[Freesurfer] Negative Longitudinal Hippocampal Subfield Values

External Email - Use Caution Dear FreeSurfer Developers, I think my earlier email may have gotten lost. I've run the longitudinal hippocampal subfield pipeline using the following command on freesurfer version 6.0: longHippoSubfieldsT1.sh PAWS001_base_FS I received no errors a

Re: [Freesurfer] mri_aparc2aseg with flag --a2005s

External Email - Use Caution Hi, I was wondering if you have any updates on this (getting the ctx-lh-primary-motor and ctx-lh-premotor labels or 9001 and 9002 from https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT ). Thank you, Anja On Fri, Ju

[Freesurfer] Dockerized version of Freesurfer 7.1

External Email - Use Caution Hi Freesurfer Team, I am working on running recon-all on a large dataset using AWS. I saw that there is a dockerized version of Freesurfer 6.0. However, I would like to use Freesurfer 7.1. I was wondering if you could give me any information on whether

Re: [Freesurfer] Dockerized version of Freesurfer 7.1

Hi Morgan, We plan to host a v7 container on dockerhub as soon as the 7.1.1 patch version is released (which should be sometime this week). Best, Andrew From: on behalf of Morgan Botdorf Reply-To: FS Help Date: Monday, July 13, 2020 at 11:59 AM To: FS Help Subject: [Freesurfer] Dockerized

Re: [Freesurfer] QAtools with Freesurfer version 6.0

Hi Kamy, The QA tools are actually developed outside of our lab. It might be helpful to contact the Reuter lab directly - https://github.com/Deep-MI/qatools-python best Andrew From: on behalf of "Wakim, Kathryn-Mary" Reply-To: FS Help Date: Thursday, July 9, 2020 at 7:51 PM To: FS Help Sub

Re: [Freesurfer] QAtools with Freesurfer version 6.0

External Email - Use Caution Hello Kamy, thanks for your mail, and sorry I missed it in last week. If I understand correctly, you are referring to the QAtools that were originally developed for Freesurfer 5.1 and 5.3, right? I.e. those at https://surfer.nmr.mgh.harvard.edu/fswi

Re: [Freesurfer] QAtools with Freesurfer version 6.0 {Disarmed}

External Email - Use Caution Hi Kersten, Thanks so much for your response. I was actually referred to the qatools-python modulate from someone in my lab in respose to my previous questions. That tool has been working great so far with Freesurfer 6.0 output. Warm regards, and th

Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment

External Email - Use Caution Hi Eugenio, I reran the segmentations after editing the aseg.presurf.mgz files and copying the edited HC to the wmparc.mgz files but the segmentations did not improve. Is there anything else you would suggest to do? Here is an example of one of my s

Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment

Hi Jenna, Would it be posible for you to share the subject? This is very weird. Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Jenna Katherine Blujus Reply-To: Freesurfer support list Date: Monday,