Your command below is missing the <surface> argument:

wb_command -volume-to-surface-mapping

<volume> - the volume to map data from

<surface> - the surface to map the data onto

<metric-out> - output - the output metric file

[-ribbon-constrained] - use ribbon constrained mapping algorithm

<inner-surf> - the inner surface of the ribbon

<outer-surf> - the outer surface of the ribbon

Which can be a repeat of one of the other surfaces I think, though we typically use the midthickness surface here.

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: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-bounces@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edu>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution

Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, then GIFTI to CIFTI, whilst keeping these functional data in the same space as the subjects FS surface. I got some information RE usign the HCP workbench, but I wondered if running mri_vol2surf could achieve the same thing as running the wb_command? For example, is it advisable to run the following command for each hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii --srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii

I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf files into .gii format (from FS format)

e.g. mris_convert lh.pial lh.pial.surf.gii

I then applied the transformation to align the filtered_func to the T1

mri_vol2vol --mov filtered_func_data.nii.gz --reg partial-to-struct.lta --fstarg --o movie_t1_space.nii.gz

I then tried to run the following wb command

wb_command -volume-to-surface-mapping /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz /home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.inflated.surf.gii /home/masontwells/Documents/Data/MovPPT_001/lh_movie.gii -ribbon-constrained /home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.white.surf.gii /home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.pial.surf.gii

Which resulted in this subsequent error.

ERROR: NAME OF FILE: movie_t1_space.nii.gz

PATH TO FILE: /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat

Unable to allocate memory for reading the file.

File Size: 3.24 Gigabytes

Note: The amount of memory required to read a data file may be substantially larger than the size of the file due to the way the file's data is organized in memory or compression of data within the file.

Any advice on how to convert NIFTI to GIFTI and then GIFTI to CIFTI whilst keeping the data in the subjects space would be really appreciated.

Best wishes,

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

Email: WellsMT1@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University webpage

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

E-bost: WellsMT1@caerdydd.ac.uk

Ffôn: 02920 879628

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