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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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

    

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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