I looked at the mri_convert code, and it appears that we are setting all
those fields (ie, dim, pixdim, and bitpix). If there is only a single
frame, I do assign 1 to pixdim[4] (and then set the dim to 4). Is this
not a reasonable thing to do?
Mark: if you can tell me which fields must be set for FSL compatibility,
I can make sure that mri_convert sets them.
doug
Mark Jenkinson wrote:
>
> Hi All,
>
> The problem with this data set would not have been that it was 8 bit.
> Flirt runs perfectly well on 8 bit data.
> There would have been some other problem associated with the
> header which stopped flirt reading the data in correctly.
> Possibly the dim0 and pixdim0 fields, or maybe bitpix.
> In general, because avwmaths uses a different input routine (very simple)
> it is able to cope with these problems and write out corrected files.
>
> It should have all worked fine if you'd kept the image at 8 bit too.
>
> All the best,
> Mark
>
> On Friday, November 8, 2002, at 10:46 AM, Darren Weber wrote:
>
> > I wonder also whether mri_convert should assign 1 to pixdim4; check the
> > differences in header values between the mri_convert and avwmaths outputs.
> > I
> > suspect that this will be one of the differences. Why would flirt not
> > work
> > with 8bit data?
> >
> > Darren
> >
> >
> > ----- Original Message -----
> > From: "Doug Greve" <[log in to unmask]>
> > To: <[log in to unmask]>
> > Sent: Friday, November 08, 2002 6:56 AM
> > Subject: Re: Freesurfer & FSL - Segmentation fault with FLIRT
> >
> >
> >> Yes, mri_convert will not change the precision, and since CORs are 8 bit
> >> ...
> >>
> >> doug
> >>
> >> Tim Souza wrote:
> >>>
> >>> Steve,
> >>>
> >>> Thanks, That worked, I guess the T1 analyze needed to be 16 bit signed
> > integer!
> >>>
> >>> Doug,
> >>>
> >>> Here is the mri_convert command line I used, and the contents of the
> > COR-.info file:
> >>> mri_convert ${SUBJECTS_DIR}/surfer/mri/T1
> > /home/jnsb/surfer_7.02/EMy/briks/
> >>> struc_fs_T1.img
> >>>
> >>> Thanks,
> >>> Tim Souza
> >>>
> >>> imnr0 1
> >>> imnr1 256
> >>> ptype 2
> >>> x 256
> >>> y 256
> >>> fov 0.256
> >>> thick 0.001
> >>> psiz 0.001
> >>> locatn 0
> >>> strtx -0.128
> >>> endx 0.128
> >>> strty -0.128
> >>> endy 0.128
> >>> strtz -0.128
> >>> endz 0.128
> >>> tr 0.000000
> >>> te 0.000000
> >>> ti 0.000000
> >>> ras_good_flag 0
> >>> x_ras -1.000000 0.000000 0.000000
> >>> y_ras 0.000000 0.000000 -1.000000
> >>> z_ras 0.000000 1.000000 0.000000
> >>> c_ras 0.000000 0.000000 0.000000
> >>
> >> --
> >> Douglas N. Greve, Ph.D.
> >> MGH-NMR Center
> >> [log in to unmask]
> >> Phone Number: 617-724-2358
> >> Fax: 617-726-7422
> >>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[log in to unmask]
Phone Number: 617-724-2358
Fax: 617-726-7422
|