Here are the errors from the trac-all.log file I sent earlier: mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/Test_FS/mri/ERROR: /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/Test_FS/mri/ERROR: /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister.nii ** ERROR (nifti_image_read): failed to find header file for '/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister ERROR: Could not open image /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister ** ERROR (nifti_image_read): failed to find header file for '/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister ERROR: Could not open image /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister ERROR: cannot open /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/reg.init.dat.fsl.mat ERROR: reading /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/anatorig2diff.bbr.dat Image Exception : #22 :: ERROR: Could not open image /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/diff/White-Matter++.flt ERROR: Could not open /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/mni2diff.bbr.mat ERROR: Could not read /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz ERROR: Could not read /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
On Thu, Mar 28, 2013 at 4:22 PM, Salil Soman <salso...@stanford.edu> wrote: > Thank you for your response. > > I tried re-running Tracula using bbr in a subject I had successfully run > using flt. trac-all prep and bedp worked without an error. Bedpostx sent me > an email confirming bedpost completed without problem. However, when I try > to run trac-all paths, I get the following error: > > Loading atlas reference volume from > /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.$ > niiRead(): error opening file > /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz > ERROR: Could not read > /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz > > recon-all did finish without error. > > Best wishes, > > -S > > > On Thu, Mar 28, 2013 at 8:43 AM, Anastasia Yendiki < > ayend...@nmr.mgh.harvard.edu> wrote: > >> >> Hi Sal, >> >> 1. I have no experience with the sun grid engine, perhaps someone else on >> the list can help with that. >> >> 2. The -bedp step needs the outputs from the -corr and -masks steps. The >> -path step needs the outputs from the -bedp step. The output files from >> each part are listed here: >> http://www.freesurfer.net/**fswiki/trac-all#** >> Outputdirectoriesandfiles<http://www.freesurfer.net/fswiki/trac-all#Outputdirectoriesandfiles> >> >> 3. Checking the aparc+aseg should be enough for tracula purposes as well, >> since that's the freesurfer output that tracula uses. Keep in mind that >> DWI resolution is usually lower than T1 resolution, so tiny changes in >> the aparc+aseg might not affect tracula at all. >> >> 4. Yes, I do recommend using bbregister. It's not surprising that it would >> give better results since it uses the additional information of the >> surfaces. If I remember correctly, Doug didn't manage to replicate your >> bbregister error, right? I'd check if you get the same error with the >> 5.1 version of bbregister. >> >> Hope this helps, >> a.y >> >> >> On Wed, 27 Mar 2013, Salil Soman wrote: >> >> Hi, >>> I have been able to implement FS 5.2 on our Sun Grid Engine Cluster >>> using the CentOS 6 >>> distribution. After modifying the fsl_sub_mgh file to work with out >>> cluster queue >>> names and to modify the email notifications, I am able to run the entire >>> processing >>> pipeline using FLT. (Everytime I try bbr I get errors. I had email doug >>> about this but >>> have not heard any response). >>> >>> I am submitting the jobs to the cluster as follows >>> >>> recon-all -i ./*.nii -s WCA_0202_T1_FS -nuintensitycor-3T -nocanorm >>> -openmp 50 >>> -hippo-subfields -all >>> trac-all -prep -no-isrunning -c /mnt/glusterfs/salsoman/SRC/** >>> WCA_0202_T1/DTI/dmrirc >>> trac-all -bedp -no-isrunning -c /mnt/glusterfs/salsoman/SRC/** >>> WCA_0202_T1/DTI/dmrirc >>> trac-all -path -no-isrunning -c /mnt/glusterfs/salsoman/SRC/** >>> WCA_0202_T1/DTI/dmrirc >>> >>> There are a few issues I am trying to sort out: >>> >>> 1) how should one conifigure the openmp flag for the Sun Grid Engine? >>> the flag I used >>> did not change processing time, and each subject is still taking ~24 hrs? >>> >>> 2) once the script starts bedpost, bedpost has controller code which >>> paralelizes all >>> of the slices (which has been great going from 12 hrs of processing to >>> 1.5 hrs). >>> However, my original script goes on to execute trace-all -path ... >>> before bepost is >>> done, generating errors. I have gotten around this by running the >>> trace-all -path >>> command again after bedpost sends me an email confirming completion. Is >>> there a way to >>> more cleanly do this (some kind of hold command I can do based on output >>> from >>> bedpost)? >>> >>> 3) In your experience, how important is quality control of freesurfer on >>> tracula >>> results? We have come to the compromise for freesurfer output to >>> manually check the >>> segmentation of aparc+aseg.mgz using free view, only correcting and >>> rerunning steps of >>> freesurfer when there are specific structures we want the volumes of (eg >>> hippocampus). >>> >>> 4) have you found a significant benefit of bbr over flt? If so, any >>> suggestions on >>> things I may need to check to get bbr to work (given flt works)? >>> >>> Best wishes, >>> >>> Sal >>> >>> >>> >>> >>> >>> >>> >> >> 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<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 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.
