Hi Anastasia I ran the command you sent me and it runs without any errors. I also attached the command line for you.
Furthermore i ran data with 12 diffusion directions and i keep getting the same kind of problems. sincerely Florian >>> Anastasia Yendiki 02.08.13 19.59 Uhr >>> Hi Florian - Can you please run this command directly on the command line and see if there are any errors? flip4fsl /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz Thanks, a.y On Fri, 2 Aug 2013, Borsodi Florian wrote: > Hi Anastasia > > Thank you for your answer. > > Yes, those files exist. > I also extracted the bvec an bval files with anotther software then dcm2nii > and i keep getting the same kind of error. > Also, about the 6 diffusion direction, those data i sent you, are just > testdata for running tracula. > > sincerely > Florian > > >>> Anastasia Yendiki 02.08.13 0.41 Uhr >>> > > Hi Florian - Do these files exist? > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvecs > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvals > > > The format of the bvecs and bvals that you sent seems fine, but (and this > has nothing to do with the error you're getting) I have to warn you that > you may not be able to get good results running probabilistic tractography > on this data. It looks like you're acquiring the same 6 diffusion > directions, repeated 8 times. Six directions is the absolute minimum for > reconstructing the tensor model, but will probably not be sufficient for > the crossing fiber model that bedpostx reconstructs (and is used by > tracula). Your scan time is better spent acquiring 48 different > directions, rather than the same 6 directions 8 times. > > a.y > > On Mon, 29 Jul 2013, Borsodi Florian wrote: > > > Hello, > > > > I have been trying to run tracula on my data and i keep getting the same > > kind of error repeatedly. > > For my imput I am using dicoms from a Siemens scanner with a stadard > > diffusion protocol. However, tracula cannot read the bvec and bval data > out > > of the dicom header. Therefore, I implemented bvec and bval files into the > > config file. > > After doing so, I got the error which says that tracula cannot find the > > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. > > I have tried many options, but still cannot find a solution. > > I am hoping to get some troubleshooting help. > > > > I have atteched my log- and config- files, as well as my bvec and bval > > files. > > To uphold patient confidentiality, I have encode the name patient's data > as > > "AAAAAA". > > > > I believe the problems are the bvec and bval files or their structures. > The > > log-file lete me assume this, especially the lines 202 - 205, 264 - 268 > and > > 1480 - 1484. > > > > Thank you in advance for your help, and your speedy response. > > > > With kind regards, > > > > Florian Borsodi > > Department of Neurology > > Medical University of Graz > > > > > > > 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
pu02neu003:/data/physics/florian/nii> flip4fsl /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 10.5469 fslswapdim /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz x -y z /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz pu02neu003:/data/physics/florian/nii>
_______________________________________________ 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.
