[Freesurfer] mris_anatomical_stats

External Email - Use Caution When using the following command line: mris_anatomical_stats -th3 -mgz- cortex ../label/?h.cortex.label -f ../stats/?h.aparc.pial.stats -b -a ../label/?h.aparc.annot -c ../label/aparc.annot.ctab subject ?h pial do we generate a pial surface area (

[Freesurfer] remark regarding tcsh with bad locale

External Email - Use Caution Hi, this is not really a question but rather a comment that, hopefully, will help those running into the issue I ran into today. I was using mri_glm-sim with --mczsim 2 option, and got an error saying that "2,0 must be 1.3, 2.0 ...". The issue is that

[Freesurfer] Postdoc Opportunity in Montréal

External Email - Use Caution Seeking Postdoctoral Fellow for Multiomics Investigations in Neurodegenerative Diseases The Multiomics Investigation of Neurodegenerative Diseases Lab, directed by Dr. AmanPreet Badhwar, is looking for a postdoctoral fellow. The successful candida

[Freesurfer] Asymmetry whole thalamus with native vs Iglesias method

External Email - Use Caution Dear freesurfer experts, I’m currently using FreeSurfer 7.1 with the thalamus subsegmentation from Iglesias et al (version 12) to subsegment the thalamus. Something we noticed is that the asymmetry between the left and right whole thalamus is reverse

[Freesurfer] group level analysis

External Email - Use Caution Hi, When conducting group-level analysis, for example comparing volumetric differences or tractography FA across subjects between groups. How we correct for the size of the brain when comparing volumetric differences or correct for the whole brain FA?

[Freesurfer] VirtualBox Ubuntu Password Request

External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to login to the Ubuntu VM disk image downloaded through the VirtualBox setup page, however I could not find the password for the "developer" account in the documentation or set up a personal account through

Re: [Freesurfer] VirtualBox Ubuntu Password Request

External Email - Use Caution Hello Eileen, I will send the password to your email shortly. - R. On Aug 31, 2020, at 11:46, XU Eileen wrote:External Email - Use CautionDear FreeSurfer Developers, I’m attempting to login to the Ubuntu VM d

[Freesurfer] tkregister2 deprecated for FS7.1?

Hi FS devs, I am following https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview? as a tutorial to fix the bad talaiarch file I have. I know that tkmedit is deprecated, but I was wondering if tkregister2 is too. If so, I was wondering what software I would use (or commands,

[Freesurfer] mri_preproc error with FS6.0

External Email - Use Caution Hello, I am running into an error while running the LGI analyses using FreeSurfer 6.0 following Jove article recommendations (  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/). The error is occuring when I try to run the following command: mris

Re: [Freesurfer] group level analysis

Hi Qi - Correcting for overall brain size is important when you are comparing measures of length/area/volume. As in, you want to know if a region specifically is bigger in population A vs. B, and not just because the whole brain is bigger. In that case, use eTIV (estimated total intracranial vol

Re: [Freesurfer] group level analysis

External Email - Use Caution Hi Anastasia, Thank you for your reply. So for segmentation.stats, should I divide the regional areas by eTIV or treat it as a covariate for a group comparison? Is it the same with Total cerebral white matter volume for wmparc.stats. For Diffusion meas

Re: [Freesurfer] group level analysis

Hi Qi - Use eTIV as a covariate for any analyses on volume, thickness, or surface area measures. In a situation where a regional FA difference is high enough to also cause a whole brain FA difference, regressing out the latter could wipe out the former. Not sure why you'd want to do that, unles

Re: [Freesurfer] group level analysis

External Email - Use Caution Hi Anastasia, Thank you for the clarification! As you said, if I regress out the global FA, I could wipe out the regional FA. But what if my question is to find out exactly which regional FA differentiate the two groups rather than if global FA is diff

Re: [Freesurfer] group level analysis

Let me put it this way. It's possible that your amygdala is bigger than mine without your brain overall being bigger than mine. But if your corpus callosum has higher average FA than mine, then your brain overall will have higher average FA than mine (assuming we don't have a reverse difference

Re: [Freesurfer] group level analysis

External Email - Use Caution Now I see. Thank you very much and have a good night! Best, Qi On Mon, Aug 31, 2020 at 11:12 PM Yendiki, Anastasia < ayend...@mgh.harvard.edu> wrote: > Let me put it this way. It's possible that your amygdala is bigger than > mine without your brain