From a.janke at gmail.com  Thu Dec  1 00:00:25 2005
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 1 Dec 2005 00:00:25 -0500
Subject: [MINC-users] help on using rawtominc and n3
In-Reply-To: <5.2.0.9.0.20051130211322.00bbf3b8@pop3-server>
References: <5.2.0.9.0.20051130211322.00bbf3b8@pop3-server>
Message-ID: <d747ed50511302100l76adf83et@mail.gmail.com>

On 30/11/05, Runa Parveen <runa at medphys.ucl.ac.uk> wrote:
> 1. I have coronal slices, dimension: 256x256x170, cubic voxel :1mm, T1
> weighted. I could not understand how I could give the command when changing
> from rawtominc? also in world coordinate space?
> the command line I use:
>
> rawtominc -coronal -short -unsigned -origin 0 0 0 -range 0 32767
> -real_range 0 32767 -orange 0 32767 -ystep 1 -zstep 1 -xstep 1 -xdircos 1 0
> 0 -ydircos 0 1 0 -zdircos 0 0 1 -mri data_pix_out.mnc 171 256 256 <
> data_pix_in.img
>
> I am worried about the right way of mentioning dimension and also what
> would be the first voxel of the data in world coordinate.

The command above looks generally right to me, I'd suggest s few
changes if you'd like to position the first voxel (say at -10,-50,-50)

   rawtominc -coronal -short -unsigned -scan_range \
   -xstep 1 -ystep 1 -zstep 1 \
   -xstart -10 -ystart -50 -zstart -50 \
    -mri data_pix_out.mnc 171 256 256 < data_pix_in.img

Although given that your data appears to be in ANALYZE/Nifti format,
the easiest thing may be this:

   nii2mnc data_pix_in.hdr data_pix_out.mnc

> 2. In mincresample, what would be the position of centre of first voxel
> along each of the world dimensions?
> the command line I use:
> mincresample data_pix_out.mnc data_pix_resample.mnc -transform
> data_pix_res.xfm -like average_305.mnc -step 1 1 1 -short -unsigned -range
> 0 32767 -nearest_neighbour -nelements 171 256 256

I am a bit confused as to what you are trying to achive in the above.
I suspect you should drop the -step argument and instead specify one
of -use_input_sampling or -like <target.mnc>.  I'd also drop the type
and range arguments unless you really do want to change the range to
be exactly this.

> The volume of the output in this stage is almost half of the rawtominc output?

Meaning the output file is now 1/2 the original size or the image data?

> 3. In display, the image is showed in some tilting position. Also I would
> like to know when the image_range is used, what would be value of the voxel
> when viewing the image in Display?

The real value of the data in a voxel is displayed in a column on the
left hand side of the image data.

> 4. Also after applying nu_correct, the program runs only for 2 iteration
> and given CV: 0.000878881, is it OK?

Possibly, but without knowing the data it is difficult to answer this.

> 5. As it is stopped after 2 iterations, I use the command:
> nu_correct -iterations 100 -stop 2.e-5 data_pix_resample.mnc data_pix_nu.mnc
> it stopped after 37 iterations and CV of field changes: 1.61641e-05.

> Also, in Display, the view of the image in tilting position. Also I would
> like to know how I could understand the non-uniformity has been corrected?

Look carefully at things like the intensity of the grey/white matter
across the image (in coronal,sagital and axial planes).  Use windowing
with say the spect colour map to best illustrate the differences in
register.

The corrections that N3 makes are often very subtle.

--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From anil.kuchinad at mcgill.ca  Tue Dec  6 11:34:29 2005
From: anil.kuchinad at mcgill.ca (Anil Ashok Kuchinad, Mr)
Date: Tue, 6 Dec 2005 11:34:29 -0500
Subject: [MINC-users] global t-test
Message-ID: <F8F248AC53796745B097DB25ACBD17EE01B96AEA@EXCHANGE2VS1.campus.mcgill.ca>

Hello,

 

I am running a VBM analysis and I wanted to obtain on statistic that I
am not sure how to find. I was curious if someone knew what command
would allow me to find an overall t-value for the comparison between all
grey matter voxel density in one group vs. another. I basically want to
find the overall difference in grey matter density across the whole
brain between two groups.

 

I am aware that glim_image has a pooled function but I couldn't get it
to work for me. I am truly shooting in the dark whether I am to use
glim_image and then run something similar to find_peaks or
tstat_threshold later on.

 

Hopefully this is possible!

 

Anil

 

 

----------------------------------------------------

Anil Kuchinad

Centre for Research on Pain

McGill University

Strathcona Anatomy and Dentistry Building

3640 University St., Room M/19

Montreal, Quebec , Canada

H3A 2B2

Tel: (514) 398-1271

Email: anil.kuchinad at mcgill.ca

 


From sylvain at bic.mni.mcgill.ca  Tue Dec  6 16:25:37 2005
From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT)
Date: Tue, 6 Dec 2005 16:25:37 -0500
Subject: [MINC-users] global t-test
In-Reply-To: <F8F248AC53796745B097DB25ACBD17EE01B96AEA@EXCHANGE2VS1.campus.mcgill.ca>
Message-ID: <Pine.SGI.4.44.0512061609200.445548-100000@shadow.bic.mni.mcgill.ca>


Hello Anil,

I haven't dealt with this kind of data personnally but you may want to have a look
here:

http://wiki.bic.mni.mcgill.ca/index.php/FullTextSearch?s=vbm

I don't know how up-to-date this is but I'm pretty certain you should find what you're
looking for!

Now concerning glim_image, it should be feasible to use it to do exactly what you want.
I doubt you should use the pooled sd measure since it requires that the sd image be
stationary. Using the voxel sd measure would be more appropriate.

It should also be possible to use Keith Worsley's latest method via fmristat's
multistat script which regularizes the random effects variance by smoothing the ratio of
fixed+random/fixed effects SD volumes and multiplying back by the fixed effects SD. Keith calls
this a form of local sd pooling. Look here for references http://www.math.mcgill.ca/keith/.
If it can be tailored to PET data, it should be feasible to taylor it to VBM data. I'm pretty sure
Jason Lerch has already done this and maybe he'll answer your call when he
gets a chance. In the meantime look at the wiki!

Hope this helps a little,

Sylvain



On Tue, 6 Dec 2005, Anil Ashok Kuchinad, Mr wrote:

> Hello,
>
>
>
> I am running a VBM analysis and I wanted to obtain on statistic that I
> am not sure how to find. I was curious if someone knew what command
> would allow me to find an overall t-value for the comparison between all
> grey matter voxel density in one group vs. another. I basically want to
> find the overall difference in grey matter density across the whole
> brain between two groups.
>
>
>
> I am aware that glim_image has a pooled function but I couldn't get it
> to work for me. I am truly shooting in the dark whether I am to use
> glim_image and then run something similar to find_peaks or
> tstat_threshold later on.
>
>
>
> Hopefully this is possible!
>
>
>
> Anil
>
>
>
>
>
> ----------------------------------------------------
>
> Anil Kuchinad
>
> Centre for Research on Pain
>
> McGill University
>
> Strathcona Anatomy and Dentistry Building
>
> 3640 University St., Room M/19
>
> Montreal, Quebec , Canada
>
> H3A 2B2
>
> Tel: (514) 398-1271
>
> Email: anil.kuchinad at mcgill.ca
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

---
Sylvain Milot (sylvain at bic.mni.mcgill.ca)
              (trinity at bic.mni.mcgill.ca)
Brain Imaging Centre
Montreal Neurological Institute
Webster 2B, Room 208
Montreal, Qc., Canada, H3A 2B4
Phone  : (514) 398-4965, Fax: 398-8948
Mobile : (514) 712-1768
Office : 527 Av Des Pins O., Room 204
         Montreal, Qc., H2W 1S4



From anil.kuchinad at mcgill.ca  Tue Dec  6 16:29:39 2005
From: anil.kuchinad at mcgill.ca (Anil Ashok Kuchinad, Mr)
Date: Tue, 6 Dec 2005 16:29:39 -0500
Subject: [MINC-users] global t-test
Message-ID: <F8F248AC53796745B097DB25ACBD17EE01B96BCA@EXCHANGE2VS1.campus.mcgill.ca>

Sounds good. I'll venture into these avenues when I get a chance!

Anil

----------------------------------------------------
Anil Kuchinad
Centre for Research on Pain
McGill University
Strathcona Anatomy and Dentistry Building
3640 University St., Room M/19
Montreal, Quebec , Canada
H3A 2B2
Tel: (514) 398-1271
Email: anil.kuchinad at mcgill.ca


-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca
[mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Sylvain MILOT
Sent: December 6, 2005 4:26 PM
To: MINC users mailing list
Subject: Re: [MINC-users] global t-test


Hello Anil,

I haven't dealt with this kind of data personnally but you may want to
have a look
here:

http://wiki.bic.mni.mcgill.ca/index.php/FullTextSearch?s=vbm

I don't know how up-to-date this is but I'm pretty certain you should
find what you're
looking for!

Now concerning glim_image, it should be feasible to use it to do exactly
what you want.
I doubt you should use the pooled sd measure since it requires that the
sd image be
stationary. Using the voxel sd measure would be more appropriate.

It should also be possible to use Keith Worsley's latest method via
fmristat's
multistat script which regularizes the random effects variance by
smoothing the ratio of
fixed+random/fixed effects SD volumes and multiplying back by the fixed
effects SD. Keith calls
this a form of local sd pooling. Look here for references
http://www.math.mcgill.ca/keith/.
If it can be tailored to PET data, it should be feasible to taylor it to
VBM data. I'm pretty sure
Jason Lerch has already done this and maybe he'll answer your call when
he
gets a chance. In the meantime look at the wiki!

Hope this helps a little,

Sylvain



On Tue, 6 Dec 2005, Anil Ashok Kuchinad, Mr wrote:

> Hello,
>
>
>
> I am running a VBM analysis and I wanted to obtain on statistic that I
> am not sure how to find. I was curious if someone knew what command
> would allow me to find an overall t-value for the comparison between
all
> grey matter voxel density in one group vs. another. I basically want
to
> find the overall difference in grey matter density across the whole
> brain between two groups.
>
>
>
> I am aware that glim_image has a pooled function but I couldn't get it
> to work for me. I am truly shooting in the dark whether I am to use
> glim_image and then run something similar to find_peaks or
> tstat_threshold later on.
>
>
>
> Hopefully this is possible!
>
>
>
> Anil
>
>
>
>
>
> ----------------------------------------------------
>
> Anil Kuchinad
>
> Centre for Research on Pain
>
> McGill University
>
> Strathcona Anatomy and Dentistry Building
>
> 3640 University St., Room M/19
>
> Montreal, Quebec , Canada
>
> H3A 2B2
>
> Tel: (514) 398-1271
>
> Email: anil.kuchinad at mcgill.ca
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

---
Sylvain Milot (sylvain at bic.mni.mcgill.ca)
              (trinity at bic.mni.mcgill.ca)
Brain Imaging Centre
Montreal Neurological Institute
Webster 2B, Room 208
Montreal, Qc., Canada, H3A 2B4
Phone  : (514) 398-4965, Fax: 398-8948
Mobile : (514) 712-1768
Office : 527 Av Des Pins O., Room 204
         Montreal, Qc., H2W 1S4


_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From sylvain at bic.mni.mcgill.ca  Tue Dec  6 16:45:05 2005
From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT)
Date: Tue, 6 Dec 2005 16:45:05 -0500
Subject: [MINC-users] global t-test
In-Reply-To: <Pine.SGI.4.44.0512061609200.445548-100000@shadow.bic.mni.mcgill.ca>
Message-ID: <Pine.SGI.4.44.0512061631000.445548-100000@shadow.bic.mni.mcgill.ca>


Hi again Anil,

concerning fmristat's multistat script, I'm not sure this will be feasible after all
since you want to look at a group effect, hence it won't be possible to include fixed subject
effect variables in this case since the independent GROUP variable will be a linear combination of the
SUBJECT effect variables. My impression is that the SD regularization process requires that
the fixed SUBJECT effect variables be included in the model but I havent yet played with this feature so don't
consider my answer to be definitive. The same reasoning applies to glim_image concerning the linear
dependency.

Sylvain

On Tue, 6 Dec 2005, Sylvain MILOT wrote:

>
> Hello Anil,
>
> I haven't dealt with this kind of data personnally but you may want to have a look
> here:
>
> http://wiki.bic.mni.mcgill.ca/index.php/FullTextSearch?s=vbm
>
> I don't know how up-to-date this is but I'm pretty certain you should find what you're
> looking for!
>
> Now concerning glim_image, it should be feasible to use it to do exactly what you want.
> I doubt you should use the pooled sd measure since it requires that the sd image be
> stationary. Using the voxel sd measure would be more appropriate.
>
> It should also be possible to use Keith Worsley's latest method via fmristat's
> multistat script which regularizes the random effects variance by smoothing the ratio of
> fixed+random/fixed effects SD volumes and multiplying back by the fixed effects SD. Keith calls
> this a form of local sd pooling. Look here for references http://www.math.mcgill.ca/keith/.
> If it can be tailored to PET data, it should be feasible to taylor it to VBM data. I'm pretty sure
> Jason Lerch has already done this and maybe he'll answer your call when he
> gets a chance. In the meantime look at the wiki!
>
> Hope this helps a little,
>
> Sylvain
>
>
>
> On Tue, 6 Dec 2005, Anil Ashok Kuchinad, Mr wrote:
>
> > Hello,
> >
> >
> >
> > I am running a VBM analysis and I wanted to obtain on statistic that I
> > am not sure how to find. I was curious if someone knew what command
> > would allow me to find an overall t-value for the comparison between all
> > grey matter voxel density in one group vs. another. I basically want to
> > find the overall difference in grey matter density across the whole
> > brain between two groups.
> >
> >
> >
> > I am aware that glim_image has a pooled function but I couldn't get it
> > to work for me. I am truly shooting in the dark whether I am to use
> > glim_image and then run something similar to find_peaks or
> > tstat_threshold later on.
> >
> >
> >
> > Hopefully this is possible!
> >
> >
> >
> > Anil
> >
> >
> >
> >
> >
> > ----------------------------------------------------
> >
> > Anil Kuchinad
> >
> > Centre for Research on Pain
> >
> > McGill University
> >
> > Strathcona Anatomy and Dentistry Building
> >
> > 3640 University St., Room M/19
> >
> > Montreal, Quebec , Canada
> >
> > H3A 2B2
> >
> > Tel: (514) 398-1271
> >
> > Email: anil.kuchinad at mcgill.ca
> >
> >
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
> ---
> Sylvain Milot (sylvain at bic.mni.mcgill.ca)
>               (trinity at bic.mni.mcgill.ca)
> Brain Imaging Centre
> Montreal Neurological Institute
> Webster 2B, Room 208
> Montreal, Qc., Canada, H3A 2B4
> Phone  : (514) 398-4965, Fax: 398-8948
> Mobile : (514) 712-1768
> Office : 527 Av Des Pins O., Room 204
>          Montreal, Qc., H2W 1S4
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

---
Sylvain Milot (sylvain at bic.mni.mcgill.ca)
              (trinity at bic.mni.mcgill.ca)
Brain Imaging Centre
Montreal Neurological Institute
Webster 2B, Room 208
Montreal, Qc., Canada, H3A 2B4
Phone  : (514) 398-4965, Fax: 398-8948
Mobile : (514) 712-1768
Office : 527 Av Des Pins O., Room 204
         Montreal, Qc., H2W 1S4



From elo at neurorx.com  Wed Dec  7 16:05:50 2005
From: elo at neurorx.com (Ernest Lo)
Date: Wed, 7 Dec 2005 16:05:50 -0500 (EST)
Subject: [MINC-users]  help on using rawtominc and n3
In-Reply-To: <mailman.5.1133456410.4650409.minc-users@bic.mni.mcgill.ca>
Message-ID: <Pine.LNX.4.44.0512071601120.29914-100000@hydra.bic.mni.mcgill.ca>

> Message: 1
> Date: Wed, 30 Nov 2005 21:59:56 +0000
> From: Runa Parveen <runa at medphys.ucl.ac.uk>
> Subject: [MINC-users] help on using rawtominc and n3
> To: minc-users at bic.mni.mcgill.ca
> Message-ID: <5.2.0.9.0.20051130211322.00bbf3b8 at pop3-server>
> Content-Type: text/plain; charset="us-ascii"; format=flowed
> 


> 4. Also after applying nu_correct, the program runs only for 2 iteration 
> and given CV: 0.000878881, is it OK?
> 
> 5. As it is stopped after 2 iterations, I use the command:
> nu_correct -iterations 100 -stop 2.e-5 data_pix_resample.mnc data_pix_nu.mnc
> 
> it stopped after 37 iterations and CV of field changes: 1.61641e-05.
> 
> Also, in Display, the view of the image in tilting position. Also I would 
> like to know how I could understand the non-uniformity has been corrected?
> 


Hi Runa,

As far as I can tell nu_correct does not provide a way to assess the
degree of non-uniformity of an image.  The CV of field change condition
does not guarantee acceptable uniformity in a single image, or consistency
in uniformity across images.

For our purposes, we find that it is useful to examine the bias field
removed by nu_correct.  You can determine this readily by dividing the nu
corrected image by the original (i.e. mincmath -div original.mnc
corrected.mnc bias_field.mnc).  We run nu_correct repeatedly until the
resultant bias field falls below a threshold variation.

When nu_correction finishes quickly - 2 or 37 iterations is relatively
quick - it could mean that there is very little non-uniformity in the
image, or that the stopping condition is too high.  You need to experiment
with reducing the stopping condition, although I would guess (given -stop
2.e-5)  that your images are quite uniform to begin with.

With regard to your last question, whether or not an image has been
corrected successfully depends on the intended application.  For example,
our goal is to perform automatic tissue classification.  So successful
nu_correction means that the tissue intensity distributions have become
narrow enough to produce acceptable classification results.  A good way to
visually assess image uniformity however is to view the images in
'spectral' - the various tissue types (sulci, white matter, gray matter,
csf) should each have a relatively consistent colour range.

Hope this helps,


Ernest Lo
NeuroRX Research
Montreal, Canada


From runa at medphys.ucl.ac.uk  Thu Dec  8 18:19:03 2005
From: runa at medphys.ucl.ac.uk (Runa Parveen)
Date: Thu, 08 Dec 2005 23:19:03 +0000
Subject: [MINC-users] help on using rawtominc and n3
In-Reply-To: <d747ed50511302100l76adf83et@mail.gmail.com>
References: <5.2.0.9.0.20051130211322.00bbf3b8@pop3-server>
	<5.2.0.9.0.20051130211322.00bbf3b8@pop3-server>
Message-ID: <5.2.0.9.0.20051208231714.03f23298@pop3-server>

Hi Andrew,

I am sending this message again as I have not received any reply. Many thanks.

Many thanks for your early response. In some points, I am still struggling 
to proper use of this package.

1.   rawtominc -coronal -short -unsigned -scan_range \
    -xstep 1 -ystep 1 -zstep 1 \
    -xstart -10 -ystart -50 -zstart -50 \
     -mri data_pix_out.mnc 171 256 256 < data_pix_in.img
According to your suggestion, I have used the above command for the 
transfer image into minc format. But when I displayed the image in DISPLAY 
menu, I have seen negative value -16321.2 in some point shown between 
bottom .1000 and .2000 in the column of colour bar in the left hand side. 
Please let me know why this one is displaying.

2. also, when I check with mincheader command of the "data_pix_out.mnc" the
image-max = 65285, 65285, 65285, 65285...................
and
image_min = _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _,

Is there any information I missed to put in the rawtominc conversion 
command line?

3. In mincresample, what would be the position of centre of first voxel 
along each of the world dimensions? the command line I use:
mincresample data_pix_out.mnc data_pix_resample.mnc -transform 
data_pix_res.xfm -like average_305.mnc -step 1 1 1 -short -unsigned -range 
0 32767 -nearest_neighbour -nelements 171 256 256

I was trying to resample the input image with average_305.mnc in mritotal 
and mincresample command before using NU_CORRECT. Which would be the better 
solution for NU_CORRECT? directly use on input image or after transforming 
data in a model (average_305) and then use the intensity correction? Please 
give me suggestion in this regard.

4. I would like to transfer the *.minc image into *.raw after the 
correction to use my own algorithm run on the intensity corrected image. I 
was using the command
minctoraw -short -unsigned -normalize data_pix_out_nu.mnc > data_pix_out_nu.raw

The value in the raw file are varied from -32767 to 32767. My original 
input image is unsigned short, intensity voxel value min is zero and  max 
1700. Please give me the appropriate command line to transfer the image format.

My sincere thanks to you for your kind help.

Yours sincerely,

Runa

******************************************************************** 

* Runa Parveen                                                            **
* Medical Imaging Group                                               **
* Dept. of Medical Physics & Bioengineering                   **
* University College London                                            **
* 2nd Floor, New Malet Place Engineering Building           **
* Gower Street, off Torrington Place                                 **
* London WC1E 6JA                                                 **
* 
UK 
**
* Tel. +44 (0) 20 7679 0246 (Dept.)
          +44 (0) 7984 084 959 (mob.)                                  **
* Fax.+44 (0) 20 7679 0255 (Dept.)                                  **
* e-mail: runa at medphys.ucl.ac.uk                                  **
*********************************************************************

At 00:00 01/12/2005 -0500, you wrote:
>On 30/11/05, Runa Parveen <runa at medphys.ucl.ac.uk> wrote:
> > 1. I have coronal slices, dimension: 256x256x170, cubic voxel :1mm, T1
> > weighted. I could not understand how I could give the command when changing
> > from rawtominc? also in world coordinate space?
> > the command line I use:
> >
> > rawtominc -coronal -short -unsigned -origin 0 0 0 -range 0 32767
> > -real_range 0 32767 -orange 0 32767 -ystep 1 -zstep 1 -xstep 1 -xdircos 1 0
> > 0 -ydircos 0 1 0 -zdircos 0 0 1 -mri data_pix_out.mnc 171 256 256 <
> > data_pix_in.img
> >
> > I am worried about the right way of mentioning dimension and also what
> > would be the first voxel of the data in world coordinate.
>
>The command above looks generally right to me, I'd suggest s few
>changes if you'd like to position the first voxel (say at -10,-50,-50)
>
>    rawtominc -coronal -short -unsigned -scan_range \
>    -xstep 1 -ystep 1 -zstep 1 \
>    -xstart -10 -ystart -50 -zstart -50 \
>     -mri data_pix_out.mnc 171 256 256 < data_pix_in.img
>
>Although given that your data appears to be in ANALYZE/Nifti format,
>the easiest thing may be this:
>
>    nii2mnc data_pix_in.hdr data_pix_out.mnc
>
> > 2. In mincresample, what would be the position of centre of first voxel
> > along each of the world dimensions?
> > the command line I use:
> > mincresample data_pix_out.mnc data_pix_resample.mnc -transform
> > data_pix_res.xfm -like average_305.mnc -step 1 1 1 -short -unsigned -range
> > 0 32767 -nearest_neighbour -nelements 171 256 256
>
>I am a bit confused as to what you are trying to achive in the above.
>I suspect you should drop the -step argument and instead specify one
>of -use_input_sampling or -like <target.mnc>.  I'd also drop the type
>and range arguments unless you really do want to change the range to
>be exactly this.
>
> > The volume of the output in this stage is almost half of the rawtominc 
> output?
>
>Meaning the output file is now 1/2 the original size or the image data?
>
> > 3. In display, the image is showed in some tilting position. Also I would
> > like to know when the image_range is used, what would be value of the voxel
> > when viewing the image in Display?
>
>The real value of the data in a voxel is displayed in a column on the
>left hand side of the image data.
>
> > 4. Also after applying nu_correct, the program runs only for 2 iteration
> > and given CV: 0.000878881, is it OK?
>
>Possibly, but without knowing the data it is difficult to answer this.
>
> > 5. As it is stopped after 2 iterations, I use the command:
> > nu_correct -iterations 100 -stop 2.e-5 data_pix_resample.mnc 
> data_pix_nu.mnc
> > it stopped after 37 iterations and CV of field changes: 1.61641e-05.
>
> > Also, in Display, the view of the image in tilting position. Also I would
> > like to know how I could understand the non-uniformity has been corrected?
>
>Look carefully at things like the intensity of the grey/white matter
>across the image (in coronal,sagital and axial planes).  Use windowing
>with say the spect colour map to best illustrate the differences in
>register.
>
>The corrections that N3 makes are often very subtle.
>
>--
>Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
>Canada->Montreal                                   Cell: +1 (514) 924 2012
>
>_______________________________________________
>MINC-users at bic.mni.mcgill.ca
>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users



From marc.schoenwiesner at mcgill.ca  Sat Dec 10 06:34:29 2005
From: marc.schoenwiesner at mcgill.ca (Marc Schoenwiesner)
Date: Sat, 10 Dec 2005 06:34:29 -0500
Subject: [MINC-users] mincbet
In-Reply-To: <Pine.SGI.4.44.0512061631000.445548-100000@shadow.bic.mni.mcgill.ca>
References: <Pine.SGI.4.44.0512061631000.445548-100000@shadow.bic.mni.mcgill.ca>
Message-ID: <1134214469.439abd453cd88@webmail.mcgill.ca>

Hi,

where do I find mincbet on the BIC drives?

Cheers,
Marc

From a.janke at gmail.com  Mon Dec 12 02:55:28 2005
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 12 Dec 2005 02:55:28 -0500
Subject: [MINC-users] mincbet
In-Reply-To: <1134214469.439abd453cd88@webmail.mcgill.ca>
References: <Pine.SGI.4.44.0512061631000.445548-100000@shadow.bic.mni.mcgill.ca>
	<1134214469.439abd453cd88@webmail.mcgill.ca>
Message-ID: <d747ed50512112355t34b5a50ay@mail.gmail.com>

Hi Marc,

mincbet is by no means an official MINC thing.  it was something that
I bashed together a while back and am now somewhat scared as to far it
has gone.. :)

You can find a binary here:

   ~rotor/opt/linux_bin/mincbet

source is somewhere in here:

   ~rotor/src/mincFSL


a

On 10/12/05, Marc Schoenwiesner <marc.schoenwiesner at mcgill.ca> wrote:
> Hi,
>
> where do I find mincbet on the BIC drives?
>
> Cheers,
> Marc
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From atsuko at bic.mni.mcgill.ca  Tue Dec 13 11:49:21 2005
From: atsuko at bic.mni.mcgill.ca (Atsuko Nagano-Saito)
Date: Wed, 14 Dec 2005 01:49:21 +0900
Subject: [MINC-users] glut
In-Reply-To: <d747ed50512112355t34b5a50ay@mail.gmail.com>
References: <d747ed50512112355t34b5a50ay@mail.gmail.com>
Message-ID: <200512131649.AA01745@QUARK.bic.mni.mcgill.ca>

Hello all,

I am now trying to install register on cygwin, but before this "glut" seems to be needed.
Where can I get glut NOW? Please help me.

Thank you in advance,

Atsuko





 


From a.janke at gmail.com  Tue Dec 13 12:04:18 2005
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 13 Dec 2005 12:04:18 -0500
Subject: [MINC-users] glut
In-Reply-To: <200512131649.AA01745@QUARK.bic.mni.mcgill.ca>
References: <d747ed50512112355t34b5a50ay@mail.gmail.com>
	<200512131649.AA01745@QUARK.bic.mni.mcgill.ca>
Message-ID: <d747ed50512130904v763c0d8dq@mail.gmail.com>

You may find it easier to download the precompiled register and
Display binaries for cygwin from here:

    packages.bic.mni.mcgill.ca/cygwin

if it is a runtime error then do a google for glut32.dll and put the
resulting file in your wondows/system directory or some such place. 
or course it would be best to get your glut dll from a somewhat
official site if you don't like viruses.

a

On 13/12/05, Atsuko Nagano-Saito <atsuko at bic.mni.mcgill.ca> wrote:
> Hello all,
>
> I am now trying to install register on cygwin, but before this "glut" seems to be needed.
> Where can I get glut NOW? Please help me.
>
> Thank you in advance,
>
> Atsuko
>
>
>
>
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From mansi at bic.mni.mcgill.ca  Tue Dec 13 12:20:14 2005
From: mansi at bic.mni.mcgill.ca (Thomas Mansi)
Date: Tue, 13 Dec 2005 18:20:14 +0100
Subject: [MINC-users] glut
In-Reply-To: <200512131649.AA01745@QUARK.bic.mni.mcgill.ca>
References: <d747ed50512112355t34b5a50ay@mail.gmail.com>
	<200512131649.AA01745@QUARK.bic.mni.mcgill.ca>
Message-ID: <439F02CE.1090907@bic.mni.mcgill.ca>

Hello Atsuko,

glut is part of the OpenGL libraries. If you hadn't installed OpenGL on 
your cygwin machine, launch the cygwin setup and  install it. You should 
find it into the dev or libraries sections, I don't remenber exactly.

Hoping this will help you
Regards,

Thomas


Atsuko Nagano-Saito a ?crit :

>Hello all,
>
>I am now trying to install register on cygwin, but before this "glut" seems to be needed.
>Where can I get glut NOW? Please help me.
>
>Thank you in advance,
>
>Atsuko
>
>
>
>
>
> 
>
>_______________________________________________
>MINC-users at bic.mni.mcgill.ca
>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>  
>

From bert at bic.mni.mcgill.ca  Tue Dec 13 12:21:01 2005
From: bert at bic.mni.mcgill.ca (Robert VINCENT)
Date: Tue, 13 Dec 2005 12:21:01 -0500
Subject: [MINC-users] glut
In-Reply-To: <d747ed50512130904v763c0d8dq@mail.gmail.com>
Message-ID: <Pine.SGI.4.44.0512131218450.1428605-100000@shadow.bic.mni.mcgill.ca>

Hi Atsuko,

If you need it, I've placed a copy of the glut32.dll I use on my Windows
XP system in my directory:

~bert/tmp/glut32.dll

This should work with the precompiled versions of Register and Display
from packages.bic.mni.mcgill.ca

	-bert

On Tue, 13 Dec 2005, Andrew Janke wrote:

> You may find it easier to download the precompiled register and
> Display binaries for cygwin from here:
>
>     packages.bic.mni.mcgill.ca/cygwin
>
> if it is a runtime error then do a google for glut32.dll and put the
> resulting file in your wondows/system directory or some such place.
> or course it would be best to get your glut dll from a somewhat
> official site if you don't like viruses.
>
> a
>
> On 13/12/05, Atsuko Nagano-Saito <atsuko at bic.mni.mcgill.ca> wrote:
> > Hello all,
> >
> > I am now trying to install register on cygwin, but before this "glut" seems to be needed.
> > Where can I get glut NOW? Please help me.
> >
> > Thank you in advance,
> >
> > Atsuko
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
> --
> Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
> Canada->Montreal                                   Cell: +1 (514) 924 2012
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From marc.schoenwiesner at mcgill.ca  Tue Dec 13 13:47:13 2005
From: marc.schoenwiesner at mcgill.ca (Marc Schoenwiesner)
Date: Tue, 13 Dec 2005 13:47:13 -0500
Subject: [MINC-users] mnc2nii
In-Reply-To: <Pine.SGI.4.44.0509231544200.1791597-100000@shadow.bic.mni.mcgill.ca>
References: <Pine.SGI.4.44.0509231544200.1791597-100000@shadow.bic.mni.mcgill.ca>
Message-ID: <1134499633.439f17316d9ba@webmail.mcgill.ca>

Hi,

where can I find nii2mnc and mnc2nii on the BIC network?

Cheers,
Marc

From tguo at imaging.robarts.ca  Tue Dec 13 17:25:26 2005
From: tguo at imaging.robarts.ca ((Jessie) Ting Guo)
Date: Tue, 13 Dec 2005 17:25:26 -0500
Subject: [MINC-users]  Questions about MNI-Autoreg
References: <006701c5f133$d34d93f0$c32914c6@irus.robarts.ca>
	<d747ed50511241740n16ac6173k@mail.gmail.com>
Message-ID: <00d701c60034$1dfb36a0$c32914c6@irus.robarts.ca>

Hey Andrew,

Do you know how to change the mni_autoreg_model? mni_autoreg uses
mni-305.mnc as the default. I want to use colin27 instead. How can I do it?

Thank you very much!

Jessie


From sylvain at bic.mni.mcgill.ca  Tue Dec 13 18:13:15 2005
From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT)
Date: Tue, 13 Dec 2005 18:13:15 -0500
Subject: [MINC-users] Questions about MNI-Autoreg
In-Reply-To: <00d701c60034$1dfb36a0$c32914c6@irus.robarts.ca>
Message-ID: <Pine.SGI.4.44.0512131753490.1246588-100000@shadow.bic.mni.mcgill.ca>


Hello,

well that can be a little tricky depending on which version of mritotal you're
using (since the model filenames and the standard directories have changed) but the options are :

mritotal -model ... -modeldir ...

I suppose mritotal -listmodels could be useful :-)

For the latest version (will look different for older versions) you can do the following to find the basename of the model files:

>grep '$ModelDir' `which mritotal`
use vars qw($ModelDir $Model $Protocol
       ["-modeldir", "string", 1, \$ModelDir,
#@GLOBALS    : site-specific: $ModelDir, $Model, $Protocol
   $ModelDir     = "$FindBin::Bin/../share/mni_autoreg";
   # Make sure that $Model has path + basename (by appending $ModelDir
   $ModelDir .= "/" if ($ModelDir ne "" && $ModelDir !~ m|/$|);
   $Model = $ModelDir . $Model unless $Model =~ m|^/|;

>which mritotal
/usr/local/bic/bin/mritotal

>ls /usr/local/bic/bin/../share/mni_autoreg/colin27*blur*
/usr/local/bic/bin/../share/mni_autoreg/colin27_t1_tal_lin_16_blur.mnc  /usr/local/bic/bin/../share/mni_autoreg/colin27_t1_tal_lin_4_blur.mnc
/usr/local/bic/bin/../share/mni_autoreg/colin27_t1_tal_lin_2_blur.mnc   /usr/local/bic/bin/../share/mni_autoreg/colin27_t1_tal_lin_8_blur.mnc

so this would translate to

mritotal -model colin27_t1_tal_lin ...

HTH,

Sylvain

On Tue, 13 Dec 2005, (Jessie) Ting Guo wrote:

> Hey Andrew,
>
> Do you know how to change the mni_autoreg_model? mni_autoreg uses
> mni-305.mnc as the default. I want to use colin27 instead. How can I do it?
>
> Thank you very much!
>
> Jessie
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

---
Sylvain Milot (sylvain at bic.mni.mcgill.ca)
              (trinity at bic.mni.mcgill.ca)
Brain Imaging Centre
Montreal Neurological Institute
Webster 2B, Room 208
Montreal, Qc., Canada, H3A 2B4
Phone  : (514) 398-4965, Fax: 398-8948
Mobile : (514) 712-1768
Office : 527 Av Des Pins O., Room 204
         Montreal, Qc., H2W 1S4




From atsuko_nagano at hotmail.co.jp  Tue Dec 13 21:37:43 2005
From: atsuko_nagano at hotmail.co.jp (nagano atsuko)
Date: Wed, 14 Dec 2005 02:37:43 +0000
Subject: [MINC-users] glut
In-Reply-To: <Pine.SGI.4.44.0512131218450.1428605-100000@shadow.bic.mni.mcgill.ca>
Message-ID: <BAY109-F891E9E374D33403B75D07D6380@phx.gbl>




>From: Robert VINCENT <bert at bic.mni.mcgill.ca>
>Reply-To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>Subject: Re: [MINC-users] glut
>Date: Tue, 13 Dec 2005 12:21:01 -0500
>
>Hi Atsuko,
>
>If you need it, I've placed a copy of the glut32.dll I use on my Windows
>XP system in my directory:
>
>~bert/tmp/glut32.dll
>
>This should work with the precompiled versions of Register and Display
>from packages.bic.mni.mcgill.ca
>
>	-bert
>
>On Tue, 13 Dec 2005, Andrew Janke wrote:
>
> > You may find it easier to download the precompiled register and
> > Display binaries for cygwin from here:
> >
> >     packages.bic.mni.mcgill.ca/cygwin
> >
> > if it is a runtime error then do a google for glut32.dll and put the
> > resulting file in your wondows/system directory or some such place.
> > or course it would be best to get your glut dll from a somewhat
> > official site if you don't like viruses.
> >
> > a
> >
> > On 13/12/05, Atsuko Nagano-Saito <atsuko at bic.mni.mcgill.ca> wrote:
> > > Hello all,
> > >
> > > I am now trying to install register on cygwin, but before this "glut" 
seems to be needed.
> > > Where can I get glut NOW? Please help me.
> > >
> > > Thank you in advance,
> > >
> > > Atsuko
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> >
> >
> > --
> > Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
> > Canada->Montreal                                   Cell: +1 (514) 924 
2012
> >
> > _______________________________________________
> > 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

_________________________________________________________________
??????????????? ?MSN Hotmail? 
http://promotion.msn.co.jp/hotmail/ 


From atsuko_nagano at hotmail.co.jp  Tue Dec 13 21:56:07 2005
From: atsuko_nagano at hotmail.co.jp (nagano atsuko)
Date: Wed, 14 Dec 2005 02:56:07 +0000
Subject: [MINC-users] batch error
In-Reply-To: <Pine.SGI.4.44.0512131218450.1428605-100000@shadow.bic.mni.mcgill.ca>
Message-ID: <BAY109-F12478BBF9D1F252A12A082D6380@phx.gbl>

Hello all,

When I try batch for "mritotal -model icbm_avg_t1_tal_lin abc.mnc abc.xfm", 
it fails.
If I use the command directly, it works.

The error command is as below;
ncopen: filename "icbm_avg_152_t1_tal_lin.mnc": No such file or directory
miopen: MINC package entry point

Please let me know a good solution.

Atsuko

P.S.

I still have problem for register-install.
Maybe I had better ask somebody directy.


Job 283793.shadow (STDIN) in the  queue on bullcalf failed.
Job started Tue Dec 13 21:25:44; finished: Tue Dec 13 21:25:44
Elapsed time: 0 s
CPU     time: 0.05 s
Output follows:

nccreate: filename "NH3.mnc": netCDF file exists && NC_NOCLOBBER
micreate: MINC package entry point





>From: Robert VINCENT <bert at bic.mni.mcgill.ca>
>Reply-To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>Subject: Re: [MINC-users] glut
>Date: Tue, 13 Dec 2005 12:21:01 -0500
>
>Hi Atsuko,
>
>If you need it, I've placed a copy of the glut32.dll I use on my Windows
>XP system in my directory:
>
>~bert/tmp/glut32.dll
>
>This should work with the precompiled versions of Register and Display
>from packages.bic.mni.mcgill.ca
>
>	-bert
>
>On Tue, 13 Dec 2005, Andrew Janke wrote:
>
> > You may find it easier to download the precompiled register and
> > Display binaries for cygwin from here:
> >
> >     packages.bic.mni.mcgill.ca/cygwin
> >
> > if it is a runtime error then do a google for glut32.dll and put the
> > resulting file in your wondows/system directory or some such place.
> > or course it would be best to get your glut dll from a somewhat
> > official site if you don't like viruses.
> >
> > a
> >
> > On 13/12/05, Atsuko Nagano-Saito <atsuko at bic.mni.mcgill.ca> wrote:
> > > Hello all,
> > >
> > > I am now trying to install register on cygwin, but before this "glut" 
seems to be needed.
> > > Where can I get glut NOW? Please help me.
> > >
> > > Thank you in advance,
> > >
> > > Atsuko
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> >
> >
> > --
> > Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
> > Canada->Montreal                                   Cell: +1 (514) 924 
2012
> >
> > _______________________________________________
> > 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

_________________________________________________________________
???250MB????????????MSN Hotmail? 
http://promotion.msn.co.jp/hotmail/ 


From atsuko_nagano at hotmail.co.jp  Tue Dec 13 22:59:41 2005
From: atsuko_nagano at hotmail.co.jp (nagano atsuko)
Date: Wed, 14 Dec 2005 03:59:41 +0000
Subject: [MINC-users] mincbet question
In-Reply-To: <BAY109-F12478BBF9D1F252A12A082D6380@phx.gbl>
Message-ID: <BAY109-F14C6CE43A4CC3A2FA04F0BD6380@phx.gbl>

Hello again,

The next problem is about mincbet.

I use mincbet with 9 anatomical T1 images.
With 8 images, the masked images have values around 'signed__ float 0 to 
100', but for one image, it is 'signed__ float 0 to 10000000000'. The range 
of signals of original images is the same, unsigned short 0 to 4095. What 
happens?

Thank you again and again,

Atsuko

_________________________________________________________________
??????????????? ?MSN Hotmail? 
http://promotion.msn.co.jp/hotmail/ 


From ed.gronenschild at mi.unimaas.nl  Wed Dec 14 04:19:13 2005
From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild)
Date: Wed, 14 Dec 2005 10:19:13 +0100
Subject: [MINC-users] How to use rawtominc with multiple files
Message-ID: <0B68BFED-3D55-47F6-B84B-959C5F81B9F5@mi.unimaas.nl>

Hi list members,

I don't know how to convert a list of 124 raw image files  
representing a coronal volume stack
with 124 slices, where each slice corresponds to a file, into a  
single minc file by means of rawtominc.

For a single file I use the following

rawtominc -coronal -short -signed -xstep 0.89843 -ystep 1.5 -zstep  
-0.89843 -mri -origin 0 0 0
-scan_range  -clobber -swap_bytes -input 1128000MR96.ids  mydata.mnc  
1 256 256

That of course will only result in a single slice stack.

System: Mac G5 OS X.3 and X.4

Kind regards,

Ed


From a.janke at gmail.com  Wed Dec 14 09:24:51 2005
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 14 Dec 2005 09:24:51 -0500
Subject: [MINC-users] How to use rawtominc with multiple files
In-Reply-To: <0B68BFED-3D55-47F6-B84B-959C5F81B9F5@mi.unimaas.nl>
References: <0B68BFED-3D55-47F6-B84B-959C5F81B9F5@mi.unimaas.nl>
Message-ID: <d747ed50512140624q6a94933dk@mail.gmail.com>

Hi Ed,

presuming you have 100 "slices" and they are sorted in alphabetic
order this will do the trick:

   cat *.ids | rawtominc -coronal -short -signed \
   -xstep 0.89843 -ystep 1.5 -zstep -0.89843 \
   -mri -origin 0 0 0 -scan_range  -clobber
   -swap_bytes  mydata.mnc  1 256 256


a

On 14/12/05, Ed Gronenschild <ed.gronenschild at mi.unimaas.nl> wrote:
> Hi list members,
>
> I don't know how to convert a list of 124 raw image files
> representing a coronal volume stack
> with 124 slices, where each slice corresponds to a file, into a
> single minc file by means of rawtominc.
>
> For a single file I use the following
>
> rawtominc -coronal -short -signed -xstep 0.89843 -ystep 1.5 -zstep
> -0.89843 -mri -origin 0 0 0
> -scan_range  -clobber -swap_bytes -input 1128000MR96.ids  mydata.mnc
> 1 256 256
>
> That of course will only result in a single slice stack.
>
> System: Mac G5 OS X.3 and X.4
>
> Kind regards,
>
> Ed
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From sylvain at bic.mni.mcgill.ca  Wed Dec 14 15:59:31 2005
From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT)
Date: Wed, 14 Dec 2005 15:59:31 -0500
Subject: [MINC-users] batch error
In-Reply-To: <BAY109-F12478BBF9D1F252A12A082D6380@phx.gbl>
Message-ID: <Pine.SGI.4.44.0512141550450.1521206-100000@shadow.bic.mni.mcgill.ca>


Hello Atsuko,

I don't see how it could work either way since your path points to
/usr/local/mni/bin/mritotal, in which case the following should work:

/usr/local/mni/bin/mritotal -model icbm_avg_152_t1_tal_lin ...

The error reported is not consistent with the command you provided though!

I may be just guessing here but be aware that

do_mritotal -model

and

mritotal -model

don't have the same meaning!

Sylvain


On Wed, 14 Dec 2005, nagano atsuko wrote:

> Hello all,
>
> When I try batch for "mritotal -model icbm_avg_t1_tal_lin abc.mnc abc.xfm",
> it fails.
> If I use the command directly, it works.
>
> The error command is as below;
> ncopen: filename "icbm_avg_152_t1_tal_lin.mnc": No such file or directory
> miopen: MINC package entry point
>
> Please let me know a good solution.
>
> Atsuko
>
> P.S.
>
> I still have problem for register-install.
> Maybe I had better ask somebody directy.
>
>
> Job 283793.shadow (STDIN) in the  queue on bullcalf failed.
> Job started Tue Dec 13 21:25:44; finished: Tue Dec 13 21:25:44
> Elapsed time: 0 s
> CPU     time: 0.05 s
> Output follows:
>
> nccreate: filename "NH3.mnc": netCDF file exists && NC_NOCLOBBER
> micreate: MINC package entry point
>
>
>
>
>
> >From: Robert VINCENT <bert at bic.mni.mcgill.ca>
> >Reply-To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> >To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> >Subject: Re: [MINC-users] glut
> >Date: Tue, 13 Dec 2005 12:21:01 -0500
> >
> >Hi Atsuko,
> >
> >If you need it, I've placed a copy of the glut32.dll I use on my Windows
> >XP system in my directory:
> >
> >~bert/tmp/glut32.dll
> >
> >This should work with the precompiled versions of Register and Display
> >from packages.bic.mni.mcgill.ca
> >
> >	-bert
> >
> >On Tue, 13 Dec 2005, Andrew Janke wrote:
> >
> > > You may find it easier to download the precompiled register and
> > > Display binaries for cygwin from here:
> > >
> > >     packages.bic.mni.mcgill.ca/cygwin
> > >
> > > if it is a runtime error then do a google for glut32.dll and put the
> > > resulting file in your wondows/system directory or some such place.
> > > or course it would be best to get your glut dll from a somewhat
> > > official site if you don't like viruses.
> > >
> > > a
> > >
> > > On 13/12/05, Atsuko Nagano-Saito <atsuko at bic.mni.mcgill.ca> wrote:
> > > > Hello all,
> > > >
> > > > I am now trying to install register on cygwin, but before this "glut"
> seems to be needed.
> > > > Where can I get glut NOW? Please help me.
> > > >
> > > > Thank you in advance,
> > > >
> > > > Atsuko
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > MINC-users at bic.mni.mcgill.ca
> > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > >
> > >
> > >
> > > --
> > > Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
> > > Canada->Montreal                                   Cell: +1 (514) 924
> 2012
> > >
> > > _______________________________________________
> > > 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
>
> _________________________________________________________________
> 無料で250MBの受信ボックスが使える「MSN Hotmail」
> http://promotion.msn.co.jp/hotmail/
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

---
Sylvain Milot (sylvain at bic.mni.mcgill.ca)
              (trinity at bic.mni.mcgill.ca)
Brain Imaging Centre
Montreal Neurological Institute
Webster 2B, Room 208
Montreal, Qc., Canada, H3A 2B4
Phone  : (514) 398-4965, Fax: 398-8948
Mobile : (514) 712-1768
Office : 527 Av Des Pins O., Room 204
         Montreal, Qc., H2W 1S4



From a.janke at gmail.com  Thu Dec 15 00:39:54 2005
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 15 Dec 2005 00:39:54 -0500
Subject: [MINC-users] mincbet question
In-Reply-To: <BAY109-F14C6CE43A4CC3A2FA04F0BD6380@phx.gbl>
References: <BAY109-F12478BBF9D1F252A12A082D6380@phx.gbl>
	<BAY109-F14C6CE43A4CC3A2FA04F0BD6380@phx.gbl>
Message-ID: <d747ed50512142139g29958c40k@mail.gmail.com>

Hi,

First and foremost, mincbet is by no means supported MINC software. It
is a dodgy hack I perpetrated a few years that has maanged to come
back to haunt me far too many times.... :)

As part of its operation it will convert all data to float. This is a
side-effect of the way data formats are/were used in FSL. I suspect
you will find that your mask is still "in" the minc file but hard to
find due to spurious range values.  I suspect that something like this
should sort  things out a bit.

  mincmath -byte -gt -const 0 bet-mask.mnc new-mask.mnc

But your mileage will vary.


Andrew

On 13/12/05, nagano atsuko <atsuko_nagano at hotmail.co.jp> wrote:
> Hello again,
>
> The next problem is about mincbet.
>
> I use mincbet with 9 anatomical T1 images.
> With 8 images, the masked images have values around 'signed__ float 0 to
> 100', but for one image, it is 'signed__ float 0 to 10000000000'. The range
> of signals of original images is the same, unsigned short 0 to 4095. What
> happens?
>
> Thank you again and again,
>
> Atsuko
>
> _________________________________________________________________
> ??????????????? ?MSN Hotmail?
> http://promotion.msn.co.jp/hotmail/
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012

From rodell at pet.auh.dk  Thu Dec 15 04:07:39 2005
From: rodell at pet.auh.dk (Anders Bertil Rodell)
Date: Thu, 15 Dec 2005 10:07:39 +0100
Subject: [MINC-users] mritotal problem
In-Reply-To: <mailman.405.1134570295.27146.minc-users@bic.mni.mcgill.ca>
References: <mailman.405.1134570295.27146.minc-users@bic.mni.mcgill.ca>
Message-ID: <1134637659.25893.69.camel@vega>

Hello Atsuko

Are you sure you are not missing the -modeldir  /path option 
and be sure your modelname icbm_avg_152_t1_tal_lin is correct
ie

mritotal -modeldir /<your model path> -model icbm_avg_t1_tal_lin 
abc.mnc abc.xfm
 

good luck Anders 
--
Anders Bertil Rodell M.Sc. C.S. Ph.D
Centre for Functionally Integrative Neuroscience, CFIN.
Aarhus PET Centre, Aarhus University Hospital,
Norrebrogade 44, 8000 Aarhus C, Denmark
phone work:   +45 89 49 40 97
mobile phone: +45 61 70 85 30
email: rodell at pet.auh.dk


From ed.gronenschild at mi.unimaas.nl  Thu Dec 15 04:46:17 2005
From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild)
Date: Thu, 15 Dec 2005 10:46:17 +0100
Subject: [MINC-users] How to use rawtominc with multiple files
In-Reply-To: <mailman.405.1134570295.27146.minc-users@bic.mni.mcgill.ca>
References: <mailman.405.1134570295.27146.minc-users@bic.mni.mcgill.ca>
Message-ID: <bad3d315cfe9f3098ffd2a1fad933c73@mi.unimaas.nl>

Hello Andrew,

Thanks for the trick, it works if I change the value for <size3> to 100
instead of 1.
So, to convert a list of say 100 files into a single mnc file the 
command
would be
cat *.ids | rawtominc ....... mydata.mnc 100 256 256

Thanks again,

Ed

>
> Message: 11
> Date: Wed, 14 Dec 2005 09:24:51 -0500
> From: Andrew Janke <a.janke at gmail.com>
> Subject: Re: [MINC-users] How to use rawtominc with multiple files
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID: <d747ed50512140624q6a94933dk at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Ed,
>
> presuming you have 100 "slices" and they are sorted in alphabetic
> order this will do the trick:
>
>    cat *.ids | rawtominc -coronal -short -signed \
>    -xstep 0.89843 -ystep 1.5 -zstep -0.89843 \
>    -mri -origin 0 0 0 -scan_range  -clobber
>    -swap_bytes  mydata.mnc  1 256 256
>
>
> a
>
> On 14/12/05, Ed Gronenschild <ed.gronenschild at mi.unimaas.nl> wrote:
>> Hi list members,
>>
>> I don't know how to convert a list of 124 raw image files
>> representing a coronal volume stack
>> with 124 slices, where each slice corresponds to a file, into a
>> single minc file by means of rawtominc.
>>
>> For a single file I use the following
>>
>> rawtominc -coronal -short -signed -xstep 0.89843 -ystep 1.5 -zstep
>> -0.89843 -mri -origin 0 0 0
>> -scan_range  -clobber -swap_bytes -input 1128000MR96.ids  mydata.mnc
>> 1 256 256
>>
>> That of course will only result in a single slice stack.
>>
>> System: Mac G5 OS X.3 and X.4
>>
>> Kind regards,
>>
>> Ed
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>


From runa at medphys.ucl.ac.uk  Thu Dec 15 12:18:30 2005
From: runa at medphys.ucl.ac.uk (Runa Parveen)
Date: Thu, 15 Dec 2005 17:18:30 +0000
Subject: [MINC-users] How to use rawtominc with multiple files
In-Reply-To: <d747ed50512140624q6a94933dk@mail.gmail.com>
References: <0B68BFED-3D55-47F6-B84B-959C5F81B9F5@mi.unimaas.nl>
	<0B68BFED-3D55-47F6-B84B-959C5F81B9F5@mi.unimaas.nl>
Message-ID: <5.2.0.9.0.20051215170729.00bbb9d0@pop3-server>

hi minc users,

I have sent this e-mail twice but nit getting any response. Please can you 
suggest me on those points.

Many thanks for your kind cooperation.

In some points, I am still struggling to proper use of this package.

1.   rawtominc -coronal -short -unsigned -scan_range \
    -xstep 1 -ystep 1 -zstep 1 \
    -xstart -10 -ystart -50 -zstart -50 \
     -mri data_pix_out.mnc 171 256 256 < data_pix_in.img
According to your suggestion, I have used the above command for the 
transfer image into minc format. But when I displayed the image in DISPLAY 
menu, I have seen negative value -16321.2 in some point shown between 
bottom .1000 and .2000 in the column of colour bar in the left hand side. 
Please let me know why this one is displaying.

2. also, when I check with mincheader command of the "data_pix_out.mnc" the
image-max = 65285, 65285, 65285, 65285...................
and
image_min = _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _,

Is there any information I missed to put in the rawtominc conversion 
command line?

3. In mincresample, what would be the position of centre of first voxel 
along each of the world dimensions? the command line I use:
mincresample data_pix_out.mnc data_pix_resample.mnc -transform 
data_pix_res.xfm -like average_305.mnc -step 1 1 1 -short -unsigned -range 
0 32767 -nearest_neighbour -nelements 171 256 256

I was trying to resample the input image with average_305.mnc in mritotal 
and mincresample command before using NU_CORRECT. Which would be the better 
solution for NU_CORRECT? directly use on input image or after transforming 
data in a model (average_305) and then use the intensity correction? Please 
give me suggestion in this regard.
THIS IS VERY URGENT :
4. I would like to transfer the *.minc image into *.raw after the 
correction to use my own algorithm run on the intensity corrected image. I 
was using the command
minctoraw -short -unsigned -normalize data_pix_out_nu.mnc > data_pix_out_nu.raw

The value in the raw file are varied from -32767 to 32767. My original 
input image is unsigned short, intensity voxel value min is zero and  max 
1700. I would like to return back the *.minc image after correction into 
the similar intensity level of input *.raw image and this is very urgent. 
Please give me the appropriate command line to transfer the image format.

My sincere thanks to you for your kind help.

Yours sincerely,

Runa

******************************************************************** 

* Runa Parveen                                                            **
* Medical Imaging Group                                               **
* Dept. of Medical Physics & Bioengineering                   **
* University College London                                            **
* 2nd Floor, New Malet Place Engineering Building           **
* Gower Street, off Torrington Place                                 **
* London WC1E 6JA                                                 **
* 
UK 
**
* Tel. +44 (0) 20 7679 0246 (Dept.)
          +44 (0) 7984 084 959 (mob.)                                  **
* Fax.+44 (0) 20 7679 0255 (Dept.)                                  **
* e-mail: runa at medphys.ucl.ac.uk                                  **
*********************************************************************


From ed.gronenschild at mi.unimaas.nl  Fri Dec 16 04:01:55 2005
From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild)
Date: Fri, 16 Dec 2005 10:01:55 +0100
Subject: [MINC-users] DICOM to mnc and vice versa for Mac OS X
Message-ID: <342CB575-2F0E-4084-A214-61B260B0A031@mi.unimaas.nl>

Hello,

I'm working on a Mac with OS X.3 and OS X.4 and I noticed
that the conversion tools DICOM-> minc and mnc->DICOM
are not present. I know that these do exist for other platforms
and are called dcm2mnc and/or dicom_to_minc, etc.. Does
somebody know how to get these for the Mac.

Kind regards,

Ed


From bert at bic.mni.mcgill.ca  Fri Dec 16 09:25:08 2005
From: bert at bic.mni.mcgill.ca (Robert VINCENT)
Date: Fri, 16 Dec 2005 09:25:08 -0500
Subject: [MINC-users] DICOM to mnc and vice versa for Mac OS X
In-Reply-To: <342CB575-2F0E-4084-A214-61B260B0A031@mi.unimaas.nl>
Message-ID: <Pine.SGI.4.44.0512160911080.1795127-100000@shadow.bic.mni.mcgill.ca>

Hi Ed,

Either dicom_to_minc or dcm2mnc should work on Mac OS X systems. I believe
that the latest version of dicom_to_minc is available here:

http://www.bic.mni.mcgill.ca/~jharlap/dicom/

dcm2mnc is part of MINC 1.4, which is available in OS X binary here:

http://packages.bic.mni.mcgill.ca/osx/minc-1.4.pkg.tar.gz

	-bert

On Fri, 16 Dec 2005, Ed Gronenschild wrote:

> Hello,
>
> I'm working on a Mac with OS X.3 and OS X.4 and I noticed
> that the conversion tools DICOM-> minc and mnc->DICOM
> are not present. I know that these do exist for other platforms
> and are called dcm2mnc and/or dicom_to_minc, etc.. Does
> somebody know how to get these for the Mac.
>
> Kind regards,
>
> Ed
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From atsuko_nagano at hotmail.co.jp  Sat Dec 17 10:23:00 2005
From: atsuko_nagano at hotmail.co.jp (nagano atsuko)
Date: Sat, 17 Dec 2005 15:23:00 +0000
Subject: [MINC-users] fmr_preprocess on cygwin
In-Reply-To: <Pine.SGI.4.44.0512141550450.1521206-100000@shadow.bic.mni.mcgill.ca>
Message-ID: <BAY109-F4457DDE2FDEE4628CF1D8D63D0@phx.gbl>

Hello all,

I tried to use fmr_preprocess on cygwin.
But, an error message comes as below, and it doesn't work.

Can't locate Getopt/Tabular.pm in @INC (@INC contain; 
/usr/lib/perl5/5.8/cygwin /usr/lib/perl5/5.8 
/usr/lib/perl5/site_perl/5.8/cygwin /usr/lib/perl5/site_perl/5.8 
/usr/lib/perl5/site_perl/5.8 /usr/lib/perl5/vendor_perl/5.8/cygwin 
/usr/lib/perl5/vendor_perl/5.8 /usr/lib/perl5/vendor_perl/5.8 .) at 
/usr/local/mni/bin/fmr_preprocess line 47.
BEGIN failed--compilation aborted at /usr/local/mni/bin/fmr_preprocess line 
47.

How can I treat this?

Best,

Atsuko

_________________________________________________________________
???250MB????????????MSN Hotmail? 
http://promotion.msn.co.jp/hotmail/ 


From a.janke at gmail.com  Sun Dec 18 22:09:48 2005
From: a.janke at gmail.com (Andrew Janke)
Date: Sun, 18 Dec 2005 22:09:48 -0500
Subject: [MINC-users] fmr_preprocess on cygwin
In-Reply-To: <BAY109-F4457DDE2FDEE4628CF1D8D63D0@phx.gbl>
References: <Pine.SGI.4.44.0512141550450.1521206-100000@shadow.bic.mni.mcgill.ca>
	<BAY109-F4457DDE2FDEE4628CF1D8D63D0@phx.gbl>
Message-ID: <d747ed50512181909s67697676l@mail.gmail.com>

Nagano,

You need to install the perl module GetOpt::Tabular from www.cpan.org in cygwin.


Andrew

On 17/12/05, nagano atsuko <atsuko_nagano at hotmail.co.jp> wrote:
> Hello all,
>
> I tried to use fmr_preprocess on cygwin.
> But, an error message comes as below, and it doesn't work.
>
> Can't locate Getopt/Tabular.pm in @INC (@INC contain;
> /usr/lib/perl5/5.8/cygwin /usr/lib/perl5/5.8
> /usr/lib/perl5/site_perl/5.8/cygwin /usr/lib/perl5/site_perl/5.8
> /usr/lib/perl5/site_perl/5.8 /usr/lib/perl5/vendor_perl/5.8/cygwin
> /usr/lib/perl5/vendor_perl/5.8 /usr/lib/perl5/vendor_perl/5.8 .) at
> /usr/local/mni/bin/fmr_preprocess line 47.
> BEGIN failed--compilation aborted at /usr/local/mni/bin/fmr_preprocess line
> 47.
>
> How can I treat this?
>
> Best,
>
> Atsuko
>
> _________________________________________________________________
> ???250MB????????????MSN Hotmail?
> http://promotion.msn.co.jp/hotmail/
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012

From ed.gronenschild at mi.unimaas.nl  Mon Dec 19 08:19:06 2005
From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild)
Date: Mon, 19 Dec 2005 14:19:06 +0100
Subject: [MINC-users] DICOM to mnc and vice versa for Mac OS X
In-Reply-To: <mailman.1.1134752409.1796594.minc-users@bic.mni.mcgill.ca>
References: <mailman.1.1134752409.1796594.minc-users@bic.mni.mcgill.ca>
Message-ID: <B07288F6-47CE-4CB1-83D1-E89C3E3AFE73@mi.unimaas.nl>

Hi Bert,

I'm a little bit confused now: I installed the MAC OS X binaries  
version 1.1 released
January 28, 2004 called MINC-tools-OS10.3-1.1.0.dmg located at
http://www.bic.mni.mcgill.ca/software/distribution/packages/
However, also at http://packages.bic.mni.mcgill.ca/osx/ i can find a  
lot of
Mac OS X stuff, amongst others minc-1.4.pkg.tar.gz which indeed includes
dcm2mnc.
My question is: what's the diference between these two sets. Should
I install all the stuff from the latter after I installed the version  
1.1 release?

Kind regards,

Ed

On 16 Dec 2005, at 18:00, minc-users-request at bic.mni.mcgill.ca wrote:

> Message: 3
> Date: Fri, 16 Dec 2005 09:25:08 -0500
> From: Robert VINCENT <bert at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] DICOM to mnc and vice versa for Mac OS X
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID:
> 	<Pine.SGI.4.44.0512160911080.1795127-100000 at shadow.bic.mni.mcgill.ca>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
>
> Hi Ed,
>
> Either dicom_to_minc or dcm2mnc should work on Mac OS X systems. I  
> believe
> that the latest version of dicom_to_minc is available here:
>
> http://www.bic.mni.mcgill.ca/~jharlap/dicom/
>
> dcm2mnc is part of MINC 1.4, which is available in OS X binary here:
>
> http://packages.bic.mni.mcgill.ca/osx/minc-1.4.pkg.tar.gz
>
> 	-bert
>
> On Fri, 16 Dec 2005, Ed Gronenschild wrote:
>
>> Hello,
>>
>> I'm working on a Mac with OS X.3 and OS X.4 and I noticed
>> that the conversion tools DICOM-> minc and mnc->DICOM
>> are not present. I know that these do exist for other platforms
>> and are called dcm2mnc and/or dicom_to_minc, etc.. Does
>> somebody know how to get these for the Mac.
>>
>> Kind regards,
>>
>> Ed
>>


From a.janke at gmail.com  Mon Dec 19 09:08:42 2005
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 19 Dec 2005 09:08:42 -0500
Subject: [MINC-users] DICOM to mnc and vice versa for Mac OS X
In-Reply-To: <B07288F6-47CE-4CB1-83D1-E89C3E3AFE73@mi.unimaas.nl>
References: <mailman.1.1134752409.1796594.minc-users@bic.mni.mcgill.ca>
	<B07288F6-47CE-4CB1-83D1-E89C3E3AFE73@mi.unimaas.nl>
Message-ID: <d747ed50512190608g4cadb7c7s@mail.gmail.com>

Hi Ed,

The 1.1 OSX distribution you describe was an earlier attempt at an
"all in one" installer that contained a lot of the MINC packages. It
was built by Jason Lerch but I don't think he has a later one.

The packages at packages.bic.mni.mcgill.ca are more up to date but
separate out the MINC "toolchain" into separate packages following the
breakdown of the source packages.

You should be safe to install the newwer ones over the top of the old ones.


Andrew

On 19/12/05, Ed Gronenschild <ed.gronenschild at mi.unimaas.nl> wrote:
> Hi Bert,
>
> I'm a little bit confused now: I installed the MAC OS X binaries
> version 1.1 released
> January 28, 2004 called MINC-tools-OS10.3-1.1.0.dmg located at
> http://www.bic.mni.mcgill.ca/software/distribution/packages/
> However, also at http://packages.bic.mni.mcgill.ca/osx/ i can find a
> lot of
> Mac OS X stuff, amongst others minc-1.4.pkg.tar.gz which indeed includes
> dcm2mnc.
> My question is: what's the diference between these two sets. Should
> I install all the stuff from the latter after I installed the version
> 1.1 release?
>
> Kind regards,
>
> Ed
>
> On 16 Dec 2005, at 18:00, minc-users-request at bic.mni.mcgill.ca wrote:
>
> > Message: 3
> > Date: Fri, 16 Dec 2005 09:25:08 -0500
> > From: Robert VINCENT <bert at bic.mni.mcgill.ca>
> > Subject: Re: [MINC-users] DICOM to mnc and vice versa for Mac OS X
> > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > Message-ID:
> >       <Pine.SGI.4.44.0512160911080.1795127-100000 at shadow.bic.mni.mcgill.ca>
> > Content-Type: TEXT/PLAIN; charset=US-ASCII
> >
> > Hi Ed,
> >
> > Either dicom_to_minc or dcm2mnc should work on Mac OS X systems. I
> > believe
> > that the latest version of dicom_to_minc is available here:
> >
> > http://www.bic.mni.mcgill.ca/~jharlap/dicom/
> >
> > dcm2mnc is part of MINC 1.4, which is available in OS X binary here:
> >
> > http://packages.bic.mni.mcgill.ca/osx/minc-1.4.pkg.tar.gz
> >
> >       -bert
> >
> > On Fri, 16 Dec 2005, Ed Gronenschild wrote:
> >
> >> Hello,
> >>
> >> I'm working on a Mac with OS X.3 and OS X.4 and I noticed
> >> that the conversion tools DICOM-> minc and mnc->DICOM
> >> are not present. I know that these do exist for other platforms
> >> and are called dcm2mnc and/or dicom_to_minc, etc.. Does
> >> somebody know how to get these for the Mac.
> >>
> >> Kind regards,
> >>
> >> Ed
> >>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From ed.gronenschild at mi.unimaas.nl  Tue Dec 20 10:27:37 2005
From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild)
Date: Tue, 20 Dec 2005 16:27:37 +0100
Subject: [MINC-users] Problems installing latest software on Mac
Message-ID: <642aaccf7044983083abadd4c267d909@mi.unimaas.nl>

Hi,

I downloaded from http://packages/bic.mni.mcgill.ca/osx the latest
packages. The installation was OK except for classify-1.0.pkg and
mni-autoreg-0.98s.pkg. For both the installer stopped with the very
informative message "There were errors installing this software".
I'm using OS X 10.3.9.
Is there some workaround possible to install this software?

Kind regards,

Ed


From a.janke at gmail.com  Tue Dec 20 08:38:20 2005
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 20 Dec 2005 08:38:20 -0500
Subject: [MINC-users] How to use rawtominc with multiple files
In-Reply-To: <5.2.0.9.0.20051215170729.00bbb9d0@pop3-server>
References: <0B68BFED-3D55-47F6-B84B-959C5F81B9F5@mi.unimaas.nl>
	<d747ed50512140624q6a94933dk@mail.gmail.com>
	<5.2.0.9.0.20051215170729.00bbb9d0@pop3-server>
Message-ID: <d747ed50512200538n35791392v@mail.gmail.com>

> 2. also, when I check with mincheader command of the "data_pix_out.mnc" the
> image-max = 65285, 65285, 65285, 65285...................
> and
> image_min = _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
>      _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
>      _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
>      _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
>      _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
>      _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
>      _, _, _, _, _, _, _, _,
>
> Is there any information I missed to put in the rawtominc conversion
> command line?

No, this is expected behaviour.


> 3. In mincresample, what would be the position of centre of first voxel
> along each of the world dimensions? the command line I use:
> mincresample data_pix_out.mnc data_pix_resample.mnc -transform
> data_pix_res.xfm -like average_305.mnc -step 1 1 1 -short -unsigned -range
> 0 32767 -nearest_neighbour -nelements 171 256 256

The position of the first voxel is defined by the start information
for each dimension. use mincinfo on the file to get thie information.

> I was trying to resample the input image with average_305.mnc in mritotal
> and mincresample command before using NU_CORRECT. Which would be the better
> solution for NU_CORRECT? directly use on input image or after transforming
> data in a model (average_305) and then use the intensity correction? Please
> give me suggestion in this regard.

Given that N3 has no knowledge of model space and the likes and works
on the raw histogram I would not expect the results to be different
beyond std interpolation and rounding errors.  Typically N3 is run on
the native data.

> 4. I would like to transfer the *.minc image into *.raw after the
> correction to use my own algorithm run on the intensity corrected image. I
> was using the command
> minctoraw -short -unsigned -normalize data_pix_out_nu.mnc > data_pix_out_nu.raw
>
> The value in the raw file are varied from -32767 to 32767. My original
> input image is unsigned short, intensity voxel value min is zero and  max
> 1700. I would like to return back the *.minc image after correction into
> the similar intensity level of input *.raw image.

I suspect you want -nonormalize as opposed to -normalize.  ('minctoraw
-help' or 'man minctoraw' explains the difference between the two.)


--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From sridar at mrs.mni.mcgill.ca  Tue Dec 20 12:45:30 2005
From: sridar at mrs.mni.mcgill.ca (Sridar Narayanan)
Date: Tue, 20 Dec 2005 12:45:30 -0500
Subject: [MINC-users] How to use rawtominc with multiple files
In-Reply-To: <mailman.5.1135098009.20384.minc-users@bic.mni.mcgill.ca>
Message-ID: <BFCDAD6A.9BD6%sridar@mrs.mni.mcgill.ca>

>> I was trying to resample the input image with average_305.mnc in mritotal
>> and mincresample command before using NU_CORRECT. Which would be the better
>> solution for NU_CORRECT? directly use on input image or after transforming
>> data in a model (average_305) and then use the intensity correction? Please
>> give me suggestion in this regard.
> 
> Given that N3 has no knowledge of model space and the likes and works
> on the raw histogram I would not expect the results to be different
> beyond std interpolation and rounding errors.  Typically N3 is run on
> the native data.

That's the usual practice, and performing the NU correction first will
likely improve the registration to the average brain.

Sridar
--
Sridar Narayanan, PhD
Magnetic Resonance Spectroscopy Unit
Montreal Neurological Institute, McGill University



From shahin at bic.mni.mcgill.ca  Tue Dec 20 13:37:02 2005
From: shahin at bic.mni.mcgill.ca (Shahin Zangenehpour)
Date: Tue, 20 Dec 2005 19:37:02 +0100
Subject: [MINC-users] MINC -> DICOM Conversion
Message-ID: <327A1FB4-C2D2-437C-AEA2-6CC77C9CF7B2@bic.mni.mcgill.ca>

Hello folks,
I was wondering if anyone knows of a quick and easy way to convert  
MINC files to DICOM format to be viewed and volume-rendered with  
Osirix for Mac OS X.
Any help or lead you can provide is much appreciated.
Thanks,
SZ
________________________________________________________________________ 
_______________________________
Shahin Zangenehpour, PhD    Postdoctoral Fellow   |   Montreal  
Neurological Institute   |   Cognitive Neuroscience Unit
3801 University Street   |   Room 276  |  Montr?al   QC   Canada    
H3A 2B4  |   P.  514  398  1717  |  F.  514  398  1338



From mdesco at cim.mcgill.ca  Tue Dec 20 16:30:56 2005
From: mdesco at cim.mcgill.ca (Maxime Descoteaux)
Date: Tue, 20 Dec 2005 16:30:56 -0500
Subject: [MINC-users] SNR question
Message-ID: <6FBE0EC6-BE5C-4282-9783-2E925959FEB7@cim.mcgill.ca>

Hi all,

Is there a minc tool to estimate the SNR of an anatomical volume  
automatically?  I have a T2 volume of the human brain and would like  
to have an approximation of the SNR.

If no tool exist can I do the following:
-take a ROI in the background and compute the standard deviation of  
the signal in that ROI, std_background
-take a ROI in the brain and find the std_data
-SNR = std_data / std_background

The obvious question is how big and in which area should my data ROI  
be.  Containing both white matter and gray matter? or it doesn't  
really matter to obtain a rough estimation of the SNR.

thanks

Max



From a.janke at gmail.com  Tue Dec 20 17:17:57 2005
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 20 Dec 2005 17:17:57 -0500
Subject: [MINC-users] SNR question
In-Reply-To: <6FBE0EC6-BE5C-4282-9783-2E925959FEB7@cim.mcgill.ca>
References: <6FBE0EC6-BE5C-4282-9783-2E925959FEB7@cim.mcgill.ca>
Message-ID: <d747ed50512201417t736eeab3o@mail.gmail.com>

> Is there a minc tool to estimate the SNR of an anatomical volume
> automatically?  I have a T2 volume of the human brain and would like
> to have an approximation of the SNR.

Nothing automatic that I know of, but....

> If no tool exist can I do the following:
> -take a ROI in the background and compute the standard deviation of
> the signal in that ROI, std_background
> -take a ROI in the brain and find the std_data
> -SNR = std_data / std_background
>
> The obvious question is how big and in which area should my data ROI
> be.  Containing both white matter and gray matter? or it doesn't
> really matter to obtain a rough estimation of the SNR.

The above approach will work.  As for the size of the ROI, you should
find than an ROI around 5000 voxels should do the trick.

--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From a.janke at gmail.com  Tue Dec 20 17:22:33 2005
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 20 Dec 2005 17:22:33 -0500
Subject: [MINC-users] MINC -> DICOM Conversion
In-Reply-To: <327A1FB4-C2D2-437C-AEA2-6CC77C9CF7B2@bic.mni.mcgill.ca>
References: <327A1FB4-C2D2-437C-AEA2-6CC77C9CF7B2@bic.mni.mcgill.ca>
Message-ID: <d747ed50512201422q550cd7f3x@mail.gmail.com>

There is no minc -> DICOM converter that I know of.

However I seem to remember that OSIRIX can read an ANALYZE file so a
mnc->analyze conversion (mnc2nii) should do the trick.  Failing that I
think the debabler can go from analyze to DICOM so this may be an
option for you.


a

On 20/12/05, Shahin Zangenehpour <shahin at bic.mni.mcgill.ca> wrote:
> Hello folks,
> I was wondering if anyone knows of a quick and easy way to convert
> MINC files to DICOM format to be viewed and volume-rendered with
> Osirix for Mac OS X.
> Any help or lead you can provide is much appreciated.
> Thanks,
> SZ
> ________________________________________________________________________
> _______________________________
> Shahin Zangenehpour, PhD    Postdoctoral Fellow   |   Montreal
> Neurological Institute   |   Cognitive Neuroscience Unit
> 3801 University Street   |   Room 276  |  Montr?al   QC   Canada
> H3A 2B4  |   P.  514  398  1717  |  F.  514  398  1338
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From a.janke at gmail.com  Tue Dec 20 17:57:29 2005
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 20 Dec 2005 17:57:29 -0500
Subject: [MINC-users] Problems installing latest software on Mac
In-Reply-To: <642aaccf7044983083abadd4c267d909@mi.unimaas.nl>
References: <642aaccf7044983083abadd4c267d909@mi.unimaas.nl>
Message-ID: <d747ed50512201457r3334dc17y@mail.gmail.com>

Hi Ed,

I have seen these "errors" with the mac packages from time to time.
Strangely enough they seem to install correctly (enough).  I'd suggest
you look in /usr/local/mni/bin too see if classfiy exists.  If so I'm
betting that the install went ok.  It seems to be an error in the
clean-up part of the install that I am yet to track down.  However
given that it doens't seem to be too much of a problem (beyond the
message) it is not too high on my list...

a

On 20/12/05, Ed Gronenschild <ed.gronenschild at mi.unimaas.nl> wrote:
> Hi,
>
> I downloaded from http://packages/bic.mni.mcgill.ca/osx the latest
> packages. The installation was OK except for classify-1.0.pkg and
> mni-autoreg-0.98s.pkg. For both the installer stopped with the very
> informative message "There were errors installing this software".
> I'm using OS X 10.3.9.
> Is there some workaround possible to install this software?
>
> Kind regards,
>
> Ed
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012


From ed.gronenschild at mi.unimaas.nl  Wed Dec 21 02:30:19 2005
From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild)
Date: Wed, 21 Dec 2005 08:30:19 +0100
Subject: [MINC-users] MINC-users] How to use rawtominc with multiple
	files
In-Reply-To: <mailman.5.1135098009.20384.minc-users@bic.mni.mcgill.ca>
References: <mailman.5.1135098009.20384.minc-users@bic.mni.mcgill.ca>
Message-ID: <134F1FB6-BEE2-44B3-A76F-A2A007D3F5A9@mi.unimaas.nl>

You should use the command:

minctoraw -short -unsigned -normalize -range 0 1700  
data_pix_out_nu.mnc > data_pix_out_nu.raw

This ensures that the intensities are between 0 and 1700 like your  
original data.

Kind regards,

Ed

On 20 Dec 2005, at 18:00, minc-users-request at bic.mni.mcgill.ca wrote:

>
>> 4. I would like to transfer the *.minc image into *.raw after the
>> correction to use my own algorithm run on the intensity corrected  
>> image. I
>> was using the command
>> minctoraw -short -unsigned -normalize data_pix_out_nu.mnc >  
>> data_pix_out_nu.raw
>>
>> The value in the raw file are varied from -32767 to 32767. My  
>> original
>> input image is unsigned short, intensity voxel value min is zero  
>> and  max
>> 1700. I would like to return back the *.minc image after  
>> correction into
>> the similar intensity level of input *.raw image.
>
> I suspect you want -nonormalize as opposed to -normalize.  ('minctoraw
> -help' or 'man minctoraw' explains the difference between the two.)
>


From vsingh at bic.mni.mcgill.ca  Wed Dec 21 08:52:13 2005
From: vsingh at bic.mni.mcgill.ca (Vivek SINGH)
Date: Wed, 21 Dec 2005 08:52:13 -0500
Subject: [MINC-users] How to use rawtominc with multiple files
In-Reply-To: <BFCDAD6A.9BD6%sridar@mrs.mni.mcgill.ca>
Message-ID: <Pine.SGI.4.44.0512210849070.85857-100000@shadow.bic.mni.mcgill.ca>

On Tue, 20 Dec 2005, Sridar Narayanan wrote:

> >> I was trying to resample the input image with average_305.mnc in mritotal
> >> and mincresample command before using NU_CORRECT. Which would be the better
> >> solution for NU_CORRECT? directly use on input image or after transforming
> >> data in a model (average_305) and then use the intensity correction? Please
> >> give me suggestion in this regard.
> >
> > Given that N3 has no knowledge of model space and the likes and works
> > on the raw histogram I would not expect the results to be different
> > beyond std interpolation and rounding errors.  Typically N3 is run on
> > the native data.

This is not exactly true.  The default behaviour of the nu_estimate script
(called by nu_correct) is to mask volumes in Talairach space using the
average_305_mask_1mm.mnc.  (This is done by attaching an -auto_mask option
when nu_estimate calls the nu_estimate_np_and_em script, for those who
care)  The decision is based on whether the 'spacetype' variables for the
x,y and z dimensions of the minc volume are set to "talairach" or not,
which is done for volumes resampled to an ICBM template using
mincresample.

>
> That's the usual practice, and performing the NU correction first will
> likely improve the registration to the average brain.
>

I believe someone investigated this and found there was little appreciable
difference in registration using mritotal if the NU correction is
performed before or after the fact (given data acquired with the ICBM
protocol), thought it probably doesn't hurt.

In my experience, performing the NU correction after registration can
sometimes improve the result, if I am unhappy with the correction before
registration.

Vivek



From elo at neurorx.com  Wed Dec 21 14:36:23 2005
From: elo at neurorx.com (Ernest Lo)
Date: Wed, 21 Dec 2005 14:36:23 -0500 (EST)
Subject: [MINC-users] How to use rawtominc with multiple files
In-Reply-To: <mailman.1.1135184409.104274.minc-users@bic.mni.mcgill.ca>
Message-ID: <Pine.LNX.4.44.0512211432190.21847-100000@hydra.bic.mni.mcgill.ca>

Some additional comments on N3:

There are arguments for using N3 (nu_correct) before and after
registration.


Reasons to use N3 (nu_correct) before registration:

1. As mentioned by Dr. Narayanan, nu_correction on images may improve
registration.  Having processed a steady stream of multi-modal scans on a
daily basis for almost a year now, I have seen a few instances where
severe image non-uniformity caused poor registration results using
mritoself (the alignment worked fine after nu_correction).  I imagine it
could cause similar effects in mritotal.  Both these algorithms use
intensity-based objective functions as convergence criteria. In any case,
nu_correction should not harm any subsequent registration processes.

2. I have heard that nu_correct works better on isotropic data.  So if one
is resampling anisotropic images to an isotropic space (meaning in this
case that the resolution or step size in the x,y,z directions are all the
same), then this may improve the result.


Reasons to use N3 after registration:

1. Since the nonlinear registration to standard space may both magnify and
reduce areas of the original image, it is possible that small
non-uniformities may be transformed into larger ones by mritotal.  Also,
assuming that N3 runs on the basis of a convergence criterion, this
criterion may no longer be satisfied after nonlinear registration.  
Therefore running N3 after mritotal ensures that all the images satisfy
the same uniformity convergence criterion.


For optimal results, you could run nu_correct both before and after
registration.  In practice, I think the differences will be small
whichever option (before or after) you choose.


Vivek, you mentioned that the default behaviour of nu_estimate is to mask
in Talairach space - are you sure about this?  I detect no nonlinear
transformation processes when nu_correct is run.


Ernest Lo
NeuroRX Research
Montreal, Canada




> ------------------------------
> 
> Message: 8
> Date: Wed, 21 Dec 2005 08:52:13 -0500
> From: Vivek SINGH <vsingh at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] How to use rawtominc with multiple files
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID:
> 	<Pine.SGI.4.44.0512210849070.85857-100000 at shadow.bic.mni.mcgill.ca>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
> 
> On Tue, 20 Dec 2005, Sridar Narayanan wrote:
> 
> > >> I was trying to resample the input image with average_305.mnc in mritotal
> > >> and mincresample command before using NU_CORRECT. Which would be the better
> > >> solution for NU_CORRECT? directly use on input image or after transforming
> > >> data in a model (average_305) and then use the intensity correction? Please
> > >> give me suggestion in this regard.
> > >
> > > Given that N3 has no knowledge of model space and the likes and works
> > > on the raw histogram I would not expect the results to be different
> > > beyond std interpolation and rounding errors.  Typically N3 is run on
> > > the native data.
> 
> This is not exactly true.  The default behaviour of the nu_estimate script
> (called by nu_correct) is to mask volumes in Talairach space using the
> average_305_mask_1mm.mnc.  (This is done by attaching an -auto_mask option
> when nu_estimate calls the nu_estimate_np_and_em script, for those who
> care)  The decision is based on whether the 'spacetype' variables for the
> x,y and z dimensions of the minc volume are set to "talairach" or not,
> which is done for volumes resampled to an ICBM template using
> mincresample.
> 
> >
> > That's the usual practice, and performing the NU correction first will
> > likely improve the registration to the average brain.
> >
> 
> I believe someone investigated this and found there was little appreciable
> difference in registration using mritotal if the NU correction is
> performed before or after the fact (given data acquired with the ICBM
> protocol), thought it probably doesn't hurt.
> 
> In my experience, performing the NU correction after registration can
> sometimes improve the result, if I am unhappy with the correction before
> registration.
> 
> Vivek


From vsingh at bic.mni.mcgill.ca  Wed Dec 21 19:47:00 2005
From: vsingh at bic.mni.mcgill.ca (Vivek SINGH)
Date: Wed, 21 Dec 2005 19:47:00 -0500
Subject: [MINC-users] How to use rawtominc with multiple files
In-Reply-To: <Pine.LNX.4.44.0512211432190.21847-100000@hydra.bic.mni.mcgill.ca>
Message-ID: <Pine.SGI.4.44.0512211935580.123844-100000@shadow.bic.mni.mcgill.ca>

>
> Vivek, you mentioned that the default behaviour of nu_estimate is to mask
> in Talairach space - are you sure about this?  I detect no nonlinear
> transformation processes when nu_correct is run.
>

Hi Ernest,

Indeed this is the default behaviour, but by registration I was referring
to volumes that are linearly registered using mritotal before applying
nu_correct.  No extra registation step is carried out and the average_305
mask is applied to the linearly registered volume.  If the volume is not
found to be in Talairach space by checking the 'spacetype' attributes, the
volume is masked based on a biModalT threshold.

Vivek