On 4/16/2020 4:30 AM, Ferraro, Pilar wrote:
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Dear Freesurfer experts,
Many thanks for your prompt reply and all the helpful information. Below are few remaining questions I have (in red), based on your responses.
Many thanks again,
Pilar
Dear Freesurfer experts,
We are conducting a PETSurfer analysis, and have some questions on the best way to proceed. Briefly, this is what we have done:
After running the standard Freesurfer analysis an all the T1 images, we have generated the segmentation for the GTM. Afterwards, we have registered the PET images with the anatomicals, obtaining the template.reg.lta. To check the preliminary results without any PVC, we have used the template.reg.lta to sample the PET volume onto the surface, with the following command: mri_vol2surf --mov subject_PET.nii \ --reg subject_template.reg.lta \ --projfrac 0.5 --interp nearest \ --hemi lh --o lh.sig.mgh
We therefore obtained the lh.sig.mgh
First question. Is this procedure correct?
Yes (though you should always check the reg.lta with tkregisterfv). Also, why are you calling the output lh.sig.mgh? My question is about "sig"; it is not wrong to call it this, but "sig" is usually reserved for significance files and I wanted to make sure you were not confused by it.
Yep yep, sorry I’ve forgotten to specify we also checked the reg.lta for each subject with tkregisterfv. As regards the name of the output you are totally right, we just called it in this way cause we found an example of the mri_vol2surf command application which used this name for the output, but yeah, without any significance it would be more appropriate to call the output in a different way to avoid any confusion.
Second question. Is the format of the of the output (.mgh) correct?
Any format (mgh, mgz, nifti) is ok.
Perfect, thanks, but it is unclear to me which would be the best way to visualize this output (and this aspect might influence the type of format we would choose). Do you have any suggestions?
It should make no difference at all.
In the wiki it is reported that: “If you are not using PVC, you can use the template.reg.lta to sample the PET volume onto the surface using mri_vol2surf, then apply standard surface-based analysis”.
Third question. At this point should we directly run the mri_glmfit with the previously obtained lh.sig.mgh?
This is probably not right. You will need to run the mri_vol2surf command above for each subject to generate an output (and using --trgsubject fsaverage to put them into the same space), then concatenate all into one file (mri_concat lh.subj1.mgh lh.subj2.mgh ... --o lh.all.mgh), then possibly smooth (mris_fwhm), then feed that output as input to mri_glmfit.
Sounds good, I’ll proceed in this way. Only one remaining question. Is it really ok to smooth even if it creates PV effects?
Yes, that is the beauty of smoothing on the surface. You still create some PVEs but it is always within the GM cortex tissue class, no PVEs across WM or CSF, which are the real killers.
Many thanks as always for the precious help,
Pilar
Like in this way:
mri_glmfit \ --y lh.sig.mgh \ --fsgd fsgd file dods\ --C cor.mtx file \ --surf fsaverage lh \ --cortex \ --glmdir glmdir
Many thanks for any information you’ll be able to provide,
Best,
Pilar Maria Ferraro
Il giorno 15 apr 2020, alle ore 5:18 PM, freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu ha scritto:
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1. Re: Trac-All Error (Hua, Jessica) 2. Re: Compiling Freesurfer 6 on Centos7 Install not working due to annex files missing (Hoopes, Andrew) 3. FreeSurfer UbuntuVM password (sapere-aude@tuta.io) 4. Re: FreeSurfer UbuntuVM password (fsbuild) 5. Re: [External] Re: Freesurfer display resolution very low compared to other viewers (Ruopeng Wang) 6. Re: [External] Re: Freesurfer display resolution very low compared to other viewers (Douglas N. Greve) 7. Re: [External] Re: Freesurfer display resolution very low compared to other viewers (Renner, Brian) 8. Re: Trac-All Error (Yendiki, Anastasia) 9. Re: Error in Tracula-all -prep (Salah Showiheen) 10. Question on using T2 or FLAIR data to improve pialsurfaces (Tim Sch?fer) 11. Data onto the Freesurfer surface (Mason Wells) 12. Manipulating MRI volume data in Matlab (Safi Ullah .)
Message: 1 Date: Tue, 14 Apr 2020 20:38:52 +0000 From: "Hua, Jessica" jphc55@mail.missouri.edu Subject: Re: [Freesurfer] Trac-All Error To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu, "AYENDIKI@mgh.harvard.edu" AYENDIKI@mgh.harvard.edu Message-ID: BY5PR01MB56524C9896B67B67B00E48AE93DA0@BY5PR01MB5652.prod.exchangelabs.com
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Attached are bvecs and bvals.
Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri