Re: [Freesurfer] Z-stat - z.mgh

On 06/16/2016 07:51 AM, Robby De Pauw wrote: > > Dear FreeSurfer users > > I am not able to extract the Z-values as they are not present in my > output: > > z.mgh -- z-stat that corresponds to the significance > > Are these Z-val

[Freesurfer] Z-stat - z.mgh

-lion-stable-pub-v5.3.0 Thank you for your response, Greetings Robby Robby De Pauw, PT, MT, drs. T +32 09 332 12 19 | Email robby.dep...@ugent.be<mailto:robby.dep...@ugent.be> Ghent University | Rehabilitation Sciences and Physiotherapy Campus Heymans 3B3 (022) De Pintelaan 185 BE-9000 Ghent

[Freesurfer] Convert ascii to .mgh

<freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Convert ascii to .mgh I would do it in matlab, eg, F = MRIread('F.mgh'); % This is to get the proper header information lfdr = load('lfdr.asc'); F.vol = fast_mat2vol(lfdr,F.volsize); MRIwrite(F,'lfdr.mgh'); On 6/15/16 4

[Freesurfer] Convert ascii to .mgh

file into an “.mgh”-overlay file. Any idea how I could approach this conversion (from asci back to .mgh)? Many thanks, Greetings Robby Robby De Pauw, PT, MT, drs. T +32 09 332 12 19 | Email robby.dep...@ugent.be<mailto:robby.dep...@ugent.be> Ghent University | Rehabilitation Sc

Re: [Freesurfer] permission denied

? Cheers Robby Robby De Pauw, drs. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent robby.dep...@ugent.be On 31 Oct 2014, at 16:35, zkauf...@nmr.mgh.harvard.edu wrote: Yes, please try running as root and get back when you have

[Freesurfer] longitudinal data processing

to the command? Thank you Greeting Robby Robby De Pauw, drs. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent robby.dep...@ugent.be ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Syntax Error: trac-all -bedp

to adjust the permission in my SUBJECTS_DIR with the recursive option -R (chmod a+rwx -R $SUBJECTS_DIR), but this doesn’t seem to fix the problem. Thanks for the already given advice, Regards, Robby Robby De Pauw, drs. Ghent University Department of Physiotherapy and Rehabilitation Sciences

[Freesurfer] Syntax Error: trac-all -bedp

Dear Anastasia, Barbara FS-community, The preprocessing step of Tracula was succesfully completed. However when I try to do the next step: fitting the Ball Stick model I get another error: mri@ge24c165:/media/mri/DATAPART11/ROBBY/FREESURFER$ trac-all -bedp -c dmrirc.info INFO:

Re: [Freesurfer] tracula: bvec-error

Hi Anastasia and Barbara I updated Tracula and now everything is running fine. Thx, Robby Robby De Pauw, drs. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent robby.dep...@ugent.be On 04 Sep 2014, at 22:01, Anastasia Yendiki

Re: [Freesurfer] tracula: bvec-error

Hi Barbara and FS-community, I tried everything you suggested, but unfortunately the same error still occurs. Have you found a solution yet? Thanks for your help Best regards, Robby Robby De Pauw, drs. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan

[Freesurfer] GLM: table with uncorrected clusters

regards Robby Robby De Pauw, dra. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent robby.dep...@ugent.be ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] tracula: bvec-error

Dear Barbara, Unfortunately I haven’t found a solution yet. I’ll keep you up to date. Greetings, Robby Robby De Pauw, dra. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent robby.dep...@ugent.be On 01 Sep 2014, at 12:22, Barbara

[Freesurfer] seed-based functional connectivity: mkcontrast-sess

. This was the command I tried to use: mkcontrast-sess -rmprestim -analysis restingstate.sm05.lh -contrast restingstate.lh I’m sure I’m missing something here, but I can’t figure out what to do. Thanks for the already given support!! Best regards, Robby Robby De Pauw, dra. Ghent University Department

Re: [Freesurfer] tracula: bvec-error

Hi Anastasia,I’m using this version of tracula.trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki ExpI’ve attached the log-file you requested. Robby De Pauw, dra.Ghent UniversityDepartment of Physiotherapy and Rehabilitation Sciences3B3De Pintelaan 185B-9000 Ghentrobby.dep...@ugent.be trac-all.log

[Freesurfer] ERROR: cannot find AFNI command 3dvolreg.afni

-per-run -fsd bold -stc upRegardsRobby preproc-GEZ_004_HACO-bold.log Description: Binary data Robby De Pauw, dra.Ghent UniversityDepartment of Physiotherapy and Rehabilitation Sciences3B3De Pintelaan 185B-9000 Ghentrobby.dep...@ugent.be ___ Freesurfer

Re: [Freesurfer] GLM: Error Matric-Scale

on a windows computer. Is that possible? Try reformatting it in linux or mac. doug On 08/20/2014 12:58 PM, Robby De Pauw wrote: Hi there FreeSurfer When trying the GLM-analysis I keep getting the following error. Could you help me with fixing it? ERROR: matrix is ill

Re: [Freesurfer] tracula: bvec-error

. error at the very beginning of your trac-all output. And it would explain why it can't find the files. Hope this helps, a.y On Thu, 21 Aug 2014, Robby De Pauw wrote: Dear FreeSurfer, When I try to use TRACULA I keep getting the following error: mv -f /Users/rdpauw/Desktop/SUBJECTS_FS/T1

[Freesurfer] tracula: bvec-error

Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64trac-preproc exited with ERRORS at Thu Aug 21 16:00:45 CEST 2014 Robby De Pauw, dra.Ghent UniversityDepartment of Physiotherapy and Rehabilitation Sciences3B3De Pintelaan 185B-9000 Ghentrobby.dep