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-values from/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmri/bv als Loading gradients from/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmri/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/subjects /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.