Try putting a slash "/" before "usr" on the input (--i) fille doug
On 02/11/2013 04:50 AM, Rotem Saar wrote: > Hi, > > My name is Rotem, I'm a PhD. student and recently started to work with > freesurfer software (freesurfer-Linux-centos4-stable-pub-v5.1.0). QUESTION > For several weeks, I have been trying to operate a script for FA > values, with no success, and would really appreciate your help with > shading some light regarding the problem and it's solution. > I have a data set, after an anatomical segmentation (file is attached, > named "Anatomical segmentation for fs", this is the script I'm using > for brain anatomical segmentation). What I'm trying to run now is the > DTI script, in which I run commands that at least for my understanding > spouse to give me at the end a table with all the FA values for each > brain region (ROI). The script I'm using to do this is attached and > called "DTI_RUN_NEW_FOR_FS". > _After running phase 5_, in which a mask file should be created > (indeed I have checked and the file is created in the same folder it > should be): > > fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> mri_mask > /usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii > /usr/local/freesurfer/subjects/FOLDER_NAME/mri/brainmask.mgz > /usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii > DoAbs = 0 > Found 16777216 voxels in mask > Writing masked volume to > /usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii...done. > > _I run phase 6, and then get the following error message:_ > > fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> mri_segstats --seg > /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii > --sum > /usr/local/freesurfer/subjects/FOLDER_NAME/stats/all_stats_fa_FOLDER_NAME > > $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ > cwd > cmdline mri_segstats --seg > /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz --ctab > /usr/local/freesurfer/FreeSurferColorLUT.txt --i > usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii --sum > /usr/local/freesurfer/subjects/FOLDER_NAME/stats/all_stats_fa_FOLDER_NAME > sysname Linux > hostname fmri4-P67A-D3-B3 > machine i686 > user fmri4 > Loading /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz > Loading > usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii > niiRead(): error opening file > usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii > ERROR: loading > usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii > > I think the problem is between phase 5 and 6, and is related to file > format (.nii) but don't have a hint regarding what can I do to solve > this:( Can someone please write me the correct code line ? > > I would really appreciate your kind help since I run out of ideas for > solutions. > > Thanks in advance, > > Rotem > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] 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.
