Re: [Freesurfer] PET-segmentattion

Can you send the terminal output and the petsuv.segstats.dat? How have you verified that the registration is correct? What version of FS are you running? On 8/5/2022 4:44 PM, Bouchra Guelib wrote: External Email - Use Caution I want to segment registered PET to T1 MRI to 45 subcortic

Re: [Freesurfer] Sclimbic segmentation fault error?

not sure. Try running mri_sclimbic_seg --i GP0050/mri/orig.mgz --o junk.mgz On 8/4/2022 4:20 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email - Use Caution Hi all, I am receiving this error when trying to run sclimbic module. It's not being very descriptive abo

Re: [Freesurfer] adding volume to aparc aseg

Try mergeseg. Run with --help to get more info On 8/3/2022 3:41 PM, Benjamin Deck wrote: External Email - Use Caution Hi there, I have extracted an ROI mask for the subthalamic nucleus from MNI space and registered this with the subject's native space orig.mgz I would like to appe

Re: [Freesurfer] Using averaged T1-images to calculate cortical thickness

If I understand correctly, you have one site that acquires two scans, one sag and one axial, and you want to register them together and compute the average, then feed the average to recon-all? Do they have the same isotropic resolution? I'd guess that this would create a systematic artifact.

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

There was something a little strange about the cases that were failing -- there were very bright values at the back of the head and around the nose. This probably messes up the normalization in the unet. I ran it with --percentile 99.9 (this eliminates the extreme voxels) and the results looked

Re: [Freesurfer] MP2RAGE sequence recon-all

If you are going to pass it the UNI, then you will probably need to mask out the stuff outside of the head. One way to do this is to run samseg on the INV1 or INV2 (INV1 probably better), the run mri_mask uni.mgz seg.mgz uni.masked.mgz Then pass uni.masked.mgz to recon-all On 8/2/2022 8:39 AM, R

Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

You should paint the template onto the sphere that is registered (i.e. sphere.reg), at which point it should look similar to the individual subject's sulc pattern. And by "bounce" I just meant send it to me Cheers, Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Trolle, Carl S

Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

I apologize but I'm not familiar with the term bounce; do you want me to re-run the mrisp_paint-command but with specifying the optional #3 parameter for the argument? The sphere and the inflated surface look more similar but still seem to differ from the fsaverage that way. Kind regards, Car

Re: [Freesurfer] Thalamus Parcellation - HCP data

Dear Asa, Rather than resampling to 2mm and then applying a linear transform, I would first transform and then resample. Cheers, Juan Eugenio Iglesias www.jeiglesias.com On Aug 9, 2022, at 3:32 PM, Asa Borzabadi Farahani mailto:asa.borzabadifarah...@mail.mcgill.ca>

[Freesurfer] Thalamus Parcellation - HCP data

External Email - Use Caution Hi, I hope this email finds you all well. I have a basic question about the right way of using ThalamicSegmentation method ( implemented by Iglesias et al. 2018). I plan to use this subject-specific atlas on the data processed via the HCP pipeline.

Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

Yes, definitely something wrong. For the paint you want to specify which frame in the tiff with #3 I believe (so $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#3). We store information in 3-frame sets, with means, variances and dofs in that order for each of inflated, sulc

Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

Sorry, been trying to get this right for some time before getting back to you, but not sure that I have. I'm attaching screenshots of the ?h.sphere.reg for the original, processed and the fsaverage-subjects with the destrieux-annotation. To me, it looks slightly worse after the mris_register co

[Freesurfer] Parcellation issue

I want to use a different template apart from the MNI for my parcellation (Yeo_JNeurophysiol11_FreeSurfer.zip). Below are the instructions given in the readme. My question is – do I need to run this code before Recon-all or after In terminal (ASSUMING shell is bash), a) "cd" to unzipped fold

[Freesurfer] Help for pass code to open Freesurfer Virtual Machine image (.7z)

External Email - Use Caution Hello, I'm a student researching Magnetoencephalography estimation and have been trying to install Freesurfer on a Windows OS using a Virtual Machine, following the instructions below: "You will be prompted for a pass code when the archive is successf