Hi Phoebe, The fslroi part extracts all the low-b images from the 4D diffusion data and creates an average low-b mask.
fslroi <input> <output> <tmin> <tsize> <tsize> is the number of 3D low-b volumes to be extracted from the 4D diffusion volume. For some reason tracula is unable to read the no. of low-b images from your dicom header (Is this an MGH acquisition?). If you know the number of low-b volumes you can specify that in the configuration file using the following command: set nb0 = *No. of low-b images* Once you set that value it should not throw that error. From what you ran in the commandline, I assume that in your dti acquisition 0 through 25 are low-b volumes. Creating the low-b image mask is the last step in the first stepwise directive of tracula (-corr). You can go through the rest of the steps by specifying any or all of the stepwise directives: Ex: trac-all -intra -inter -masks -tensor -prior -c ./scripts/dmrirc_single_subject Please let us know if you have any questions or problems running the same. Thanks, Priti > Hi, > > I do the pre-processing with the following command: > > trac-all -prep -c ./scripts/dmrirc_single_subject > > THe process exits with error when it comes to fslroi (attached pls find > the log file). I try to re-run the fslroi command as follow: > > fslroi > /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi.nii. > gz > /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz > > 0 25 > > It works and the lowb.nii.gz looks normal. In case if I have the same > problem with another dataset, how can I incorporate the number of frames > (25) in the trac-all command for the fslroi? Can I continue the remaining > procedures of trac-all from this point? > > Thank you. > > Phoebe. > -- > ___________________________________ > Phoebe Suk-tak Chan, Ph.D. > Athinoula A. Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Bldg. 149, 13th St., mailcode 149-2301 > Charlestown, MA 02129 > pho...@nmr.mgh.harvard.edu > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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.
