Hello Bruce, Doug and Emanuel,

I tried what you suggested (ln -s orig.mgz norm.mgz), and I also downloaded the development version and tried that, but neither procedures fixed the problem.

In the meantime, my father-in-law took a week and fixed the script and now it runs smoothly and finishes without error. The following code segment of the make_average_subject file needed to be fixed:

Erroneous code segment:

…

if($DoSurfaces && $DoVolumes) then

  set cmd = (recon-all -s $average_subject -cortribbon -aparc2aseg)

  echo $cmd

  $cmd

  if($status) exit 1;

endif

…

New, corrected code segment:

if($DoSurfaces && $DoVolumes) then

  #set cmd = (recon-all -s $average_subject -cortribbon -aparc2aseg)

  set cmd = (recon-all -s $average_subject -nuintensitycor -gcareg -canorm -careg -calabel -cortribbon -aparc2aseg)

  echo $cmd

  $cmd

  if($status) exit 1;

endif

…

The code that is highlighted with red and a hashtag is what caused the script to exit with errors. The one below that (highlighted with green) is the fixed line of code that finishes without errors.

The patched make_average_subject file is also attached. Feel free to use it.

Best,
Marta (and my father-in-law)

On Tue, Jan 22, 2019 at 2:45 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

This has been fixed in our development version. I can give you a new
script or you can try this:
cd $SUBJECTS_DIR/*avgsubjectPRUEBAESTASI!
ln -s orig.mgz norm.mgz
Then re-run make_average_subject

*
On 12/14/18 1:43 PM, Emanuel Alvaredo wrote:
>
>         External Email - Use Caution
>
> Thanks Greve. The output is attached now.
>
>
> Emanuel
>
>
> On Fri, Dec 14, 2018 at 1:01 PM Greve, Douglas N.,Ph.D.
> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>
>   can you include the full terminal output?
>
> On 12/13/18 7:45 AM, Emanuel Alvaredo wrote:
>>
>>          External Email - Use Caution
>>
>> Hello Bruce, thanks for your anwer. Sure. The command is
>>
>> *make_average_subject --out avgsubjectPRUEBAESTASI! --subjects
>> Bartley_Recon Baez_Recon Bonilla_Recon*
>>
>> The output is in the attached file
>>
>> Thanks!
>>
>> Emanuel
>>
>>
>> On Wed, Dec 12, 2018 at 7:05 PM Bruce Fischl
>> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>
>> wrote:
>>
>> Hi Emanuel,
>>
>> can you include the full command line and output?
>>
>> cheers
>> Bruce
>> On Wed, 12 Dec 2018,
>> Emanuel Alvaredo wrote:
>>
>> >
>> >         External Email - Use Caution
>> >
>> > Thanks for your answer Douglas. I replaced the
>> make_average_surface file with the new one but I
>> > have the same message error.
>> > ASeg Vox2RAS: -----------
>> > -1.00000 0.00000 0.00000 128.00000;
>> > 0.00000 0.00000 1.00000 -128.00000;
>> > 0.00000 -1.00000 0.00000 128.00000;
>> > 0.00000 0.00000 0.00000 1.00000;
>> > mghRead(mri/norm.mgz, -1): could not open file
>> > -------------------------
>> >
>> > Labeling Slice
>> > relabeling unlikely voxels in interior of white matter
>> > mri/norm.mgz: could not load norm volume from (null)
>> >
>> > Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP
>> Tue Oct 2 17:16:02 UTC 2018 x86_64 x86_64
>> > x86_64 GNU/Linux
>> >
>> > Thanks
>> >
>> > Emanuel
>> >
>> >
>> > On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D.
>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>> > Sorry, the disk that held that patch failed and we
>> did not have a backup so not
>> > everything was restored. I just put this file there:
>> >
>> >
>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface
>> >
>> > Copy it to $FREESURFER_HOME/bin. Let me know how it goes
>> >
>> >
>> > On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:
>> >
>> >          External Email - Use Caution
>> >
>> > Thanks Bruce. The following is the command.
>> >
>> > make_average_subject --out avgsubjectPRUEBAESTASIEmac
>> --subjects subject1
>> > subject2 subject3
>> >
>> >
>> > And I made a mistake in may last mail. I use the word path
>> instead of patch
>> >
>> > I have found this page with a patch for de issue
>> >
>> >
>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>> >
>> > But I dont know how to apply the patch. Can you give some
>> information about this?
>> >
>> >
>> > Emanuel
>> >
>> >
>> > On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl
>> <fischl@nmr.mgh.harvard.edu
>> <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
>> > Hi Emanuel
>> >
>> > you need to send us the full command you ran and
>> output of it if you want
>> > us to be able to help you
>> >
>> > cheers
>> > Bruce
>> > On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:
>> >
>> > >
>> > >         External Email - Use Caution
>> > >
>> > > Hello!, I am getting the following error using the
>> > command make_average_subject
>> > >
>> > > mri/norm.mgz: could not load norm volume from (null)
>> > >
>> > > I have found this page with a path for de issue
>> > >
>> > >
>> >
>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>> > >
>> > > But I dont know how to apply the path. Can you give
>> some information about
>> > this?
>> > >
>> > > Thanks!
>> > >
>> > >
>> > >
>> > > Emanuel
>> > >
>> > >_______________________________________________
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>> >
>> >
>> >
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