External Email - Use Caution 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. < dgr...@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. > > <dgr...@mgh.harvard.edu <mailto:dgr...@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 > >> <fis...@nmr.mgh.harvard.edu <mailto:fis...@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. > >> <dgr...@mgh.harvard.edu <mailto:dgr...@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 > >> <fis...@nmr.mgh.harvard.edu > >> <mailto:fis...@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 > >> > > > >> > >_______________________________________________ > >> > 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> > >> 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 > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Marta Korom | *PhD Candidate University of Delaware, Clinical Science e-mail: mko...@udel.edu phone: 646 861 8461 http://www.abcintervention.org/
make_average_subject
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
