[Freesurfer] mri_surf2vol with inflated surfaces

External Email - Use Caution Greetings freesurfuer community, I've been working on a research project for which I need to simulate different levels of inflation for a given brain MRI, to achieve so I have tried the following so far: 1. To run recon-all for a test subject 2.

Re: [Freesurfer] Synthsr

Dear Gonzalo, I’m incredibly sorry for the inconvenience but SynthSR is indeed broken right now. It should be fixed in 1-2 days; please try downloading the development version next week and it should all be fine! Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (

[Freesurfer] Synthsr

External Email - Use Caution Hello FreeSurfer, I am trying to run the following comand: :~$ synthsr --i $SUBJECTS_DIR/super_resolve/ --o $SUBJECTS_DIR/super_resolved/ --ct --threads 4 --cpu synthsr: command not found Is this due to the synthsr being broken or with my installat

Re: [Freesurfer] A question regarding a Freeview command (Douglas N. Greve) 8/10/21

External Email - Use Caution Dear FreeSurfer developers, First, thank you Douglas very much for your reply. I have a follow up question, and for some reason I wasn't able to continue the thread, so I have copied the thread with Douglas's answer and my first question below. Her

Re: [Freesurfer] Segmentation of thalamic nuclei - misplaced position

Dear Edyta, The smaller nuclei are definitely less accurate than the bigger ones in the atlas. Is it only the VM giving you trouble? Is it in every case, or only on this case? Cheers, Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeigle

[Freesurfer] ACPC alignment before processing

External Email - Use Caution Hello FreeSurfer Developers, I wonder if we have a function that could automatically align T1w to ACPC before running recon-all? Or if we have an option in recon-all that could do this ACPC alignment automatically? I noticed there are such ways after r

[Freesurfer] Different pixel spacing for scans in the same cohort

External Email - Use Caution Dear Freesurfer, I was wonderign wether processing scans and comparing their stats, e.g. cortical thickness and area, could be not recommended if the pixel spacing across all the scans was different, i.e. the range is between .9375x.9375x1.2 and 1.3