On 4/14/2020 5:40 AM, Ferraro, Pilar wrote:
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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.
Second question. Is the format of the of the output (.mgh) correct?
Any format (mgh, mgz, nifti) is ok.
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.
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 7 apr 2020, alle ore 6:00 PM, freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu ha scritto:
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1. vertex number to MNI coordinates (Marina Fern?ndez) 2. Install Freesurfer on Ubuntu (Stephan) 3. Re: vertex number to MNI coordinates (Douglas N. Greve) 4. Re: Install Freesurfer on Ubuntu (Peer Herholz) 5. Re: Install Freesurfer on Ubuntu (fsbuild) 6. Permutation with Non-Orthogonal Matrices (Hua, Jessica) 7. Re: Permutation with Non-Orthogonal Matrices (Douglas N. Greve) 8. Error in Tracula-all -prep (Salah Showiheen) 9. hippocampus subfield segmentation using Siemen and GEscans (Kate Marvel) 10. Chorid-plexus in Freesurfer reconall (Lijun An) 11. Re: Chorid-plexus in Freesurfer reconall (Bruce Fischl) 12. whether freesurfer version 7 still support GPU (Frank Robert) 13. Re: hippocampus subfield segmentation using Siemen and GE scans (Iglesias Gonzalez, Juan E.) 14. Re: whether freesurfer version 7 still support GPU (Hoopes, Andrew) 15. Re: hippocampus subfield segmentation using Siemen and GE scans (Kate Marvel) 16. Re: whether freesurfer version 7 still support GPU (Frank Robert) 17. Re: whether freesurfer version 7 still support GPU (Hoopes, Andrew)
Message: 1 Date: Mon, 6 Apr 2020 22:06:24 +0200 From: Marina Fern?ndez marina.fdez.alvarez@gmail.com Subject: [Freesurfer] vertex number to MNI coordinates To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAALjZmd_9caMAE8uHbn_vu4o_4Lkc8mWyXTatSUr4AAQpznq0w@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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Dear Freesurfer experts,
I hope you can help me with the following questions:
- What is the best way to know the MNI coordinates to which a vertex
of a surface corresponds?
- I have projected the surfaces of the subjects onto the average subject
from this dataset. Can I know the MNI coordinates corresponding to a vertex of the average subject of my dataset? Or do I need to project it onto the fsaverage to know the correspondence to de MNI space?
- I know that the average surface is constructed by computing the MNI305
coordinate at each vertex, But how can I obtain the MNI152 coordinates (instead of MNI305) to which a vertex corresponds? (if it is possible).
Thank you very much in advance.
Best regards, Marina