Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30065 discussions

Re: [Freesurfer] Infant Freesurfer - manual edits
by Kang, Jee Won 06 Mar '23

06 Mar '23

External Email - Use Caution Dear Freesurfer experts, Hello, I have started experimenting with Infant Freesurfer (version 4a14499), and we have run into a problem with very poor segmentation of the thalamus in one of our subjects. Is there a way to incorporate manual edits, as in adult Freesurfer, to improve the segmentation? From this post: https://secure-web.cisco.com/1A3X8CGDC9HIB1-7GzN2d3Jhl_jxtbWw34-Ck5nrUNk5fV…, it looks like the option to make manual edits was a feature in the works, but I am not sure if that is still the case. I am guessing it would be inadvisable to re-run the infant data after making edits (to wm or aseg.presurf) in adult Freesurfer? Thank you for your advice on this! Sincerely, Jee Won

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How to get individual betas (parameter estimates) in certain ROI?
by Andy Kim 06 Mar '23

06 Mar '23

External Email - Use Caution Dear FreeSurfer Developers, Hi. Thanks to FreeSurfer, I finished a group activation analysis with FS-FAST. Now I want to draw a ROC curve to check how well my task conditions can distinguish M1 and S1. (M1 is more activated under certain condition of my task and S1 is more activated under another condition.) To do so, I need to get every betas of individual nodes in certain ROIs (which I created my own, but let's just say M1 and S1). Betas are in beta.mgh file which is a product of mri_glmfit. Then how do I get betas of only M1 nodes or only S1 nodes? Kind Regards, Andy (Junghyun) Kim

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Mac OS 13 Ventura
by Elmira Hassanzadeh 06 Mar '23

06 Mar '23

External Email - Use Caution Hi everyone, Could someone please direct me to the workaround instructions on installing Freesurfer on Mac M1 ultra on OS 13.0 Ventura? Thank you, Elmira

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cvs clarifications with petsurfer
by Federica Di Antonio 06 Mar '23

06 Mar '23

External Email - Use Caution Dear Freesurfer experts, I'm using PETsurfer. I've done the standard pipeline for all my subjects, using the cvs registration. I was wondering (maybe it's very stupid) when the standard pipeline "uses" the cvs resulting files (except for subcortical volume-based analysis and final resampling). Moreover, when I obtain a resampled file (like subctxgm.cvs.2mm.sm00.nii.gz ) should I process it with freesurfer? Sorry for my english, maybe what I ask is not very clear, but I hope you can help me. Thank you so much for your time and kindness! Sincerely, Federica

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Samseg cortex parcellation
by Stepanov, Valentin 06 Mar '23

06 Mar '23

External Email - Use Caution Hello, I hope this email finds you well. I am using Samseg for the MS patients' data and am very impressed with its performance in terms of lesions segmentation along with posteriors and probability maps saving. Also, compared to freesurfer, it has a remarkably better quality of cortical gray matter segmentation, particularly in subjects with juxta/intracortical lesions. However, to my knowledge, it does not allow doing a cortex parcellation. I used it with the —recon option, but in that case, the output (aparc+aseg.mgz) is identical or very close to those freesurfer provides and commonly has some segmentation errors, whereas seg.mgz saved in samseg directory demonstrates significantly better segmentation. I wonder if there is any way to run cortex parcellation using exact samseg seg.mgz output? I have attached a couple of images demonstrating the difference of segmentation output for freesurfer and samseg. Thank you, Best regards Valentin Valentin Stepanov Postdoctoral Fellow Center for Biomedical imaging Department of Radiology NYU Grossman School of Medicine 660 1st Avenue, office 212 New York, NY 10016

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Re: [Freesurfer] -pctsurfcon --fsvol default
by Antonio #30 06 Mar '23

06 Mar '23

External Email - Use Caution Hello again, I would like to ask one last thing. How can the class averages computed from csdbase.y.ocn.dat not match the gamma.mgh values in the cluster? e.g. How can gamma show +29 in a vertex that is part of the significantly positive cluster in an A-B contrast, while the average of all values taken from csdbase.y.ocn.dat referring to class A in that same cluster is lower than that of class B (average of values of input y for class A = 20.367; average for class B = 20.401)? Are the values in csdbase.y.ocn.dat not corrected by the variables chosen as covariates? Thanks again! Antonio Bonifanti Il giorno mer 15 feb 2023 alle ore 18:36 Antonio #30 < toni.bonif2511(a)gmail.com> ha scritto: > Hi, > > 1. I was wondering why the --fsvol argument in -pctsurfcon takes > rawavg.mgz by default, when most literature on grey/white contrast tends to > compute it from nu.mgz. > Is the intensity-corrected volume to be preferred in all cases or was > there a reason for choosing rawavg as a default while writing the script? > > 2. I would also like to ask whether or not you believe the values of > smoothing kernels seen in literature for grey-white contrast (which often > are over 20mm) to be adequate for such a measure. > > 3. As a final note, would you say it is appropriate, from a statistical > standpoint, to compare the results of group analyses conducted on the two > hemispheres with different covariates? (e.g. with mean left cortical > thickness and mean right cortical thickness rather than mean whole cortical > thickness) > > Thank you for your time! > > Antonio Bonifanti >

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WMH in aparc+aseg
by Alberto Del Cerro Leon 06 Mar '23

06 Mar '23

External Email - Use Caution Hello FS team! I am using the volumetric data of WMH obtained during the recon-all in the apar+aseg.mgz file. Where I could find the description of the method throught it is segmented? I find the Automated Labeling of Neuroanatomical Structures in the Human Brain but the label WMH doesn't figure on that. Thanks in advance

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Re: [Freesurfer] Recon-all exited without errors
by Goeckner, Bryna 06 Mar '23

06 Mar '23

External Email - Use Caution Thanks for the response. I should have been more clear in my first email. I have used tkregister2 in the past to fix talairachs, but this one does not appear to be fixable with the in-plane shifting, scaling, and rotating that is available within the tkregister2 GUI. The moveable appears to be in a different plane than the target. I’m attaching a screenshot from tkregister2. Is there a different way to fix the talairach or another recon fix (especially considering the apparent brainmask issue) that should be pursued? Thanks again for your help! Bryna Goeckner (she/her) Graduate Student Meier Lab Medical College of Wisconsin Neuroscience Doctoral Program Date: Fri, 10 Feb 2023 20:48:26 +0000 From: "Huang, Yujing" <YHUANG43(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all exited with errors To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <MN2PR04MB5982D0100E4EC48D6FD8A2949DDE9(a)MN2PR04MB5982.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi Bryna, In this tutorial, it talks about how to fix bad output from the talairach registration: https://secure-web.cisco.com/1AsdowaGUQbpsRB4dUWGRiDD2RdKWB-n1kUwwmPwq1WQ9Y…<https://secure-web.cisco.com/1YTUJIwB-u_KNhoI17IHgKhkMu-K4cxIGnnOeSiooClREn…> Best, Yujing From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Goeckner, Bryna Sent: Friday, February 10, 2023 3:35 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all exited with errors External Email - Use Caution Hi All, I am using FS 7.2.0 and have one subject that exited recon-all with errors (looks like for talairach issues) but I am not able to use tkregister2 to view and make manual adjustments to the talairach since surf/lh.orig was not generated. I then tried recon-all with the -notal-check flag, which exited "without errors" although the talairach is nowhere near correctly aligned and while aparc & aseg in freeview appear ok, the brainmask appears to have issues (when I turn it off, the entire background displays as white). I'm including the recon-all logs (original & notal-check flag) and have listed the actual commands used below as well. Any help you can provide in figuring out how to run this subject is greatly appreciated. Thanks! The original code was: recon-all -subject subj# \ -i rawT1.nii.gz \ -T2 rawT2.nii.gz \ -T2pial \ -parallel -openmp 12 \ -3T \ -all And for the second run, -notal-check was added after -all For tkregister2: tkregister2 --s subj# --fstal --surf orig Bryna Goeckner (she/her) Graduate Student Meier Lab Medical College of Wisconsin Neuroscience Doctoral Program

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Question on mri_nu_correct for 3 Tesla data
by Saemann, Philipp 06 Mar '23

06 Mar '23

External Email - Use Caution Hi FreeSurfer specialists, we have problems with a strong non-intensity in 3 Tesla data of GE (mainly temporal poles and occipital area). We managed to rescue the occipital errors by a pre-Bias-field correction using SPM, but would of course try to optimize this in recon-all itself. When I open the recon-all scrip tin FS v7.1.1 I can find no difference in the parameters depending on if the the flag "-3T" is set or not. In both cases the parameters forwarded are: --n 1 --proto-iters 1000 --distance 50 (in line 1536 and line 1540 of /bin/recon-all.) Could someone explain this? What could be done (manual corrections etc. are obsolete due to the large sample size...) to improve the WM detection in the temporolateral/polar area (subsequently cortex detection)? The brainmask looks okay; the ribbon.mgz shows the cut off lateral parts of the cortex. Thanks in advance for any hints, Philipp

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pass code to open the Ubuntu compressed image with Freesurfer
by Chloe Lin 06 Mar '23

06 Mar '23

External Email - Use Caution Hi, I do not have the pass code to open the Ubuntu compressed image with Freesurfer, can you provide me with that? Thank you very much. Best regards, Chloe

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