Many thanks Anastasia. So, do you think it would work if I exclude this tracts from the analysis and ask for the remaining ones? thanks again, Gari
On Fri, Sep 27, 2013 at 4:35 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Gari - Just looked at your subject. The bottom of the brain is > truncated in the DWIs. The slices stop in the middle of the angular bundle, > which is why the -prior step failed in that pathway. But I expect there'd > be problems with other tracts that reach that inferior, even if they didn't > fail completely - corticospinal, uncinate, inferior longitudinal fasciculus. > > > a.y > > On Thu, 26 Sep 2013, Garikoitz Lerma-Usabiaga wrote: > > Hi Anastasia, >> I was testing just with one subject and it finished the -prep part with >> error. >> Please find attached the trac-all.log file. >> As this is a test user you will see some other invocations of trac-all. >> The >> last build_stamp starts at row 54.500 aprox. >> (just in case: I started new from de DICOMS and the dcm2nii, and I am >> using >> the resulting .nii, .bvec and .bval, just in case I attached the dmrirc >> too). >> >> Thanks again for your help! >> Gari >> >> >> On Thu, Sep 26, 2013 at 8:01 AM, Anastasia Yendiki >> <ayend...@nmr.mgh.harvard.edu> wrote: >> >> Hi Gari - Yes, that's your best option right now. Sorry for the >> inconvenience. I'll make sure to add the option to have one >> gradient file per subject in the next version. >> >> a.y >> >> On Thu, 26 Sep 2013, Garikoitz Lerma-Usabiaga wrote: >> >> Hi! Thanks for the fast answer. If I do: diff >> id1.bvec id2.bvec >> I can see some clear differences. >> >> I was told that in FSL I should use the bvecs and >> bvals created in dcm2nii >> per subject, so I understand I should do the same >> now? >> Do you think an option would be to script the >> creation of a dmrirc file per >> each subject and then launch as many trac-alls as >> subjects? >> >> Thanks again, >> Gari >> >> On Thursday, September 26, 2013, Anastasia Yendiki >> wrote: >> >> Hi Gari - Sorry, right now the assumption is >> that the gradient >> vectors are the same for all subjects. How >> different are they? >> >> a.y >> >> On Wed, 25 Sep 2013, Garikoitz Lerma-Usabiaga >> wrote: >> >> Hi Anastasia,I am setting up the dmrirc >> file to run >> Tracula. I am using >> Siemens Dicoms, so I did not specify any >> setting for >> bval and bvec, but when >> trac-all -prep starts running it gives >> the following >> error: mv: cannot stat >> >> 'paths.../SubjectID/dmri/dwi_**orig_flip.mghdti.bvecs': >> No such file or >> directory >> >> Ok, so I understand that our problem is >> that we >> don't have MGH Siemens >> Dicom. >> >> So I used dcm2nii to convert it to .nii >> files and >> each conversion gives me a >> SubjectID.bval and SubjectID.bvec. Every >> .bval is >> the same file, but every >> .bvec file is a different one. >> >> I can edit "set dcm_list = " to include >> all the >> newly created .nii files, >> but >> >> My question is: >> - How can I specify every .bvec value >> for every >> subject? In the dmrirc file >> everything I see is a "set bvecfile = " >> option. >> >> Thank you very much, >> Gari >> >> >> >> >> 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<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. >> >> >> >> >>
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