Dear Darren and Matthew
Thank you for your explanation. That solved my questions and concerns.
Best regards,
Kiyotaka
2010/11/11 Darren Gitelman <[log in to unmask]>:
> Kiyotaka
> The script doesn't know anything about left or right handed coordinates. It
> simply reorganizes the header so that it conforms to the SPM2 version of
> analyze. It uses the transformation matrix stored in the nifti header, and
> keeps in the same orientation as the nifti file. However, it will flip the
> images to maintain them in neurological orientation just as was the
> convention for SPM2, depending on the setting in the spm_flip_analyze_images
> file.
> Darren
>
> On Wed, Nov 10, 2010 at 4:53 PM, Kiyotaka Nemoto <[log in to unmask]>
> wrote:
>>
>> Darren,
>>
>> Thank you for showing the useful script.
>> I'm wondering how your script handles the coordinate system.
>> I have some niftii dataset. Some are right-handed, and others are
>> left-handed.
>> As long as those are niftii, it shouldn't be much problems, but when
>> it comes to Analyze format, problems arise.
>>
>> I'm looking for the function which converts all of the niftii files
>> either left- or right-handed coordinate system into specific
>> coordinate analyze format files. (All analyze files are right-handed
>> or left-handed.)
>>
>> Best regards,
>>
>> Kiyotaka
>>
>> 2010/11/10 Darren Gitelman <[log in to unmask]>:
>> > Try this function
>> > http://brainimaging.tiddlyspot.com/#nifti2ana
>> >
>> > --------------------
>> > Darren Gitelman, MD
>> > Sent from my mobile.
>> > Office Ph: (312) 908-8614
>> > Fax: (312) 908-5073
>> > On Nov 10, 2010, at 7:08 AM, Vanessa Sochat <[log in to unmask]> wrote:
>> >
>> > How about the BXH/XCEDE tools? They were developed by Syam Gadde here
>> > at
>> > Duke, and they are excellent for jumping around between image types.
>> >
>> > http://www-calit2.nbirn.net/tools/bxh_tools/index.shtm
>> >
>> > You can use bxhabsorb to fit the data with a bxh header, and then
>> > bxh2analyze to convert from nifti to analyze. There are a bunch of
>> > options
>> > that you can look at to check orientation as well!
>> >
>> > Best,
>> >
>> > Vanessa
>> >
>> > On Mon, Nov 8, 2010 at 2:19 PM, Matthew Brett <[log in to unmask]>
>> > wrote:
>> >>
>> >> Hi,
>> >>
>> >> > Our lab here has an in house software package that only reads analyze
>> >> > images. I'm trying to do some reorientation and registration in
>> >> > SPM5/8, but
>> >> > I need to then convert to analyze hdr/img pair and write out the
>> >> > image in
>> >> > the new orientation. I've tried a few programs, but they all also
>> >> > generate
>> >> > the *.mat file needed by older versions of SPM to store the
>> >> > orientation.
>> >> > What I really need is something that will take a nii format file and
>> >> > write
>> >> > out an analyze format file where the the image volume is actually
>> >> > physically
>> >> > written in the correct orientation.
>> >>
>> >> If the .mat file only encodes some axis flips or axis rearrangements,
>> >> then you could try our 'nibabel' python package [1]:
>> >>
>> >> easy_install nibabel
>> >> python
>> >> >>> import nibabel as nib
>> >> >>> img = nib.load('nifti_image.nii')
>> >> >>> better_img = nib.as_closest_canonical(img)
>> >> >>> nib.analyze.save(img, 'better_analyze_image.img')
>> >>
>> >> By the way - this will generate a 'neurological' orientation image
>> >> (first pixel is the right-most pixel).
>> >>
>> >> If there are rotations and translations so that the image does not
>> >> align down any reorganization of the axes, you'll have to reslice the
>> >> image to some canonical volume...
>> >>
>> >> Best,
>> >>
>> >> Matthew
>> >>
>> >> [1] http://nipy.sourceforge.net/nibabel/
>> >
>> >
>> >
>> > --
>> > Vanessa Villamia Sochat
>> > Laboratory of Neurogenetics
>> > Duke University, 2009
>> > (603) 321-0676
>> >
>>
>>
>>
>> --
>> Kiyotaka Nemoto, M.D.
>> Department of Psychiatry
>> Graduate School of Comprehensive Human Sciences
>> University of Tsukuba
>> 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan
>> E-mail: [log in to unmask]
>
>
>
> --
> Darren Gitelman, MD
> 710 N. Lake Shore Dr., 1122
> Chicago, IL 60611
> Ph: (312) 908-8614
> Fax: (312) 908-5073
>
--
Kiyotaka Nemoto, M.D.
Department of Psychiatry
Graduate School of Comprehensive Human Sciences
University of Tsukuba
1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan
E-mail: [log in to unmask]
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