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