Hi Thomas the seed sets the random number generator to the same starting point so that the algorithm is repeateable.
Maybe Doug can comment on the second question. How are you visualizing it? cheers Bruce On Fri, 19 Feb 2016, 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? > > 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... > > 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.
