Hi Max,

Please try putting each command as a separate line, like this:

-v scan1/mri/T1.mgz -v scan1/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 etc..

Best, Ruopeng

On Dec 17, 2015, at 5:30 AM, BAUTISTA-PERPINYA Maximilià maximila.bautista-perpinya@etu.unistra.fr wrote:

Hi FS experts,

I have an script (screenshots.txt) that takes screenshots of freeview of several scans:

It looks like this:

-v scan1/mri/T1.mgz ; -v scan1/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 ; -viewport sagittal -slice 80 127 127 -ss sag1_scan1 ; -v scan2/mri/T1.mgz ; -v scan2/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 ; -viewport sagittal -slice 80 127 127 -ss sag1_scan2 ; ... and so on

Then I run freeview -cmd screenshots.txt and it gives me this error: MRIread failed: Unable to read from /home/freesurfer/Desktop/test005/subjects/;

This path is my cwd. The scan folders (scan1, scan2, and so on) are contained within the above mentioned cwd, but the cwd is not mentioned in the script. I tried specifying the complete path (/home/freesurfer/Desktop/test005/subjects/scan1 and so on) but gives the same error.

As well, the only output from this is the screenshot from the last scan (sag1_scan2 in this case). The other ones before are missing.

Anybody knows a way around this? Any help would be much appreciated

Best regards,

Max Bautista

btw:

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

RedHat release: CentOS release 6.7 (Final)

Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64

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