I also use Mac to convert images but I use AFNI's to3d program which
works easily in a GUI. You still have to create a .hdr using
avwcreatehd which you can get instructions for on the FSL web site.
Andy
On Saturday, November 9, 2002, at 02:50 AM, Mark Jenkinson wrote:
> Hi John,
>
> If you don't have the voxel dimensions set correctly then I would
> expect
> you to have problems with BET like you describe.
>
> There are two things to do about this.
> Firstly, see if there is an easy way to fix the ImageJ conversion.
> To do this, create your own analyze header using avwcreatehd.
> Then compare your header with the one from ImageJ (you can list the
> fields with avwhd) and if there is a difference in some of the critical
> fields like dim1 to dim4, pixdim1 to pixdim3, sizeof_hdr or datatype
> then
> this is the problem and you can easily write a script using avwval and
> avwcreatehd to fix the problem.
>
> The second alternative is to just use avwcreatehd every time as part
> of your conversion process. To do this you would need to get the
> appropriate values (like voxel dimensions) from somewhere. Once you
> have the header file all the .img file must contain is a
> straightforward binary list of intensity values, voxel by voxel,
> incrementing x first, then y, then z. So, if you can get something to
> save the image data like this then that's all you'll need for a
> successful conversion.
>
> All the best,
> Mark
>
>
>
> John Grinstead wrote:
>> I was having problems using BET (it was drawing the contours much too
>> small) when I used images that I had converted from Dicom to Analyze
>> format
>> with ImageJ (using the Analyze Writer plugin from
>> http://rsb.info.nih.gov/ij/plugins/analyze.html to write out a stack
>> of
>> T2-wtd anatomical images). When I converted them with MRIcro then BET
>> worked fine. Anyone had this problem and know how to fix it within
>> ImageJ?
>> Perhaps ImageJ throws out some header information (such as field of
>> view)
>> that BET requires?
>>
>> This is really only an issue for me because I run FSL on a Mac, and
>> MRIcro
>> is for windows only. If someone knows a reliable way to convert these
>> files
>> with some other simple to use Mac friendly software that would be
>> great.
>>
>> Thanks,
>> John
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