Hi,
I also wrote a perl script to convert PAR/REC into NIFTI format.
As for Mikael Hanke, I wrote my own converter due to some limitations of
available softwares (for example, old version of 3dPAR2AFNI.pl doesn't
convert sagittal and coronal acquisitions, maybe it's no true any more
with newer version).
My perl script needs PDL (pdl.perl.org) and FSL from version 3, it's a
frontend to the very useful avw- or newer fsl-tools.
Note that for DWI exported in the last version 4.2, order of weighted
volumes have changed. I choose to reorder data as before according to :
b0 - DW - mean of DWI
Hope that it can help someone
Franck Le 26/03/2010 02:51, Michael Hanke a écrit :
> On Thu, Mar 25, 2010 at 06:15:36PM -0700, Connolly, Colm wrote:
>
>> On Mar 25, 2010, at 2:46 PM, Michael Hanke wrote:
>>
>>
>>> Hi,
>>>
>>> On Thu, Mar 25, 2010 at 08:19:53PM +0000, Greg H wrote:
>>>
>>>> Dear FSL experts,
>>>>
>>>> I am a new user of FSL and this is the first time I've collected
>>>> data on a Philips 3T scanner. I am using dcm2nii for this
>>>> conversion because based on the program it appears that it will
>>>> convert these files to nifti format. I noticed that it has some
>>>> trouble setting the scaling so some of our files can not be viewed
>>>> in fslview. I was able to find the min and max intensities using
>>>> fslstats -t image.par -r and then the file can be viewed in
>>>> fslview. I am wondering if anyone has had any trouble converting
>>>> par files with dcm2nii. Sometimes it looks like it cannot
>>>> completely read the par file and I noticed that the cal_min and
>>>> cal_max are always set to 0. Does anyone have any suggests as to
>>>> why this may happen or what I can do to fix it? Is there a better
>>>> program available? I went through the archives, but I didn't find
>>>> anything relevant to this problem.
>>>>
>>> I recently started toying with a (from scratch) parrec2nii converter
>>> based on nibabel, because people in the department complained about
>>> insufficiencies of available software. There is some code already,
>>> but right now, I don't expect it to be any less buggy than other
>>> tools, but my intentions are good ;-)
>>>
>>> Maybe it can help you in the future. Or you can help me by testing
>>> things out and offer feedback!?
>>>
>>> The current code is here:
>>>
>>> http://github.com/hanke/nibabel/blob/mh/master/bin/parrec2nii
>>>
>>>
>>> Michael
>>>
>>>
>>> PS: Right now it will set the scaling to match the method documented
>>> in the PAR header. However, Phillips own tools seem to ignore that
>>> (there are actually two different scaling values in the header). I
>>> will add support to choose between the two possibilities.
>>>
>>
>> There is a program called 3dPAR2AFNI.pl which is part of afni which
>> will do this job for you. It, however, has some limitations, such as
>> only handling axial slices. But you make be able to make there
>> relatively minor modifications to it handle other orientations.
>>
> It should be mentioned that this is a perl script that serves as a
> frontend for other AFNI tools -- so you actually need AFNI too. It also
> doesn't handle the more recent "clincial tryout" variant of the 4.2 PAR
> images.
>
> Michael
>
>
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