Doug, Sorry for the repeated questions. Could this be due to the fact that only the 'minsig' and 'sig' files were generated by intergroupavg-sess. I don't have any files like sig.bhdr.
I had already managed to create a symlink to fsaverage called 'talairach' for an earlier stage in the analysis. However, I am still getting the error. Just to double check, the symlink goes from 'talairach' in the analysis structural folder to the fsaverage folder in '/apps/freesurfer/freesurfer/subjects/fsaverage/' Once again here is the tkmedit-sess command and the resulting error. tkmedit-sess -analysis taumax30_stc_smooth6 -s LowTrauma_v_HighTrauma -isxavg random -contrast Rcue_v_Ncue -space tal -d . -------------------------------------------------------------- tkmedit-sess logfile is /Raid/shared/exp/REfMRI/fMRI_FPPREW/functional/log/tkmedit-sess.log -------------------------------------------------------------- setenv SUBJECTS_DIR /exp/REfMRI/fMRI_FPPREW/structural/ INFO: Found session in: ./LowTrauma_v_HighTrauma INFO: LowTrauma_v_HighTrauma is a group average INFO: Found session in: ./LowTrauma_v_HighTrauma INFO: LowTrauma_v_HighTrauma is a group average INFO: subject is talairach INFO: subject is talairach /exp/REfMRI/fMRI_FPPREW/structural//talairach/mri/orig: No such file or directory. Oh and when I search in fsaverage I can locate a 'orig.mgz' file 'fsaverage/mri' Thanks, Avram ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: [EMAIL PROTECTED] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Quoting Doug Greve <[EMAIL PROTECTED]>: > Create a sym link in your SUBJECTS_DIR from fsaverage to talairach > > doug > > Avram Holmes wrote: > > >To anyone not outside enjoying the nice weather, > > > >I have recently completed running intergroupavg-sess > > > >intergroupavg-sess -analysis taumax30_stc_smooth6 -contrast Rcue_v_Ncue > -group1 > >LowTrauma -group2 HighTrauma -intergroup LowTrauma_v_HighTrauma -space tal > > > >Only 'minsig' and 'sig' files were generated. However, no sig.bhdr files > were > >created. I just wanted to check to see if everything is as it should be. > > > >Also, when I run tkmedit-sess in an attempt to view the data on both the > between > >and within group (where all the normal files were created) analyses... > > > >tkmedit-sess -analysis taumax30_stc_smooth6 -s LowTrauma_v_HighTrauma > -isxavg > >random -contrast Rcue_v_Ncue -space tal -d . > > > >I recieve the following error... > > > >-------------------------------------------------------------- > >tkmedit-sess logfile is > >/Raid/shared/exp/REfMRI/fMRI_FPPREW/functional/log/tkmedit-sess.log > >-------------------------------------------------------------- > >setenv SUBJECTS_DIR /exp/REfMRI/fMRI_FPPREW/structural/ > >INFO: Found session in: ./LowTrauma_v_HighTrauma > >INFO: LowTrauma_v_HighTrauma is a group average > >INFO: Found session in: ./LowTrauma_v_HighTrauma > >INFO: LowTrauma_v_HighTrauma is a group average > >INFO: subject is talairach > >INFO: subject is talairach > >ERROR: subject talairach does not exist in data base > >SUBJECTS_DIR: /exp/REfMRI/fMRI_FPPREW/structural/ > > > >Do I have to take any steps to add the talairach brain to my studies > >'structural' folder so that I can use tkmedit-sess or is this error related > to > >something else. > > > >Thanks in advance for any help you can offer, > >Avram > > > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >Avram Holmes > >Department of Psychology > >Harvard University > >1210 William James Hall Phone:(617) 495-0790 > >33 Kirkland Street Fax:(617) 495-3728 > >Cambridge, MA 02138, USA Email: [EMAIL PROTECTED] > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > > > > > > > > > > > >_______________________________________________ > >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 > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
