[Freesurfer] ?????? Recon-all run error

that failed directly on the command line and see if it works? Was anything else running on the machine at the time? We do report total and free memory at the start of the recon in the recon-all.log file cheers Bruce On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution

[Freesurfer] Triangular mesh sampling problem

External Email - Use Caution Dear FS We now have high and low resolution images, we want to resample each triangular surface mesh generated from low-resolution data onto the corresponding triangular surface mesh generated from high-resolution data and vice versa as follows: For

[Freesurfer] Recon-all run error

External Email - Use Caution Dear FS, When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the mri_convert command is executed. The specific errors are as follows: /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted

[Freesurfer] 回复： 回复： Recon-all run error

ion of netcdf. I've attached a screenshot of the code. You could try setting all the soft limits for the shell to be unlimited, e.g., in bash, $ ulimit -c unlimited 1013364183 November 5, 2018 at 21:22 via Postbox External Email - Use Caution

[Freesurfer] ?????? ?????? Recon-all run error

fit ix. On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I found the error location in the recon-all.log folder. Here is the place > where it went wrong??I > don't think it's the reason for insufficient mem

[Freesurfer] Calculated thickness

External Email - Use Caution Dear FS?? I now have two different surfaces, the two surfaces have intersecting parts, I want to calculate their signed distance, what should I do?I want to calculate the thick std and mean mgh files through mris_surface_stats, but there is no

[Freesurfer] gray intensity

External Email - Use Caution Dear Bruce, I want to get the percent gray-white contrast((white-gray)/(white + gray).100%) and gray intensity sampled at 30% cortical depth. What should I do? yours yujunjie___ Freesurfer mailing list

[Freesurfer] ?????? Calculated thickness

at you want. cheers Bruce On Fri, 7 Dec 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear FS?? > I now have two different surfaces, the two surfaces have intersecting > parts, I want to calculate > their signed distance, what should I do?I wa

[Freesurfer] ?????? Calculated thickness

ist"; : Re: [Freesurfer] Calculated thickness Hi yujunjie you can use mris_distance_transform -vol to compute a volumetric map of distances to the surface if that is what you want. cheers Bruce On Fri, 7 Dec 2018, 1013364183 wrote: > > External Email - Use Caution >

[Freesurfer] ?????? ?????? Calculated thickness

ple the full command line you ran and the full output of it (in text, not a screen shot!) cheers Bruce On Sat, 8 Dec 2018, 1013364183 wrote: > > External Email - Use Caution > > The problem is in the fourth step of ThicknessRepea

[Freesurfer] ???????????? ?????? Calculated thickness

diff.mgh Best, Tim > On December 8, 2018 at 2:08 PM 1013364183 wrote: > > > External Email - Use Caution > > Dear Bruce, > I run the following command: > > mris_surface_stats -nsmooth 60 -surf_name $SUBJECTS_DIR/1001/surf/lh.white > -out_na

[Freesurfer] Surface displacement

External Email - Use Caution Dear FS, We want to calculate the displacement of different surfaces, what should we do? yours yujunjie___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Surface displacement

? -- Original -- From: "Bruce Fischl"; Date: Mon, Dec 3, 2018 11:49 PM To: "Freesurfer support list"; Subject: Re: [Freesurfer] Surface displacement Hi yujunjie you need to give us more information than this. cheers Bruce On Mon, 3 Dec 201

[Freesurfer] ?????? ?????? Triangular mesh sampling problem

ve any complete code that will do exactly what you want though, so you will have to poke around in the source yourself I'm afraid. cheers Bruce On Thu, 29 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I want to do the followi

[Freesurfer] ?????? ?????? ?????? Triangular mesh sampling problem

quot;Freesurfer support list";"Jonathan Polimeni"; : Re: [Freesurfer] ?? ?? Triangular mesh sampling problem hmm, maybe Jon (ccd) can help? Bruce On Sat, 1 Dec 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, >

[Freesurfer] fdr correction problem

External Email - Use Caution Dear Bruce?? I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected graphs are all 0. Why is this, the instructions and the running results are as follows: mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh

[Freesurfer] fdr correction problem

External Email - Use Caution Dear Bruce?? I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected graphs are all 0. Why is this, the instructions and the running results are as follows: mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh

[Freesurfer] ?????? Triangular mesh sampling problem

your own, although it will be a bit of a project. cheers Bruce On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear FS > We now have high and low resolution images, we want to resample each > triangular surface mesh >

[Freesurfer] ?????? ?????? ?????? Triangular mesh sampling problem

be someone else can?). The only alternative I can think of is to use the various fsaverage meshes instead of the subject meshes. Then the "projection" becomes trivial as the lower res meshes are just the first N vertices in the higher res ones. cheers Bruce On Fri,

[Freesurfer] ?????? ?????? ?????? ?????? Triangular mesh samplingproblem

: "Jonathan Polimeni"; : Re: [Freesurfer] ?? ?? ?? Triangular mesh samplingproblem Hi yujunjie I included him in the previous (and this) email cheers Bruce On Sun, 2 Dec 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bru

[Freesurfer] ?????? ?????? ?????? Recon-all run error

ischl"; : 2018??11??18??(??) 11:15 ??: "Freesurfer support list"; : Re: [Freesurfer] ?? ?? Recon-all run error Instructions on how you can upload tarred and gzipped files here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Sun, 18 No

[Freesurfer] ?????? ?????? ?????? Recon-all run error

quot;Freesurfer support list"; : Re: [Freesurfer] ?? ?? Recon-all run error Instructions on how you can upload tarred and gzipped files here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Sun, 18 Nov 2018, 1013364183 wrote: > > Ex

[Freesurfer] multi-threaded question

External Email - Use Caution Dear FS, I would like to ask if freesurfer can run multi-threaded. If so, can you give us some guidance on this? Thanks in advance yours yujunjie___ Freesurfer mailing list

[Freesurfer] ?????? multi-threaded question

ischl"; : 2018??11??17??(??) 11:03 ??: "Freesurfer support list"; : Re: [Freesurfer] multi-threaded question Yes, use the -openmp option in recon-all Cheers Bruce On Nov 16, 2018, at 9:52 PM, 1013364183 wrote: External Email - Use Caution

[Freesurfer] ?????? ?????? ?????? Recon-all run error

or cerebellum still attached. Follow the tutorial for checking for and fixing defects. On 11/14/2018 02:59 AM, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce Fischl, > I am very sorry that I have not reply to you last week. > Our data has been running

[Freesurfer] trilinear interpolation

External Email - Use Caution Dear Bruce, Hello, we used mri_convert ?Cvs [] ?CI [] ?Co[] ?Crt interpolate to perform the trilinear interpolation on the image, and also used the trilinear interpolation in the torch to process the image. We found the result obtained by the

Re: [Freesurfer] recon-all error

-- From: "Bruce Fischl"; Date: Wed, Apr 24, 2019 09:52 PM To: "Freesurfer support list"; Subject: Re: [Freesurfer] recon-all error hmmm, how long did you let it run? I've never seen this before. Can you upload your subject to our ftp site? cheers Bruce On Wed, 24

[Freesurfer] recon-all error

External Email - Use Caution Dear freesurfer We run the recon-all command of freesurfer, but when it runs to the randomSeed 0 step below, it will not run anymore, that is, the running terminal has been stuck in the following statement for more than 10 days.We want to ask why