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 <fis...@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 > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- Joerg Pfannmoeller <pfannmo...@uni-greifswald.de>
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