External Email - Use Caution
You can use Connectome Workbench’s wb_command -volume-to-surface-mapping (recommend using the -ribbon-constrained option with the white and pial surfaces). You can then use wb_command -cifti-create-dense-timeseries to merge the two hemispheres and subcortical grey matter data into a CIFTI file. If you want a pipeline that does this for you, the ciftify pipeline (https://github.com/edickie/ciftify) might be a good choice if you have already done your preprocessing, or you could use the HCP Pipelines to do all of your preprocessing.
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells WellsMT1@cardiff.ac.uk Reply-To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Date: Wednesday, June 24, 2020 at 7:42 AM To: "freesurfer-bounces@nmr.mgh.harvard.edu" freesurfer-bounces@nmr.mgh.harvard.edu, Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Nifti to gifti conversion
External Email - Use Caution Hi Experts,
I have a set of resting state data in nifti format. I want to get these data into gifti format, so I can then convert them into cifti format and run melodic ICA. I suspect using mri_vol2surf would do the trick, but I know you need to specify which hemisphere you want the projection to take place on. However, I wondered if it was possible to do this for both hemisphere, or whether there is a command to merge the two hemisphere back together into a single gifti file after running vol2surf separately? The command I am currently running is:
Mri_vol2surf –src filtered_func.nii.gz –out resting_surface.gii –srcreg partial-to-struct.lta –hemi lh –projfrac 0.5 –out_type gii
Any advice would be great. Thanks, Mason
Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU
E-bost: WellsMT1@caerdydd.ac.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628
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