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
|