I've had fairly good luck (with one exception) with r2agui
http://r2agui.sourceforge.net/
requires matlab.
Dave Kennedy
On Fri, Mar 26, 2010 at 4:33 AM, lamberton <[log in to unmask]> wrote:
> 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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