Dear Douglas, The wm.mgz is in the mri folder so it's in:
Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz. Best Regards, Mahtab. Sent from myMail for iOS Thursday, May 19, 2016, 16:19 +0100 from gr...@nmr.mgh.harvard.edu <gr...@nmr.mgh.harvard.edu>: >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
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