Hi Greg,
The images that you've sent show that the labels in FSLView are greyed
out in the radiological case. This is what happens when there is no
orientation information (sform or qform) contained in the image, and
FSLView must resort to its defaults. This is no doubt why the axes are
wrong.
So I think that something must have gone wrong in your conversion
from "neurological order" to "radiological order". Try the following
instead:
avwswapdim nodif -x y z nodif_swapped
avworient -swaporient nodif_swapped
and see if nodif_swapped is correct. This is what we advocate on the
FSL FAQ for swapping between the different orderings, so hopefully
it will work fine for your data.
Let us know how you get on.
All the best,
Mark
Kirk, Gregory wrote:
>Hi Tim,
>
>Note as the listserver refused my jpegs in attachment I have uploaded
>the two jpegs
>neurological.jpg,radiological.jpg
>
>I am a bit confused, neurological.jpg abobe is a gimp of the fslview
>shot of the Original nii created by freesurfer. It comes up in
>neurological convention and the AP seems to be correct. The second is a
>snapshot after the steps you prescribed where it is now in radiological
>convention but the AP appears to be backwards.
>
>I also uploaded data, the same one I am quite sure , called now
>nodif2.nii just to make sure.
>
>Hummm ?
>
>Thanks
>
>Greg.
>
>-----Original Message-----
>From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>Behalf Of Tim Behrens
>Sent: Friday, January 05, 2007 5:07 AM
>To: [log in to unmask]
>Subject: Re: [FSL] NIFTI conversion
>
>
>Hi - I misunderstood.
>Your data was already A/P swapped before the change from Neurological
>to Radiological.
>
>This often happens with scanners that define the phase encode
>direction from nose backwards.
>
>You can solve this by flipping Y in the avwswapdim command exactly as
>you suggest, but make sure the read direction is also defined as you
>expect.
>(i.e. that left-right is correct in your final image)
>
>Cheers
>
>Tim
>
>On 4 Jan 2007, at 21:15, Kirk, Gregory wrote:
>
>
>
>>Hi Tim,
>>
>>I uploaded nodif.nii - upload ref number 103521.
>>This is the no diffusion b0 data, the file was as I said before
>>created
>>with
>>The mri_convert function in freesurfer. If you wanted I could send the
>>anonymized Siemens DICOM
>>
>>Thanks a lot
>>
>>Greg.
>>
>>
>>-----Original Message-----
>>From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>>Behalf Of Tim Behrens
>>Sent: Thursday, January 04, 2007 6:35 AM
>>To: [log in to unmask]
>>Subject: Re: [FSL] NIFTI conversion
>>
>>
>>That would certainly fix it, but I don't know why this happens.
>>
>>If you like, you could upload your data onto
>>http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>>
>>and we'll take a quick look.
>>
>>T
>>
>>
>>On 3 Jan 2007, at 18:31, Kirk, Gregory wrote:
>>
>>
>>
>>>I tried it out on my nodif.nii b0 volume. Works like a charm To
>>>change
>>>
>>>
>>>it to radiological convention. Small fly in the ointment. The AP is
>>>backwards now.
>>>
>>>Do I need to change avwswapdim data -x y z data
>>>To avwswapdim data -x -y z data ?
>>>
>>>Thankx
>>>
>>>Greg.
>>>
>>>-----Original Message-----
>>>From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>>>Behalf Of Tim Behrens
>>>Sent: Wednesday, January 03, 2007 3:50 AM
>>>To: [log in to unmask]
>>>Subject: Re: [FSL] NIFTI conversion
>>>
>>>
>>>Sorry - my mistake!
>>>
>>>
>>>>1) get the qform information out of the diffusion data avworient
>>>>-getorient data > tmp.txt
>>>>
>>>>
>>>This should read
>>>
>>>1) get the qform information out of the diffusion data avworient
>>>-getqform data > tmp.txt
>>>
>>>
>>>I'm sorry about this.
>>>Hopefully the rest should still work.
>>>
>>>T
>>>
>>>
>>>
>>>On 2 Jan 2007, at 21:22, Kirk, Gregory wrote:
>>>
>>>
>>>
>>>>Hi Tim,
>>>>
>>>>Tried your ideas, got through the first couple but when I got to
>>>>
>>>>4) edit tmp.txt replacing the first number with its own negative
>>>>(this
>>>>
>>>>
>>>>should be easy to script if you have to do it a lot of times)
>>>>
>>>>I found there was one thing in tmp.txt, the word NEUROLOGICAL -
>>>>nothing else, No numbers. Humm , I think the qform is not set. This
>>>>nii was
>>>>created
>>>>with mri_convert
>>>>From freesurfer. I asked Doug Greve about it, and the rel;ated fact
>>>>that
>>>>the structural data from the same subject
>>>>Came out in RADIOLOGICAL convention -- and upside down and sideways
>>>>when
>>>>displayed in fslview. The data is Siemens
>>>>DICOM from an Avanto Scanner version VB 11D. Doug said the data will
>>>>come out Neurological or radiological, however
>>>>It is set at the scanner. I do not, and I asked the MR physicist,
>>>>know
>>>>where this would be getting set Neurological
>>>>For the diffusion data... I am thinking this must be a common
>>>>thing, to
>>>>set datafrom a modern Siemens scanner, diffusion
>>>>And structural into the same convention and orientation so they
>>>>can be
>>>>registered and use the structural to guide the seed placement ?
>>>>
>>>>Is there possibly better software I could use to import the Siemens
>>>>data into NIfTI. I looked a bit And the software I found mricro etc.
>>>>
>>>>
>
>
>
>>>>all seemed to have spaggetii dependencies and such and I was
>>>>Never able to quite get it to work. I have the idea with software
>>>>that
>>>>if something like load data does not work without a lot of effort
>>>>Then one should mot likely not use the software.
>>>>
>>>>
>>>>-----Original Message-----
>>>>From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>>>>Behalf Of Tim Behrens
>>>>Sent: Wednesday, December 27, 2006 3:34 AM
>>>>To: [log in to unmask]
>>>>Subject: Re: [FSL] NIFTI conversion
>>>>
>>>>
>>>>Hi - again, I'm not sure I'll get this completely right, but I'll
>>>>have a go.
>>>>
>>>>My advice would be to ensure everything ends up in radiological
>>>>conventions. I think this will be very important when you do
>>>>tracking, as otherwise there will be a great deal of confusion
>>>>between the gradient orientations and the image convention. (fslview
>>>>
>>>>
>
>
>
>>>>always displays the eigenvectors in radiological coordinates,
>>>>ignoring the q-form, but it displays the images in neurological if
>>>>the q-form is set, so it can get very confusing - we will fix this
>>>>for the next release.)
>>>>
>>>>To put the diffusion data into radiological convention, you
>>>>should be
>>>>
>>>>
>>>>able to do the following:
>>>>
>>>>1) get the qform information out of the diffusion data avworient
>>>>-getorient data > tmp.txt
>>>>
>>>>2) delete all orientation information
>>>>avworient -deleteorient data
>>>>
>>>>3) swap the image axes so the data are stored in radiological
>>>>convention:
>>>>avwswapdim data -x y z data
>>>>
>>>>4) edit tmp.txt replacing the first number with its own negative
>>>>(this should be easy to script if you have to do it a lot of times)
>>>>
>>>>5) reload the data with the newly relevant q-form matrix: avworient
>>>>-setqform `cat tmp.txt` data
>>>>
>>>>6) check that this has also set the q-form code ( I am not sure
>>>>if it
>>>>
>>>>
>>>>does or not). If it doens't, set it with avworient.
>>>>
>>>>7) enjoy your new radiologically stored data.
>>>>
>>>>T
>>>>
>>>>On 22 Dec 2006, at 20:27, Gregory Kirk wrote:
>>>>
>>>>
>>>>
>>>>>We are experiencing a few problems with NIFTI images created from
>>>>>Siemens DICOM data using either MRI convert (Freesurfer) or our own
>>>>>
>>>>>
>
>
>
>>>>>in house software written in IDL. We want to use structural (3D T1
>>>>>weighted
>>>>>data)
>>>>>data to define ROIs for probabilistic fibre tracking. The diffusion
>>>>>
>>>>>
>
>
>
>>>>>images are acquired in an axial plane tipped to give an approx
>>>>>AC-PC
>>>>>angulation
>>>>>while the structural images are in sagittal plane, typically with
>>>>>small
>>>>>tilts to align the slices with midline of the brain. When we
>>>>>convert these
>>>>>images to NIFTI format and import them in to FSL we consistently
>>>>>get a
>>>>>mismatch between the orientation of the diffusion data and the
>>>>>structurals
>>>>>with the diffusion data being in neurological convention while the
>>>>>structurals appear in radiological convention. The options for
>>>>>converting
>>>>>radiological to neurological orintation don't seem to have any
>>>>>effect (but
>>>>>changing qform does switch the slice ordering as one would expect).
>>>>>Thus
>>>>>we were wondering exactly how FSL determines which convention to
>>>>>display
>>>>>NIFTI images in? Obviously what we require is to get both data sets
>>>>>to be
>>>>>displayed in the same convention so that we can register the data
>>>>>sets
>>>>>prior to doing the fibre tracking.
>>>>>
>>>>>Thanks in advance.
>>>>>
>>>>>Greg
>>>>>
>>>>>
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