[Freesurfer] About FreeSurfer source code

External Email - Use Caution Dear community: I was curious about how the software is made and I decided to write an email to Dr. Bruce Fischl who answered all of the questions I asked, but he gave me the input to ask these questions also in FreeSurfer Community. I first asked

Re: [Freesurfer] Freeview: Load multiples overlays for one surface

External Email - Use Caution It's works! Thanks a lot! El vie., 7 sept. 2018 a las 16:46, Ruopeng Wang () escribió: > Yes, it is possible. But you should use ':' as separator like this: > > -f > surf/lh.inflated:overlay=surf/lh.sulc:overlay=surf/lh.thickness:overlay_threshold=1,5

Re: [Freesurfer] Freeview: Load multiples overlays for one surface

Yes, it is possible. But you should use ':' as separator like this: -f surf/lh.inflated:overlay=surf/lh.sulc:overlay=surf/lh.thickness:overlay_threshold=1,5 Ruopeng On 09/07/2018 03:11 PM, Emanuel Alvaredo wrote: External Email - Use Caution Hi! I would like from command line to

[Freesurfer] Freeview: Load multiples overlays for one surface

External Email - Use Caution Hi! I would like from command line to open one surface with multiple ovelays. For example, intead of this ..-f surf/lh.inflated:overlay=surf/lh.sulc surf/lh.inflated:overlay=surf/lh.thickness:overlay_threshold=1,5 I would like to do something

[Freesurfer] longitudinal hippocampal aseg editing

External Email - Use Caution Martin, That is the point. I have edited the hippocampus in the -long 2 times and the recon does not maintain my edits. I would love any help to changes I should be making to my recon statement to maintain my edits. Rebecca Hi Rebecca, aseg

Re: [Freesurfer] recon-all error

The terminal output is evrything that gets printed to the screen. The analysis in the recon-all.log file looks  like it did not finish right away (and there is no error msg in it) On 9/7/18 11:51 AM, Song, Da-Yea wrote: External Email - Use Caution I have attached the recon-all.log

Re: [Freesurfer] FsPalm patch

Actually, I figured it out. Everything is there now, just follow the instructions in the README. On 9/7/18 11:48 AM, Douglas Greve wrote: > I have recreated the patch. The only problem is that I don't quite > remember what should be in it. The wiki says that there are 3 files to > install, but I

Re: [Freesurfer] FsPalm patch

I have recreated the patch. The only problem is that I don't quite remember what should be in it. The wiki says that there are 3 files to install, but I can only remember two. Tom, can you install those two files and run it and see what fails? That will tell me what the 3rd file is. thanks doug

Re: [Freesurfer] recon-all error

can you send the terminal output and recon-all.log? thanks On 9/7/18 9:58 AM, Song, Da-Yea wrote: External Email - Use Caution Hello, I’m running some subjects through recon-all but have noticed that some error out (terminate the job) within seconds of starting. Any suggestions

Re: [Freesurfer] FsPalm patch

External Email - Use Caution Hi Tom and Zahra, >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> on behalf of Tom Parker >> I am attempting to download the FsPalm patch >> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm) > On September 7, 2018 at 4:10 PM "Nasiriavanaki,

Re: [Freesurfer] FsPalm patch

Hi I downloaded it from this link. https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide PALM/UserGuide - FslWiki - University of Oxford fsl.fmrib.ox.ac.uk Downloading and installing PALM. To download latest packaged version, please

[Freesurfer] recon-all error

External Email - Use Caution Hello, I'm running some subjects through recon-all but have noticed that some error out (terminate the job) within seconds of starting. Any suggestions would be really appreciated. Here is the recon-all.cmd error message:

Re: [Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield Matlab runtime Java error

External Email - Use Caution Hi all, Not sure if this was resolved off-list or not, but I just ran into it myself and it turned out to be a permissions-related error in that the user didn't have read access to some of the required files in the Matlab runtime. Setting them

[Freesurfer] FsPalm patch

External Email - Use Caution Dear Freesurfer developers, I am attempting to download the FsPalm patch (https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm ) using: the link described in the wiki -

Re: [Freesurfer] Fwd: longitudinal hippocampal aseg editing

Hi Rebecca, aseg edits to subcortical structures need to be done in the -long stage. (see here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits ) Best, Martin On Thu, 2018-09-06 at 14:37 -0700, Rebecca Ray wrote: > External Email - Use Caution > HELP > --

Re: [Freesurfer] Did not find any volume info. Warning: MatrixInverse failed

External Email - Use Caution Thanks for your quick answer Ruopeng. They are loaded with the same command and we check that the freeview's build time is the same in both computers: _Version 2.0_ _Build Jan 18 2017 16:48:55_ _Copyright (c) 2016_ Do you know what else can