Hi Gari - It looks from the output like something has gone wrong with the registration, either diffusion to anatomical, or individual to atlas. If you upload for me here all the directories that tracula has created so far (dmri, dmri.bedpostX, dlabel), I'll take a look. http://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks, 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 ayendiki@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 . 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.