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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 CautionThanks 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_aver...
> > 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....
> > 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....
> > > > But I dont know how to apply the path. Can you give some information about > this? > > > > Thanks! > > > > > > > > Emanuel > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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