External Email - Use Caution
Also I missed that you upsampled the volume fMRI file massively as well.
Indeed, this is not how I would recommend going about things, particularly in a
memory limited environment.
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Glasser, Matthew"
<glass...@wustl.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, June 29, 2020 at 1:11 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>,
"freesurfer-boun...@nmr.mgh.harvard.edu"
<freesurfer-boun...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion
External Email - Use Caution
Yes you are probably low on memory (3.5GB is really low for brain imaging these
days). Like I said, probably best to use the ciftify outputs if you have them
and then resample the ICA maps back to the native mesh.
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mason Wells
<wells...@cardiff.ac.uk>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, June 29, 2020 at 12:50 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>,
"freesurfer-boun...@nmr.mgh.harvard.edu"
<freesurfer-boun...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion
External Email - Use Caution
Hi Matt,
I have 3.5GB free on my 64 bit linux machine, do you think the wb_command issue
is due to memory alone then? Perhaps I misunderstood your previous emails about
this, I thought that using the workbench commands was the best way. E.g.
running volume-to-surface to get the functional data resampled to the subjects
lh and rh surface, and then cifti-create-dense-timerseries to create a a single
cifti file with the functional data on the subjects surface? Then I was going
to use the matlab code you suggest to get an estimation of dimensionality and
finally run melodic. Is this not the best route to go down with my aims in
mind? This was also why I asked the FS list whether the same thing can be done
with mri_vol2surf or other FS commands.
Cheers,
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: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University
webpage<https://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: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Glasser, Matthew"
<glass...@wustl.edu>
Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 29 June 2020 at 17:28
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>,
"freesurfer-boun...@nmr.mgh.harvard.edu"
<freesurfer-boun...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion
External Email - Use Caution
Scratch that, I guess you did include a surface. How much RAM do you have
available and are you on a 64bit OS? As I mentioned last week, what you are
trying to do is not computationally efficient and not really the best approach
to go about things.
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Glasser, Matthew"
<glass...@wustl.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, June 29, 2020 at 11:24 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>,
"freesurfer-boun...@nmr.mgh.harvard.edu"
<freesurfer-boun...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu> on behalf of Mason Wells
<wells...@cardiff.ac.uk>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu"
<freesurfer-boun...@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
UK
Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University
webpage<https://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: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628
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or the taking of any action in reliance on the contents of this information is
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