Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

Re: [Freesurfer] matlab: command not found - How can I solve this?
by fsbuild 01 Oct '21

01 Oct '21

External Email - Use Caution Hello Camila, Did you try using the script fs_install_mcr, e.g., in the linux 7.2.0 release as freesurfer/7.2.0/bin/fs_install_mcr to install Matlab R2014b ?   Please note that there is a currently an issue with running it on M1 Macs. - R. On Oct 1, 2021, at 15:51, Camila Fernandes da Silva <camila.fernandes.silva(a)usp.br> wrote:        External Email - Use Caution        Hey, I'm totally new into Freesurfer and I need some help with my Matlab.I tried to do "recon-all -s <.....>/ -lgi But as you can see, It shows an error related to matlab...I tried everything! But nothing is working.I have heard that we should modify the startup.m file...But, what am I supposed to do with it?I'm using the Freesurfer 7.1.0 version-----------------------------------------------------------------------#@# Local Gyrification Index lh Fri Oct  1 15:25:01 EDT 2021 mris_compute_lgi --i lh.pial matlab: Command not found.matlab5: Command not found.ERROR: Matlab is required to run mris_compute_lgi!Command exited with non-zero status 1@#@FSTIME  2021:10:01:15:25:01 mris_compute_lgi N 2 e 0.01 S 0.00 U 0.01 P 94% M 2784 F 0 R 736 W 0 c 11 w 15 I 0 O 0 L 0.05 0.12 0.10@#@FSLOADPOST 2021:10:01:15:25:01 mris_compute_lgi N 2 0.05 0..12 0.10Linux developer-VirtualBox 5.4.0-87-generic #98~18.04.1-Ubuntu SMP Wed Sep 22 10:45:04 UTC 2021 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s controle01_T1 exited with ERRORS at Fri Oct  1 15:25:01 EDT 2021For more details, see the log file /home/developer/freesurfer/controle01_T1/scripts/recon-all.logTo report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1vxWcbz-IO91ksjI-7f0BIIkVTrTYBYHERFTGDy… FernandesLicenciatura em Física - IFUSP_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] FreeSurfer 7.1.0 VirtualBox Installation password
by fsbuild 01 Oct '21

01 Oct '21

External Email - Use Caution Sending the info to your private email shortly. - R. On Oct 1, 2021, at 14:51, Lester Melie-Garcia <lester_melie(a)yahoo.com> wrote:        External Email - Use Caution        Dear Freesurfer team,Could you provide me the password for the user 'developer' of the VM Freesurfer installation?Many thanks in advance,Best regards,Lester Melie-Garcia, PhDDepartment of Biomedical EngineeringUniversity of Basel. Switzerland._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FreeSurfer 7.1.0 VirtualBox Installation password
by Lester Melie-Garcia 01 Oct '21

01 Oct '21

External Email - Use Caution Dear Freesurfer team, Could you provide me the password for the user 'developer' of the VM Freesurfer installation? Many thanks in advance, Best regards, Lester Melie-Garcia, PhD

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Control for eTIV on Voxelwise Wholebrain Analysis?
by Wakim, Kathryn-Mary 01 Oct '21

01 Oct '21

External Email - Use Caution Hi all, I'm currently running a voxelwise whole-brain analysis on my recon-all data using the procedure outlined here: https://secure-web.cisco.com/1ltFRrUt9VeFo_xsJaFu_MKrnVu0LBNxjHernMBBefXqT5… If I am performing this analysis on volume (not cortical thickness), do I need to include eTIV as a covariate in my FSGD file? Thanks! Kamy

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What does Freesurfer do with a T2 if you do not use the t2pial flag
by Aaron Tanenbaum 01 Oct '21

01 Oct '21

External Email - Use Caution What does Freesurfer do with a T2 if you do not use the t2pial flag?

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Color LUT after coregister and reslice aparc/aseg.nii
by Ryan Wales 01 Oct '21

01 Oct '21

External Email - Use Caution Hello, I'm using fmriprep's aparcaseg_dseg.nii (still FreeSurfer code, right?) to create ROI masks. I wish to coregister and reslice this segmentation file to match the native space for another image (PET), then extract SUVR values for each ROI. However, after coregistration, the lookup values are no longer faithful to their original values. Would there be a way to view or create a new color LUT that reflects that aparcaseg_dseg.nii map in a different space? Thank you, Ryan -- Ryan Wales (he/him), M.A. Ph.D. Candidate Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wales(a)stonybrook.edu <ryanwales(a)stonybrook.edu>

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unpacking Diffusion data
by Nasiriavanaki, Zahra,M.D. 30 Sep '21

30 Sep '21

Hello Freesurfers, I have 6 runs of DTI data per subject in a sample of 50, and I want to unpack the dicoms, so it outputs the bval bvec values, to use in dt_recon. I realized I can use either dcm2nii or mri_convert to do this. Could you please let me know what the command should be? and also should I do it separately for each run? subject’s scan info is attached. I used the below command in dev environment but didn’t get any bval bvec values. mri_convert /${subj}/IMAGES/IM01113 /${subj}/DTI/IM_13.nii Appreciate your help. Mona 1 Localizer ok 512 512 13 1 IM00269 2 SagT2FLAIRSPACE ok 512 512 176 1 IM00273 3 SagT2FLAIRSPACE ok 512 512 171 1 IM02084 4 SagT1MPRAGE1mmiso_P3 ok 256 256 176 1 IM00449 5 SagT2FLAIRSPACE ok 512 512 227 1 IM02311 6 SagT1MPRAGE1mmiso_P3 ok 256 256 171 1 IM02482 7 SagT1MPRAGE1mmiso_P3 ok 256 256 239 1 IM02721 8 AxWaveSWI ok 288 252 88 1 IM00793 9 AxWaveSWI ok 288 252 88 1 IM00881 10 AxWaveSWI ok 288 252 81 1 IM00705 11 AxWaveSWI ok 288 252 88 1 IM00969 12 Diffusion ok 990 990 1 70 IM00970 13 Diffusion ok 110 110 74 1 IM01113 14 Diffusion ok 110 110 74 1 IM01187 15 Diffusion ok 110 110 74 1 IM01261 16 Diffusion ok 110 110 74 1 IM01335 17 Diffusion ok 110 110 1 74 IM01336 Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

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Fill between two surfaces
by I. Kelleher-Unger 30 Sep '21

30 Sep '21

External Email - Use Caution Hi there, Apologies if this is a basic question: I have two surfaces and I would like to make a ribbon/mask of the area between the surfaces. How could I go about this? Is mris_fill the right tool to use? Thanks for your help! Isaac

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Longitudinal Hypothalamic Subunits
by Pedersen, Walker Scott 29 Sep '21

29 Sep '21

I see that generating the hippocampal subfields in the longitudinal pipeline has its own script (segmentHA_T1_long.sh), but am not seeing a corresponding script or command to do the same for the hypothalamic subunits. Would simply running mri_segment_hypothalamic_subunits on my subject_session.long.template folders get me there, or would that be violating the logic of the logitudinal pipeline, by not taking advantage of the unbiased template?

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Freesurfer: Version of development version?
by Tobias Ruzok 29 Sep '21

29 Sep '21

External Email - Use Caution Dear Sir or Madam, first of all, thanks a lot for providing such a great tool like Freesurfer! I only have a minor question regarding the version I used: As I am writing a Paper for a Journal right now, I also wanted to quote the Freesurfer Version I used. We downloaded the development version of Freesurfer on 02.02.2021. But now I wanted to know if this downloaded development version is Freesurfer version 7.0 or 7.1.0/7.1.1 or even another version. Is it possible to detect the version with the information I provided? That would be really great! Thanks a lot! All the best, Tobias Ruzok

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