[Freesurfer] ATTACHMENT REMOVED--asegstats2table

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[Freesurfer] FS educ links

External Email - Use Caution Hi, We're implementing freesurfer and other neuroimaging applications on the High Performance Computing center. To help more users get up to speed quickly, I'm trying to pull together up-to-date freesurfer/freeview educational materials into a

[Freesurfer] SC20

External Email - Use Caution I thought some people from this list might want to attend SC20, the 2020 supercomputing conference. It looks interesting, and could be relevant to your work. Examples of activities at SC can be found in the previous year's program at the SC19

[Freesurfer] unable to create symbolic link, and GPU error

External Email - Use Caution Hi, I am testing a new installation of freesurfer. Two errors occurred, and I'm hoping someone can help me troubleshoot: First, recon-all exits with error indicating that it is unable to create a symbolic link: [GHS\026278@vmcntdsktp10 fs_sample1]$

[Freesurfer] GPU/supercomputer adaptation of freesurfer?

External Email - Use Caution Hi, I'm planning a freesurfer analysis of a large MRI dataset, and want to use the "380 GPU nodes" (and other cores/nodes) on the Palmetto Cluster (https://www.palmetto.clemson.edu/palmetto/userguide_palmetto_overview.html) to speed up the process.

[Freesurfer] Sag T1 3D post-contrast

External Email - Use Caution Has anyone else tried to do recon-all with Sagittal 3D T1 post-contrast volumes? We're getting hung in recon-all at the Talairach registration step, and I wonder if the vascular enhancement at the pial surface might be throwing the algorithm off.

[Freesurfer] symbolic link problem

External Email - Use Caution Hi, Running recon-all on sag T1 post-contrast MRI (for archival study) on virtualBox with centOS7 and freesurfer 6. The virtual box runs on a windows server and is allocated 8 processors and 16 GB memory by the windows server on which it resides. A

[Freesurfer] parallel openmp

External Email - Use Caution We are trying to run many subjects through recon-all in batches on an 8 core Windows Server on which we have virtualBox running CentOS7 and freesurfer 6. Can you tell me if this command will utilize all 8 cores effectively to process all 8 subjects

[Freesurfer] degrees of freedom

External Email - Use Caution In group analysis, is it better to have matched controls (1:1) or to use age, education and other characteristics as confounds in the glm? In the latter situation, we would control for these demographic variables in the glm and the control group n

[Freesurfer] Analyzing slice data with freesurfer?

External Email - Use Caution We are attempting to analyze archival MRI data obtained during routine clinical care. Unfortunately, the standard clinical MR sequences do not include 3D volumes. Will the freesurfer algorithm work on slice data so that each slice could be marked

[Freesurfer] segmentation and parcellation advances

During the last lectures of the recent 4/2-5 course, Dr. Fischl referenced code that would properly segment/parcellate sub-par images. If we don't have a good 3D MPRAGE or SPGR T1 image, is there a specific command I need to use for these alternate/sub-par inputs into recon-all ? If not, when

[Freesurfer] MCR

Hi, I was pleased to learn freesurfer runs with the standalone matlab runtime, and installed this on CentOS7. It seems to be working well. I noticed that there's also a version of spm12 that runs using this runtime, "with limitations." Two questions: 1. Are there freesurfer limitations