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[#9982] Intensity boundary is not calculated for cal_min=cal_max=0
Date: 2021-10-28 11:07 |
Priority: more information 3 |
Submitted By:
spenhouet (spenhouet)
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Assigned To: more information
Nobody (None) |
Hardware: None | Product: None |
Operating System: other | Component: None |
Version: None | Severity: normal |
Resolution: None |
Summary: more information Intensity boundary is not calculated for cal_min=cal_max=0 |
| Detailed description |
In the file hippo.nii.gz the cal_min and cal_max are set to 0.
When loading the orig.nii.gz and hippo.nii.gz, then the
"Darkest" value is wrong (-128).
Reproduction:
- Open orig.nii.gz in MRIcroGL
- Overlay hippo.nii.gz
Expected behavior:
The hippo.nii.gz file should load with "Darkets" set to 0 and
"Brightest" set to 5.
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Response
| Message |
Date: 2021-10-28 15:09
Sender: Chris Rorden
Hello
This will be fixed in the next release, alternatively recompile the
latest commit on Github:
https://github.com/rordenlab/MRIcroGL/commit/c755d83a23fd431641807a5769255c7880a0a6f1
The core issue is that your image is saved as INT8. While legal,
this is an exceptionally rare data type (indeed, it did not exist
in NIfTI's predecessor the Analyze format). This may cause unusual
behavior in many tools. I would suggest saving images like this as
UINT8 data. Here is a Python script to convert INT8 data types to
UINT8:
import nibabel as nib
import numpy as np
fnm = 'hippo.nii.gz'
nii = nib.load(fnm)
img = nii.get_fdata()
nii.set_data_dtype(np.ubyte)
nii = nib.Nifti1Image(img, nii.affine, nii.header)
nii.header['scl_slope'] = 1.0
nii.header['scl_inter'] = 0.0
outnm = 'hippo8.nii.gz'
nib.save(nii, outnm)
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Attached Files:
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Changes:
| Field |
Old Value |
Date |
By |
| New Message | | 2021-10-28 15:09 | crlab |
| File Added | 1166: hippo.nii.gz | 2021-10-28 11:07 | spenhouet |
| File Added | 1165: orig.nii.gz | 2021-10-28 11:07 | spenhouet | |
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