The second one is a valid command (1st is not). What is the full path to the wm.mgz file that is in your anlayzed data?
On 05/19/2016 10:33 AM, Mahtab Farahbakhsh wrote: > Dear Bruce, > > This is the input command and the output that I get: > > bash-3.2$ mris_anatomical_stats -l anon/label/lh.BA45.label -f anon lh > anon lh > limiting computations to label anon/label/lh.BA45.label. > reading volume > /Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz... > mghRead(/Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz, > -1): could not open file > mris_anatomical_stats: could not read input volume > /Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz > > or: > > mris_anatomical_stats -l anon/label/lh.BA45.label anon lh > limiting computations to label anon/label/lh.BA45.label. > reading volume > /Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz... > mghRead(/Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz, > -1): could not open file > mris_anatomical_stats: could not read input volume > /Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz > > > This is the SUBJECTS_DIR > > export SUBJECTS_DIR=/Applications/freesurfer/experimental_data/TG/anon > > cd $SUBJECTS_DIR > > Best Regards, > Mahtab. > > > On 19 May 2016 at 13:41, Bruce Fischl <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > > Hi Mahtab > > can you please send the screen output of the command you ran and > what it printed, and also what the environment variable > SUBJECTS_DIR is? > > cheers > Bruce > > On Thu, 19 May 2016, Mahtab Farahbakhsh wrote: > > Dear FreeSurfer, > I have a problem when I use mris_anatomical_stats. It gives me > an error > saying that it couldn't read the input volume which is the > wm.mgz file. > would you please help me how I should fix this problem? > > Best Regards, > Mahtab. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
