Difference between revisions of "Documentation/4.1/FAQ"
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Sometimes the header information that describes the orientation and size of the image in physical space is incorrect or missing. Slicer displays images in physical space, in a RAS orientation. If images appear flipped or upside down, the transform that describes how the image grid relates to the physical world is incorrect. In proper RAS orientation, a head should have anterior end at the top in the axial view, look to the left in a sagittal view, and have the superior end at the top in sagittal and coronal views.<br> | Sometimes the header information that describes the orientation and size of the image in physical space is incorrect or missing. Slicer displays images in physical space, in a RAS orientation. If images appear flipped or upside down, the transform that describes how the image grid relates to the physical world is incorrect. In proper RAS orientation, a head should have anterior end at the top in the axial view, look to the left in a sagittal view, and have the superior end at the top in sagittal and coronal views.<br> | ||
Yes, you can flip images and change the axis orientation of images in slicer. But we urge to use great caution when doing so, since this can introduce subtantial problems if done wrong. Worse than no information is wrong information. '''Below the steps to flip the LR axis of an image''':<br> | Yes, you can flip images and change the axis orientation of images in slicer. But we urge to use great caution when doing so, since this can introduce subtantial problems if done wrong. Worse than no information is wrong information. '''Below the steps to flip the LR axis of an image''':<br> | ||
| − | #Go to the ''Data'' module, right click on the node labeled "Scene" and select "Insert Transform" from the pulldown menu | + | #Go to the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Data ''Data'' module], right click on the node labeled "Scene" and select "Insert Transform" from the pulldown menu |
#Move/drag your image into/onto the newly created transform | #Move/drag your image into/onto the newly created transform | ||
#Go to the ''Transforms'' module and select the newly created transform from the "Transform Node" menu. | #Go to the ''Transforms'' module and select the newly created transform from the "Transform Node" menu. | ||
Revision as of 19:46, 3 May 2012
Home < Documentation < 4.1 < FAQContents
User FAQ: Installation & Generic
Is slicer really free?
Yes, really, truly, free. Not just a free trial. No pro version with all the good stuff. Slicer is free with no strings attached. You can even re-use the code in any way you want with no royalties and you don't even need to ask us for permission. (Of course we're always happy to hear from people who've found slicer interesting).
See the Slicer License page for the legal version of this.
Can I use slicer for patient care?
Slicer is intended for research work and has no FDA clearances or approvals of any kind. It is the responsibility of the user to comply with all laws and regulations (and moral/ethical guidelines) when using slicer.
User FAQ : Registration
How do I fix incorrect axis directions? Can I flip an image (left/right, anterior/posterior etc) ?
Sometimes the header information that describes the orientation and size of the image in physical space is incorrect or missing. Slicer displays images in physical space, in a RAS orientation. If images appear flipped or upside down, the transform that describes how the image grid relates to the physical world is incorrect. In proper RAS orientation, a head should have anterior end at the top in the axial view, look to the left in a sagittal view, and have the superior end at the top in sagittal and coronal views.
Yes, you can flip images and change the axis orientation of images in slicer. But we urge to use great caution when doing so, since this can introduce subtantial problems if done wrong. Worse than no information is wrong information. Below the steps to flip the LR axis of an image:
- Go to the Data module, right click on the node labeled "Scene" and select "Insert Transform" from the pulldown menu
- Move/drag your image into/onto the newly created transform
- Go to the Transforms module and select the newly created transform from the "Transform Node" menu.
- Double-Click inside one of the field of the 3x3 matrix, where you see a number 1.0.
- replace the 1.0 with "-1.0", then hit the RETURN key again. You should see a flip immediately, assuming you have the volume in the proper view. Depending on which of the axes you want flipped, select the corresponding field in the 3x3 matrix.
- Go back to the Data module, right click on your image and select Harden Transform from the pulldown menu.
- The image will move back outside the transform onto the main level. Your change of axis orientation has now been applied.
- Note that this change was applied to the header information that stores the physical orientation, not the image data itself. Hence you will only see this flip in software that reads and accounts this header orientation info.
- Save your image under a new name, do not use a format that doesn't store physical orientation info in the header (jpg, gif etc).; also consider saving the transform as documentation to what change you have applied. You can also use these saved transforms as templates to quickly flip an image.
- Again: the change is saved as part of the image orientation info and not as an actual resampling of the image, i.e. if you save your image and reload it in another software that does not read the image orientation info in the header (or displays in image space only), you will not see the change you just applied.
To flip the other axes do the same as above but edit the diagonal entries in the 2nd and 3rd row, for flipping anterior-posterior and inferior-superior directions, respectively.
