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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