Re: [Freesurfer] need for help

External Email - Use Caution Dear Doug, Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, th

[Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not found

External Email - Use Caution To whom it may concern, I am trying to run hippocampal and amygdala segmentation (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala) on FreeSurfer v6.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c). I wa

[Freesurfer] Research Assistant Position available at Brown University

External Email - Use Caution Dear colleagues: We are looking for a Research Assistant who will join a group of researchers on Aging and Alzheimer's disease at Brown University. 50% of time of the position will be devoted to behavioral and fMRI experiment preparation, data collecti

Re: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not found

External Email - Use Caution Dear CC, You need the development version of FreeSurfer, since the amygdala was added to the atlas after the 6.0 release. Kind regards, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesia

Re: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not found

External Email - Use Caution Hello, Thank you for the response! I just want to double check before I install the development version, will installing the development version amend, delete, or override any of the previous FreeSurfer files or scripts we have with the non-developm

Re: [Freesurfer] Mass-Univariate LME - help please!

External Email - Use Caution Hi Tom, regarding the first question: I think that here the issue is that non-transformed and transformed p-values are mixed: the spval file should contain non-transformed values between p=0 and p=1, while the '1.3' (which is used as the threshold)

Re: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not found {Disarmed}

External Email - Use Caution Nope, unless you rerun your subjects, which you totally shouldn’t (just run segmentHA_T1.sh) And of course, install on a different directory than 6.0 😉 Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (

[Freesurfer] Running FSL randomise on FS cortical thickness data

External Email - Use Caution Dear Freesurfer experts, Hi. We are analyzing cortical thickness data in Freesurfer, longitudinal data in 55 subjects using the linear mixed effects package. We are finding a number of siginificant clusters, and would like to correct for multiple c