[Freesurfer] recon-all: Same MRI, different execution tame

the performed work on each execution? I'm thinking on the number of GPU kernels executed, the number of the iterations of the methods... Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona http://www.pic.es Avis - Aviso

[Freesurfer] Fwd: Recon-all different execution time for same subjects

in each execution? I'm thinking on the number of GPU kernels executed, the number of the iterations of the methods... Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html

[Freesurfer] Fwd: Recon-all different execution time for same subjects

in each execution? I'm thinking on the number of GPU kernels executed, the number of the iterations of the methods... Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html

Re: [Freesurfer] recon-all complete in 10 hours!!!!

and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jordi

Re: [Freesurfer] recon-all CUDA error

? - Bryan -- *From:* Jordi Delgado [jordi...@pic.es] *Sent:* Thursday, July 03, 2014 12:36 AM *To:* Chiu, Bryan (PHTH) *Cc:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] recon-all CUDA error Hi again, Sorry I think that we have

Re: [Freesurfer] recon-all CUDA error

but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jordi Delgado Mengual PIC (Port d'Informació Científica) -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586

Re: [Freesurfer] recon-all CUDA error

Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jordi Delgado Mengual PIC (Port d'Informació Científica

Re: [Freesurfer] Advice: Freesurfer Parallel Processing on Large Dataset

Dear Elijah, If I'm right, there are two options to accelerate FS execution: 1) The first option is using the FS openmp implementation http://surfer.nmr.mgh.harvard.edu/fswiki/OpenMP. I haven't tested this way but openmp allows to open multiple processing threads, and it is supported for the

[Freesurfer] CUDA binaries

Dear freesurfers, I'm trying to exploit CUDA capabilities by using recon-all with -use-gpu. On the freesurfer wiki I found an approximate speedups for the main CUDA implementations in Freesurfer ( http://ftp.nmr.mgh.harvard.edu/fswiki/CUDADevelopersGuide). But I can't found mri_watershed_cuda

[Freesurfer] MRI artifacts detection

in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html

Re: [Freesurfer] MRI artifacts detection

will correct for intensity bias. You can have it generate two series - one with and one withour the correction. What other artifacts do you mean? There are lots of possibilities cheers Bruce On Mon, 13 May 2013, Jordi Delgado wrote: Dear FS experts, I'm studying the most common

[Freesurfer] mri_segstats SNR calculation

Dear Freesurfers, After running the first tests of freesurfer 5.2, I found a file named $hemi.w-g.pct.stats on the stats folder. The last column of the file is a SNR calculation, i found on the help manual, that is required to add --snr to perform this calculation. I'm interested to know how

[Freesurfer] mri_segstats SNR calculation

this SNR is calculated. Is there any method or paper related? Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http

[Freesurfer] Gray matter

Dear FS experts, I have a double question about the gray matter calculations in FS: - Revising the aseg.stats, I noticed that there is a Total Gray Volume calculation. Is there a mgz volume with the gray matter? I cannot find it on the output mri folder... - How this total Gray Volume is

Re: [Freesurfer] Gray matter

in FreeSurferColorLUT.txt Cheers, Gabriel. El 22/03/13, *Jordi Delgado * jordi...@pic.es escribió: Dear FS experts, I have a double question about the gray matter calculations in FS: - Revising the aseg.stats, I noticed that there is a Total Gray Volume calculation. Is there a mgz volume

Re: [Freesurfer] cuda error...

contact the sender and properly dispose of the e-mail. -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html

[Freesurfer] FreeSurfer Compiling error

/mri_em_register' make[2]: *** [all] Error 2 make[2]: Leaving directory `/home/neuro/dev/mri_em_register' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/neuro/dev' make: *** [all] Error 2 I don't know what is going wrong... Any idea? Thank you in advance! -- Jordi Delgado

Re: [Freesurfer] Error compiling freesurfer

, Jordi Delgado wrote: ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lGLU -lGL -L/usr/X11R6/lib -lX11 -lm ../glut/libglut.a -lz -lm -lcrypt -ldl -lpthread -lnetcdf -lvolume_io -lminc -lvnl_algo -lvnl

[Freesurfer] Download source code from repository

Hi Freesurfers, I'm trying to download the FreeSurfer's source code from de repository using: cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev and I obtain this message: cvs checkout: authorization failed: server fsvm.nmr.mgh.harvard.edu rejected access

Re: [Freesurfer] recommende pc and cuda

, please contact the sender and properly dispose of the e-mail. -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html

Re: [Freesurfer] new GPU binaries

contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus

[Freesurfer] recon-all using cuda

] ff60-ffe0 ---p 00:00 0 [vdso] I attached the output log of the execution. Any idea will be apreciated! Thank you in advance!! -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax

[Freesurfer] Missing structures lh.aparc.stats

Dear FS experts, We are using the 4.3.1 version of FreeSurfer, and we have noticed that in the lh.aparc.stats/rh.aparc.stats file there are 35 structures calculated and not 36 structures, only corpuscallosum is missing. We have also compared it with an old subject processing (using 4.0.2 version

[Freesurfer] QDEC Multigroupal analysis

in Analyze: command failed: mri_glmfit --y ../path/qdec/qdecUntitled/y.mgh --fsgd ../path/qdec/Untitled/qdec.fsgd dods --glmdir ../path/qdec/Untitled --surf fsaverage lh --label ../path/fsaverage/label/lh.cortex.label Any idea? Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació

[Freesurfer] Fwd: FreeSurfer Error: bits = 0 not supported.

-- Forwarded message -- From: Jordi Delgado jordi...@pic.es Date: 2009/10/30 Subject: FreeSurfer Error: bits = 0 not supported. To: freesurfer@nmr.mgh.harvard.edu Hello*, * My name is Jordi Delgado, I work with FreeSurfer on a cluster of machines. Yesterday I sent some subjects