[Freesurfer] TOPO_DEF

External Email - Use Caution Hi My name is Halil Ibrahim akçay. I am a neurologist. I have been used FreeSurfer for a while. And I cannot understand some part of troubleshooting process. I am sending a screenshot of my question. How can I understand whether gray zone as marked

[Freesurfer] Segmentation fault

External Email - Use Caution Hi, I am trying to use Freeview in my MacBook Pro. However, every time I tried to open it from terminal I get this error: /Applications/freesurfer/7.2.0/bin/freeview: line 2: 5984 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS

[Freesurfer] fs_install permission denied

External Email - Use Caution Dear Freesurfer experts, I was tiring to install fs_install using the below command. cd $FREESURFER_HOME/bin && curl https://secure-web.cisco.com/186mRL7xDETIpN5cZS-wivuTmyhZn0PmwqT8bMpnWm3D4D_WUHYglUgqCALj1K0RLMMNugABxNcqPDrvA0L2GjDjTujRrsnTCSBefUDtO

Re: [Freesurfer] Segmentation of thalamic nuclei: LGN volume

Hi Marco, Would you mind sharing a representative case with us, please? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On Aug 30, 2021, at 04:17, Marco Aiello mailto:marcoaiello1...@gmail.com>> wrote: Ext

[Freesurfer] Freesurfer Matlab LME tool: problem with function lme_mass_RgGrow

External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to analyze thickness changes in a longitudinal design using a mass-univariate approach, as described on the Linear Mixed Effects tutorial at https://secure-web.cisco.com/1HwLf5wG3aIAhV84T5KTL4VUiVpoa1DISeYUy

Re: [Freesurfer] Hippocampal subfields

External Email - Use Caution Hi Eugenio, Thanks so much for you reply. I will do that so. Just by way understanding the outputs I have , so the extract script only pulls the HBT automatically, and you need to simply add these together for the FS60 measures ? You can't modify th

Re: [Freesurfer] Hippocampal subfields

Oh, now I understand. Yeah you can add the head, body and tail segments of each subfield to get 6.0 type of measurements ;-) Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On Aug 28, 2021, at 08:20, Erik O'Hanlon

[Freesurfer] Segmentation of thalamic nuclei: LGN volume

External Email - Use Caution Dear Freesurfer experts, I'm running (FS 7.1.1) segmentThalamicNuclei.sh on T1 scan from recon-all. On a sample of about 100 subjects I've found an average volume of 250 mm^3 and 290 mm^3 for LGN-left and LGN-right, respectively. Consistent with liter

[Freesurfer] ERROR: mri_ca_register with non-zero status 11

External Email - Use Caution Hello FreeSurfer Developers, when I run the recon-all command: $ export SUBJECTS_DIR=`pwd` $ cd /lustre/home/acct/zjzhu/project/zzu_MRI/T1/test $ ls *nii | parallel --jobs 12 recon-all -s {.} -i {} -all -qcache I get the following error ERROR: mr