External Email - Use Caution
I wanted to keep data in the same space as the subjects surface as I have retinotopically defined borders which are on the subjects surface, I want to compare these borders
to the ICA component on the subjects surface.
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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.uk Tel: 02920
879628 |
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.uk Ffôn: 02920
879628 |
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Glasser, Matthew" <glasserm@wustl.edu>
Reply to: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 24 June 2020 at 14:41
To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>, "freesurfer-bounces@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edu>
Cc: Erin Dickie <Erin.Dickie@camh.ca>
Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}
External Email - Use Caution
Here is an example of how we do it in the HCP Pipelines: MailScanner has detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" claiming to be
https://github.com/Washington-University/HCPpipelines/blob/master/fMRISurface/scripts/RibbonVolumeToSurfaceMapping.sh Line 135
You will need to make sure that all your data are NIFTI/GIFTI/CIFTI to use wb_command (you can convert to these from FreeSurfer formats using mri_convert and mris_convert).
That said, what is the reason to keep the data super upsampled to FreeSurfer’s original irregular mesh? The 32k standard mesh we usually use has an average vertex spacing of 2mm. We also have a 59k mesh with an average vertex spacing
of 1.6mm, but have not yet shown that this has advantages. Particularly since you said on the FSL list you plan to smooth the data, I would just use the standard mesh outputs. The HCP Pipelines (and possibly ciftify) produce surfaces in both MNI space and
the subject’s physical (undeformed) space on standard meshes. Keep in mind that the volume space and surface mesh are independent of each other, and one can have standard meshes in subject’s physical space and FreeSurfer original meshes in MNI space.
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 8:27 AM
To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>, "freesurfer-bounces@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}
External Email - Use Caution
Hi Matt,
Thanks for this. I had previously been using
cifitfy (a great tool), but I want to keep my data in the native T1 surface space, which isn’t possible with
ciftify, hence me looking for a different way to do this.
I don’t suppose you know of any
documentation that shows an example of how to run the volume-surface-mapping command correctly (other
than this)? I am a little unsure as to what is required for the flags you suggest (also unsure if I need to use a -flag before the paths to the data?). I have tired the below, but as you can see I get a couple of errors, one of which I believe is due to
memory.
While running:
/home/masontwells/Documents/Analysis/workbench/bin_linux64/../exe_linux64/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
/home/masontwells/Documents/Data/MovPPT_001/lh_movie.gii -ribbon-constrained /home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.white /home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.pial
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.
|
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.uk Tel: 02920
879628 |
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.uk Ffôn: 02920
879628 |
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Glasser, Matthew" <glasserm@wustl.edu>
Reply to: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 24 June 2020 at 14:01
To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>, "freesurfer-bounces@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Nifti to gifti conversion
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 (MailScanner
has detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" claiming to be
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.uk Tel: 02920
879628 |
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.uk Ffôn: 02920
879628 |
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