Send me one sequence (raw dicoms and analyze image). Do you use any
fiducials (vitamin E)?
Did you use any other converters like vb2img (part of VoxBo)
http://voxbo.org/wiki/index.php/Using_vb2img ?
Thanks,
Mikolaj
On Nov 9, 2007 4:34 PM, Jennifer Bramen <[log in to unmask]> wrote:
> We were using a Seiemens Allegra 3T scanner. The script for dicom to
> analyze was written in house. That being said, we are certain that the
> images are in ASR when converted to Analyze format via our method.
>
> I did try the following and got the correct RPI orientation.
>
> fslswapdim z -x -y
>
> However I got wraparound (f 1/3 for the anterior portion ended up in
> the posterior section of the screen, followed by a gap and the actual
> posterior boundary of the brain) I can send an image if my text does
> not sufficiently describe the problem.
>
> Is there someway to fix this without having to create an identity
> matrix in flirt, edit the .mat file to move the image in the y
> direction? The point of this was to simplify my data path, and this
> would actually do the opposite.
>
> Thanks for your assistance.
>
> Jen
>
>
> On Nov 9, 2007, at 12:54 PM, Mikolaj Pawlak wrote:
>
> > What scanner and dicom>analyze converter you use?
> >
> > On Nov 9, 2007 3:46 PM, Jennifer Bramen <[log in to unmask]>
> > wrote:
> >> Hi Mikolaj,
> >>
> >> First, using fsl view the original image displays an axial image,
> >> oriented A - P, a coronal image oriented S -> I and on the bottom a
> >> sagittal image oriented A - >P and upside down.
> >>
> >> If I use fslswapdim z -x y: I get an axial image, oriented P - >A, a
> >> coronal image with no change and on the bottom a sagittal image
> >> oriented P -> A and upside down.
> >>
> >> Another note, all the orientations in the nifti header are incorrect.
> >> It assumes that the original image is in RPI to start because our
> >> dicom-> analyze -> niftii does not have any useful orientation info to
> >> start, though I do know it starts ASR.
> >>
> >> Thanks for your help
> >>
> >> Jen
> >>
> >>
> >>
> >> On Nov 9, 2007, at 12:20 PM, Mikolaj Pawlak wrote:
> >>
> >>> Hi,
> >>>
> >>> What happens when you use avwswapdim input z -x y output
> >>> or fslswapdim input z -x y output (using current version of FSL)?
> >>>
> >>> Thanks,
> >>>
> >>> Mikolaj
> >>>
> >>> --
> >>> ****************************************
> >>> Mikolaj A. Pawlak, MD PhD
> >>> Neuroradiology Research Division
> >>> Department of Radiology
> >>> University of Pennsylvania
> >>> 3600 Market Street Suite 370
> >>> Philadelphia, PA 19104
> >>> Phone: 215-662-3688
> >>> Fax: 215-615-3681
> >>> mail: [log in to unmask]
> >>>
> >>>
> >>> On Nov 9, 2007 2:37 PM, Jennifer Bramen <[log in to unmask]>
> >>> wrote:
> >>>> Hi all,
> >>>>
> >>>> I have tried every possible permutation of the fslswapdim command to
> >>>> axialize my sagitally acquired T1 images. They start in ASR format.
> >>>> I
> >>>> need
> >>>> to be able to rotate 90 degrees, not only 180 to do this. Is there
> >>>> some tool
> >>>> I need in addition to fslswapdim? Are there additional orientation
> >>>> codes not
> >>>> listed in the help? I would prefer to use your tools as the method I
> >>>> have
> >>>> been using is unscriptable and takes too much time.
> >>>>
> >>>> Best regards
> >>>>
> >>>> Jennifer Bramen
> >>>> UCLA
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> ****************************************
> >>> Mikolaj A. Pawlak, MD PhD
> >>> Neuroradiology Research Division
> >>> Department of Radiology
> >>> University of Pennsylvania
> >>> 3600 Market Street Suite 370
> >>> Philadelphia, PA 19104
> >>> Phone: 215-662-3688
> >>> Fax: 215-615-3681
> >>> mail: [log in to unmask]
> >>>
> >>
> >>
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> >
> >
> > --
> > ****************************************
> > Mikolaj A. Pawlak, MD PhD
> > Neuroradiology Research Division
> > Department of Radiology
> > University of Pennsylvania
> > 3600 Market Street Suite 370
> > Philadelphia, PA 19104
> > Phone: 215-662-3688
> > Fax: 215-615-3681
> > mail: [log in to unmask]
> >
>
>
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> IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the recipient, please immediately notify us by return email, and delete this message from your computer.
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> IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the recipient, please immediately notify us by return email, and delete this message from your computer.
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--
****************************************
Mikolaj A. Pawlak, MD PhD
Neuroradiology Research Division
Department of Radiology
University of Pennsylvania
3600 Market Street Suite 370
Philadelphia, PA 19104
Phone: 215-662-3688
Fax: 215-615-3681
mail: [log in to unmask]
|