Re: [Freesurfer] Help Download FreeSurfer Windows VM

2024-02-06 Thread fsbuild
External Email - Use Caution We don’t expect things to work reliably with 8G total RAM for the machine.  The host machine itself will always consume some memory when running its OS, probably up to a few Gig, leaving even  less than 8G to be used for running the VM with freesurfe

[Freesurfer] Fwd: Vertex / voxel lesion symptom mapping

2024-02-06 Thread Martin Juneja
External Email - Use Caution Dear FreeSurfer community and experts, I would greatly appreciate any help/response with the following. Thanks. -- Forwarded message - From: Martin Juneja Date: Wed, Jan 31, 2024 at 7:51 PM Subject: Vertex / voxel lesion symptom mapp

[Freesurfer] Using funcroi-sess with per-run analysis

2024-02-06 Thread Akkoyunlu, Beyza
External Email - Use Caution Hi, We are trying to do % signal change within a ROI. However, when we run funcroi-sess function (after funcroi-config), we get following output in terminal set: variable name must begin with a letter When we run the function with -debug, we saw th

Re: [Freesurfer] calculation of sulcal depth

2024-02-06 Thread Linn Christin Bonaventure Norbom
External Email - Use Caution OK perfect, thank you so much for the clarification! Kind regards Linn From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD Sent: 06 February 2024 15:35:16 To: Freesurfer support list Sub

Re: [Freesurfer] calculation of sulcal depth

2024-02-06 Thread Fischl, Bruce R.,PHD
Hi Linn The text you cite is how we measure it. It is the signed distance each points moves to get from the white to the inflated surface, where outwards movement is positive (along the surface normal direction) and inwards distance is negative. Cheers Bruce From: freesurfer-boun...@nmr.mgh.ha

Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat

2024-02-06 Thread Huang, Yujing
I can’t reproduce the error here with FS 6.0. Not sure where you downloaded the script. Can you run this “tcsh -x $FREESURFER_HOME/bin/mri_glmfit-sim –help”? I’m hoping it will give some hints. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Sven Kühn Sent: Sunday, Feb

[Freesurfer] Help Download FreeSurfer Windows VM

2024-02-06 Thread lioudadracacci
External Email - Use Caution Hello FreeSurfer Developers, I am attempting to start Ubuntu via VirtualBox 7.0 on Windows 10. But I have few problems. First, I do not have the access to the compressed VM Image file (FS_7_3_2_course_ubuntu_18_04_06.ova.7z), is it still possible

Re: [Freesurfer] if: Expression Syntax - preproc-sess

2024-02-06 Thread Huang, Yujing
Not sure where this happened. Does it produce any log files that you can share? Maybe both logs with and without the -nomc option. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Stefano Delli Pizzi Sent: Saturday, February 3, 2024 2:33 PM To: freesurfer@nmr.mgh.harvard

Re: [Freesurfer] ERROR: mri_ca_register with non-zero status 9

2024-02-06 Thread Huang, Yujing
It looks like your recon-all was killed. Is it possible that your recon-all ran out of the job limit (time, memory, ...). I also noticed you have these options to recon-all '-3T -no-isrunning'. Make sure you don't have other instance of recon-all running on the same subject. Best, Yujing From

[Freesurfer] calculation of sulcal depth

2024-02-06 Thread Linn Christin Bonaventure Norbom
External Email - Use Caution Dear experts, I am assessing different morphological aspects of the cortex including sulcal depth but am struggling to understand how this is calculated in FreeSurfer. I see that a previous correspondence (https://secure-web.cisco.com/130Tf81zvPk_60

[Freesurfer] Cortical WM parcellation for DKT atlas?

2024-02-06 Thread Hamied Haroon
External Email - Use Caution Hello Freesurfer Gurus, Is it possible to obtain "wmparc" but for the DKT cortical atlas, please? Many thanks. Best wishes, Hamied Dr Hamied A Haroon [he/him/his], MSc, PhD, MInstP Research Fellow in Quantitative Biomedical MR Imaging The Universi