CIFTI Parcellation of the Cerebellum

[Kodibagkar, Alisha]

Hello,

Thank you for answering my earlier question about pre-excluding the volumes and slice time correction!

I had another question, for which I found a similar post in the forum but wasn't sure how to interpret the answer. ​

Our group is interested in parcellating HCP-Aging data using the cerebellar atlas mentioned in this paper:

https://www.sciencedirect.com/science/article/abs/pii/S1053811909000809?via%3Dihub​

​However, I was unable to find a CIFTI version of this cerebellum atlas. I was wondering if something like this exists, and if not, is it possible to convert the NIFTI version of this atlas into a CIFTI file or find another way to parcellate the cerebellum with this atlas?

Thank you,

Alisha Kodibagkar

[Glasser, Matthew]

You should be able to import it into CIFTI using wb_command -volume-label-import and wb_command -cifti-create-dense-label.

 

Matt.

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[Coalson, Timothy Scott (S&T-Student)]

If you want it to match by index to other cifti files, would suggest wb_command -volume-label-import and then -cifti-dense-create-from-template.  You may need to resample it to our 2mm space first to use it with standard 91k cifti data.

Tim

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From: Glasser, Matthew <glas...@wustl.edu>
Sent: Thursday, July 22, 2021 4:12 PM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Subject: Re: [hcp-users] CIFTI Parcellation of the Cerebellum

 

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[Grace Shearrer]

Hello, I am also trying to transform the Buckner 2011 cerebellum parcellation into a cifti to use with the PTN ICA files. I have done the following steps:

wb_command -volume-label-import Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz color.txt update_Buck.nii

WARNING: datatype disagrees with bitpix in file 'Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz'

wb_command -cifti-create-dense-from-template HCP_S1200_997_tfMRI_ALLTASKS_level2_cohensd_hp200_s4_MSMSulc.dscalar.nii Buck_cifti.dlabel.nii -volume CEREBELLUM update_Buck.nii -from-cropped

ERROR: -volume option specified for structure CEREBELLUM, but template cifti file does not contain this volume structure

I am not sure what the error message means. Should I use a different cifti as a template?

Thank you,

Grace

[Glasser, Matt]

Use:

      CEREBELLUM_LEFT

      CEREBELLUM_RIGHT

 

Matt.

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[Grace Shearrer]

Hi Matt,

thank you so much for the quick reply. I changed my command to:

wb_command -cifti-create-dense-from-template HCP_S1200_997_tfMRI_ALLTASKS_level2_cohensd_hp200_s4_MSMSulc.dscalar.nii Buck_cifti.dlabel.nii -volume CEREBELLUM_LEFT update_Buck.nii -from-cropped

I now get this error:

ERROR: volume file 'update_Buck.nii' does not match volume space of template cifti file

How do I change the space to match the template? 

Thank you again,

Grace

[Glasser, Matt]

Are the data lined up with the same voxel size and FOV?

Matt.

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[Grace Shearrer]

Hi Matt,

shoot, no.... it looks like they are slightly different. I am assuming I will need to do some combination of FLIRT FNIRT to get them in the same space? 

Grace

[Glasser, Matt]

You would want them as well lined up and on the same voxel grid as you can.

[Grace Shearrer]

Got it! Thank you so much!

Grace