[Freesurfer] Pial in the thalamus

Dear all, We have this issue around the thalamus that is recurring in several of our scans and there does not seem to be a problem with the white matter mask in that area. Is it a problem? Does anyone have an idea how to fix this? We are using Freesurfer v5.3. Thanks. Yann _

Re: [Freesurfer] Pial in the thalamus

t; Bruce > On Thu, 16 Mar 2017, Yann Quidé wrote: > >> Hi Bruce, >> >> Thanks for your reply. Most of the voxels are not labelled as thalamus on >> the aseg, only few partially cross the wm/pial lines (see screenshot >> attached). >> Any recommendation? &g

[Freesurfer] Problem with fsgd file

Dear all,I am sure it is something obvious, but I am stuck with that error.I am trying to analyse data and prepared my fsgd file, but when trying to use mri_glmfit, Terminal returns me the errorgdfReadHeader: reading group_age_sex.fsgdERROR: gdfRead: group_age_sex.fsgd is not formatted properly.  T

Re: [Freesurfer] Problem with fsgd file

> are you on? > > > On 03/29/2017 04:01 PM, Yann Quidé wrote: >> Dear all, >> >> I am sure it is something obvious, but I am stuck with that error. >> I am trying to analyse data and prepared my fsgd file, but when trying >> to use mri_glmfit, Terminal

Re: [Freesurfer] Medial Surface Problem

ps://twitter.com/neuraustralia> > <https://www.facebook.com/NeuroscienceResearchAustralia> > <http://www.neura.edu.au/help-research/subscribe> >> On 28 Mar 2017, at 10:51 pm, Yann Quidé > <mailto:yannqu...@gmail.com>> wrote: >> >> Dear all, >> >> I

[Freesurfer] ROI extraction using functional masks

Dear FS experts, I am trying to extract values for cortical thickness, surface area and volumes, from different functional ROIs. These cortical ROIs have been defined using SPM tools, and are in .nii format. My scans have been processed using FS v5.3. Although the conversion seems to go well, t

[Freesurfer] Correction for multiple comparisons

External Email - Use Caution Dear all, Using Freesurfer 5.3, I would like to limit my whole-brain analyses to a mask I already defined (ie, small volume correction-like analysis). To correct for multiple comparisons, I want to use the mri_glmfit-sim option. As I am looking withi

Re: [Freesurfer] ROI extraction using functional masks

las N Greve wrote: > > At what step is the failure happening? Do the masks look ok on the surface? > > > On 02/12/2018 08:06 PM, Yann Quidé wrote: >> Dear FS experts, >> >> I am trying to extract values for cortical thickness, surface area and >> volu

[Freesurfer] Postdoctoral or experienced research position in a Neuroscience/Resilience/Twin Research Program

External Email - Use Caution Posted on behalf of Dr Justine Gatt. Dear Colleagues Our team is currently advertising a postdoc / experienced research assistant position in a neuroscience research program focusing on wellbeing and resilience in twins. Applications close 28t

[Freesurfer] Matlab runtime installation error for Freesurfer v7.1.0

External Email - Use Caution Hi team, I am trying to install fs_install_mcr R2014b, but encounter an error just at the end of it: mv: rename /var/folders/1f/4_zl7p9n795c2yq1dgb3hvt4gq/T/tmp.Xvv7Ku4d/install-target/v84 to /Applications/freesurfer/7.1.0/MCRv84: Permission de

Re: [Freesurfer] Matlab runtime installation error for Freesurfer v7.1.0

lesias > Senior research fellow > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > http://www.jeiglesias.com <http://www.jeiglesias.com/> > > > > From: <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Yann Quidé > mailto:yannqu...@gmai

Re: [Freesurfer] Error recon-all mri_cc

s" (no quotes) > It will ask you for a password: use "anonymous" (no quotes) > cd transfer/incoming > binary > put subject.tar.gz > Send an email that the file has been and the name of the file. > > > > On 6/15/2020 8:28 PM, Yann Quidé wrote: >>

Re: [Freesurfer] Error recon-all mri_cc

External Email - Use Caution Hi team, I was just wondering if you received my file and if you had time to look at it? Thanks, Yann > On 18 Jun 2020, at 7:08 am, Yann Quidé wrote: > > Hi Doug, > > Thanks for this. I sent the file; it’s called yannquide.ta

Re: [Freesurfer] Error recon-all mri_cc

External Email - Use Caution Hi team, I appreciate everyone is busy, but did anyone have time to look at my subject? It was uploaded on June 18. It’s called yannquide.tar.gz Thanks for your time. Yann > On 22 Jun 2020, at 12:51 pm, Yann Quidé wrote: > > Hi team, &

Re: [Freesurfer] Error recon-all mri_cc

> Please let us know if this does not solve your issue. > Andrew > > From: <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Yann Quidé > mailto:yannqu...@gmail.com>> > Reply-To: FS Help <mailto:freesurfer@nmr.mgh.harvard.edu>> >

[Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use Caution Hi team, I am trying to run the thalamic nuclei pipeline with FS7.3.2, on scans processed with recon-all from FS5.3 (mac OSX10.13). However, I receive the below error. Any idea how I could solve this? Thanks in advance. Yann ---

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

by the script ./freesurfer/bin/fs_install_mcr > > - R. > >> On Aug 19, 2022, at 07:33, Yann Quidé wrote: >> >> External Email - Use Caution >> >> >> Hi team, >> >> I am trying to run the thalamic nuclei pipeline with

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

RS at Sat 27 Aug 2022 10:28:44 AEST It seems that FS is looking for v84 files that are missing in v93? Does anyone have an idea of what I am doing wrong? Thanks in advance. Yann > On 20 Aug 2022, at 9:42 am, Yann Quidé wrote: > > Not a good news for me, but thanks! > > Yann

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use Caution Hi all, Just bumping this one up. Any help would be really appreciated. Thanks in advance, Yann > On 27 Aug 2022, at 10:47 am, Yann Quidé wrote: > > Hi team, > > I have been having troubles with processing my scans for thalamic

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.java.com/en/download/manual.jsp- R.On Aug 29, 2022, at 20:26, Yann Quidé <yannqu...@gmail.com> wrote:External Email - Use CautionHi all,Just bumping this

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use Caution Thanks again for your help. I tried with both R2017b and R2019b but no luck. When I soft link either of these versions to MCRv84, I receive the following error: sub-BA_IGP001 Setting ITK threads to 1 # #@#

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use Caution Interesting… when I leave the folders named MCRv93 or MCRv97 (one at a time, not present together at the same time), then FS tells me I need to install MCRv84! FS7.2.0 seems to only recognise MCRv84, hence why I used for example, sudo ln -s v93 MCRv8

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use Caution This is the error I get when for example, I use MCRv93 sub-BA_IGP001 ERROR: cannot find Matlab 2014b runtime in location: /Applications/freesurfer/7.2.0/MCRv84 It is looking for either: bin/glnxa64/libmwlaunchermain.so(Linux 64

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

wrong? Thanks for your time. Yann > On 31 Aug 2022, at 2:12 pm, Yann Quidé wrote: > > This is the error I get when for example, I use MCRv93 > > sub-BA_IGP001 > > ERROR: cannot find Matlab 2014b runtime in location: > > /Applications/freesurfer/7.2.0/MC

Re: [Freesurfer] mri_sclimbic_seg patch issue?

External Email - Use Caution Hi all, I have the same issue on Ubuntu 22.04, patch is installed. Many thanks, Yann > On 20 Dec 2022, at 04:29, daedalu...@aol.com wrote: > > External Email - Use Caution > > > Dear FreeSurfer Developers, > > We are interested i