Re: [Freesurfer] Hippocampal/amygdala subfields hemisphere error

External Email - Use Caution Dear Juan, Thank you for the reply. In the base/tmp directory there is one folder, "hippoSF_T1_long.v22_right" and an empty text file "filled.edits.txt". I don't see any directory pointing to the left hemisphere. In the right hemisphere directory,

[Freesurfer] Freesurfer archive password

External Email - Use Caution Hello, Could you please provide the password required to open the archive containing the freesurfer ubuntu virtual machine. Thanks in advance. Best regards, Dan ___ Freesurfer mailing list Freesurfer@nmr.mgh

[Freesurfer] Any large stash of labelled brain MRIs for CNN training?

External Email - Use Caution Hi, First samseg and mri_reg are amazing tools. Thank you! I am running them on an internal dataset of images to create labelled MRIs. This is taking 45 min to an hour per grouping (T1, T1ce, T2 and FLAIR) to align and segment. It made me

Re: [Freesurfer] creating average labels

External Email - Use Caution I am basically looking for a way to create an average of the labels for the L subcallosal cingulate cortex (SCC) and then make an average of the labels for the R SCC across all subjects and use these 2 average labels as a mask to see if the average la

[Freesurfer] free view crash report

External Email - Use Caution hi, i have downloaded 7.3.2 version on my macbook pro ,os 13.1. When i am trying to load volume from subjec > bert > T1.mgz or other .nii volume freeview crashing unexpectedly. below the error log,,please kindly help.God bless. ---

[Freesurfer] VM freesurfer version

External Email - Use Caution Hello, We’d like to set up the virtual machine version of freesurfer, but need a password to unzip the ova.7z file. Would you be able to send it when you get a chance? Thank you so much! Best regards, Fred

[Freesurfer] postdoctoral position available at the University of Toronto Brain, Body, and Perception Research Program

External Email - Use Caution A postdoctoral scholar position is available in the Brain, Body, and Perception Research Program

Re: [Freesurfer] creating average labels

External Email - Use Caution Hi Carlos, mri_concat concatenates input .mgz files. The following command will output C.mgz with A.mgz as the first frame, and B.mgz as the second frame, assuming both A and B have only one frame. mri_concat --i A.mgz --i B.mgz --o C.mgz I’m not su

[Freesurfer] questions about mri_normalize

External Email - Use Caution Dear experts, I have been using the mri_normalize in FSv7.3.2 to standardize the intensity of FLAIR images , and I've observed that increasing the sigma parameter up to 25 is effective in improving the quality of the normalized images for noisy datasets