External Email - Use Caution Hi Juan,
If I want to seed T1 hippocampus.mgz to fill the ProbtrackX. How should I do that? Is it something like below: mris_convert lh.white lh.white.gii mri_convert lh.hippocampus.mgz lh.hippocampus.nii.gz and then label2surf -s lh.white.gii -o lh.hippocampus.nii.gz -l hippocampus.txt Thank you so much ! Best, Qi On Fri, Jun 5, 2020 at 4:13 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Removing the -U ;-) > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Zeng, Qi" < > qi.z...@icahn.mssm.edu> > *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Date: *Friday, June 5, 2020 at 16:02 > *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Get hippocampus segmention from > [lr]h.hippoAmygLabels-T1.v21.mgz > > > > * External Email - Use Caution * > > Thanks. I was wondering If there is another way around to get the amygdala > mgz. > > > > Best, > > Qi > > > > On Fri, Jun 5, 2020 at 2:44 PM Iglesias Gonzalez, Juan E. < > jiglesiasgonza...@mgh.harvard.edu> wrote: > > Yes 😊 the amydala labels are in the 7000 range and the hippocampal in > the 200s. Feel free to use eg 4129 next time! > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Zeng, Qi" < > qi.z...@icahn.mssm.edu> > *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Date: *Friday, June 5, 2020 at 14:42 > *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Get hippocampus segmention from > [lr]h.hippoAmygLabels-T1.v21.mgz > > > > * External Email - Use Caution * > > Thanks, it works. Does the code mean that it only allows labels under 300 > to pass through? > > > > Best, > > Qi > > > > On Fri, Jun 5, 2020 at 12:37 PM Iglesias Gonzalez, Juan E. < > jiglesiasgonza...@mgh.harvard.edu> wrote: > > Dear Qi, > > You can try: > > mri_threshold -U [lr]h.hippoAmygLabels-T1.v21.mgz 300 > [lr]h.hippoLabelsNoAmyg-T1.v21.mgz > > > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Zeng, Qi" < > qi.z...@icahn.mssm.edu> > *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Date: *Friday, June 5, 2020 at 11:54 > *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject: *[Freesurfer] Get hippocampus segmention from > [lr]h.hippoAmygLabels-T1.v21.mgz > > > > * External Email - Use Caution * > > Hi, > > > > I conducted longitudinal segmentation of both hippocampus and amygdala > from running segmentHA_T1_long.sh. But is it possible for me to segment > only the hippocampus region "mgz" from the stored > [lr]h.hippoAmygLabels-T1.long.v21.mgz ? > > > > Best, > > Qi > > > -- > > > > Ph.D. candidate > > Icahn School of Medicine at Mount Sinai > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > > > Ph.D. candidate > > Icahn School of Medicine at Mount Sinai > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > > > Ph.D. candidate > > Icahn School of Medicine at Mount Sinai > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Ph.D. candidate Icahn School of Medicine at Mount Sinai
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