Re: [Freesurfer] consistency in recon-all parallel pipeline

-parallel’ or ‘recon-all –threads ’? From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Horn, Mitchell Jacob Sent: Friday, February 23, 2024 12:28 PM To: Freesurfer support list mailt

Re: [Freesurfer] consistency in recon-all parallel pipeline

: [Freesurfer] consistency in recon-all parallel pipeline So, is the bottom line that when you run 7.4.1 on COS8 in parallel that you get (slightly) different results each time? On 2/2/2024 11:20 AM, Horn, Mitchell Jacob wrote: Hi FS Devs, I’m experiencing unreproducible thickness results when

Re: [Freesurfer] aparcstats2table - append option

is added to aparcstats2table and asegstats2table. It should be available tomorrow in Freesurfer dev version. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Horn, Mitchell Jacob Sent: Monday, December 18, 2023 9:06 AM To: Freesurfer support list Subject: Re: [Freesurfer

Re: [Freesurfer] aparcstats2table - append option

, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Horn, Mitchell Jacob Sent: Tuesday, December 12, 2023 10:10 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.

[Freesurfer] aparcstats2table - append option

Hi FS Devs, Would it be possible to add an "append" flag for use with aparcstats2table and asegstats2table? If I understand their usage correctly, each time one of them are run they will create (or overwrite) a new file. Not urgent but would be useful. Thanks, Mitch

Re: [Freesurfer] HPC Usage - Moving On from CentOS7

, i.e., the libs may not be the same. I also don’t see that RedHat CentOS8* releases include CentOS7 versions of libraries. - R. On Mar 30, 2023, at 12:12, Horn, Mitchell Jacob wrote: As an update I’ve tested another run (bert, 7.2.0, no flags, recon-all) on an OS-8 system but set LD_PRELOAD

[Freesurfer] Neuroimaging Scientist Position - Massachusetts General Hospital, Department of Neurology

Senior Research Technologist - (3220849) Background The Senior Research Technologist will perform duties in structural and functional magnetic resonance imaging at the Massachusetts General Hospital Stroke Research Center and the Athinoula A. Martinos Center for Biomedical Imaging. The

Re: [Freesurfer] Scalable recon workflow

, Mitchell Jacob mailto:mjh...@mgh.harvard.edu>> wrote: Hi Experts, If I have 100s of subjects to recon and have access to an HPC with both GPU and CPU options what is the recommended flags to maximize speed performance? Is … -parallel -openmp 4 … still the best approach? And if so,

[Freesurfer] Scalable recon workflow

Hi Experts, If I have 100s of subjects to recon and have access to an HPC with both GPU and CPU options what is the recommended flags to maximize speed performance? Is … -parallel -openmp 4 … still the best approach? And if so, is 2GB memory/core best (keeping it 8GB memory/subject) or is

[Freesurfer] mri_vol2surf; --projfrac-avg and --projfrac-max

Dear FS Experts, When using --projfrac-max or --projfrac-avg, how is the “min” component defined? If I specify: --projfrac-max -2 1 0.1 Is the min (-2) simply 2x the thickness at each vertex below/inside the GM/WM boundary? Thanks in advance! Mitch

Re: [Freesurfer] Cerebellar Segmentation Definitions

Hi Doug, Thanks for your reply. Would it be safe to say that these deep grey nuclei are included in the cerebellar white matter? Thanks, Mitch ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Cerebellar Segmentation Definitions

Hi FS Experts, I am planning to use the cerebellar segmentations in the routine recon-all which parcellates the cerebellum into cerebellar-white-matter and cerebellar-gray-matter. I am trying to define the two terms, as it appears that the cerebellar-white-matter label includes much if not all

Re: [Freesurfer] vol2surf: lesion overlap across group into surfaces

10:25 AM, Horn, Mitchell Jacob wrote: Thanks so much Douglas. Many of the lesions are in the white matter, and many span across WM and GM. In the case where the lesions on not strictly cortical, is this surface mapping not possible? Or perhaps a representative surface map showing the occurrences

Re: [Freesurfer] vol2surf: lesion overlap across group into surfaces

Thanks so much Douglas. Many of the lesions are in the white matter, and many span across WM and GM. In the case where the lesions on not strictly cortical, is this surface mapping not possible? Or perhaps a representative surface map showing the occurrences of lesions in any lobe/ROI? Best,

[Freesurfer] vol2surf: lesion overlap across group into surfaces

Dear FS Experts, I would like to show the distribution and overlap of lesions on an average inflated brain surface as a heat map. I have a 150 subjects of which I’ve made masks of T2 lesions and moved into their respective subject-T1w-spaces (using T1.mgz as reference) where I have

[Freesurfer] Lesion Correction

Hi Freesurfer Team, I have a couple cases with large hemispheric ICH that have caused my recon to hit the default wall-time of 96 hours. It seems to get hung up on the correcting topology defects step for the affected hemisphere. My goal is to have the recon at least finish so I can analyze