Re: [Freesurfer] Recon Reprocessing Issues

2016-03-06 Thread Bruce Fischl
Hi Champe can you send us the recon-all.log file? cheers Bruce On Sun, 6 Mar 2016, Champe Barton wrote: Hi Freesurfer People, I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I have System Integrity Protection disabled (though I hadn’t experienced any issues that c

Re: [Freesurfer] mean thickness

2016-03-06 Thread Bruce Fischl
Hi Caroline how did you generate the Gnumeric file? And what operating system/hardware are you using? Also, please send us the recon-all.log for one of the subjects that you see this happening cheers Bruce On Fri, 4 Mar 2016, Caroline Beelen wrote: Dear Freesurfer team,   Forgive me

Re: [Freesurfer] Cortical thickness using freesurfer

2016-03-06 Thread Bruce Fischl
Hi Sahil I believe with that command you are mapping the lh_cuneus.nii file to the surface of that subject, not fsaverage. Try visualizing it on the S01_LP inflated surface instead of fsaverage. If you want to map to fsaverage you can use surf2surf. cheers Bruce On Fri, 4 Mar 2016, Sahil B

Re: [Freesurfer] recon-all -lgi issue with MATLAB Student version - Help!

2016-03-06 Thread Marie Schaer
Hi all, To follow-up on this issue if anyone else has the same problem, you need to modify one of the LGI functions as described in the release notes (http://freesurfer.net/fswiki/ReleaseNotes): * LGI: issue when using Matlab 2013. the fix is to edit the file $FREESURFER_HOME/matlab/SearchP

[Freesurfer] mri_surf2surf dev vs stable

2016-03-06 Thread marmaduke woodman
Hi The command mri_surf2surf --srcsubject tvb --trgsubject fsaverage5 --hemi lh --sval-xyz pial --tval pial.tvb --tval-xyz ./tvb/mri/T1.mgz works on dev (mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve), but on stable fails with ERROR: Option ./tvb/mri/T1.mgz unknown Is there a simple wor

Re: [Freesurfer] mri_surf2surf dev vs stable

2016-03-06 Thread marmaduke woodman
On 03/06/2016 08:23 PM, marmaduke woodman wrote: > mri_surf2surf ...--tval-xyz ./tvb/mri/T1.mgz just to follow up, it seems --tval-xyz is a flag (no argument) on stable, but on dev takes an argument. So, on stable, just mri_surf2surf ... --tval-xyz will run, but the resulting surface doesn't

[Freesurfer] mris_anatomical_stats -th3

2016-03-06 Thread Kaiming Yin
Dear guys, I checked one of my subjects file /stats/lh.aparc.stats, in which it said the commandline as: mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject1 lh white what does the flag "-t

Re: [Freesurfer] T2pial shrinks pial surface

2016-03-06 Thread Matt Glasser
What FreeSurfer version are you using? Very small changes to the input images (e.g. a different random see for FreeSurfer) may be able to kick mris_make_surfaces out of that bug, though perhaps Bruce has fixed it. Peace, Matt. From: on behalf of Chris Adamson Reply-To: Freesurfer support li

Re: [Freesurfer] T2pial shrinks pial surface

2016-03-06 Thread Chris Adamson
5.3.0 stable From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser Sent: Monday, 7 March 2016 11:50 AM To: Freesurfer support list Subject: Re: [Freesurfer] T2pial shrinks pial surface What FreeSurfer version are you using? Very

Re: [Freesurfer] T2pial shrinks pial surface

2016-03-06 Thread Bruce Fischl
Hi Chris if you upload that dataset I'll try to take a look soon cheers Bruce On Mon, 7 Mar 2016, Chris Adamson wrote: The T2pial option mostly works beautifully. I have a few cases where the pial surface just shrinks globally and wraps over the white surface (see attached). I have checked

Re: [Freesurfer] T2pial shrinks pial surface

2016-03-06 Thread Chris Adamson
How can I upload it to you? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, 7 March 2016 1:25 PM To: Freesurfer support list Subject: Re: [Freesurfer] T2pial shrinks pial surface Hi C

Re: [Freesurfer] T2pial shrinks pial surface

2016-03-06 Thread Bruce Fischl
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Mon, 7 Mar 2016, Chris Adamson wrote: How can I upload it to you? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, 7 Mar

Re: [Freesurfer] mysterious fsgd format error (not the end of line problem)

2016-03-06 Thread Joseph Dien
never mind! It turned out I was forgetting to run a script to move copies of the fixed fsgd files into their final locations. Once I did so the files I posted worked fine. Sorry for the false alarm and thanks for getting back to me! Joe > On Mar 3, 2016, at 12:18, Douglas N Greve wrote: >

Re: [Freesurfer] T2pial shrinks pial surface

2016-03-06 Thread Chris Adamson
It is checkT2pial.zip -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, 7 March 2016 1:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] T2pial shrinks pial surface https://su

Re: [Freesurfer] T2pial shrinks pial surface

2016-03-06 Thread Chris Adamson
Thanks Bruce. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson Sent: Monday, 7 March 2016 1:54 PM To: Freesurfer support list Subject: Re: [Freesurfer] T2pial shrinks pial surface It is checkT2pial