# 5ttgen warning poor registration
**URL:** https://community.mrtrix.org/t/5ttgen-warning-poor-registration/5936
**Category:** Uncategorized
**Tags:** connectomics, error, preprocessing
**Created:** [August 13, 2022, 6:32pm UTC](https://community.mrtrix.org/t/5ttgen-warning-poor-registration/5936 "2022-08-13T18:32:49Z")
**Posts on this page:** 10
**Page:** 1
### Author:  [@andraderenew](https://community.mrtrix.org/u/andraderenew)
#### Post date: [August 13, 2022, 6:32pm UTC](https://community.mrtrix.org/t/5ttgen-warning-poor-registration/5936/1 "2022-08-13T18:32:49Z")
Dear community:
I have run the code below,
5ttgen fsl anat.mif 5tt\_nocoreg.mif -mask mask.mif -force
and it gavem me this warning
5ttgen: [WARNING] Generated image does not perfectly conform to 5TT format:
5ttgen: [WARNING] 5ttcheck: [WARNING] Image “result.mif” contains 44 brain voxels with non-unity sum of partial volume fractions
5ttgen: [WARNING] 5ttcheck: [WARNING] Input image does not perfectly conform to 5TT format, but may still be applicable (suggest re-running using the -masks option to see voxels where tissue fractions do not sum to 1.0)
if i continue the processing towards the structural connectome
tck2connectome: [WARNING] The following nodes do not have any streamlines assigned:
tck2connectome: [WARNING] 1, 3, 7, 8, 10, 14, 17, 18, 19, 21, 23, 26, 29, 30, 31, 33, 36, 37, 38, 39, 40, 42, 43, 44, 46, 80
tck2connectome: [WARNING] (This may indicate a poor registration)
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### Author:  [@j-tseng](https://community.mrtrix.org/u/j-tseng)
#### Post date: [August 14, 2022, 8:46pm UTC](https://community.mrtrix.org/t/5ttgen-warning-poor-registration/5936/2 "2022-08-14T20:46:02Z")
Hey there - a few questions/suggestions for troubleshooting:
1. Did you inspect the `5tt_nocoreg.mif` image after you generated it? Does the segmentation into gray matter, white matter, etc. make sense? If you’re using the gmwm boundary, overlay that on the image as a sanity check.
2. Did anything funky happen when you generated whole-brain streamlines? Do you find streamlines across the whole-brain when you overlay the tractography on the diffusion image? (Warning: don’t overlay the main streamline output, but a tck file with a smaller number of streamlines to avoid crashing your computer.)
3. What about QAing the atlas-related outputs in the steps between `5ttgen` and `tck2connectome`? The `tck2connectome` suggestion about poor registration means you should probably make sure that nothing went wrong for: atlas parcellation of your T1 anat image, the transformation from T1-space to diffusion space?
Good luck!
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### Author:  [@andraderenew](https://community.mrtrix.org/u/andraderenew)
#### Post date: [August 24, 2022, 2:44am UTC](https://community.mrtrix.org/t/5ttgen-warning-poor-registration/5936/3 "2022-08-24T02:44:55Z")
5tt\_nocoreg.mif makes no sense. It seems everything is condensed in one image. I don’t know how to explain just that you don’t have all the views normally but just one square with all brain views superimposed. Anyways thats the issue. I don’t know if just omit this subject from the study or there is any fix.
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### Author:  [@andraderenew](https://community.mrtrix.org/u/andraderenew)
#### Post date: [October 11, 2022, 11:45am UTC](https://community.mrtrix.org/t/5ttgen-warning-poor-registration/5936/4 "2022-10-11T11:45:19Z")
Is there any fix? sorry if I wasn’t explicit enough in the question.
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### Author:  [@mblesac](https://community.mrtrix.org/u/mblesac)
#### Post date: [October 11, 2022, 12:14pm UTC](https://community.mrtrix.org/t/5ttgen-warning-poor-registration/5936/5 "2022-10-11T12:14:15Z")
Hi,
Just to be sure about this, are you using adult human data right?
If 5tt\_nocoreg.mif makes no sense, could you post an image of the anat.mif and the mask.mif?
Best regards,
Manuel
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### Author:  [@andraderenew](https://community.mrtrix.org/u/andraderenew)
#### Post date: [October 11, 2022, 12:52pm UTC](https://community.mrtrix.org/t/5ttgen-warning-poor-registration/5936/6 "2022-10-11T12:52:24Z")
yes adult human data!!
anat.mif and mask.mif files?
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### Author:  [@mblesac](https://community.mrtrix.org/u/mblesac)
#### Post date: [October 11, 2022, 12:53pm UTC](https://community.mrtrix.org/t/5ttgen-warning-poor-registration/5936/7 "2022-10-11T12:53:45Z")
Hi,
Yes, the ones you use for the 5ttgen command:
> [@andraderenew](#):
>
> 5ttgen fsl anat.mif 5tt\_nocoreg.mif -mask mask.mif -force
Best regards,
Manuel
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### Author:  [@andraderenew](https://community.mrtrix.org/u/andraderenew)
#### Post date: [October 11, 2022, 12:55pm UTC](https://community.mrtrix.org/t/5ttgen-warning-poor-registration/5936/8 "2022-10-11T12:55:27Z")
I don’t have them with me when I do I’ll post them.
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### Author:  [@andraderenew](https://community.mrtrix.org/u/andraderenew)
#### Post date: [January 27, 2023, 11:06am UTC](https://community.mrtrix.org/t/5ttgen-warning-poor-registration/5936/9 "2023-01-27T11:06:47Z")
here are the files requested [Transfer - Dropbox](https://www.dropbox.com/t/a2fWe05XkaNfF15m)
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### Author:  [@andraderenew](https://community.mrtrix.org/u/andraderenew)
#### Post date: [January 30, 2023, 11:19am UTC](https://community.mrtrix.org/t/5ttgen-warning-poor-registration/5936/10 "2023-01-30T11:19:43Z")
I understand a lot of time has passed since this post originally was posted. Anyways I decided to discard this subject.