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-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 12:07 PM 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 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: 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
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, 24 June 2020 at 15:46 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,
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: 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
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 15:02 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 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-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 8:54 AM 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 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: 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
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/fMRISurfac...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-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 thishttps://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: 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
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/ciftifyhttps://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-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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________________________________ 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.