Hi Priti, Thank you for your help. I get through the fslroi successfully by setting the nb0 variable. The lowb.nii.gz looks fine. However, when the process comes to bet, there's another error prompt for lowb.nii.gz.hdr.
fslmaths /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz -Tmean /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz bet /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb_brain.nii.gz -m -f 0.3 Can't open /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz.hdr Linux guasha 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux Kindly help. Phoebe. > 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 > > > -- ___________________________________ 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 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.
