mirror? different interpretation of coordinates

classic Classic list List threaded Threaded
7 messages Options
Reply | Threaded
Open this post in threaded view
|

mirror? different interpretation of coordinates

andreas_fe
Hello,

when I display specific slices with 3dslicer it seems that they are
mirrored,

in other words the acitivity which is on the right side when displaying
the activity of an fMRI experiment with slover (shipped by SPM) is on
the left side when I use 3Dslicer?

where can I change this behavoir?

Thanks
Andreas
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: mirror? different interpretation of coordinates

pieper
Administrator
Hi Andreas -

Are your images in analyze format (.hdr/.img) format?  Interpretation of
these files is inconsistent across programs and their use if not
recommended.  Instead, nifti files (.nii or .nii.gz) files should be
used.  If you are still having trouble with nifti files perhaps you can
share example data for investigation.

Best,
Steve

On 02/01/2011 06:15 AM, An Fe wrote:

> Hello,
>
> when I display specific slices with 3dslicer it seems that they are
> mirrored,
>
> in other words the acitivity which is on the right side when displaying
> the activity of an fMRI experiment with slover (shipped by SPM) is on
> the left side when I use 3Dslicer?
>
> where can I change this behavoir?
>
> Thanks
> Andreas
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: mirror? different interpretation of coordinates

inorton
Hi Andreas,

Slicer does not know anything about the spm.analyze.flip setting which controls the display (radiological vs neuro.) in SPM. The problem is that SPM actually writes the data to file in a different order based on this setting. SPM Analyze is similarly not interoperable with other programs depending on the flip setting.

You can manually flip by putting a negative sign in front of the x-spacing field in the Volumes editor but this is obviously not recommended as a regular practice.

Another problem is that SPM Analyze does not have compatible origin information so it is necessary to set the offsets manually. I always center the Analyze image and its space-defining image -- or avoid Analyze and burn-in to DICOM from SPM.

So use Nifti if you can!

-Isaiah

On Tue, Feb 1, 2011 at 7:32 AM, Steve Pieper <[hidden email]> wrote:
Hi Andreas -

Are your images in analyze format (.hdr/.img) format?  Interpretation of
these files is inconsistent across programs and their use if not
recommended.  Instead, nifti files (.nii or .nii.gz) files should be
used.  If you are still having trouble with nifti files perhaps you can
share example data for investigation.

Best,
Steve

On 02/01/2011 06:15 AM, An Fe wrote:
> Hello,
>
> when I display specific slices with 3dslicer it seems that they are
> mirrored,
>
> in other words the acitivity which is on the right side when displaying
> the activity of an fMRI experiment with slover (shipped by SPM) is on
> the left side when I use 3Dslicer?
>
> where can I change this behavoir?
>
> Thanks
> Andreas
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: mirror? different interpretation of coordinates

andreas_fe
Hello,

thanks for the answer, but I already use nifit as image format.

Where can I place the nifti file (601K) ? which causes trouble?

(I think a solution for me is just to add what kind of view
- radiological vs neuro -  was used)

Thanks

Andreas



Am 01.02.2011 15:53, schrieb Isaiah Norton:
Hi Andreas,

Slicer does not know anything about the spm.analyze.flip setting which controls the display (radiological vs neuro.) in SPM. The problem is that SPM actually writes the data to file in a different order based on this setting. SPM Analyze is similarly not interoperable with other programs depending on the flip setting.

You can manually flip by putting a negative sign in front of the x-spacing field in the Volumes editor but this is obviously not recommended as a regular practice.

Another problem is that SPM Analyze does not have compatible origin information so it is necessary to set the offsets manually. I always center the Analyze image and its space-defining image -- or avoid Analyze and burn-in to DICOM from SPM.

So use Nifti if you can!

-Isaiah

On Tue, Feb 1, 2011 at 7:32 AM, Steve Pieper <[hidden email]> wrote:
Hi Andreas -

Are your images in analyze format (.hdr/.img) format?  Interpretation of
these files is inconsistent across programs and their use if not
recommended.  Instead, nifti files (.nii or .nii.gz) files should be
used.  If you are still having trouble with nifti files perhaps you can
share example data for investigation.

Best,
Steve

On 02/01/2011 06:15 AM, An Fe wrote:
> Hello,
>
> when I display specific slices with 3dslicer it seems that they are
> mirrored,
>
> in other words the acitivity which is on the right side when displaying
> the activity of an fMRI experiment with slover (shipped by SPM) is on
> the left side when I use 3Dslicer?
>
> where can I change this behavoir?
>
> Thanks
> Andreas
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject



_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: mirror? different interpretation of coordinates

andreas_fe
http://dl.dropbox.com/u/20188918/l_zer_pp1_26_ee5_k11.nii
http://dl.dropbox.com/u/20188918/l_zer_pp1_26_ee5_k12.nii

are the files where slover and 3Dslicer display the activity in different views?

Does use slover the radiological oder neuro view?

Thanks

Andreas

Am 02.02.2011 14:25, schrieb Isaiah Norton:
try http://www.letscrate.com/ or rapidshare or dropbox

On Wed, Feb 2, 2011 at 6:24 AM, An Fe <[hidden email]> wrote:
Hello,

thanks for the answer, but I already use nifit as image format.

Where can I place the nifti file (601K) ? which causes trouble?

(I think a solution for me is just to add what kind of view
- radiological vs neuro -  was used)

Thanks

Andreas
    



Am 01.02.2011 15:53, schrieb Isaiah Norton:
Hi Andreas,


Slicer does not know anything about the spm.analyze.flip setting which controls the display (radiological vs neuro.) in SPM. The problem is that SPM actually writes the data to file in a different order based on this setting. SPM Analyze is similarly not interoperable with other programs depending on the flip setting.

You can manually flip by putting a negative sign in front of the x-spacing field in the Volumes editor but this is obviously not recommended as a regular practice.

Another problem is that SPM Analyze does not have compatible origin information so it is necessary to set the offsets manually. I always center the Analyze image and its space-defining image -- or avoid Analyze and burn-in to DICOM from SPM.

So use Nifti if you can!

-Isaiah

On Tue, Feb 1, 2011 at 7:32 AM, Steve Pieper <[hidden email]> wrote:
Hi Andreas -

Are your images in analyze format (.hdr/.img) format?  Interpretation of
these files is inconsistent across programs and their use if not
recommended.  Instead, nifti files (.nii or .nii.gz) files should be
used.  If you are still having trouble with nifti files perhaps you can
share example data for investigation.

Best,
Steve

On 02/01/2011 06:15 AM, An Fe wrote:
> Hello,
>
> when I display specific slices with 3dslicer it seems that they are
> mirrored,
>
> in other words the acitivity which is on the right side when displaying
> the activity of an fMRI experiment with slover (shipped by SPM) is on
> the left side when I use 3Dslicer?
>
> where can I change this behavoir?
>
> Thanks
> Andreas
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject





_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: mirror? different interpretation of coordinates

inorton
Hi Andreas,
Your images are displayed consistently in Slicer, FSLView, and mricron. I don't have SPM (well, matlab) available here, but screenshots of the other three are attached.

Here is the canonical L/R nifti standard if you want to investigate further:
http://afni.nimh.nih.gov/pub/dist/data/avg152T1_LR.nii.gz

Orientation-related links:
http://nifti.nimh.nih.gov/nifti-1/documentation/faq
http://www.grahamwideman.com/gw/brain/orientation/orientterms.htm
http://www.slicer.org/slicerWiki/index.php/Coordinate_systems

Hope this helps,
-Isaiah

On Wed, Feb 2, 2011 at 8:51 AM, An Fe <[hidden email]> wrote:
http://dl.dropbox.com/u/20188918/l_zer_pp1_26_ee5_k11.nii
http://dl.dropbox.com/u/20188918/l_zer_pp1_26_ee5_k12.nii

are the files where slover and 3Dslicer display the activity in different views?

Does use slover the radiological oder neuro view?

Thanks

Andreas

Am 02.02.2011 14:25, schrieb Isaiah Norton:
try http://www.letscrate.com/ or rapidshare or dropbox

On Wed, Feb 2, 2011 at 6:24 AM, An Fe <[hidden email]> wrote:
Hello,

thanks for the answer, but I already use nifit as image format.

Where can I place the nifti file (601K) ? which causes trouble?

(I think a solution for me is just to add what kind of view
- radiological vs neuro -  was used)

Thanks

Andreas
    



Am 01.02.2011 15:53, schrieb Isaiah Norton:
Hi Andreas,


Slicer does not know anything about the spm.analyze.flip setting which controls the display (radiological vs neuro.) in SPM. The problem is that SPM actually writes the data to file in a different order based on this setting. SPM Analyze is similarly not interoperable with other programs depending on the flip setting.

You can manually flip by putting a negative sign in front of the x-spacing field in the Volumes editor but this is obviously not recommended as a regular practice.

Another problem is that SPM Analyze does not have compatible origin information so it is necessary to set the offsets manually. I always center the Analyze image and its space-defining image -- or avoid Analyze and burn-in to DICOM from SPM.

So use Nifti if you can!

-Isaiah

On Tue, Feb 1, 2011 at 7:32 AM, Steve Pieper <[hidden email]> wrote:
Hi Andreas -

Are your images in analyze format (.hdr/.img) format?  Interpretation of
these files is inconsistent across programs and their use if not
recommended.  Instead, nifti files (.nii or .nii.gz) files should be
used.  If you are still having trouble with nifti files perhaps you can
share example data for investigation.

Best,
Steve

On 02/01/2011 06:15 AM, An Fe wrote:
> Hello,
>
> when I display specific slices with 3dslicer it seems that they are
> mirrored,
>
> in other words the acitivity which is on the right side when displaying
> the activity of an fMRI experiment with slover (shipped by SPM) is on
> the left side when I use 3Dslicer?
>
> where can I change this behavoir?
>
> Thanks
> Andreas
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject






_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject

Screenshot-1.png (236K) Download Attachment
Screenshot-2.png (418K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: mirror? different interpretation of coordinates

andreas_fe
Hello Isaiah

thank you for the pictures,

I'm little suprised, why SPM changes right to left
(http://imaging.mrc-cbu.cam.ac.uk/imaging/DisplaySlices )

or something from my script, but I don't know...


ok, orientation seem a bit strange.... when I would like to use
the notation of  SPM .... would it be very unusual to speak about LAS
coordinates?  When I display slices in an axial view... maybe S=-10,..,15 and
change right to left.... I get LAS instead of RAS?  

Thanks

Andreas

Am Sonntag, 6. Februar 2011, um 20:28:07 schrieb Isaiah Norton:

> Hi Andreas,
> Your images are displayed consistently in Slicer, FSLView, and mricron. I
> don't have SPM (well, matlab) available here, but screenshots of the other
> three are attached.
>
> Here is the canonical L/R nifti standard if you want to investigate
> further: http://afni.nimh.nih.gov/pub/dist/data/avg152T1_LR.nii.gz
>
> Orientation-related links:
> http://nifti.nimh.nih.gov/nifti-1/documentation/faq
> http://www.grahamwideman.com/gw/brain/orientation/orientterms.htm
> http://www.slicer.org/slicerWiki/index.php/Coordinate_systems
>
> Hope this helps,
> -Isaiah
>
> On Wed, Feb 2, 2011 at 8:51 AM, An Fe <[hidden email]> wrote:
> >  http://dl.dropbox.com/u/20188918/l_zer_pp1_26_ee5_k11.nii
> >
> > http://dl.dropbox.com/u/20188918/l_zer_pp1_26_ee5_k12.nii
> >
> > are the files where slover and 3Dslicer display the activity in different
> > views?
> >
> > Does use slover the radiological oder neuro view?
> >
> > Thanks
> >
> > Andreas
> >
> > Am 02.02.2011 14:25, schrieb Isaiah Norton:
> >
> > try http://www.letscrate.com/ or rapidshare or dropbox
> >
> > On Wed, Feb 2, 2011 at 6:24 AM, An Fe <[hidden email]> wrote:
> >>  Hello,
> >>
> >> thanks for the answer, but I already use nifit as image format.
> >>
> >> Where can I place the nifti file (601K) ? which causes trouble?
> >>
> >> (I think a solution for me is just to add what kind of view
> >> - radiological vs neuro -  was used)
> >>
> >> Thanks
> >>
> >> Andreas
> >>
> >>
> >>
> >>
> >>
> >> Am 01.02.2011 15:53, schrieb Isaiah Norton:
> >>
> >> Hi Andreas,
> >>
> >>
> >> Slicer does not know anything about the spm.analyze.flip setting which
> >> controls the display (radiological vs neuro.) in SPM. The problem is
> >> that SPM actually writes the data to file in a different order based on
> >> this setting. SPM Analyze is similarly not interoperable with other
> >> programs depending on the flip setting.
> >>
> >> You can manually flip by putting a negative sign in front of the
> >> x-spacing field in the Volumes editor but this is obviously not
> >> recommended as a regular practice.
> >>
> >> Another problem is that SPM Analyze does not have compatible origin
> >> information so it is necessary to set the offsets manually. I always
> >> center the Analyze image and its space-defining image -- or avoid
> >> Analyze and burn-in to DICOM from SPM.
> >>
> >> So use Nifti if you can!
> >>
> >> -Isaiah
> >>
> >> On Tue, Feb 1, 2011 at 7:32 AM, Steve Pieper
<[hidden email]>wrote:

> >>> Hi Andreas -
> >>>
> >>> Are your images in analyze format (.hdr/.img) format?  Interpretation
> >>> of these files is inconsistent across programs and their use if not
> >>> recommended.  Instead, nifti files (.nii or .nii.gz) files should be
> >>> used.  If you are still having trouble with nifti files perhaps you
> >>> can share example data for investigation.
> >>>
> >>> Best,
> >>> Steve
> >>>
> >>> On 02/01/2011 06:15 AM, An Fe wrote:
> >>> > Hello,
> >>> >
> >>> > when I display specific slices with 3dslicer it seems that they are
> >>> > mirrored,
> >>> >
> >>> > in other words the acitivity which is on the right side when
> >>> > displaying the activity of an fMRI experiment with slover (shipped
> >>> > by SPM) is on the left side when I use 3Dslicer?
> >>> >
> >>> > where can I change this behavoir?
> >>> >
> >>> > Thanks
> >>> > Andreas
> >>> > _______________________________________________
> >>> > slicer-users mailing list
> >>> > [hidden email]
> >>> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> >>> > To unsubscribe: send email to
> >>>
> >>> [hidden email] with unsubscribe as the
> >>> subject
> >>> _______________________________________________
> >>> slicer-users mailing list
> >>> [hidden email]
> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> >>> To unsubscribe: send email to
> >>> [hidden email] with unsubscribe as the
> >>> subject

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject