Hi Phoebe - I don't have permission to access your files, but do you have FSLOUTPUTTYPE set to anything other than nifti by any chance?
a.y On Thu, 14 Jul 2011, pho...@nmr.mgh.harvard.edu wrote: > 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 >> >> >> > > > _______________________________________________ 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.
