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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 <glass...@wustl.edu>:
>
> External Email - Use Caution
>
> 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 on behalf of
> Alina Rojas" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> 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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