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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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.
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