On Tue, 2012-05-29 at 21:24 +0100, Marta Penedo wrote:
> I said this because I tried it both ways. But yes, I already tried
> that.
>
>
> The name's change was only another attempt.
>
>
>
>
> Marta
>
> 2012/5/29 Michael Harms <
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> So, you had a single folder with the complete set of 3640
> DICOMs from
> the run, and ran dcm2nii on that folder? Because you
> initially wrote
> that you ran dcm2nii and MRIconvert on the incomplete folders.
>
> As far as I know, the actual filename of the DICOMs are
> irrelevant, as
> the NIFTI is assembled based on the fields in the DICOMs.
>
> cheers,
> -MH
>
> On Tue, 2012-05-29 at 20:49 +0100, Marta Penedo wrote:
> > I put all dicom images in a unique folder and changed their
> filename
> > to the same filename (in sequence), and then I tried to
> convert images
> > of this folder, but the convertion does 4 nii files such as
> the images
> > are separated.
> >
> >
> > Is that what you asked me?
> >
> > 2012/5/29 Michael Harms <
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> > Hi Marta,
> > Did you try moving all the DICOMs from a given run
> into a
> > single
> > directory PRIOR to converting to NIFTI? You can't
> convert to
> > NIFTI
> > using an incomplete set of DICOMs and expect the
> converter to
> > necessarily handle it cleanly.
> >
> > cheers,
> > -MH
> >
> >
> > On Tue, 2012-05-29 at 19:59 +0100, Marta Penedo
> wrote:
> > > Yes, I see this in mricron too.
> > >
> > >
> > > In this case, the number of slices is 26 and 140
> volumes, of
> > a total
> > > of 3640 images, but this information is not in
> images. I
> > think that
> > > acquisition was not well done, but the files have
> been used.
> > >
> > >
> > >
> > > 2012/5/29 Jesper Andersson <
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> > > Hi again Marta,
> > >
> > > >
> > > >
> > > > First nii file: dim1=64, dim2=64,
> dim3=973
> > > > Second nii file: dim1=64, dim2=64,
> dim3=999
> > > > Third nii file: dim1=64, dim2=64,
> dim3=999
> > > > Fourth nii file: dim1=64, dim2=64,
> dim3=669
> > > >
> > > >
> > > > In all cases, the matrix are 64x64 and
> the dim3
> > > > corresponding at number of images in
> each folder
> > and nii
> > > > file appears such a 3D file.
> > >
> > >
> > > I am a little confused by this. Usually
> dim1 and
> > dim2 are the
> > > matrix size (which seems to be true here
> too) and
> > dim3 are
> > > number of slices (which it is clearly not
> here).
> > What do you
> > > see if you open one of those nifti files
> in fslview?
> > Do you
> > > get a bunch of brains stacked on top of
> each other?
> > >
> > >
> > > Jesper
> > >
> > >
> > >
> > > >
> > > > 2012/5/29 Jesper Andersson
> <
[log in to unmask]>
> > > > Chose one of the cases that
> doesn't work
> > and type
> > > >
> > > >
> > > > fslhd my_nifti | grep dim
> > > >
> > > >
> > > > for each of your nifti files and
> check the
> > values of
> > > > dim1 to dim3
> > > >
> > > >
> > > > Jesper
> > > >
> > > > On 29 May 2012, at 13:05, Marta
> Penedo
> > wrote:
> > > >
> > > > > The command that I used was:
> fslmerge -t
> > FFfmri7
> > > > > F*
> > > > >
> > > > >
> > > > > I think that the command is
> correctly.
> > The problem
> > > > > is that images are grouped, in
> same
> > cases, in 4
> > > > > folders (one with 976, 2
> folders with
> > 999 images
> > > > > and other folder with 627) and
> in other
> > cases in 2
> > > > > folders (one with 984 and
> other with
> > 617). The
> > > > > different information between
> images of
> > each
> > > > > folders are in
> SeriesInstanceUID, Series
> > Number,
> > > > > Instance Number, Image
> Position Patient
> > and Slice
> > > > > Location.
> > > > >
> > > > >
> > > > > I tried to merge the two
> folders with
> > 999 images,
> > > > > for experience, and the
> warning
> > disappear. But I
> > > > > have to merge all of them.
> > > > >
> > > > >
> > > > > Is There any way to change the
> > information without
> > > > > interfering with images?
> > > > >
> > > > > 2012/5/29 Jesper Andersson
> > <
[log in to unmask]>
> > > > > Dear Marta,
> > > > >
> > > > >
> > > > > > I tried to convert
> dicom
> > images,
> > > > > acquired from 1.5T GE
> CVi/NVi,
> > to NIfTI.
> > > > > This device allows
> only acquire
> > 999 images
> > > > > at a time, but the
> complete
> > sequence have
> > > > > 3640 images. So,
> software put
> > each group
> > > > > of images in different
> folders,
> > such as
> > > > > "RTIP_6" and
> "RTIP_26".
> > > > > >
> > > > > > I tried to convert
> and merge
> > all images
> > > > > using dcm2nii and
> MRIConvert,
> > but this
> > > > > softwares shows me one
> file .nii
> > for each
> > > > > folder. Then, I tried
> to merge
> > all
> > > > > files .nii obtained
> using
> > fslmerge but the
> > > > > command shows me this
> warning:
> > > > > >
> > > > > > Error in size-match
> along
> > non-
> > > > > concatenated
> dimension.
> > > > >
> > > > >
> > > > > If you have run
> fslmerge
> > correctly this
> > > > > would imply that you
> have
> > different image
> > > > > sizes for the
> different "sub
> > series",
> > > > > which sounds very
> strange. If
> > that is the
> > > > > case you should look
> into the
> > reason for
> > > > > that.
> > > > >
> > > > > Can you send us the
> exact
> > fslmerge command
> > > > > you used?
> > > > >
> > > > > Jesper
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> > >
> > >
> >
> >
> >
>
>
>