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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 <alinacol...@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 <glass...@wustl.edu
>> <mailto:glass...@wustl.edu>>:
>>
>> External Email - Use Caution
>>
>> I 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&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
>>
>> <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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