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
You may have to transpose the bval and bvec files.
On 07/29/2013 11:17 AM, 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
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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
freesurfer@nmr.mgh.harvard.edu
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Anastasia Yendiki -
Borsodi Florian -
Chris Watson