Closed Renatar18 closed 3 years ago
Which version of nibabel are you using? Using an older version might be a quick workaround.
Hi Jakob, Thank you very much for your reply! I adressed your question to our IT engineer, and he replied:
'Now I've installed older nibabel version (2.5.2) in the conda environment for tractseg on your server. But just as a warning, dipy 1.1.1 requires nibabel>=3.0.0. So I'll really need an exact version to not have compatibility issues'.
What do you say? Which version should we install?
Thank you, Renata.
On Mon, Oct 5, 2020 at 8:10 AM Jakob Wasserthal notifications@github.com wrote:
Which version of nibabel are you using? Using an older version might be a quick workaround.
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Which nibabel version did you use when the error occured?
We had version 3.0.1 on it before. When downgraded it to 2.5.2 it told: "dipy 1.1.1 has requirement nibabel>=3.0.0"
On Tue, Oct 6, 2020, 03:00 Jakob Wasserthal notifications@github.com wrote:
Which nibabel version did you use when the error occured?
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I just tested TractSeg with nibabel 3.1.1 and it worked fine for me. I guess there is another error. What is the complete error message when it stops?
This is the complete message when it stops. For some reason it works well for some subjects and doesn't work for the others from the same sample. What could be the problem?
On Fri, Oct 9, 2020 at 8:49 AM Jakob Wasserthal notifications@github.com wrote:
I just tested TractSeg with nibabel 3.1.1 and it worked fine for me. I guess there is another error. What is the complete error message when it stops?
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Probably your FA image has different dimensions than your endpoint_segmentation images.
Could you post the dimensions / affine of those?
Did you use the --preprocess
option?
On the preprocessing I ran eddy_correct and rotated the vectors before starting tractSeg.
On Mon, Oct 12, 2020 at 10:47 AM Jakob Wasserthal notifications@github.com wrote:
Probably your FA image has different dimensions than your endpoint_segmentation images. Could you post the dimensions / affine of those? Did you use the --preprocess option?
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The affine matrices in the header of the images (your diffusion image, peak image, segmentation and FA image) have to be the same. Probably this is causing the error.
They all seem to be the same. Are you willing to see the data? Should I upload one of the "wrong" subjects?
On Wed, Oct 14, 2020 at 3:38 AM Jakob Wasserthal notifications@github.com wrote:
The affine matrices in the header of the images (your diffusion image, peak image, segmentation and FA image) have to be the same. Probably this is causing the error.
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Hello!
The command stops at 16%: Tractometry -i ${i}/tractseg_output/TOM_trackings/ -o results/FA/${i}_FA.csv -e ${i}/tractseg_output/endings_segmentations/ -s ${i}/FA.nii.gz --tracking_format tck
What is wrong?
Thank you!