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Thank you for the quick answer! For the archive and my understanding…the pscalar gives out a column with 360 values, these values are the average thickness of my one subject and finally, the data I was searching for: cortical thickness values from my subject obtained with Freesurfer but with the parcellation of the HCP-MMP1. Is there a document or a command where I can correlate these values with the name/number of cortical area?
Regards,
Alina
Am 20.07.2020 um 11:32 schrieb Alina Rojas alinacolora@gmail.com:
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? 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 <glasserm@wustl.edu mailto:glasserm@wustl.edu>:
External Email - Use CautionI would find using something like ciftify (https://github.com/edickie/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&a... 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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alina Rojas" <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of alinacolora@gmail.com mailto:alinacolora@gmail.com> wrote:
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External Email - Use CautionHello 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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