mincresample (2.1.01) shows nothing obvious to do this, but maybe I'm
overlooking something as I'm pretty new to these tools.

Of course, I can always just run a pass of mincconvert to compress my
outputs as I go, but it would be handy to be able to do this in a single
step.

Thanks,
Jon.

From jason at phenogenomics.ca  Fri Jun 22 11:39:09 2012
From: jason at phenogenomics.ca (Jason Lerch)
Date: Fri, 22 Jun 2012 11:39:09 -0400
Subject: [MINC-users] mincresample MINC 2.0 compression
In-Reply-To: <CAKS_Keoe9GOJYs0xBxFO2ZDJn9kYScP8yj2BVR=HFS=g0u01bQ@mail.gmail.com>
References: <CAKS_Keoe9GOJYs0xBxFO2ZDJn9kYScP8yj2BVR=HFS=g0u01bQ@mail.gmail.com>
Message-ID: <D8B5E41B-51CF-428B-876F-A78E691622CF@phenogenomics.ca>

Set the MINC_COMPRESS environment variable (4 is a good setting) to force compression of all MINC2 volumes.

Jason

On 2012-06-22, at 11:27 AM, jon pipitone wrote:

> Hey all,
> 
> I'm currently doing some processing work in which I need to take care of
> the storage space I'm consuming, so I'd like to keep my minc volumes
> compressed where possible.  I see that mincconvert has the option to
> compress a volume in 2.0 format, but is there any way to *produce* a
> compressed volume as the output of mincresample and friends?  The help for
> mincresample (2.1.01) shows nothing obvious to do this, but maybe I'm
> overlooking something as I'm pretty new to these tools.
> 
> Of course, I can always just run a pass of mincconvert to compress my
> outputs as I go, but it would be handy to be able to do this in a single
> step.
> 
> Thanks,
> Jon.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From jon.pipitone at utoronto.ca  Fri Jun 22 11:53:07 2012
From: jon.pipitone at utoronto.ca (jon pipitone)
Date: Fri, 22 Jun 2012 11:53:07 -0400
Subject: [MINC-users] mincresample MINC 2.0 compression
In-Reply-To: <D8B5E41B-51CF-428B-876F-A78E691622CF@phenogenomics.ca>
References: <CAKS_Keoe9GOJYs0xBxFO2ZDJn9kYScP8yj2BVR=HFS=g0u01bQ@mail.gmail.com>
	<D8B5E41B-51CF-428B-876F-A78E691622CF@phenogenomics.ca>
Message-ID: <CAKS_KeoHYeDroVgvfo=GZ6mr1XcM1Fi9K1ZoU5UtaLU9uYgdZw@mail.gmail.com>

>
> Set the MINC_COMPRESS environment variable (4 is a good setting) to force
> compression of all MINC2 volumes.
>

Magic!

Thanks Jason,
Jon.

From a.janke at gmail.com  Sun Jun 24 06:52:36 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Sun, 24 Jun 2012 20:52:36 +1000
Subject: [MINC-users] installing mni_autoreg
In-Reply-To: <790582915299864F9DC262BDDC538DF51699B5@EXMBX2010-1.campus.MCGILL.CA>
References: <FC413AEB-A273-4B10-BBBE-C86314410EFD@phenogenomics.ca>
	<36FAE925-5BFD-48B6-8173-636FE5A71124@phenogenomics.ca>
	<790582915299864F9DC262BDDC538DF51626E4@EXMBX2010-2.campus.MCGILL.CA>
	<CAG0CB20X+VapLq-gccr=QdGxO65gcjz2mkJYfOavZYbyJPXx8g@mail.gmail.com>
	<790582915299864F9DC262BDDC538DF51699B5@EXMBX2010-1.campus.MCGILL.CA>
Message-ID: <CAG0CB22_NxeAj0seuk1Nw9bAHRGNmm=yzSqmYJsEM3cy0-XSHg@mail.gmail.com>

> So, after running the commands below, I get the following:
>
> Ayman-Oweidas-MacBook-Pro:mni_perllib-0.08 Ayman$ sudo make install
> Password:
> Manifying blib/man3/MNI::DataDir.3pm
> Not a HASH reference at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 557.
> make: *** [pure_site_install] Error 2

I am guessing that by this stage everything up until this has
completed OK? I am guessing you are using the inbuilt perl in OSX? On
older versions of OSX I found this problematic and used the macports
or fink version but am not sure if this is still the case.

There are others on here who use OSX and MINC so I am hoping they will
chime in here.


a

From zijdenbos at gmail.com  Sun Jun 24 17:20:54 2012
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Sun, 24 Jun 2012 23:20:54 +0200
Subject: [MINC-users] mincblur with FWHM =?utf-8?Q?<=3D_?=voxel dims
In-Reply-To: <CAG0CB22ToqGK5j3Soj8FEcx+mJ7xw3N+c9qypxNaB+_OuRyvdQ@mail.gmail.com>
References: <0A683A0DC4174CFDBCB6651E4B3DF5E3@gmail.com>
	<CAG0CB22ToqGK5j3Soj8FEcx+mJ7xw3N+c9qypxNaB+_OuRyvdQ@mail.gmail.com>
Message-ID: <B7EB53C7B0834D548E1F147DB8755A2E@gmail.com>

On Thursday, 21 June, 2012 at 8:34 AM, Andrew Janke wrote:
> On 21 June 2012 13:53, Alex Zijdenbos <zijdenbos at gmail.com (mailto:zijdenbos at gmail.com)> wrote:
> > Empirically, when you reduce the FWHM to below the voxel dimension, the voxel value of the blurred image increases. Moreover, for an image with 1mm isotropic voxels, the FWHM at which the voxel values of the result are about equivalent to those in the source image seems to be around 1.3, give or take. See this image:
> >  
> > mni_icbm_00102_t1_blurs.png (http://cl.ly/2A1m3Y470P0M3S3J2Q0j)
> >  
> > which shows in the top row the original, 1mm isotropic, volume, followed by the result of running mincblur on it with decreasing FWHM from 1.5 to 0.5mm. I used spectral with a fixed range across all rows to bring out the signal difference.
> >  
> > So - is this expected? Surprising? Follows theory or bad behaviour of mincblur? After scribbling a few pages with normal distributions and looking through the mincblur code I still can't quite figure it out. Anybody can explain this to me?
>  
> I'd say expected (given how mincblur works) and I'd also say is the
> correct behaviour. If you think of the blur as fitting a Gaussian to
> your noisy peak then as the width of this peak decreases, the height
> of it increases to the same given amount of signal.
>  
>  

That is also the explanation I managed to come up with; however, having studied this a bit further, I disagree with this being the "correct" behaviour. (Gaussian) blurring is expected to adhere to "average grey level invariance", meaning that the filter should not modify the mean value of the image. And that is not a resolution-dependent principle, so I would say that mincblur should adhere to this regardless of the relationship between the kernel width and voxel size.   

I did some experimenting by blurring a binary cube in an image and monitoring the mean value (generously padded and away from the image edge to avoid edge effects). See this graph: ?mincblur_mean.png (http://cl.ly/2V472I092L3U3R3e0k02) which shows the mean value of the 1mm isotropic image as a function of kernel FWHM running from 0.2 to 5.0mm with 0.1mm steps. You can see that for FWHM < 2*voxel_dim the mean signal starts to go up rather steeply. By contrast, the orange HR line is from the same image, but obtained by first upsampling it to a relatively high (0.1mm) resolution, performing the blur at that resolution, and downsampling the result. I would argue that, barring some resampling effects, these curves should be the same.

I should note that the blurring implemented in FSL for example, does adhere to the average grey level invariance principle (regardless of voxel size).
> As for if it should happen when you (or a script) doesn't sanitize
> inputs then you probably have an argument that mincblur should give a
> warning. I would argue that the script should check the input sampling
> though, certainly I remember doing this in a few scripts of mine. I
> won't be so bold to say that I do check in all scripts I write though!
>  
>  

:) neither would I. But I actually think that mincblur should be fixed, in which case it won't need to produce a warning. I would imagine this means changing the kernel normalization. Of course a wrapper script could also fix this simply by scaling the image; but figuring out the right scaling factor would probably involve padding the images prior to blurring to not be affected by edge effects.

-- A 

From vladimir.fonov at gmail.com  Sun Jun 24 20:07:22 2012
From: vladimir.fonov at gmail.com (Vladimir S. Fonov)
Date: Sun, 24 Jun 2012 20:07:22 -0400
Subject: [MINC-users] mincblur with FWHM <= voxel dims
In-Reply-To: <B7EB53C7B0834D548E1F147DB8755A2E@gmail.com>
References: <0A683A0DC4174CFDBCB6651E4B3DF5E3@gmail.com>
	<CAG0CB22ToqGK5j3Soj8FEcx+mJ7xw3N+c9qypxNaB+_OuRyvdQ@mail.gmail.com>
	<B7EB53C7B0834D548E1F147DB8755A2E@gmail.com>
Message-ID: <4FE7ABBA.3060802@gmail.com>

Hello,

I have my own implementation of gaussian blurring in EZminc:
https://github.com/vfonov/EZminc/blob/master/tools/fast_blur.cpp
(fast_blur binary in the minc-toolkit) .
I think it behaves properly for any blurring kernel size, and it 
produces the same results as mincblur when fwhm> 2*voxel size

On 24/06/2012 5:20 PM, Alex Zijdenbos wrote:
> I did some experimenting by blurring a binary cube in an image and
> monitoring the mean value (generously padded and away from the image
> edge to avoid edge effects). See this graph: ?mincblur_mean.png
> (http://cl.ly/2V472I092L3U3R3e0k02) which shows the mean value of the
> 1mm isotropic image as a function of kernel FWHM running from 0.2 to
> 5.0mm with 0.1mm steps. You can see that for FWHM<  2*voxel_dim the
> mean signal starts to go up rather steeply. By contrast, the orange
> HR line is from the same image, but obtained by first upsampling it
> to a relatively high (0.1mm) resolution, performing the blur at that
> resolution, and downsampling the result. I would argue that, barring
> some resampling effects, these curves should be the same.

-- 
Best regards,

  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com

From zijdenbos at gmail.com  Mon Jun 25 17:44:51 2012
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Mon, 25 Jun 2012 23:44:51 +0200
Subject: [MINC-users] mincblur with FWHM =?utf-8?Q?<=3D_?=voxel dims
In-Reply-To: <4FE7ABBA.3060802@gmail.com>
References: <0A683A0DC4174CFDBCB6651E4B3DF5E3@gmail.com>
	<CAG0CB22ToqGK5j3Soj8FEcx+mJ7xw3N+c9qypxNaB+_OuRyvdQ@mail.gmail.com>
	<B7EB53C7B0834D548E1F147DB8755A2E@gmail.com>
	<4FE7ABBA.3060802@gmail.com>
Message-ID: <1DDC786AF7C54760BB45F75C40D0426A@gmail.com>

Thanks, Vladimir - this is very interesting. Tried, tested, and true - I ran the same series of blurring experiments, and comparing mincblur to fast_blur you are absolutely correct that it maintains grey level across all kernel widths, see this snap:
 ?
mincblur-fastblur_4.00mm.png (http://cl.ly/3o3f0l1o0J330s3X3M42)  

The image comparison on the right is the mincblur result of the 5mm blurring kernel (left column) and the difference (simple subtraction) between the mincblur and fast_blur result at that scale. Some things of note:

- fast_blur maintains average grey level to at least 6 decimals; you can see in the graph above that mincblur deviates somewhat even all the way out to 5x voxel size

- mincblur also generates some odd artifacts (the dot pattern) that I haven't been able to explain so far.

- as the 'picture frame' image on the right shows, there are some slight differences between both methods. The amplitude of that diff is very small though, in the range [-2e-5,2e-5] so that is probably just quantization (the in-/and output volumes are short).

- fast_blur uses about 40% more memory.

With the exception of that last point, I think fast_blur wins this contest hands down?

Question perhaps is: should we "MINC" have multiple pieces of code for doing the exact same thing, slightly differently? Me thinks not, but?  

-- A

--  
Alex Zijdenbos
Sent with Sparrow (http://www.sparrowmailapp.com)


On Monday, 25 June, 2012 at 2:07 AM, Vladimir S. Fonov wrote:

> Hello,
>  
> I have my own implementation of gaussian blurring in EZminc:
> https://github.com/vfonov/EZminc/blob/master/tools/fast_blur.cpp
> (fast_blur binary in the minc-toolkit) .
> I think it behaves properly for any blurring kernel size, and it  
> produces the same results as mincblur when fwhm> 2*voxel size
>  
> On 24/06/2012 5:20 PM, Alex Zijdenbos wrote:
> > I did some experimenting by blurring a binary cube in an image and
> > monitoring the mean value (generously padded and away from the image
> > edge to avoid edge effects). See this graph: ?mincblur_mean.png
> > (http://cl.ly/2V472I092L3U3R3e0k02) which shows the mean value of the
> > 1mm isotropic image as a function of kernel FWHM running from 0.2 to
> > 5.0mm with 0.1mm steps. You can see that for FWHM< 2*voxel_dim the
> > mean signal starts to go up rather steeply. By contrast, the orange
> > HR line is from the same image, but obtained by first upsampling it
> > to a relatively high (0.1mm) resolution, performing the blur at that
> > resolution, and downsampling the result. I would argue that, barring
> > some resampling effects, these curves should be the same.
> >  
>  
>  
> --  
> Best regards,
>  
> Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca (mailto:MINC-users at bic.mni.mcgill.ca)
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>  
>  



From vladimir.fonov at gmail.com  Mon Jun 25 20:24:45 2012
From: vladimir.fonov at gmail.com (Vladimir S. Fonov)
Date: Mon, 25 Jun 2012 20:24:45 -0400
Subject: [MINC-users] mincblur with FWHM <= voxel dims
In-Reply-To: <1DDC786AF7C54760BB45F75C40D0426A@gmail.com>
References: <0A683A0DC4174CFDBCB6651E4B3DF5E3@gmail.com>
	<CAG0CB22ToqGK5j3Soj8FEcx+mJ7xw3N+c9qypxNaB+_OuRyvdQ@mail.gmail.com>
	<B7EB53C7B0834D548E1F147DB8755A2E@gmail.com>
	<4FE7ABBA.3060802@gmail.com>
	<1DDC786AF7C54760BB45F75C40D0426A@gmail.com>
Message-ID: <4FE9014D.602@gmail.com>

Hello,

fast_blur uses FFTW library to perform it's calculations, which is 
distributed under GPL license.
So, effectively EZminc should also be distributed under GPL license.

On the other hand mincblur is part of mni_autoreg with it's own 
implementation of FFT (?) and also distributed under it's own license ( 
see https://github.com/BIC-MNI/mni_autoreg/blob/master/COPYING ).

On 12-06-25 05:44 PM, Alex Zijdenbos wrote:
> With the exception of that last point, I think fast_blur wins this
> contest hands down?
>
> Question perhaps is: should we "MINC" have multiple pieces of code
> for doing the exact same thing, slightly differently? Me thinks not,
> but?

-- 
Best regards,
  Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com



From a.janke at gmail.com  Mon Jun 25 21:21:15 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 26 Jun 2012 11:21:15 +1000
Subject: [MINC-users] mincblur with FWHM <= voxel dims
In-Reply-To: <4FE9014D.602@gmail.com>
References: <0A683A0DC4174CFDBCB6651E4B3DF5E3@gmail.com>
	<CAG0CB22ToqGK5j3Soj8FEcx+mJ7xw3N+c9qypxNaB+_OuRyvdQ@mail.gmail.com>
	<B7EB53C7B0834D548E1F147DB8755A2E@gmail.com>
	<4FE7ABBA.3060802@gmail.com>
	<1DDC786AF7C54760BB45F75C40D0426A@gmail.com> <4FE9014D.602@gmail.com>
Message-ID: <CAG0CB20-SoujLhgz07HwiX1PSYhRtBBgTAHxkxkMhNma-BiyEA@mail.gmail.com>

On 26 June 2012 10:24, Vladimir S. Fonov <vladimir.fonov at gmail.com> wrote:
> On the other hand mincblur is part of mni_autoreg with it's own
> implementation of FFT

My understanding is that louis based his fft upon the NR in C version.
mincblur has also long been on my list of things to re-implement with
support for arbitrary bluring in multiple dimensions (>4) but haven't
got to it.

There is also mincfft that uses fftw but it is a separate package for
this same licensing issue.

a

From zijdenbos at gmail.com  Wed Jun 27 11:15:13 2012
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Wed, 27 Jun 2012 17:15:13 +0200
Subject: [MINC-users] mincblur with FWHM =?utf-8?Q?<=3D_?=voxel dims
In-Reply-To: <CAG0CB20-SoujLhgz07HwiX1PSYhRtBBgTAHxkxkMhNma-BiyEA@mail.gmail.com>
References: <0A683A0DC4174CFDBCB6651E4B3DF5E3@gmail.com>
	<CAG0CB22ToqGK5j3Soj8FEcx+mJ7xw3N+c9qypxNaB+_OuRyvdQ@mail.gmail.com>
	<B7EB53C7B0834D548E1F147DB8755A2E@gmail.com>
	<4FE7ABBA.3060802@gmail.com>
	<1DDC786AF7C54760BB45F75C40D0426A@gmail.com> <4FE9014D.602@gmail.com>
	<CAG0CB20-SoujLhgz07HwiX1PSYhRtBBgTAHxkxkMhNma-BiyEA@mail.gmail.com>
Message-ID: <0A07FDDA9EF248D2A11CC2FEECD43192@gmail.com>

Hrm those pesky licensing issues :-}

Not that I necessarily want to continue to harp on mincblur (where is Louis anyways?), but I just stumbled across something else with mincblur that has me a bit stumped. I had to dig this one fairly deep out of a registration script which seemed to be behaving oddly.

Take a look at this image: ?test_blur.png (http://cl.ly/2E362x310I231C1T1W3u)

These are two virtually identical images with the standard 1mm stx sampling (top two rows); the third row is the difference between them (simple subtraction); and the 4th and 5th rows are the result of mincblurring each of them with an 8mm FWHM kernel. For some reason, the blurred result of (only) one of the two produces a strong edge artifact.

Adding the -no_apodize option removed the edge effect; but that doesn't seem to explain why two almost-identical images would result in such different blurring behaviour.

-- A

On Tuesday, 26 June, 2012 at 3:21 AM, Andrew Janke wrote:

> On 26 June 2012 10:24, Vladimir S. Fonov <vladimir.fonov at gmail.com (mailto:vladimir.fonov at gmail.com)> wrote:
> > On the other hand mincblur is part of mni_autoreg with it's own
> > implementation of FFT
> >  
>  
>  
> My understanding is that louis based his fft upon the NR in C version.
> mincblur has also long been on my list of things to re-implement with
> support for arbitrary bluring in multiple dimensions (>4) but haven't
> got to it.
>  
> There is also mincfft that uses fftw but it is a separate package for
> this same licensing issue.
>  
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca (mailto:MINC-users at bic.mni.mcgill.ca)
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>  
>  



From a.janke at gmail.com  Wed Jun 27 21:15:07 2012
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 28 Jun 2012 11:15:07 +1000
Subject: [MINC-users] mincblur with FWHM <= voxel dims
In-Reply-To: <0A07FDDA9EF248D2A11CC2FEECD43192@gmail.com>
References: <0A683A0DC4174CFDBCB6651E4B3DF5E3@gmail.com>
	<CAG0CB22ToqGK5j3Soj8FEcx+mJ7xw3N+c9qypxNaB+_OuRyvdQ@mail.gmail.com>
	<B7EB53C7B0834D548E1F147DB8755A2E@gmail.com>
	<4FE7ABBA.3060802@gmail.com>
	<1DDC786AF7C54760BB45F75C40D0426A@gmail.com> <4FE9014D.602@gmail.com>
	<CAG0CB20-SoujLhgz07HwiX1PSYhRtBBgTAHxkxkMhNma-BiyEA@mail.gmail.com>
	<0A07FDDA9EF248D2A11CC2FEECD43192@gmail.com>
Message-ID: <CAG0CB21APN-ebzCMfExRcP_WqvQzX+QgqE_sJZcOrQ92edQffg@mail.gmail.com>

You'll find that this is because the second image (69) has been
cropped aggressively. If your image "touches" the edge then the way
that mincblur works will cause this effect.

I tend to autopad all input images to such registration pipes for this
(And other) reasons.


a

On 28 June 2012 01:15, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> These are two virtually identical images with the standard 1mm stx sampling (top two rows); the third row is the difference between them (simple subtraction); and the 4th and 5th rows are the result of mincblurring each of them with an 8mm FWHM kernel. For some reason, the blurred result of (only) one of the two produces a strong edge artifact.

From zijdenbos at gmail.com  Fri Jun 29 06:15:54 2012
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 29 Jun 2012 12:15:54 +0200
Subject: [MINC-users] mincblur with FWHM <= voxel dims
In-Reply-To: <CAG0CB21APN-ebzCMfExRcP_WqvQzX+QgqE_sJZcOrQ92edQffg@mail.gmail.com>
References: <0A683A0DC4174CFDBCB6651E4B3DF5E3@gmail.com>
	<CAG0CB22ToqGK5j3Soj8FEcx+mJ7xw3N+c9qypxNaB+_OuRyvdQ@mail.gmail.com>
	<B7EB53C7B0834D548E1F147DB8755A2E@gmail.com>
	<4FE7ABBA.3060802@gmail.com>
	<1DDC786AF7C54760BB45F75C40D0426A@gmail.com>
	<4FE9014D.602@gmail.com>
	<CAG0CB20-SoujLhgz07HwiX1PSYhRtBBgTAHxkxkMhNma-BiyEA@mail.gmail.com>
	<0A07FDDA9EF248D2A11CC2FEECD43192@gmail.com>
	<CAG0CB21APN-ebzCMfExRcP_WqvQzX+QgqE_sJZcOrQ92edQffg@mail.gmail.com>
Message-ID: <CABEEk151dehV0W4iihW4N2GVBHnv-JEb-kmrZm2_z+c88-X=wA@mail.gmail.com>

True that padding 1 voxel all around also makes the problem go away;
however the egge "touchiness" of these two is really quite similar so
it's still not clear to me what sets this off. But then I do also tend
to pad images in registration pipes but not always; and I hadn't
actually seen this behaviour before. Good to know :)

Thanks,

-- A

On Thu, Jun 28, 2012 at 3:15 AM, Andrew Janke <a.janke at gmail.com> wrote:
> You'll find that this is because the second image (69) has been
> cropped aggressively. If your image "touches" the edge then the way
> that mincblur works will cause this effect.
>
> I tend to autopad all input images to such registration pipes for this
> (And other) reasons.
>
>
> a
>
> On 28 June 2012 01:15, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
>> These are two virtually identical images with the standard 1mm stx sampling (top two rows); the third row is the difference between them (simple subtraction); and the 4th and 5th rows are the result of mincblurring each of them with an 8mm FWHM kernel. For some reason, the blurred result of (only) one of the two produces a strong edge artifact.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>