Does talairach appear in your SUBJECTS_DIR? If not, then

cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage .

I would have thought that the .bhdr files would be there, but that might be another problem.

doug

Avram Holmes wrote:

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

---

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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Whoops. Disregard the previous question. Somehow I forgot to add the subjectname file.

Sorry for cluttering up everyone's inbox, 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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Tue, 15 May 2007, Avram Holmes wrote:

All,

I'm an getting an error when I attempt to run autoreg-sess

This is the command I am running...

autoreg-sess -s c07 -d . -fsd Flanker

The following is the error I get.

Logfile is /net/daplab1/Raid/shared/exp/CONCON/fMRI/functional/log/autoreg-sess.log setenv SUBJECTS_DIR /exp/CONCON/fMRI/structural/

---

--- /net/daplab1/Raid/shared/exp/CONCON/fMRI/functional/c07 ----------- _______________________________________________________ ERROR: (/net/daplab1/Raid/shared/exp/CONCON/fMRI/functional/c07) cannot find /net/daplab1/Raid/shared/exp/CONCON/fMRI/functional/c07/subjectname ... Continuing Tue May 15 11:05:35 EDT 2007 autoreg-sess completed with ERRORS

Any ideas about what I could do to fix this?

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

On Thu, 10 May 2007, 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