Hi Anastasia, Here are the bvec and bval files you asked me about.
Sincerely, Florian >>> Anastasia Yendiki 18.08.13 22.52 Uhr >>> Hi Florian - Can you please also attach the bvecs/bvals files from the dmri directory? Thanks, a.y On Sun, 18 Aug 2013, Borsodi Florian wrote: > Hi Anastasia, > > Thanks for your help. I renamed the directories and reran trac-all. It > worked for the moment. > However, then I got another error: "bvecs and bvals don't have the same > number of entries." > I don't know why, because they actually have the same number of entries. > > I attached the logfile so that you may see what is going on. The error > occours at line 1463. > > Thank you in advance for your help. > > Sincerely, > Florian > > > >>> Anastasia Yendiki 15.08.13 18.01 Uhr >>> > > Hi Florian - I see what's going on. Can you please rename the directory > /data/physics/florian/nii into something that doesn't include "nii", and > rerun? Because "nii" is a file extension, this confuses some of the > scripts. > > Thanks, > a.y > > On Thu, 15 Aug 2013, Borsodi Florian wrote: > > > 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.bvec > s > > > > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bval > s > > > > > > > > > > > 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 > > > > > >
bvecs
Description: Binary data
bvals
Description: Binary data
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