Freesurfer February 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
143 discussions

Re: [Freesurfer] PetSurfer questions
by Soo-Jong Kim 31 Jan '20

31 Jan '20

External Email - Use Caution I ran gtmseg for my partial volume correction 1. but I have a question. What regions are for the detail?? in this option. mri_gtmpvc --default-seg-merge. I searched mri_gtmpvc --help but it is default schema for merging ROIs. So I wanna know what regions you use as default. for example, in FreeSurferLUT. 1000, 1010, etc.. Can you tell me what regions freesurfer uses. 2. In general, After PVC (i.e.MG or RBV), Does some smoothing kernel apply to pv-corrected images from rbv as rbv.nii.gz? If then, how large smoothing kernel? Best, Soo

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orig2rawavg transformation matrix
by Sam W 31 Jan '20

31 Jan '20

External Email - Use Caution Hello! How can I get a transformation matrix that maps orig.mgz to rawavg.mgz? I only see examples bringing freesurfer results into original anatomical space with mri_vol2vol, but I really just want the transformation matrix. Thanks! Best regards, Sam

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Re: [Freesurfer] medial wall metric file
by Alexopoulos, Dimitrios 31 Jan '20

31 Jan '20

External Email - Use Caution Having difficulty with how to use label2label for this purpose. Just need a binary mask of medial wall (vertex number and 0 or 1s) on native surface. What's would this command be? On Jan 28, 2020 5:42 PM, "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> wrote: Attention: This email originated from outside the university. Do you mean you want a binary mask of the medial wall? You can create a mask of the cortical label (?h.cortex.label) with mri_label2label You can then invert that with something like fscalc lh.cortex.mask.mgz not -o lh.medialwall.mask.mgz On 1/28/2020 6:31 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Is there a freesurfer file that contains metric info that delineates the medial wall in the native surface output for an individual? It appears to be associated with the ?lh.aparc.annot file (below). I’d like to be able to export the medial wall metric into Worbench. Thanks. Jim [cid:part1.330140F5.A370F13A@mgh.harvard.edu] ________________________________ 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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ________________________________ 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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Freesurfer February 2020