[Freesurfer] HIRING: Postdoc and Research Tech

I am hiring at the Martinos Center, MGH. For details, see 1. Postdoc: https://scholar.harvard.edu/lillazollei/jobs 2. Research technician: https://partners.taleo.net/careersection/ghc/jobdetail.ftl?job=3156502 If you have any questions, let me know. Best, Lilla

[Freesurfer] which file is freesurfer autoseg result?

External Email - Use Caution hello, FSI do the brain region parcellation, I have label(ground truth) for each subject. I want to use my own neural network segmentation results and Freesurfer automatic segmentation results comparison, to get a qualitative and quantitative results

Re: [Freesurfer] In Freesurfer, the sulc value of the gyrus is NOT positive, on the contrary, they are negative?

Maybe a better way to think about curvature is that it indicates whether the surface is locally above (positive) or below (negative) the tangent plane On Jun 14, 2021, at 10:29 PM, Fischl, Bruce wrote:  Sulc is the integrated dot product of the movement vector with the (outwards pointing) sur

Re: [Freesurfer] the white matter surface is from the individual sMRI?

Yes, if it is high enough quality Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of 1248742467 Sent: Monday, June 14, 2021 9:32 PM To: freesurfer Subject: [Freesurfer] the white matter surface is from the individual sMRI? External Email - Use Caution Hello, Fs ca

Re: [Freesurfer] In Freesurfer, the sulc value of the gyrus is NOT positive, on the contrary, they are negative?

Sulc is the integrated dot product of the movement vector with the (outwards pointing) surface normal during inflation. In gyral regions the movement vector is consistently inwards and has a negative dot product with the surface normal, which is why it is negative. As for your second question,

[Freesurfer] can the white matter surface is from the individual sMRI?

External Email - Use Caution Hello, Fs can I get the white matter surface from individual smri??___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] the white matter surface is from the individual sMRI?

External Email - Use Caution Hello, Fs can I get the white matter surface from individual smri??___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Error in hippocampal subfields longitudinal processing

External Email - Use Caution Hi Eugenio, No problem at all, thanks for getting back to me! All the subjects should have been acquired exactly the same way with the same parameters, so I don't understand... So far I've only gotten through a few subjects but decided to reach out w

[Freesurfer] In Freesurfer, the sulc value of the gyrus is NOT positive, on the contrary, they are negative?

External Email - Use Caution Hello, Fs  In Freesurfer, the sulc value of the gyrus is NOT positive, on the contrary, they are negative?? by the way, how the mean curvature reflects the degree of fold? Since the mean curvature is a local measurement, does the mean curvature map re

Re: [Freesurfer] Edits to White Matter (wm.mgz)

External Email - Use Caution Hi colleagues, Just following up on this if anyone has an input =) Thanks Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Cent

Re: [Freesurfer] Error in hippocampal subfields longitudinal processing

Sorry for not having replied earlier, Kaija. This is very strange. Do these subjects have more time points or a larger field of view? Did you run all the subjects on the same platform? Is the issue with these few subjects reproducible? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fell

[Freesurfer] Fwd: Running FreeSurfer with fmriprep

External Email - Use Caution Dear Freesurfer's experts, I have run recon-all all to one subject with fmriprep. The work finished without errors. However, after inspecting the results, I have seen that there are some *grey regions* (mainly frontal and temporal ones) that have not

[Freesurfer] nu correction

External Email - Use Caution Dear experts, I would like to create myelin maps calculating the T1w/T2w ratio. Should I apply bias field correction and intensity normalization (i.e., "nu correction" in the Freesurfer pipeline) to T1w and T2w images separately before calculating the

Re: [Freesurfer] FreeSurfer cortical thickness

External Email - Use Caution Hi Rosie, For cortical thickness, check out *.aparc.*.stats files (e.g, lh.aparc.stats, lh.aparc.a2009s.stats, lh.aparc.DKTatlas.stats). There is more info in the ROI analysis tutorial: - https://secure-web.cisco.com/15BXH9iwkvAUJ2mnf7udx7SdsKrQQYNr

Re: [Freesurfer] Samseg pallidum issue

External Email - Use Caution Hi Andrew, No, I don't think we have seen something like that before. I'm a bit doubtful about the "enhanced T1 images", though - for sure there is more information for samseg to work on when you feed it both T1 and FLAIR, compared to some fused image

Re: [Freesurfer] Error in hippocampal subfields longitudinal processing

External Email - Use Caution Hello, I just wanted to follow up on this issue as it seems other people experience problems with hippocampal subfields segmentation but not this same issue. Does anyone please have any idea how to help?? Thank you very much, Kaija _

[Freesurfer] FreeSurfer cortical thickness

External Email - Use Caution Dear Freesurfer's experts, I run FreeSurfer and I got the following stats: rosalia@rosalia-Lenovo-Y520-15IKBN /media/rosalia/Nuevo_vol/ARTICO/derivatives/freesurfer/sub-003/stats $ ls aseg.stats lh.BA_exvivo.thresh.stats rh.aparc.stats

Re: [Freesurfer] Finding equivalent vertices on fsaverage_sym lh and rh surfaces

External Email - Use Caution Dear Paul, thanks a lot, that did it. Best, Tim > On 06/11/2021 6:23 PM Paul Wighton wrote: > > > External Email - Use Caution > > Hi Tim, > > I think this is possible with mris_left_right_register, e.g. > > mris_left_right_register -

[Freesurfer] Infant FreeSurfer: volumes

External Email - Use Caution Hi FreeSurfer team, I using the latest version of Infant FreeSurfer to assess brain volumes on very young kids. When looking at the brain volume (aka 'BrainSegVolNotVent') extracted from the aseg statistical file I got a very different volume than do