Hi Anatasia, Thank you for your reply, I'm sorry for responding so later, I have been trying a few different things in order to get tracula to work. I did what you suggested and compiled the bvals and bvecs into one file, in the same order as the images. This got me further, but the trac-all -prep step is still not completing without error. The lastest problem I can't get past is this:
"WARNING!!!! Multiple image files detected: /users/marchaut/Documents/myprojects/R01/TESTS/TEST1/dmri/dwi.nii /Users/marchaut/Documents/myprojects/R01/TESTS/TEST1/dmri.dwi.nii.gz STOPPING PROGRAM Darwin Marcs-Macbook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016, root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Nov 11 14:46:42 EST 2016" But since I'm combining the AP and PA images files, wouldn't it be necessary for there to be multiple image files? Marissa On Wed, Sep 14, 2016 at 9:54 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > 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 >> >> > _______________________________________________ > 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. > >
_______________________________________________ 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.
