External Email - Use Caution
I’m not sure what algorithm mri_vol2surf uses for this purpose and I don’t know
what level of compatibility there is with CIFTI in FreeSurfer currently.
Perhaps one of the FreeSurfer developers can comment more on that.
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: Wednesday, June 24, 2020 at 12:07 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] Nifti to gifti conversion {Disarmed}
External Email - Use Caution
Matt,
Just another point. Is it not possible to use mri_vol2surf to project the
functional data onto the lh and then rh surfaces and then using a second
command to convert these into a single CIFTI format, such as
cifti-create-dense-timeseries?
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 Mason Wells
<wells...@cardiff.ac.uk>
Reply to: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 24 June 2020 at 15:46
To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>,
"freesurfer-boun...@nmr.mgh.harvard.edu"
<freesurfer-boun...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}
External Email - Use Caution
Hi Matt,
Are you referring to using the volume-to-surface wb command and then using
create-dense-timeseries to merge the two hemispheres together into a CIFTI
before running melodic? Can you run this using the freesurfer outputs? E.g.
using the lh.inflated as the surface and the lh.white and lh.pial as the inner
and outer surfaces? The metric-out flag, can this just be lh_functional.gii? If
so, have you any idea what might be causing the error I showed in the previous
email?
Thanks for your help.
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: Wednesday, 24 June 2020 at 15:02
To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>,
"freesurfer-boun...@nmr.mgh.harvard.edu"
<freesurfer-boun...@nmr.mgh.harvard.edu>
Cc: Erin Dickie <erin.dic...@camh.ca>
Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}
External Email - Use Caution
I see, our (Connectome Workbench) border format can be easily resampled to
different surfaces, but perhaps FreeSurfer’s cannot. If you do as I suggest
below, you will be able to make a native mesh CIFTI file. Doing sICA on that
will potentially be more computationally intensive than on the original volume
given the upsampling; however. I wonder if it would be better to resample the
sICA maps computed in CIFTI standard space back to the native FreeSurfer mesh
based on the ciftify output?
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: Wednesday, June 24, 2020 at 8:54 AM
To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>,
"freesurfer-boun...@nmr.mgh.harvard.edu"
<freesurfer-boun...@nmr.mgh.harvard.edu>
Cc: Erin Dickie <erin.dic...@camh.ca>
Subject: Re: [Freesurfer] Nifti to gifti conversion {Disarmed}
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.
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: Wednesday, 24 June 2020 at 14:41
To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>,
"freesurfer-boun...@nmr.mgh.harvard.edu"
<freesurfer-boun...@nmr.mgh.harvard.edu>
Cc: Erin Dickie <erin.dic...@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<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines%2Fblob%2Fmaster%2FfMRISurface%2Fscripts%2FRibbonVolumeToSurfaceMapping.sh&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cd57311b709b14eb0bda508d8184d6dd1%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637286068139188141&sdata=OG5Wxqd7dvoC%2BLktphideRwMSFvGk1bltqYZXRfFrII%3D&reserved=0>
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-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: Wednesday, June 24, 2020 at 8:27 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] 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<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.humanconnectome.org%2Fsoftware%2Fworkbench-command%2F-volume-to-surface-mapping&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cd57311b709b14eb0bda508d8184d6dd1%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637286068139198089&sdata=6mBeBGZtNFrm2Aw0TuBd91gZZFnHFCaTf3STTHS9%2Bv0%3D&reserved=0>)?
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: 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: Wednesday, 24 June 2020 at 14:01
To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>,
"freesurfer-boun...@nmr.mgh.harvard.edu"
<freesurfer-boun...@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<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fedickie%2Fciftify&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cd57311b709b14eb0bda508d8184d6dd1%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637286068139198089&sdata=8ptc1XMh8bsv5EwrcWSoxfy2ZLMvMoh37hp40j3eRHI%3D&reserved=0>)
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-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: Wednesday, June 24, 2020 at 7:42 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu"
<freesurfer-boun...@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: 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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intended recipient, be advised that any unauthorized use, disclosure, copying
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immediately notify the sender via telephone or return mail.
________________________________
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.
________________________________
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.
________________________________
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.
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