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[Idea] addition to the wiki about wrong labels on images #59
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Hi Julien, this seems like a smart solution, and I see no reason for it not to work universally. |
I agree. You have wiki editing rights, right? Just add a section. I'd suggest you present as you did here, that this solution works in your lab (perhaps @niksirbi can add a nudge if he confirms it on his data) so readers know it hasn't been tested on an extensive range of different datasets (even though I don't expect problems either). This is what the wiki is for: if people find that it doesn't work for them, or see ways to improve we can always adjust. |
Thank you Niko for your fast answer! Yes you are right, R-L is always very tricky and without a marker it may be difficult to know which is which. If you happen to know how the animal was registered at the console and how it was actually positioned in the tunnel, you may guess how wrong is the label. It happened to us recently: |
Thank you also Chris! Yes I have editing rights.I will write with this cautionary note. |
You are completely right about the LR thing. Just trying to think through your example gave me a headache :). Plus, sometimes we don't know how the animal was registered during scanning. Markers are the only fail-proof way. Meanwhile, I did some testing of your method. I loaded a misaligned macaque T1 image into fsleyes, and determined that the data orientation was RIA (x, y, z displays were increasing towards right, inferior, and anterior respectively). Then I ran: Anyhow, I don't know why |
ok! Thank you for checking! Would you mind sharing the file you wanted to correct to see if it something to do with your AFNI or with the file itself? or maybe just share the output of 3dinfo for this image? |
I can confirm that freesurfer uses the same convention as FSL: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert
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Sure! You can download the file from here: https://drive.google.com/file/d/1B8vq7V1N6KEC151YT3zYCBy4cvS7BGSh/view?usp=sharing It's the original, unaltered nifti. You can assume that the R label is correct. Below is a screenshot from the |
It is also very good to know that this works also with freesurfer, it can be useful for users who don't use AFNI on their system! |
Thank you for sharing! It was a perfect counter example! I also got a headache when I discover that AFNI 3drefit did not do anything to this file. I tried many thing, convert the nifti file to AFNI format, delete orientation before... Before: |
This is fantastic @julfou81 ! Thanks for zeroing on the problem. We should definitely include this knowledge in the wiki now! |
Thank you @niksirbi for showing the |
Anyone willing to add a section to the wiki, or did that already happen? |
My bad @pcklink , I am supposed to do it and got side-tracked. I will do it very soon. |
No rush. I was just scrolling through the issues as a reminder of things initiated but perhaps not completed 🙂 |
Hi @pcklink @niksirbi ,
I would like to report a procedure that we use now in our lab to correct for the wrong label issue in some NHP acquisitions (like when the animal is in sphinx position, or that there is any kind of mismatch between the registration at the subject on the scanner and the actual position of the animal in the scanner).
Here is an example:
The solution we use now lies in in two lines using AFNI and FSL: The labels are wrong so don't look at them. First you need to look at the data storage (in FSLeyes for example) (you have to determine toward each direction each dimension is increasing):
=> The data storage is 'IPL' in FSL convention, and 'SAR' in AFNI convention (opposite convention between AFNI and FSL, why keep things simple? ;-) )
So the first command is from AFNI:
3drefit -orient SAR your_image_to_correct.nii.gz
=> the label are now correct but the display is not standard in FSLeye
So to have a correct display, we now use FSL:
fslreorient2std your_image_to_correct.nii.gz your_image_corrected.nii.gz
=> the image is now ready to work with!
Do you think it is a sound procedure?
Do you think I should add this in the wiki?
Thank you for your answer!
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