Re: [Freesurfer] trac-all -prep error

Hi Ela - Do you know what phase-encode direction your DWIs were collected with (e.g. AP, PA, LR, etc.)? Then add it to the config file like this: "set pedir = (AP)" Otherwise, if your data are stored in BIDS format, there's a new script that will figure all this out and generate the

Re: [Freesurfer] FREESURFER

External Email - Use Caution That worked, thanks so much! On Thu, 9 Dec 2021 at 16:14, Fischl, Bruce wrote: > Hi Ali > > > > What directory are you running from? You need to specify the full paths > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >

Re: [Freesurfer] FREESURFER

Hi Ali What directory are you running from? You need to specify the full paths Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Alison McDonnell Sent: Thursday, December 9, 2021 11:11 AM To: Freesurfer support list Subject: Re: [Freesurfer] FREESURFER External Email

Re: [Freesurfer] FREESURFER

External Email - Use Caution Hi Bruce, Thank you for clearing up the differences. Im getting an error to say there is no such file and that couldn't open the file. was wondering if you had any ideas why this would be as I can see the file in the folder. Thanks, Ali [image:

Re: [Freesurfer] FREESURFER

Hi Ali mris_convert converts surface while mri_convert converts volumes (in general these prefixes hold across all our binaries – the mris_ ones do surfaces and the mri_ ones do volumes). To convert a patch you need to tell mris_convert that it is a patch and not a complete surface by giving

[Freesurfer] trac-all -prep error

External Email - Use Caution Dear freesurfer developers and Dr. Yendiki, I am trying to run trac-all -prep -c dmriEla, dmriEla being my config file. I am attaching the config file here. If I perform registration-based correction with eddy_correct, doeddy=1, things start to run.

Re: [Freesurfer] Error: recon-all exited with ERRORS: failing without generating all surf files: How to modify wm.mgz to make it work?

Hi Sumit Can you post some images? It looks like the topo fixer ran out of memory: CORRECTING DEFECT 0 (vertices=2851, convex hull=1075, v0=1654) An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to

[Freesurfer] FREESURFER

External Email - Use Caution Hi all, I'm trying to use mris_convert and can't get it to work. current command I'm using: mris_convert lh.full.flat.patch.3D lh.full.flat.patch.3D.asc also can't seem to find the difference between mris convert and mri convert so don't know if I

[Freesurfer] Doubts about analysis of hippocampal subfields and nuclei of the amygdala

External Email - Use Caution Hello FreeSurfer Developers, I would like to know if the analysis of hippocampal subfields and nuclei of the amygdala can only be done through ROI-based analysis or is there any way to perform GLM analysis with these data in freesurfer? Thanks in