[MINC-users] mincaverage error

[Andrew Janke]

Hi Lisa,

I think this bug might be related to one I have seen as of late (only
on Ubuntu Maverick and the latest Debian release). In combination with
various phases of the moon you get this self same error. Even
something as simple as changing the input files order can make it go
away. I have noticed it more with register than anything else but
still haven't seen anything all that consistent yet to track it down.
:(

If changing the input file order fixes things then it most likely is
the same as I have seen.  Another thing that seems to exacerbate the
problem is a mix of MINC 1 and MINC 2 files. What does "file" return
on all your input files?


a

On Sat, Mar 5, 2011 at 08:14, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> Hi Vladimir,
> Yes, I specified all the file names.
> I also re-ran it including the full path in the filelist, but it still gave
> me the same error.
> I re-ran it without a filelist (just listed all filenames in the command),
> but it failed.
>
> Hi Alex,
> Yes, I have writing permission and that there is ample free space (over
> 120GB) in my current location.
> I copied all of my input file to a different location, made sure I had the
> correct permission and ample space, and re-ran mincaverage, but failed
> again.
>
> Another tidbit:
> The output file is created (3.2MB), but when I open it in register, it is
> just a black image.
>
>
> Thanks.
>
>
> Best,
> Lisa
>
>
> On Fri, Mar 4, 2011 at 12:44 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
>
>> Hi Lisa,
>>
>> On the off-chance that this is the problem - are you sure you have
>> write access and free disk space in the location where you are trying
>> to write the output file?
>>
>> -- Alex
>>
>> On Fri, Mar 4, 2011 at 3:17 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
>> >
>> > Hi Andrew,
>> >
>> > I double checked each minc file (displayed them in register) and they all
>> > seemed to be fine...
>> >
>> > Don't know if this helps at all..., but here are some more information:
>> >
>> > 1. A correction to what I wrote earlier:
>> >
>> > > I am trying to run mincaverage on 43 minc files, all which have been N3
>> > > intensity nonuniformity normalized, neck portion cropped off,
>> mincnorm-ed,
>> > > *and linearly (9parameter) registered to a standard template*.
>> >
>> >
>> > 2. I am using the -filelist option. I have a .txt file with each file
>> name
>> > listed on separate lines. Is this the correct format for the filelist?
>> >
>> > 3. The version I am using:
>> >
>> > > > mincaverage -version
>> > > program: 2.1.00
>> > > libminc: 2.1.00
>> > > netcdf : 4.1.1 of May 15 2010 04:10:51 $
>> > > HDF5   : 1.8.4
>> >
>> >
>> >
>> > Thanks.
>> >
>> >
>> > Best,
>> > Lisa
>> >
>> > On Fri, Mar 4, 2011 at 11:52 AM, Andrew Wood <andrew at biospective.com>
>> wrote:
>> >
>> > > Hi Lisa,
>> > >
>> > > Is there any chance that the problem is with your input minc files? I
>> just
>> > > gave minc average a few good minc volumes plus a filename that didn't
>> exist
>> > > and I got back your error message.
>> > >
>> > > Andrew
>> > >
>> > >
>> > > On Fri, Mar 4, 2011 at 2:23 PM, Lisa F. Akiyama <lrisa87 at uw.edu>
>> wrote:
>> > >
>> > > > Hi Jared,
>> > > >
>> > > > I tried re-running mincaverage with the -clobber extention.
>> > > > I also ran it using a totally new output filename too, but it still
>> gives
>> > > > me
>> > > > the same error message.
>> > > >
>> > > > Thanks.
>> > > >
>> > > >
>> > > > Best,
>> > > > Lisa
>> > > >
>> > > >
>> > > >
>> > > > On Fri, Mar 4, 2011 at 11:05 AM, Jared Rowley <
>> jared.rowley at gmail.com
>> > > > >wrote:
>> > > >
>> > > > > Hi Lisa,
>> > > > >
>> > > > > I think you need to to do mincaverage -clobber.
>> > > > >
>> > > > > My guess is that the output.mnc already exists and you need to do
>> > > > -clobber
>> > > > > to overwrite it.
>> > > > >
>> > > > > Jared
>> > > > >
>> > > > >
>> > > > > On Fri, Mar 4, 2011 at 2:00 PM, Lisa F. Akiyama <lrisa87 at uw.edu>
>> > > wrote:
>> > > > >
>> > > > > > Hello,
>> > > > > >
>> > > > > > I am trying to run mincaverage on 43 minc files, all which have
>> been
>> > > N3
>> > > > > > intensity nonuniformity normalized, neck portion cropped off, and
>> > > > > > mincnorm-ed.
>> > > > > > The following is the error that I receive:
>> > > > > >
>> > > > > > Processing:........................miicv_attach: MINC package
>> entry
>> > > > point
>> > > > > > > *ncvarid: ncid -1: NetCDF: Not a valid ID*
>> > > > > >
>> > > > > >
>> > > > > > When I run mincaverage on individual files and on subsets of the
>> 43
>> > > > > files,
>> > > > > > mincaverage runs fine.
>> > > > > > What is the issue?
>> > > > > >
>> > > > > > Thank you in advance.
>> > > > > >
>> > > > > >
>> > > > > > Best,
>> > > > > > Lisa
>> > > > > > _______________________________________________
>> > > > > > 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
>> > > >
>> > > _______________________________________________
>> > > 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
>>
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