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I would map your data to individual subjects surfaces (which you can make with Freesurfer), not to a group average surface, and then register on the surface. I believe some folks have made hacks of the HCP Pipelines to process legacy data without T2w
scans (and I think they posted something to the list), but there isn’t currently an officially supported hack for this. The basic idea is to create appropriately named files and run the parts of the pipeline one needs for volume atlas registration, surface
generation, conversion of FreeSurfer surfaces to standard formats, and then running the fMRI preprocessing.
Peace,
Matt.
From: <[email protected]> on behalf of Iason Nikolas <[email protected]>
Date: Wednesday, July 22, 2015 at 6:38 AM To: "[email protected]" <[email protected]> Subject: [HCP-Users] Co-register tfMRI data to brain surface. Hello HCP users,
I am new to this field and I’d love to work with HCP pipelines. Workbench is the best brain visualization tool and is still under heavy development (congratulations to the developers). What I want to do, is to compare tfMRI from two different subjects. The problem is that I have tfMRI data and T1 weighted data but not T2. So as I read, (correct me if I am wrong) I cannot follow the HCP pipelines to create the CIFTI file. Is any other way to create the dtseries.nii file? What I have done so far is to project the preprocessed tfMRI to the standard Conte69 32K surface using the –volume-to-surface-mapping command. But I also want to co-register the tfMRI data based on the subjects’ surface that I can extract from T1 weighted MRI data (I don’t know how). Based on the transformation that converts the vertices from subjects’ surface to Conte69 surface, I want to co-register the tfMRI data and map them on top of Conte69 surface. I believe this way would be easier to compare side by side the two subjects. Can someone kindly point me in the right direction on how doing something like this? (If it’s possible.) Thank you in advance.
Best Regards, Jason _______________________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ |
- [HCP-Users] Co-register tfMRI data to brain surface. Iason Nikolas
- Re: [HCP-Users] Co-register tfMRI data to brain surf... Glasser, Matthew
