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I would use https://balsa.wustl.edu/file/show/3VLx which is the CIFTI label
file. The pscalar is not a label file, but rather the average thicknesses in
each cortical area. You can view the average thicknesses in Connectome
Workbench or print out the results with wb_command -cifti-convert -to-text.
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alina Rojas
<alinacol...@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, July 20, 2020 at 4:32 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
External Email - Use Caution
Thank you, the ciftify was run successfully! But now I have questions to the
wb-command -cifti-parcellate:
wb_command -cifti-parcellate
<cifti-in> - the cifti file to parcellate
<cifti-label> - a cifti label file to use for the parcellation
<direction> - which mapping to parcellate (integer, ROW, or COLUMN)
<cifti-out> - output - output cifti file
I understand that <cifti-in> should be
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii,
but what should I use as label? The
Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii
from https://balsa.wustl.edu/WN56? And the output from the -cifty-parcellate is
.pscalar.nii..how do I get from there to GIFTI?
And for the GIFTY to .annot I would do:
mris_convert --annot lh.aparc.gii lh.white.gii lh.aparc.annot (Freesurfer
example)
Thank you,
Alina
Am 14.07.2020 um 16:17 schrieb Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>>:
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I would find using something like ciftify (https://github.com/edickie/ciftify)
potentially more straightforward (and then you can just use wb_command
-cifti-parcellate on
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
It is possible to go the other direction too (e.g. using this link:
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
and then perhaps someone on the list can explain how to go from GIFTI on
fsaverage to .annot on the native meshes and extract the stats.
Matt.
On 7/14/20, 8:54 AM,
"freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Alina Rojas"
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of alinacol...@gmail.com<mailto:alinacol...@gmail.com>> wrote:
* External Email - Caution *
External Email - Use Caution
Hello Freesurfer support list,
I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my
subjects to get the values of the parcellation, like aparc.stats but aparc
being HCP-MMP1. The aim ist to compare the cortical thickness of the
Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the
archive and didn’t find the solution. It would be so great if you could help me!
Thank you and regards,
Alina Rojas
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