Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Creating intermediate surfaces between white and pial?
by Tim Schäfer 12 Dec '19

12 Dec '19

External Email - Use Caution Dear FreeSurfer experts, I know that I can sample data from a certain depth between the white and pial surfaces, but is there any way to create an intermediate surface file (i.e., mesh)? I would like to create, e.g., a surface file that is at 10% of the distance between the white and pial surface. I had a look at mris_create_surface, but unless I misinterpreted the description of the command line arguments, it does not seem to be the proper tool for the job. Background: This is for visualization purposes. I would like to create a figure similar to Figure S1 from Bletsch et al. 2018 in tkmedit: https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fhbm… Thanks for your time and all the best, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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selxavg in native space vs fsaverage space
by Nasiriavanaki, Zahra 12 Dec '19

12 Dec '19

Dear Freesurfer experts Hi I was trying to do selxavg in native space for individual subjects which I have analyzed them in "fsaverage" space before. I have two sessions of functional data for each subject. In order to register them on one T1, I put the functional data from both sessions in one bold folder and registered all of them to one T1. The maps that I acquired from these analysis are slightly different from "fsaverage" maps. In "fsaverage" analysis, I analyzed each session separately (selxavg) and then concatenated (isxconcat) the two sessions at the end. I believe it is not possible to do this in "native" space, since I have to register all the functional data to one T1, right? I need to know what is causing the differences in "native" and "fsaverage" maps? I appreciate if you could reply. Thanks a lot Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Re: [Freesurfer] MacOS Catalina
by fsbuild 11 Dec '19

11 Dec '19

External Email - Use Caution Yes, you can disable the gatekeeper security software and allow software to be installed anywhere.  This may not be the best choice for everyone if you prefer to have this security (or do not have sudo privs).   Anyway, we will endeavor to not require this. - R. On Dec 11, 2019, at 05:03, nayan wadhwani <nayanw775(a)gmail.com> wrote:sudo spctl - -master -disable

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(no subject)
by fsbuild 11 Dec '19

11 Dec '19

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Hippocampal subfields: exporting results
by Steve Petersen 11 Dec '19

11 Dec '19

External Email - Use Caution Dear Freesurfer experts, I used the freesurfer dev version to estimate hippocampal subfields using mode B (additional scan). All have worked fine although when I tried to export the results I can not find the txt file created This is the output rmnlab1:~ neucoga$ quantifyHippocampalSubfields.sh HIPOAMYG HipoAmyg_results.txt /Applications/freesurfer/subjects/4001T1 Gathering results from subjects in: /Applications/freesurfer/subjects/4001T1 Using the suffix name: HIPOAMYG And writing them to: HipoAmyg_results.txt Where is saved the HipoAmyg_results.txt file?? I have searched it and I can't find it... Excuse me for this basic question. Thanks in advance. Best regards,

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Re: [Freesurfer] MacOS Catalina
by fsbuild 11 Dec '19

11 Dec '19

External Email - Use Caution Hello CM, We are looking at how Freesurfer can work with the new security and file system changes added in Catalina (Mac OS 10.15).  I am not aware of an issue if Freesurfer had been installed on a machine running an older version of Mac OS, e.g., Mojave (Mac OS 10.14), that was subsequently upgraded to run Mac OS 10.15.  But we still need to testing - including new Apple hardware that comes with Catalina installed out of the box.  Like other software vendors, at this time we do not recommend upgrading to Catalina if you want to continue to run existing (Freesurfer) software releases on Mac OS. - R. On Dec 11, 2019, at 03:13, Chantal Miller <cm954(a)cam.ac.uk> wrote:        External Email - Use Caution        Dear all,I keep getting a warning on my Mac that Freesurfer will not be compatible with the latest update to MacOS Catalina. Does anyone have any information about how critical this issue is/ if Freesurfer will be updated to be compatible with this?Thank you for the help,CM_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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MacOS Catalina
by Chantal Miller 11 Dec '19

11 Dec '19

External Email - Use Caution Dear all, I keep getting a warning on my Mac that Freesurfer will not be compatible with the latest update to MacOS Catalina. Does anyone have any information about how critical this issue is/ if Freesurfer will be updated to be compatible with this? Thank you for the help, CM

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tkregisterfv problems
by Vicky Yang 10 Dec '19

10 Dec '19

External Email - Use Caution Dear Freesurfer experts, I am using bbregister to register my functional template image into T1 image. The bbregister is running fine. But when I tried to view registration using tkregisterfv, the window opened and closed quickly with an error message: Warning: Transformation can only apply to volumes for now. If your data includes ROI/Surface/Way Points, please do not use this feature yet. INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. LTAchangeType: src geometry must be valid terminate called after throwing an instance of 'int' Abort (core dumped). My command: bbregister --s subj_ID --mov template.nii --reg bbr_template_T1.reg --bold --init-fsl tkregisterfv --mov template.nii --reg bbr_template_T1.reg --surfs Can anyone help me with this? Thank you so much! VY

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Using pre-segmented results
by Jordi Huguet 10 Dec '19

10 Dec '19

External Email - Use Caution Hi there, I wonder if its somehow possible to feed FreeSurfer's recon-all with pre-existing segmented maps (based on prior segmentation procedure e.g. SPM or ANTs) to "improve" FreeSurfer results. For some images I am working with the FreeSurfer's WM segmentation output is not optimal so I am looking for alternatives to improve the final results on such specific cases without requiring any manual intervention. Any comments, examples or shared reflections on this regard are kindly welcome. Thanks in advance, Jordi Huguet

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Problem for cortical thickness analysis
by Gwang-Won Kim 10 Dec '19

10 Dec '19

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