Hi Marissa - You have to specify as many b-values and gradient vectors as there are volumes in your DWI data file. This means that, if you combine the AP and PA volumes, you also have to concatenate the bvals from the two into one file, and do the same with the bvecs. Make sure that the order in which the AP and PA volumes are combined is the same as the order in which the corresponding bvals and bvecs are combined.
Hope this helps, a.y On Wed, 14 Sep 2016, Marissa Pifer wrote:
Hello freesurfer experts, I am trying to run tracula on subjects that have separate AP/PA direction DTI files. We combined the data into one using topup, and would now like to run tracula on the subject. The problem is, the combined file doesn't have a bvals/bvecs file. When I try to use the original bval/bvec files, I get the error that the bvals and bvecs don't match up. I have tried combining the files into one, and then running a dicom to nifty conversion to get a combined bvals/bvecs output, but that results again in two separate bvals/bvecs files as well. I then tried just have two specified bvals and bvecs. This did not give us an error message, but trac-prep took only a few seconds and did not complete the steps it was supposed to to create the directories for trac-bedp to complete. I have attached our dmrirc.example file and the log for the trac-prep step for your reference. The questions then are; is there a way to get one bvals/bvecs file that has the correct parameters for the AP and PA combined file. Or, if not, is there a way to run tracula with two sets of bvals and bvecs (one for the AP and one for the PA direction)? In case you need this information, the process is being run with freesurfer 5.3, on a macbook pro OS X version 10.9.5. Thank you in advance, Marissa
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