Re: [Freesurfer] data sharing of freesurfer processed data

External Email - Use Caution Hi Stacey, aren't participant IDs already anonymized or at least pseudonymized? In any case, if that ID is part of the file name, you should delete or change the recon-all.cmd, recon-all.done, recon-all.log files as the input file name is written in

Re: [Freesurfer] Issue with the hypothalamic segmentation

External Email - Use Caution Yes, so I tried both installing missing libraries and removing some outdated ones to no effect. This was the result of mri_convert --help: mri_convert: mri_convert: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not found (required by mr

Re: [Freesurfer] Issue with the hypothalamic segmentation

Thanks. Can you run something like `mri_convert --help` to check if this is an issue with all the FS binaries? It seems like this is a known ubuntu bug: https://ubuntuforums.org/showthread.php?t=2438576 https://askubuntu.com/questions/1254845/upgrade-from-19-10-to-20-04-fails It might require up

[Freesurfer] Lesion heat map question

External Email - Use Caution Dear Freesurfers, I’m working on generating a heat map of white matter lesions in a disease group. I have the lesion probability maps for each individual generated in SAMSEG and I was wondering what the best method would be to place the maps of each

Re: [Freesurfer] comparing long and cross FS aparc+aseg

Hi Michele I guess after running the long you could launch a cross recon on the spatially registered time points. You’ll have to be careful about extra interpolations though Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Michele Valotti Sent: Wednesday, February 3, 20

[Freesurfer] comparing long and cross FS aparc+aseg

External Email - Use Caution Hi all, I am running a test of long FS on some subjects to see if I can improve the segmentation accuracy compared to cross FS. The aparc+aseg.mgz output of long FS, however, is not aligned with the original timepoint structural scan, but rather to the

[Freesurfer] FIR Analysis and task regressor

External Email - Use Caution Hi everyone, Is it possible to do an FIR analysis using a task regressor instead of (or additional to) a paradigm file? More precisely, we want to use pupil size as task regressor. It was recorded during an auditory detection task (event related).

Re: [Freesurfer] Issue with the hypothalamic segmentation

External Email - Use Caution Hi Andrew We are running Ubuntu 19.10 on our computer and as for Freesurfer were we tried to run this on freesurfer 7 and the development version but both produced this error. (freesurfer 7: freesurfer-linux-centos7_ x86_64-7.1.0-20200511-813297 Freesur

Re: [Freesurfer] white matter volume

Not from a group analysis, but you can get it from running asegstats2table. See our tutorial on ROIs https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI On 2/2/2021 11:44 AM, Sara Lyn wrote: External Email - Use Caution If that's the correct way to do it then yes since

Re: [Freesurfer] Issue with the hypothalamic segmentation

Hi Mackenzie, Can you let us know what OS and version you’re running this on? Thanks, Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Langan, Mackenzie Date: Wednesday, February 3, 2021 at 10:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Issue with the hypo

[Freesurfer] Issue with the hypothalamic segmentation

External Email - Use Caution Good Morning, I have been trying to run the hypothalamic segmentation and get the following error: *aalqadi@athena:/zstore/data/aalqadi/aalqadi/mPFC/data$ mri_segment_hypothalamic_subunits --s S05486* *Traceback (most recent call last):* * File "/u

Re: [Freesurfer] FIR Analysis and task regressor

Did you demean the task regressor? Is the problem that you cannot run tksurfer-sess? Or are you reporting multiple problems? On 2/3/2021 8:32 AM, Doll, Laura wrote: External Email - Use Caution Hi everyone, Is it possible to do an FIR analysis using a task regressor instead of (or

Re: [Freesurfer] define freeview colormap from command line

You can specify custom colors like this: freeview -f lh.inlfated:overlay=xxx:overlay_custom=val,r,g,b,val2,r2,g2,b2 ... val is the value of the color point, r, g, b are RGB values in the range of 0 to 255. You can find more details from ‘freeview -h’. Best, Ruopeng > On Feb 3, 2021, at 6:38

[Freesurfer] define freeview colormap from command line

External Email - Use Caution Dear all, Using your precious hints in a past thread, I'm now displaying several surface analyses and taking a screenshot for each of them, everything from command line using the command freeview -f ***/mni152.fnirt/surf/lh.inflated:overlay=***mni152.fn

Re: [Freesurfer] White matter parcellation

External Email - Use Caution Hey, Douglas. Thanks for the answer and the references. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Tuesday, February 2, 2021 5:57:33 PM To: freesurfer@nmr.mgh.harvard.edu Subjec