Hi,
I corrected my proceeding and separated the echoes using the pipeline:
recon-all -s subj_name -i /.../dicom_images.dcm recon-all -s subj_name -use-gpu -mprage -all
mri_convert -odt float -f 0 ./... .dcm $SUBJECTS_DIR/subj_name/mri/000.mgz mri_convert -odt float -f 1 ./... .dcm $SUBJECTS_DIR/subj_name/mri/001.mgz mri_convert -odt float -f 2 ./... .dcm $SUBJECTS_DIR/subj_name/mri/002.mgz mri_convert -odt float -f 3 ./... .dcm $SUBJECTS_DIR/subj_name/mri/003.mgz
mris_make_surfaces -dura %03d.mgz 4 subj_name lh mris_make_surfaces -dura %03d.mgz 4 subj_name rh
recon-all -autorecon-pial -subjid subj_name -use-gpu -mprage .
I see a difference in the cortical atlas after doing "recon-all -autorecon-pial", but if I take a look at the 3D-Volume I still find pieces of the dura included in the cortex. Please check the figure attached to this mail. The red cross signals the location.
Regards Joerg
On Wed, 12 Jun 2013 09:03:21 -0400 (EDT) Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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
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