Re: [Freesurfer] bbr problem run
Hi Sal - Had you ever tried running this in 5.1? Just trying to figure out if it's 5.2-specific. Thanks, a.y On Thu, 28 Mar 2013, Salil Soman 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_end 1_dil.nii.$ niiRead(): error opening file/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end 1_dil.nii.gz ERROR: Could not read/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end 1_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 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
Re: [Freesurfer] bbr problem run
Hi Sal - Would it be possible for you to run the bbregister command that fails (you can find the command line in trac-all.log) using both the 5.1 and 5.2 version of bbregister and see if one of them works on your system? a.y On Fri, 29 Mar 2013, Salil Soman wrote: Hi Anastasia, Because I did not have a compatible older version of fsl on the SGE, I was not able to run tracula with 5.1. Thank you, Sal On Fri, Mar 29, 2013 at 8:32 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Sal - Had you ever tried running this in 5.1? Just trying to figure out if it's 5.2-specific. Thanks, a.y On Thu, 28 Mar 2013, Salil Soman 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 volumefrom/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr _end 1_dil.nii.$ niiRead(): error openingfile/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr _end 1_dil.nii.gz ERROR: Could notread/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr _end 1_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 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?
Re: [Freesurfer] bbr problem run
There was a problem with bbregister running on the new CentOS 6 machines. I've attached a new version that should work. doug On 03/29/2013 11:41 AM, Anastasia Yendiki wrote: Hi Sal - Would it be possible for you to run the bbregister command that fails (you can find the command line in trac-all.log) using both the 5.1 and 5.2 version of bbregister and see if one of them works on your system? a.y On Fri, 29 Mar 2013, Salil Soman wrote: Hi Anastasia, Because I did not have a compatible older version of fsl on the SGE, I was not able to run tracula with 5.1. Thank you, Sal On Fri, Mar 29, 2013 at 8:32 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Sal - Had you ever tried running this in 5.1? Just trying to figure out if it's 5.2-specific. Thanks, a.y On Thu, 28 Mar 2013, Salil Soman 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 volumefrom/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr _end 1_dil.nii.$ niiRead(): error openingfile/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr _end 1_dil.nii.gz ERROR: Could notread/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr _end 1_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 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,
Re: [Freesurfer] bbr problem run
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#** Outputdirectoriesandfileshttp://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
