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Number of DWIs, b-vals and b-vecs mismatch #1095
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Hi @ta4218 Thanks for reporting. Best, |
Hi Nicolas, I am currently using Clinica 0.7.7. My OS is Red Hat Enterprise Linux 8.5 (Ootpa). As for the input data, it is in BIDS format; could you clarify what you mean by what the input data looks like? The command line is: The error traceback looks like this:
Thanks, |
Thanks for clarifying a bit @ta4218 ! By looking at the traceback, it seems like the pipeline is crashing right at the beginning because of the dimensions mismatch between the DWI image and the b-vectors and b-values. You can verify these issues by opening the related files and checking the shapes. Here is an example from data that we use in our CI: >>> import numpy as np
>>> import nibabel as nib
>>> img = nib.load("sub-PREVDEMALS0010025PG_ses-M000_dwi.nii.gz")
>>> img.shape
(96, 96, 59, 139)
>>> bvals = np.loadtxt("sub-PREVDEMALS0010025PG_ses-M000_dwi.bval")
>>> bvals
>>> bvals.shape
(139,)
>>> bvecs = np.loadtxt("sub-PREVDEMALS0010025PG_ses-M000_dwi.bvec")
>>> bvecs.shape
(3, 139) I'm wondering whether your input dataset contains other subjects or sessions on which you could try running this to see if you get the same problem. It might just be an issue with this specific subject / session. |
I have another example here. I'm not able to confirm at the moment how many more there are. It is peculiar that the shape is 3d and not 4d for the dwi img.
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@ta4218 Thanks for looking into it. |
@NicolasGensollen Thanks for your help. Don't worry, I have gone through a few that are working OK; my initial investigations suggest that this is a subject-specific issue. Thanks, |
This issue is considered stale because it has not received further activity for the last 14 days. You may remove the |
This issue is considered stale because it has not received further activity for the last 14 days. You may remove the |
Hello,
I am running the dwi-preprocessing-using-t1 pipeline on some ADNI data. I have been receiving the following error which causes the pipeline to crash:
"OSError: Number of DWIs, b-vals and b-vecs mismatch (# DWI = 34, # B-vec = 32, #B-val = 32)"
I can remove the specific image from my .tsv file but then a new image error occurs with a new mismatch. Is there a way to identify all images that have mismatches prior to running, or to ignore this error and run without the pipeline crashing.
Thanks,
Tom
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