Re: [Freesurfer] what is the right manual correction when ?h.white extends into gray matter

Hi Carolin yes, there are ways. You can modify the intensity thresholds that mris_make_surfaces auto-detects. Sounds like they are a bit off. If you send us the recon-all.log and the intensity of a few voxels that are included in the ?h.white surface and should not be we can suggest some thin

[Freesurfer] Call for Nominations – OHBM Student and Postdoc Special Interest Group

External Email - Use Caution Dear All, The OHBM Student and Postdoc Special Interest Group (SIG) is seeking nominations for open seats on the 2019-2020 SIG Committee. The SIG provides a community of shared interests for OHBM trainees. The Committee aims to provide professional, p

Re: [Freesurfer] what is the right manual correction when ?h.white extends into gray matter

External Email - Use Caution Hello Freesurfer experts, I would like to follow up on my previous question. As Doug recommended, I did the manual editing to the wm.mgz by deleting voxels in the wm.mgz file, which I thought are gray matter. I rerun recon-all using the command below b

Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hi Tristan, Thanks for the files. I have no problem loading them with the latest dev build and stable 6.0 build. I do not have an Ubuntu system, though. If I’m not mistaken you use dev version of freeview binary along with stable 6.0 FS binary. Is that correct? Is there any chance you can try

Re: [Freesurfer] mris_convert segmentation fault on R hemisphere aparc.a2009s only?

yup, sounds good. Good luck Bruce On Thu, 22 Aug 2019, Damion V Demeter wrote: External Email - Use Caution Hi Bruce,  I have been doing some investigating on our side and I believe the issue may have to do with something in our environment. It appeared to happen across system

Re: [Freesurfer] mris_convert segmentation fault on R hemisphere aparc.a2009s only?

External Email - Use Caution Hi Bruce, I have been doing some investigating on our side and I believe the issue may have to do with something in our environment. It appeared to happen across systems, but we are not experiencing the error on another system. I am trying to identify

Re: [Freesurfer] mris_convert segmentation fault on R hemisphere aparc.a2009s only?

Hi Damion you can upload them to our ftp site https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange cheers Bruce On Sun, 18 Aug 2019, Damion V Demeter wrote: External Email - Use Caution Hi Bruce,  My apologizes, I just saw this reply because I didn't realize I had

[Freesurfer] Gender and age based reconstruction

External Email - Use Caution Hello FreeSurfer Support, I reached out the other day about if there was a way to specify the data is from a specific gender or age during the recon all code, such as a tag at the end. I was told that there is not way to tell recon-all about demographi

Re: [Freesurfer] Converting surface coordinates to MNI coordinates

External Email - Use Caution Hi, Thank you so much for your reply I reviewed the link you sent and now know how to convert MNI305 to MNI 152 coordinates based on example of Case 8. However, I am still confused regarding my question number 1... When I use QDEC to do my own analys

[Freesurfer] FreeSurfer development version masks

Hello, I am trying to freeze the development freesurfer version for today and I am denied access to copy the following files: /usr/local/freesurfer/dev.backup/average/mult-comp-cor/fsaverage/rh/cortex/mask.mgh /usr/local/freesurfer/dev.backup/average/mult-comp-cor/fsaverage/lh/cortex/mask.mgh /

Re: [Freesurfer] freeview crash -- petsc error when opening volume

External Email - Use Caution Ruopeng, I've uploaded the files to the FTP drop (transfer/incoming/freesurfer_data.tar.gz). The command my user is running against these files is: freeview -v brainmask.mgz T1.mgz -f lh.white:edgecolor=yellow lh.pial:edgecolor=magenta rh.white:edg

Re: [Freesurfer] freeview crash -- petsc error when opening volume

External Email - Use Caution Absolutely, Ruopeng, happy to provide. Would the best avenue for sharing these files be the FTP drop (into transfer/incoming) or some other avenue? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Ruopeng Wa

Re: [Freesurfer] freeview crash -- petsc error when opening volume

Hi Tristan, Would it be possible to send us the files and the command-line you run? Best, Ruopeng > On Aug 21, 2019, at 12:18 PM, TRISTAN J PAUTSCH wrote: > > External Email - Use Caution > Adding more details provided by my user: > > The crash only happens when loading surfa

[Freesurfer] bug in freesurfer-dev (T2-specific parameters not passed to second call of mri_make_surfaces)

External Email - Use Caution Hi, I would like to report a bug in freesurfer-dev. I have encountered this bug in a version downloaded on July 11th, 2019, and again in a version downloaded two days ago (August 20th). In short, it seems that parameters specified via an expert fil