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.
Regards,
--
Colm G. Connolly, Ph. D.
Dept of Psychiatry
University of California, San Diego
9500 Gilman Dr. #0855
La Jolla, CA 92093-0855
Tel: +1-858-246-0608
Fax: +1-858-534-9450
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