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
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