Back to PLS Helpsave current region to IMG?
Posted on 02/02/07 12:40:35
Number of posts: 100
Author: Agatha (---.csbmb.Princeton.EDU)
Date: 01-16-07 11:12
hello ~
i would like to export the maps to nifti files. i have tried all three options for saving to IMG files. when i read the result into AFNI, however, the saved file is read as an anatomical file rather than as a functional file (an spm)... and the image displays my background image used in PLS and the brain areas from PLS results.
i.e., the save to IMG option appears to be saving the image not the results directly to IMG format... saving 'brain region to IMG' results in a "mask" of the brain region but does not save an ROI (which i thought it would)...
1. i seem to be mis-understanding how the export function works - how is it meant to be used (the User Guide does not explain)?
2. is the saved-to IMG format ANALYZE or NIfTI?
3. can one save just the activation results (e.g., saliences, bootsrap ratio) as an parametric map (without the underlying background image)?
Thanks!
Agatha
Date: 01-16-07 11:12
hello ~
i would like to export the maps to nifti files. i have tried all three options for saving to IMG files. when i read the result into AFNI, however, the saved file is read as an anatomical file rather than as a functional file (an spm)... and the image displays my background image used in PLS and the brain areas from PLS results.
i.e., the save to IMG option appears to be saving the image not the results directly to IMG format... saving 'brain region to IMG' results in a "mask" of the brain region but does not save an ROI (which i thought it would)...
1. i seem to be mis-understanding how the export function works - how is it meant to be used (the User Guide does not explain)?
2. is the saved-to IMG format ANALYZE or NIfTI?
3. can one save just the activation results (e.g., saliences, bootsrap ratio) as an parametric map (without the underlying background image)?
Thanks!
Agatha
Replies:
Re: save current region to IMG?
Posted on 02/02/07 12:41:03
Number of posts: 100
Author: Jimmy (---.rotman-baycrest.on.ca)
Date: 01-16-07 11:48
> i would like to export the maps to nifti files. i have tried
> all three options for saving to IMG files.
There are only 2 options to export maps to NIfTI files:
1. Save Current Display to IMG file
2. Save BLV (or BSR) result to IMG file
You probably also considered "Save brain region to IMG file" as the third option, right? Please see the following link in the PLS User's Guide for further help:
http://rotman-baycrest.on.ca/pls/UserGuide.htm#_Toc146699261
> when i read the
> result into AFNI, however, the saved file is read as an
> anatomical file rather than as a functional file
AFNI read NIfTI file using its only colormap. I heard people here are using "Save BLV (or BSR) result to IMG file" option to export IMG file (functional map), and they load it to AFNI and manually choose colormap from AFNI. However, you will never get exactly the color displayed in PLS result window.
In the future, if AFNI can also load user's own colormap, you can then choose "Save Current Display to IMG file" option, which also export ".mat" file with the same file name. In that ".mat" file, it only contains colormap (cmap variable). Currently, people only use this option to reproduce what exactly displayed on the PLS result window for publication purpose.
> (an spm)...
> and the image displays my background image used in PLS and the
> brain areas from PLS results.
>
> i.e., the save to IMG option appears to be saving the image not
> the results directly to IMG format...
> saving 'brain region to
> IMG' results in a "mask" of the brain region but does not save
> an ROI (which i thought it would)...
That has already been described in the above link .
> 1. i seem to be mis-understanding how the export function works
> - how is it meant to be used (the User Guide does not explain)?
It explained.
As described in PLS User's Guide (above link):
... "Save brain region to IMG file" takes the coordinates of the common brain region from the result file, and saves it to a brain region image file...
> 2. is the saved-to IMG format ANALYZE or NIfTI?
It is saved to NIfTI format, and ANALYZE is merely a subset of NIfTI format.
> 3. can one save just the activation results (e.g., saliences,
> bootsrap ratio) as an parametric map (without the underlying
> background image)?
As described in PLS User's Guide (above link):
... "Save the BLV (or BSR) result to IMG files" saves the result values (either Brain LV or Bootstrap Ratio) that are currently displayed to image files...
Date: 01-16-07 11:48
> i would like to export the maps to nifti files. i have tried
> all three options for saving to IMG files.
There are only 2 options to export maps to NIfTI files:
1. Save Current Display to IMG file
2. Save BLV (or BSR) result to IMG file
You probably also considered "Save brain region to IMG file" as the third option, right? Please see the following link in the PLS User's Guide for further help:
http://rotman-baycrest.on.ca/pls/UserGuide.htm#_Toc146699261
> when i read the
> result into AFNI, however, the saved file is read as an
> anatomical file rather than as a functional file
AFNI read NIfTI file using its only colormap. I heard people here are using "Save BLV (or BSR) result to IMG file" option to export IMG file (functional map), and they load it to AFNI and manually choose colormap from AFNI. However, you will never get exactly the color displayed in PLS result window.
In the future, if AFNI can also load user's own colormap, you can then choose "Save Current Display to IMG file" option, which also export ".mat" file with the same file name. In that ".mat" file, it only contains colormap (cmap variable). Currently, people only use this option to reproduce what exactly displayed on the PLS result window for publication purpose.
> (an spm)...
> and the image displays my background image used in PLS and the
> brain areas from PLS results.
>
> i.e., the save to IMG option appears to be saving the image not
> the results directly to IMG format...
> saving 'brain region to
> IMG' results in a "mask" of the brain region but does not save
> an ROI (which i thought it would)...
That has already been described in the above link .
> 1. i seem to be mis-understanding how the export function works
> - how is it meant to be used (the User Guide does not explain)?
It explained.
As described in PLS User's Guide (above link):
... "Save brain region to IMG file" takes the coordinates of the common brain region from the result file, and saves it to a brain region image file...
> 2. is the saved-to IMG format ANALYZE or NIfTI?
It is saved to NIfTI format, and ANALYZE is merely a subset of NIfTI format.
> 3. can one save just the activation results (e.g., saliences,
> bootsrap ratio) as an parametric map (without the underlying
> background image)?
As described in PLS User's Guide (above link):
... "Save the BLV (or BSR) result to IMG files" saves the result values (either Brain LV or Bootstrap Ratio) that are currently displayed to image files...
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