Re: [Freesurfer] Dividing surface overlays

External Email - Use Caution Hi Dylan, Give this a try: fscalc gm_lh.nii.gz div wm_lh.nii.gz --o gmwmratio_lh.nii.gz On Wed, Feb 23, 2022 at 12:24 PM Tisdall, Dylan < mtisd...@pennmedicine.upenn.edu> wrote: > External Email - Use Caution > > Hi all, > > I've generated

[Freesurfer] Dividing surface overlays

External Email - Use Caution Hi all, I've generated two surface overlays, using mri_vol2surf with positive and negative projfrac to get a GM and WM samples (gm_lh.nii.gz and wm_lh.nii.gz). I'd now like to take the vertex-wise ratio of these two overlays, and make a new one

[Freesurfer] PhD Position in Neuroimaging and Deep Learning at Karolinska Institute, Stockholm, Sweden

External Email - Use Caution Dear all, We are looking for a PhD student to work in an interdisciplinary and internationally competitive environment at Karolinska Institute, one of the top medical universities in the world and the home for the Nobel Prize in Medicine. We combine

Re: [Freesurfer] Incorrect SI/AP swap from bbregister

External Email - Use Caution My apologies, it ends up that this swap was because my initial registration .lta file wasn't referencing the correct source and destination files. Once I figured out how to export the correct initial transfrom from freeview, everything works.

Re: [Freesurfer] cortical measurments

External Email - Use Caution If you want region-based measurements (e.g., for Desikan atlas), you can use the 'aparcstats2table' tool that comes with FreeSurfer to generate a CSV file with aggregated data for several subjects. For vertex-wise measurements, you most likely want

[Freesurfer] Incorrect SI/AP swap from bbregister

External Email - Use Caution Thanks for the help with my previous question on formatting the bbregister command line. Now that I've got it running, I'm seeing that 1 of my two subjects ends up with a 90 degree rotation (swapping SI and AP axes) when I try to register my 7T T1

[Freesurfer] cortical measurments

External Email - Use Caution Hello Freesurfer experts How can I get a text file of the cortical measurements of a group of images after they have been processed with recon -all?? Best, Reem ___ Freesurfer mailing list

Re: [Freesurfer] convert .mgz to .nii

External Email - Use Caution Thank you very much, but I want to implement tf.train.F Feature of python or numpy data type. This is an essential step towards building any TFRecords database. The method I found requires nii files to be extracted and read by SimpleITK ‫في الأربعاء،