Absolutely perfect!
Cheers, M
2009/2/19 Rajeet Saluja <[log in to unmask]>
> Hi Markus,
>
> Thanks for your quick reply. But I'm not sure I quite understood the
> procedure. Starting from the beginning, is this what should be done:
>
> -run eddy-current correction on the patient_diff.nii.gz file producing
> data.nii.gz
> -run bet on the data.nii.gz file producing data_brain.nii.gz and
> data_brain_mask.nii.gz
> -rename data_brain_mask.nii.gz to nodif_brain_mask.nii.gz
> -run DTIFIT on the directory
> -run bedpostX etc.
>
> Does that sound right?
>
> Rajeet
>
>
> On Thu, 19 Feb 2009 19:03:31 +0100, Markus Gschwind
> <[log in to unmask]> wrote:
>
> >Hi Rajeet!
> >
> >This time the problem seems resolvable ,-)
> >
> >it says **data dimensions do not match mask dimensions**
> >
> >and it shows:
> >
> >/home/rajeet/Desktop/new/data
> >data_type INT16
> >dim1 128
> >dim2 128
> >dim3 63
> >dim4 100
> >[...]
> >
> >and
> >/home/rajeet/Desktop/new/nodif_brain_mask
> >data_type FLOAT32
> >dim1 176
> >dim2 256
> >dim3 256
> >dim4 1
> >[...]
> >
> >It looks as you took the nodif_brain_mask form a T1.
> >You should take it form the dti data also.
> >That is just run
> >
> >bet yourDTI_data yourDTI_data_brain -m
> >
> >(the -m mode gives you the nodif_brain_mask)
> >
> >I think having dont this: Enjoy!
> >
> >Markus
> >
> >
> >2009/2/19 Rajeet Saluja <[log in to unmask]>
> >
> >> Hi,
> >>
> >> So after about a week of loading and re-loading FSL, I think I finally
> have
> >> it installed correctly...Only problem is I'm still having a problem with
> >> FDT-bedpostx step.
> >>
> >> When I run FEEDS, everything seems to pass including FDT. Doing "echo
> >> $FSLDIR" yeilds "/usr/share/fsl", but when I try it out I get the
> following
> >> issues: After running DTIFIT, everything seems to be okay except that
> at
> >> the very end, I get the following error message in a separate window,
> while
> >> in the terminal all it says is "Done"
> >>
> >> window name "prompt" already exists in parent
> >> window name "prompt" already exists in parent
> >> while executing
> >> "toplevel .prompt -borderwidth 5"
> >> (procedure "MxPause" line 4)
> >> invoked from within
> >> "MxPause " Done! " "
> >> (procedure "fdt:apply" line 317)
> >> invoked from within
> >> "fdt:apply .fdt keep"
> >> invoked from within
> >> ".fdt.apply invoke"
> >> ("uplevel" body line 1)
> >> invoked from within
> >> "uplevel #0 [list $w invoke]"
> >> (procedure "tk::ButtonUp" line 22)
> >> invoked from within
> >> "tk::ButtonUp .fdt.apply"
> >> (command bound to event)
> >>
> >>
> >> Also, if I try running bedpostx_datacheck, I get the following info:
> >>
> >> /home/rajeet/Desktop/new/data
> >> data_type INT16
> >> dim1 128
> >> dim2 128
> >> dim3 63
> >> dim4 100
> >> datatype 4
> >> pixdim1 2.0000000000
> >> pixdim2 2.0000000000
> >> pixdim3 2.0000000000
> >> pixdim4 1.0000000000
> >> cal_max 0.0000
> >> cal_min 0.0000
> >> file_type NIFTI-1+
> >>
> >> /home/rajeet/Desktop/new/nodif_brain_mask
> >> data_type FLOAT32
> >> dim1 176
> >> dim2 256
> >> dim3 256
> >> dim4 1
> >> datatype 16
> >> pixdim1 1.0000000000
> >> pixdim2 1.0000000000
> >> pixdim3 1.0000000000
> >> pixdim4 1.0000000000
> >> cal_max 0.0000
> >> cal_min 0.0000
> >> file_type NIFTI-1+
> >>
> >> num lines in /home/rajeet/Desktop/new/bvals
> >> 1
> >> num words in /home/rajeet/Desktop/new/bvals
> >> 100
> >> num lines in /home/rajeet/Desktop/new/bvecs
> >> 3
> >> num words in /home/rajeet/Desktop/new/bvecs
> >> 300
> >> data dimensions do not match mask dimensions
> >>
> >>
> >> Now, I understood that you don't necessarily need to run DTIFIT in order
> to
> >> go through the FDT procedure, but running the bedpostx_datacheck prior
> to
> >> the DTIFIT stage yielded the exact same message. Any ideas? Could this
> >> mean that the bvals and bvecs files are no good? Thanks in advance...
> >>
> >> Rajeet
> >>
> >
> >
> >
> >--
> >Dr. med. Markus Gschwind, M.D.
> >Laboratory for Neurology and Imaging of Cognition
> >Dept of Neurosciences
> >University Medical Center (CMU)
> >1 Michel-Servet - 1211 GENEVA - CH
> >
> >Tel 0041 (0) 22 379 5324
> >Fax 0041 (0) 22 379 5402
> >email: [log in to unmask]
> >http://labnic.unige.ch
> >
>
--
Dr. med. Markus Gschwind, M.D.
Laboratory for Neurology and Imaging of Cognition
Dept of Neurosciences
University Medical Center (CMU)
1 Michel-Servet - 1211 GENEVA - CH
Tel 0041 (0) 22 379 5324
Fax 0041 (0) 22 379 5402
email: [log in to unmask]
http://labnic.unige.ch
