Hi Joerg
you need to convert the individual echoes to be in conformed space without scaling the intensities, then run it with something like
mris_make_surfaces -dura echo%d.mgz 4 subj_name lh
otherwise it will just load 001.mgz 4 times and think it is the different echoes. That is, name the echoes echo0.mgz echo1.mgz echo2.mgz and echo3.mgz
cheers Bruce
On Wed, 12 Jun 2013, Joerg Pfannmoeller wrote:
Hello FSexperts,
I used the mgh memprage and the dura correction scheme described in:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28479.html .
Afterwards I applied
recon-all -autorecon-pial -subjid subj_name
to the subjects in order to include the changes in the subsequent FS-Fast analysis. Currently I do not see any effect in tksurfer if I proceed like this. Please correct me if I am wrong with my effect size expectation. For completeness I add the command pipeline used:
recon-all -s subj_name -i /.../dicom_images.dcm recon-all -s subj_name -use-gpu -mprage -all mri_convert -odt float ./... .dcm $SUBJECTS_DIR/subj_name/mri/001.mgz mris_make_surfaces -dura 001.mgz 4 subj_name lh mris_make_surfaces -dura 001.mgz 4 subj_name rh recon-all -autorecon-pial -subjid subj_name _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer