[Freesurfer] SOLVED? recon on all subjects error: on "CA Reg Inv" but "CA Reg" fails cause "CUDA Error in file '../include/ctfactory.hpp' on line 76 : out of memory."
Hi.
only to notify that witout -use_gpu it worked :)
Riccardo
- Messaggio inoltrato da r.nava...@itab.unich.it -
Data: Sat, 20 Jul 2013 11:59:47 +0200
Da: r.nava...@itab.unich.it
Oggetto: recon on all subjects error: on "CA Reg Inv" but "CA Reg"
fails cause "CUDA Error in file '../include/ctfactory.hpp' on line 76
: out of memory."
A: freesurfer@nmr.mgh.harvard.edu
Hi list,
I have seven subject named 101 to 107 with a couple of T1 each one.
I ran
for i in $(seq 101 107) ; do \
recon-all \
-i DATA/WHOLE/10${i}_1_T1.nii.gz \
-i DATA/WHOLE/10${i}_2_T1.nii.gz \
-subject $ii -all -use_gpu & done
but I got error on "#@# CA Reg Inv ..." because "#@# CA Reg" fails
(cuda out of memory).
An extract of recon-all-status.log and recon-all.log:
###
#--
#@# CA Reg Sat Jul 20 03:24:55 CEST 2013
/FS/101/mri
mri_ca_register_cuda -nobigventricles -T transforms/talairach.lta
-align-after -mask brainmask.mgz norm.mgz
/DATA/grid/share/freesurfer53/average/RB_all_2008-03-26.gca
transforms/talairach.m3z
nvcc
...
CUDA Error in file '../include/ctfactory.hpp' on line 76 : out of memory.
...
Abort
ERROR: mri_ca_register with non-zero status 134
but continuing despite the error
#--
#@# CA Reg Inv Sat Jul 20 11:05:26 CEST 2013
/FS/101/mri
mri_ca_register -invert-and-save transforms/talairach.m3z
Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z
ERROR: cannot find or read transforms/talairach.m3z
ERROR: mri_ca_register with non-zero status 0
Linux FSLSERVER02 2.6.32-48-generic #110-Ubuntu SMP Fri May 31
18:32:53 UTC 2013 x86_64 GNU/Linux
recon-all -s 101 exited with ERRORS at Sat Jul 20 11:05:28 CEST 2013
###
bugr:
###
FREESURFER_HOME: /DATA/grid/share/freesurfer53
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Debian version: squeeze/sid
Kernel info: Linux 2.6.32-48-generic x86_64
###
full files attached. Please help! Thank you.
Now I'm going to try without -use_gpu options...
Riccardo
- Fine messaggio inoltrato. -
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[Freesurfer] [Tracula] ERRORS in Tracula Preprocessing
Hi Vivian, did you solve your issue? I got (almost) same error, not "Too many )'s." but "ERROR: flag ; unrecognized" and the final "trac-preproc exited with ERRORS ... IsRunningFile: Undefined variable." Thank you. Riccardo [Freesurfer] ERRORS in Tracula Preprocessing Vivian Roger Steiger Sat, 25 May 2013 03:43:14 -0700 Dear Freesurfer experts I am trying to process the data of a Longitudinal DTI Study with 2 Timepoints I have encountered the following error while running the tracula pre-processing: freesurfer-Darwin-lion-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/ FSFAST_HOME /Applications/freesurfer//fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Users/zenso/Subjects/structural_23VPs FSL_DIR /Applications/fsl MNI_DIR /Applications/freesurfer//mni FSL_DIR /Applications/fsl [iMac:Subjects] zenso% trac-all -prep -c /Users/zenso/Subjects/Tracula/dmrirc.long.sad Too many )'s. INFO: SUBJECTS_DIR is /Users/zenso/Subjects/structural_23VPs INFO: Diffusion root is /Users/zenso/Subjects/Tracula Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Users/zenso/Subjects/Tracula/1Pre_VP3/scripts/dmrirc.local -log /Users/zenso/Subjects/Tracula/1Pre_VP3/scripts/trac-all.log -cmd /Users/zenso/Subjects/Tracula/2Post_VP3/scripts/trac-all.log -cmd /Users/zenso/Subjects/Tracula/2Post_VP3/scripts/trac-all.cmd ; trac-preproc -c /Users/zenso/Subjects/Tracula/VP3_Base/scripts/dmrirc.local -log /Users/zenso/Subjects/Tracula/VP3_Base/scripts/trac-all.log -cmd /Users/zenso/UZH/MSc/FS2013/Psychologie/Masterarbeit/Subjects/Tracula/VP3_Base/scripts/trac-all.cmd ; ERROR: flag ; unrecognized -c /Users/zenso/Subjects/Tracula/1Pre_VP3/scripts/dmrirc.local -log /Users/zenso/Subjects/Tracula/1Pre_VP3/scripts/trac-all.log -cmd /Users/zenso/Subjects/Tracula/1Pre_VP3/scripts/trac-all.cmd ; trac-preproc -c /Users/zenso/Subjects/Tracula/2Post_VP3/scripts/dmrirc.local -log /Users/zenso/Subjects/Tracula/2Post_VP3/scripts/trac-all.log -cmd /Users/zenso/Subjects/Tracula/2Post_VP3/scripts/trac-all.cmd ; trac-preproc -c /Users/zenso/Subjects/Tracula/VP3_Base/scripts/dmrirc.local -log /Users/zenso/Subjects/Tracula/VP3_Base/scripts/trac-all.log -cmd /Users/zenso/Subjects/Tracula/VP3_Base/scripts/trac-all.cmd ; Darwin iMac.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Sa 25 Mai 2013 11:28:57 CEST IsRunningFile: Undefined variable. Please let me know if this is not enough information. Thanks a lot for your support. Vivian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error 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.
Re: [Freesurfer] possible to use multiple B value DTI in Tracula?
Hi, did you try specifying values in bvals file? (set bvalfile=... ) Riccardo Salil Soman ha scritto: > Hi, > > I was wondering - is it possible to use DTI data of multiple B values in > Tracula (acquired during the same session and same TE)? > > Best wishes, > > Sal > > Salil Soman, MD, MS > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error 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.
[Freesurfer] [Tracula] Run trac-all with 2 time points for DTI scan but 1 time point for T1 scan. How to?
Hi, I need to run trac-all on subjects scanned first time in T1 and DTI, second time DTI only. How to configure dmrirc? I've seen long.example but it seems that it require T1 second run too. Tnx, Riccardo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error 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.
[Freesurfer] mgz to nii.gz... T1 and ROIs. Is there a way to do (5) from command line?
Hi FS expert. I need to port my T1 and a couple of ROIs from mgz to nii.gz. The same for many subjects. The issue's about dimensions. When I use fslview, it respond me that "All overlays must have same dimensions as the base image!". Indeed T1's 256x256x256 with voxel sizee 1mm3, ROIs are differents dimensions and 0.5mm3 voxel size. To work now I use this pipeline: ( command line :) ) 1) mri_convert ---> nii 2) gzip ---> nii.gz 3) fslmaths t1 -sub t1 t1_zero 4) mricron t1_zero -l 0 -h 100 -o roi1.nii.gz ( GUI only :( ) 5) (from mricron) save as nifti roi1_ok.nii.gz Is there a way to do (5) from command line? Thanx Riccardo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error 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.
Re: [Freesurfer] mgz to nii.gz... T1 and ROIs. Is there a way to do (5) from command line?
Hi Bruce, (4) open in mricon t1_zero and use roi1 as overlay...anyway -rl option is what I was looking for! :D Thank you New pipiline is: (command line:) (a) mri_convert t1.mgz t1.nii.gz (b) for roiX -> mri_convert roiX.mgz roiX.nii.gz -rl t1.mgz (it works with t1.nii.gz also ) Thank you so much! Riccardo Quoting Bruce Fischl : > Hi Riccardo, > > I don't understand what 4) is. A couple of points: > > 1. if you give mri_convert .nii.gz as an output extension it will do the > gzipping for you. > > 2. If you give mri_convert the flag -rl it will reslice > the input volume "like" the template. > > not sure if that solves your problem. Can you describe in more detail what > you are trying to accomplish? > > cheers, > Bruce > > > On Tue, 19 Jul 2011, > r.nava...@itab.unich.it wrote: > >> Hi FS expert. >> I need to port my T1 and a couple of ROIs from mgz to nii.gz. The same >> for many subjects. The issue's about dimensions. When I use fslview, >> it respond me that "All overlays must have same dimensions as the base >> image!". Indeed T1's 256x256x256 with voxel sizee 1mm3, ROIs are >> differents dimensions and 0.5mm3 voxel size. >> To work now I use this pipeline: >> >> ( command line :) ) >> 1) mri_convert ---> nii >> 2) gzip ---> nii.gz >> 3) fslmaths t1 -sub t1 t1_zero >> 4) mricron t1_zero -l 0 -h 100 -o roi1.nii.gz >> ( GUI only :( ) >> 5) (from mricron) save as nifti roi1_ok.nii.gz >> >> Is there a way to do (5) from command line? >> >> Thanx >> >> Riccardo >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error 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. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
