[Freesurfer] Freesurfer 7.1 processing error MacOS, manual fix code not working

External Email - Use Caution Dear all, As evidently experienced by others, a certain percentage of subjects failed to run on freesurfer 7.1 version, stopping at the segmentation step, while they could run in version 6. I read that this is bug is present in Mac os, which I am us

[Freesurfer] Freesurfer license file error

External Email - Use Caution Hi Expets, I am trying to work with the Ciftify package, a great tool for converting non-HCP data into cifti format. I am running the following docker command. However, I get an error with the return code 255 sudo docker run --entrypoint ciftify_rec

Re: [Freesurfer] Freesurfer 7.1 processing error MacOS, manual fix code not working

External Email - Use Caution The 2nd line are actually 2 commands, you have to split them: The first one downloads a file: sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init -o rca-long-tp-init The second command makes it executable

Re: [Freesurfer] Ventricular location

External Email - Use Caution To find the code, look at FreeSurferColorLUT.txt, e.g., you may be interested in a subset of these: grep -i vent $FREESURFER_HOME/FreeSurferColorLUT.txt The last 4 values on each line make up a color code (RGBA, in range 0-255 per channel). The fi

[Freesurfer] total vertices does not match between results and labels

External Email - Use Caution Dear experts, I am using the mri_surfcluster function to cluster the surface results: mri_surfcluster --subject fbb_average --mask mask.mgh --hemi lh --olab label --in sig_results_tvalues.mgh --thmin 0.001 When I count vertices different

Re: [Freesurfer] Ventricular location

External Email - Use Caution Hi Doug, just an FYI that I think this requires extra recon-all files that are only output by v7 ? ./mri_segcentroids --i freesurfer/surf --o results.txt error: corRead(): can't open file freesurfer/surf/COR-.info On 16/06/2020 15:44, Douglas N. Grev

Re: [Freesurfer] freeview of freesurfer 7.1 incompatible with merged overlays

Hi Nick, Would it be possible to send us the surface file and the merged gift file so we can take a look? Best, Ruopeng On Jun 17, 2020, at 1:14 AM, Nick Blauch mailto:bla...@cmu.edu>> wrote: External Email - Use Caution Hello Freesurfer experts, I recently upgraded to Freesurfer

Re: [Freesurfer] Ventricular location

External Email - Use Caution Are the ventricles currently in V6 Surf directory as a set of vertices, or a labelled list of voxels, or anything like that? Ian On 16/06/2020 13:39, Ian wrote: External Email - Use Caution Hi Freesurfers. I'm looking to find the center o

Re: [Freesurfer] Ventricular location

External Email - Use Caution Perfect, thanks Tim. On 17/06/2020 10:50, Tim Schäfer wrote: > External Email - Use Caution > > To find the code, look at FreeSurferColorLUT.txt, e.g., you may be interested > in a subset of these: > >grep -i vent $FREESURFER_HOME/FreeSur

Re: [Freesurfer] Ventricular location

you're not running it correctly. Run it with just --help to get info on how to set up the command line On 6/17/2020 3:48 AM, Ian Hardingham wrote: External Email - Use Caution Hi Doug, just an FYI that I think this requires extra recon-all files that are only output by v7 ? ./mri_s

Re: [Freesurfer] total vertices does not match between results and labels

Maybe those 88 vertices have a value lower than the thresh or are not in the mask. On 6/17/2020 6:42 AM, Marina Fernández wrote: External Email - Use Caution Dear experts, I am using the mri_surfcluster function to cluster the surface results: mri_surfcluster --subject fbb_average -

Re: [Freesurfer] Freesurfer license file error

Hi Mason, My guess is that freesurfer is still grabbing the initial license. Have you been sure to remove the original one? It might be hiding as a .license file Best Andrew From: on behalf of Mason Wells Reply-To: FS Help Date: Wednesday, June 17, 2020 at 5:34 AM To: "freesurfer-boun...@nm

Re: [Freesurfer] version 7 docker container

Yes, we will release a v7 container on dockerhub as soon as we can. Hopefully by next week once we release a new 7.1 patch. From: on behalf of David Pagliaccio Reply-To: FS Help Date: Tuesday, June 16, 2020 at 4:20 PM To: FS Help Subject: [Freesurfer] version 7 docker container Ext

Re: [Freesurfer] Error recon-all mri_cc

External Email - Use Caution Hi Doug, Thanks for this. I sent the file; it’s called yannquide.tar.gz. Yann > On 16 Jun 2020, at 11:56 pm, Douglas N. Greve wrote: > > Can you upload the subject so I can take a look? Instructions below > > > From the linux command line, > Crea

Re: [Freesurfer] Correcting recon-all output (missing parts in pial surface)

Phew! From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Michael Sent: Wednesday, June 17, 2020 5:18 PM To: Freesurfer support list Subject: Re: [Freesurfer] Correcting recon-all output (missing parts in pial surface) External Email - Use Caution Thank you for your quick respo

[Freesurfer] How to get access to the coordinate data of specified area

External Email - Use Caution Hello, I found FreeSurfer can segment brain areas automatically these days, and it really meets my requirements. therefore, this tool is really useful for me! But this process is only a part of my work, and I notice FreeSurfer isn't designed for third-p