[Freesurfer] Obtaining single file from segmented images

External Email - Use Caution Dear sir/madam, I have successfully segmented my participants' hippocampus thanks to "segmentHA_T2.sh" command, which provided me both right and left hippocampal segmented files. However, I was wondering if it is possible to obtain single files for eac

Re: [Freesurfer] Hippocampal Subfield Definition Errors

Definitely an ASEG problem that the subfield routine couldn’t recover from. Bruce: any ideas on what may have gone wrong? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On Jul 17, 2021, at 23:46, Franchesca Kuhney mailto:fk

[Freesurfer] Drawing ROIs

External Email - Use Caution Dear FS experts, I am planning to extract early visual region ROIs from my retinotopy scan. Is it possible group vertices according to radian values? (Like it is done in functional scans, filling an area according to the threshold). Or is there any

Re: [Freesurfer] Obtaining single file from segmented images

External Email - Use Caution Hi Gregorio, You should be able to use mri_binarize to create masks from the hippocampal seg files https://secure-web.cisco.com/1qpMewyxfLa5R6eiYrzcf1qqqYJYO4CO0D3YKhBtxNKEZ97mm-iZPnbTazVbnV6aErI2Y4G6Iodqtpa7eRC6MzifD_tow_ROWRGLcJnlSoJoMvp7kVi4-NzdGcgO

Re: [Freesurfer] Drawing ROIs

External Email - Use Caution I realised my e-mail wasn’t to really saying what I meant to, sorry for the confusion. My correction, I delineated early visual areas, and I would like to create ROIs for my polar angle and eccentricity interest. For instance I would like to create a

[Freesurfer] Developer password

External Email - Use Caution Dear Freesurfer Team, I am currently setting up freesurfer using the Ubuntu VM but I can't log in because I don't have the developer password. Would it be possible to provide me with the password? Thank you! Best, Clemens___

[Freesurfer] Joining Hippocampal files

External Email - Use Caution Dear sir/madam, After the segmentation I obtained the hippocampal segmented file for each hemisphere. Since I want to use them as mask for my functional scans, I wanted to join the the 2 hemisphere files together (otherwise I would obtain a different M

Re: [Freesurfer] Joining Hippocampal files

Dear Gregorio, There’s 2 options: 1. Merge the 1mm segmentations (i.e., the *.FSvoxelSpace.mgz). This is easy as they live in the same voxel space, you can directly sum the images. The problem is that they have less resolution. 2. Merge at higher resolution. This will create HUGE volumes. You

Re: [Freesurfer] Developer password

External Email - Use Caution I’ll send the info to your private email shortly. - R. On Jul 19, 2021, at 07:07, Clemens M wrote:External Email - Use CautionDear Freesurfer Team,I am currently setting up freesurfer using the Ubuntu VM but I

[Freesurfer] Announcing FreeSurfer version 7.2

We are  please to announce version 7.2. Mostly bug fixes and behind-the-scenes enhancements. But there are a few new goodies and one new "known issue" about defacing. Check out https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes doug ___ Freesurfer

Re: [Freesurfer] Announcing FreeSurfer version 7.2

External Email - Use Caution Dear Doug, Thank you for the announcement of 7.2.0 update. I updated using freesurfer-linux-ubuntu18_amd64.tar.gz and noticed that the 'mni' directory is missing. As a result, now the shell shows warning about MNI = freesurfer-linux-ubun

Re: [Freesurfer] Claustrum segmentation

No, we don't segment it (there are many regions in that table that are aspirational). It is on our list ... On 7/16/2021 11:06 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email - Use Caution ​Hi all, I was wondering if any of you guys have had experience wanting

[Freesurfer] MNI to RAS conversion

External Email - Use Caution Dear Mailing List, I have a set of MNI coordinates (from SPM2) that I need to visualise relative to the Desikan-Killiany Atlas parcellation. However, I'm unsure how to convert these coordinates so that I can load up Freeview and visualise their loca

Re: [Freesurfer] Announcing FreeSurfer version 7.2

External Email - Use Caution Hello Kiyotaka, You may not need to be concerned about that warning.  You can suppress it by setting the following in your shell environment. $ export NO_MINC=1 For Ubuntu linux, if you have sudo/root/admin privileges, then you could try running the i