you can use mri_aparc2aseg. Look in the recon-all.log file for an example command line.
On 02/22/2016 07:33 AM, Thomas Jacquemont wrote: > Dear, > > Thank you for all your advice. I have a last question, at the end of the > process I have two different volumes containing the right and the left > hemisphere parcellation. > How can I combine these two parcellation to get one whole brain parcellation? > Thank you, have a nice day. > > Yours faithfully, > > Thomas > > > >> On 2/19/16 11:00 AM, Thomas Jacquemont wrote: >>> Dear FreeSurfer experts, >>> >>> I would like to use the P. Hagmann atlas (Lausanne 2008 available here >>> https://github.com/LTS5/cmp/tree/master/cmp/data/colortable_and_gcs) on >>> my >>> subjects. I ran Recon all on their T1 images and then these two commands >>> to get the Hagmann parcellation for my subject: >>> >>> mris_ca_label -dir ../subject_dir/003_S_2374 rh sphere.reg >>> /aramis/home/jacquemont/DataAramis/Atlas/Hagmann/myatlas_250_rh.gcs >>> ./test_sub_003_S_2374.rh.Hagmann500.annot >>> >>> mri_label2vol --subject 003_S_2374 --hemi rh --annot >>> ./test_sub_003_S_2374.rh.Hagmann500.annot --temp >>> ../subject_dir/003_S_2374/mri/orig/001.mgz --o >>> annoted_volume_Hagmann500_003_S_2374.mgz --identity >>> >>> I have two questions. First, looking at the recon all log file I saw >>> that >>> the command is used this way: >>> >>> #@# Cortical Parc lh mardi 19 janvier 2016, 23:32:45 (UTC+0100) >>> mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz >>> -seed >>> 1234 NameSubject_M0 lh ../surf/lh.sphere.reg >>> /path/to/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs >>> ../label/lh.aparc.annot >>> >>> I would like to know what is the "seed" option? Do I need it? >> There is some randomness built into mris_ca_label, and the seed is the >> seed for the random generator. We want the results to be dterministic >> (ie, gives the same answer when re-run in the same way) so we always >> seed with the same number. Probably you will want this too, so use the >> seed option. >>> Secondly, By surperimposed the resulting parcellation file (output of >>> the >>> mri_label2vol command) to the repective T1 image it seems that they are >>> not in the same space. How could I have the pacellated file in the same >>> space as the T1 image? Is the way I am using these two command good? >>> What >>> inputs should I change? The sphere file (for mris_ca_label), the --temp >>> (for mri_label2vol), etc... >> Use --regheader orig.mgz instead of --identity >> doug >> >>> Thank you for your help, >>> >>> Yours faithfully, >>> >>> Thomas >>> >>> _______________________________________________ >>> 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. >> > > _______________________________________________ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
