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
