[Freesurfer] extracting values from signifciant clusters

External Email - Use Caution Dear FreeSurfer Team, We are doing a longitudinal analysis with Freesufer 7.1.1 (two-stage longitudinal model), and we would like to extract the Cortical thickness values from the significant clusters (before and after treatment changes) to visualize

[Freesurfer] Subcortical regions of Brainnetome Atlas

External Email - Use Caution Hi FreeSurfer Experts, I am using Brainnetome Atlas in FreeSurfer to calculate the brain volume. The cortical regions are done smoothly by using mris_ca_label->mris_anatomical_stats with materials on https://secure-web.cisco.com/1p7TY1frW67uqViolqd9

Re: [Freesurfer] Hippocampal/amygdala subfields hemisphere error

External Email - Use Caution Dear Chris, This is a pretty weird one! Question: what files are there in the temporary directory subjectDir/subjectBase/tmp/hippoSF_T1_long.v22_left/ ? Cheers, /E -- Juan Eugenio Iglesias http://secure-web.cisco.com/1FmaPIPrt8VADXFs3ezSt_rWHcBh_tWsK4

[Freesurfer] Hippocampal/amygdala subfields hemisphere error

External Email - Use Caution Dear experts, I'm getting an error running the longitudinal hippocampal/amygdala subfields analysis and hoping for help. I've been able to complete this analysis without problems for all but one of my subjects. The issue is that only the left hemi

Re: [Freesurfer] TIV from manually corrected aseg+aparc.mgz

External Email - Use Caution Hi Daniela, On this page https://secure-web.cisco.com/1eUQpVvxrVeNEfeuknfSJu6n3plR5yKIy8iRlfATB5XV2S4Wq_68rpEnw4YyVZM9BjK4jMfItVUk3EBKG85JZGFeYB67XqxzUaW3sx_iQBKkuPpJnxHb70EvrWDP21B9zMFJAXpCVKvaAGxd2BG1YToPdu2TLDfqVo880z9p3OfdSus4qO0uJPBNy3Vb9DNri0QsN

[Freesurfer] creating average labels

External Email - Use Caution Good afternoon, I would like to verify that the subcallosal cingulate cortex (SCC) segmentation of my subjects are correct. I want to do this by creating an average label of the left SCC and an average label of the right SCC which I can then map onto e

Re: [Freesurfer] is it possible to run a longitudinal study on 2 "-base" images?

External Email - Use Caution You can run longitudinal analysis with 2 timepoints - https://secure-web.cisco.com/1jQQ0cVi7lI0yGhk44hY2J-io2CWVn1H8Pa0LTIgv7lJoY6DvAzdL-94yJFuUJgiTBTy90dccfUzUHS74CitHvEMQPm31joNosyoZGVcpO0GnFgFpHpm-PYiOjWcw_hH1AS_OZXMTT517S1fM6Ldxek4-QJbcuzYXEjTS-R7

[Freesurfer] License key

External Email - Use Caution Hello could you please guide me where I should copy the license.txt file in Linux Ubuntu There is no installation demo video for Linux and I am totally confused I couldn't install freesurfer, not only the DEB file but also tar.gz . Unfortunately, all th

[Freesurfer] Fw: freesurfer download zip password

External Email - Use Caution Hi I reached out previously but haven't heard back -- can you please provide me with the password for the zip file? Thanks! From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Parmaksiz, Deniz Sent: Tuesday, A

[Freesurfer] TIV from manually corrected aseg+aparc.mgz

External Email - Use Caution Hi FreeSurfer Developers, For our study we had to manually correct some recon-all outputs due to some ROIs underestimation. For the purpose we manually edited the aparc+aseg.mgz file using the "voxel edit” command from Freeview. Then we use the mri_s

[Freesurfer] Fwd: Password to VirtualMachine request

External Email - Use Caution Hi, I would like to kindly ask you for the password for FreeSurfer 7.2.0 Virtual Machine. I tried using old password (brain.map), but that doesn't work anymore. Also, is there a possiblity of getting sudo password? It was quite annoying to work on pr

[Freesurfer] Extracting statistical values from significant ROIs after running GLM

External Email - Use Caution Hi I have run a GLM using cortical thickness and a behavioural measure on specific ROIs, I have a query about extracting the statistical values, specifically the test statistic from the significant regions after running the GLM but prior to multiple