Creating Cifti Thickness File from FreeSurfer Output

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Hi all!

I would like to create a cortical-thickness-file in the Cifti-file-format using the FreeSufer output. More specifically, I would like to use the fs_subjects/$subject/surf/lh.thickness and fs_subjects/$subject/surf/rh.thickness files, merge them and project them onto the fsaverage_LR32k Cifti-surface, i.e. create one single $subject.thickness.32k_fs_LR.dscalar.nii file. Does anybody know a way to achieve this?

Thanks in advance,
Marlene.

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Hi @mtahedl, and welcome to neurostars!

I know that fMRIPrep will do this as part of its anatomical workflow as of the recently released 23.0.0, as long as you specify —cifti-outputs 91k in your command. You can try that (if you don’t have BOLD images you can try using the —anat-only flag too).

Best,
Steven

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Hi Steven,

thanks for getting back :slight_smile: However, I’m particularly interested in doing that conversion independent of the (entire) fMRIPrep pipeline. Are you aware of a simple and quick line of commands to achieve that?

Thanks!
Marlene.

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Not off the top of my head, but perhaps looking through the code that was added to enable this workflow could provide some clues ENH: Enable resampling morphometrics to fsLR CIFTI-2 files by effigies · Pull Request #325 · nipreps/smriprep · GitHub.

Best,
Steven

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Hi @mtahedl, one option to try is the ciftify_recon_all command from ciftify. This is meant to convert a freesurfer output directory to CIFTI space and should be able to run outside of the full ciftify workflow - independent from the fMRIPrep-based processing.

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Hi @pcamach2 , thank you! Yes, I’m aware of the Ciftify toolbox including the ciftify_recon_all command. You’re right, it does the conversion I’m looking for. However, one pre-requisite of using cifitfy_recon_all is to have the full FreeSurfer output at hand. I’m trying to find out whether there is a solution if you only have the lh.thickness file (and not the rest of the FreeSurfer output). Any input would be appreciated :slight_smile:

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@mtahedl, I doubt this is possible with only the morphometric file. Those files are basically just data vectors, and do not contain geometric/anatomical information, which would be in the surface meshes (such as those output by recon-all). At some point you will need to register between native and fs_LR space, which is probably informed by outputs from recon-all.

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Hm, I see. Then let’s re-formulate my problem: I’m looking for the minimum number of files from the FreeSurfer output to create a cortical thickness file in the cifti-file format.

The following strategy came close to my solution: I’ve first created a metric file off the lh.thickness using anatomical information as follows:

mris_convert -c lh.thickness lh.white lh.thickness.gii

I repeated that for the right hemisphere. Then, I used a tool from workbench to do the gitft-to-cifti conversion:

wb_command -cifti-create-dense-scalar thickness.dscalar.nii -left-metric lh.thickness.gii -right-metric rh.thickness.gii

The result is indeed a cortical thikness file in the cifti-file format (“thickness.dscalar.nii”). However, it does not have the dimensions of the fs_LR_32k space (neither of the fs_LR_164k space, but it has 272439 vertices…). I’m now wondering how to register my result to the fs_LR_32k space.

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I’m not sure what the minimum would be, but also do not think it matters, as it is likely the easiest one-line command to get them would be to run recon-all. What are your concerns about running recon-all?

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If you really know what you’re doing, ?h.sphere.reg might be enough, in addition to the ?h.thickness files. I don’t personally know what I’m doing enough to make a suggestion beyond that.

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Hi, Sorry for interrupting the discussion. I recently tried creating a cortical thickness file in a cifti-file format using FreeSurfer outputs (l/rh.thickness).
The command you mentioned would be correct, but I cannot understand the role of lh.wihte in this command line.
mris_convert -c lh.thickness lh.white lh.thickness.gii
I know that if I don’t put lh.white here, I get an error, but I don’t quite understand why lh.white is needed here.
If you have any idea, could you teach me?

Sincerely,

Izumi