23 Aug
2012
23 Aug
'12
4:01 p.m.
This probably means that bedpostx didn't process all the slices in your DWIs. Someone else reported something like that recently, not sure what may be causing it, but since it's independent of trac-all, I'd check on the FSL list archives.
On Thu, 23 Aug 2012, Natalia Sánchez wrote:
they are not. The z dimension of the bedpost images is 52 (from FSL) and for the dmri FS images it is 72.
-- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering & Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611
On Thu, Aug 23, 2012 at 2:08 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Can you please check that the x-y-z dimensions of the bedpostx output files are the same as the dimensions of the DWIs? On Thu, 23 Aug 2012, Natalia Sánchez wrote: Thanks for your response!Attached are the requested files The error occurs here are shown on my terminal: Loading b-valuesfrom/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmr i/bv als Loading gradientsfrom/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmr i/bv ecs Segmentation fault Darwin dhcp-165-124-9-141.phystherapy.northwestern.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering & Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Thu, Aug 23, 2012 at 1:48 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Natalia - I'd need to see at which point in the processing the error occurs, since this is a very generic error message. Can you please include your trac-all.log and dmrirc? Thanks, a.y On Thu, 23 Aug 2012, Natalia Sánchez wrote: Hi Anastasia!I finally made tracula -prep work without errors, using the 1mm T1 MNI template (i tried using the 2mm one but the vertices for registering white matter came out as NaN). However, I was not able to get bedpost to work. After looking at other posts on the FS archive, I think the reason why -bedp does not work is because of my FSL version. I tried running bedpost on FSL and then just copying those files on my dmri.bedpost folder and using those files for reconstructing the white matter tracts. However, I get a "Segmentation Fault" error. Do you have any idea what this error may mean? My dpath folder is empty and I my trac-all.log file has no errors related to -path Thanks! -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering & Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Fri, Aug 10, 2012 at 5:05 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Natalia - This is an error that will occur if lowb_brain_mask does not exist. The command that generates lowb_brain_mask is "bet" - can you find that line in the log file and run it directly on the command line and see if you get an error? On a separate note, have you opted to use a DWI mask instead of an anatomical mask by setting usemaskanat = 0? If not, then it may be that it's trying to use the DWI mask b/c it can't find the anatomicals, in which case I'd check if SUBJECTS_DIR has been set properly and a freesurfer recon of the same subject exists there. But this is a separate issue than the DWI mask not being generated. Hope this helps, a.y On Fri, 10 Aug 2012, Natalia Sánchez wrote: The required files were not generated. the error occurs at rh.slft_PP_roi2.flt.nii.gz--bmask/Users/Natalia/Desktop/freesurfer/subject s /Justin/cJD/dlabel/mni/low b_brain _mask.flt.nii.gz--fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/ d mri/mni/dtifit_F A.fl t.nii.gz --ncpts 5 --trunc --debug ERROR: fio_pushd: /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni ERROR: Must specify brain mask volume for output subject does the brain mask have to be input manually in the configuration file, or is this part of the pre-processing? since I set the bet thr to 0.23 in the config file i thought the brain mask was also created during the preprocessing stage. Attached is my log file. I am familiar with FSL but I am using Free surfer since i think automating the entire process, including tracking is a great advantage, but I'm just starting to get the hang of it Thanks! -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering & Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Fri, Aug 10, 2012 at 4:28 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: dtifit_FA.fl t.nii.gz 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.