Re: [Freesurfer] How to join certain segmentation with T1.mgz and save them in one file with nifti format

To merge the two hippocampi together in one file you can fscalc left-hippo.mgz sum right-hippo.mgz -o both.hippo.mgz If you want a binary mask of the brainmask, you can run mri_binarize --i brainmask.mgz --min 0.5 --o brainmask.bin.mgz Then run mergeseg --src brainmask.bin.mgz --merge both.hippo.m

Re: [Freesurfer] How to join certain segmentation with T1.mgz and save them in one file with nifti format

External Email - Use Caution Hello Freesufer developers, I just want to know how to merge the right and left-hypocampus in one file (hypocampus.gmz), and then merge hypocampus.gmz with brainmask.gmz so that I can get one mgz file having the segmentations with the brainmask. I wa

Re: [Freesurfer] Not able to find corresponding files for the paper: "Functional–anatomical validation and individual variation of diffusion tractography-based segmentation of the human thalamus"

sorry, no idea. They probably merged labels from the aparc or the aparc+a2009s to create those labels. You might also try mri_annotatoin2label with the --lobes option On 8/4/2021 5:28 AM, Sumit Sharma wrote: External Email - Use Caution Hi Freesurfer Developers I am trying to reprod

Re: [Freesurfer] How to join certain segmentation with T1.mgz and save them in one file with nifti format

I don't understand what you mean by "join". Can you elaborate? On 8/4/2021 1:16 AM, Ammar Shujaa wrote: External Email - Use Caution Hello FreeSurfur Developers, I have used binary mask and got the segmentations: right and left-hypocampus.mgz. I just want to know how to join these

Re: [Freesurfer] mri_glmfit-sim error

This happens because the cached p-values were generated from a simulation that only went up to 30mm FWHM of smoothing. lGI has lots of internal smoothness which often pushes it over this level. You can try not using any smoothing, or, even better, try using permutation instead. https://surfer.n

Re: [Freesurfer] How to extract individual structures after recon-all

and you can use mri_binarize --i aseg.mgz --match index1 index2 --o yourmask.mgz On 8/3/2021 10:07 AM, Fischl, Bruce wrote: Hi Ammar In the mri dir there are segmented volumed called aseg.mgz and aparc+aseg.mgz where every voxel has an index into the FreeSurferColorLUT.txt lookup file Chee

[Freesurfer] Not able to find corresponding files for the paper: "Functional–anatomical validation and individual variation of diffusion tractography-based segmentation of the human thalamus"

External Email - Use Caution Hi Freesurfer Developers I am trying to reproduce your work in the below paper using freesurfer: Johansen-Berg, Heidi, et al. "Functional–anatomical validation and individual variation of diffusion tractography-based segmentation of the human thalamus

[Freesurfer] How to join certain segmentation with T1.mgz and save them in one file with nifti format

External Email - Use Caution Hello FreeSurfur Developers, I have used binary mask and got the segmentations: right and left-hypocampus.mgz. I just want to know how to join these segmentations with T1.mgz so that I can get one file containing T1 image with the two segmentations.