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: holmes@fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
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: holmes@fas.harvard.edu
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