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MASILab / Synb0-DISCO

Distortion correction of diffusion weighted MRI without reverse phase-encoding scans or field-maps
https://my.vanderbilt.edu/masi
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Could not open matrix file /tmp/tmp.CAniyjLkgw/epi_reg_d.mat #67

Closed mmelmendili closed 2 months ago

mmelmendili commented 3 months ago

Hi, I got an error related to epi_regt:

Copying user provided T1 Mask

epi_reg distorted b0 to T1 epi_reg --epi=/INPUTS/b0.nii.gz --t1=/INPUTS/T1.nii.gz --t1brain=/tmp/tmp.CAniyjLkgw/T1_mask.nii.gz --out=/tmp/tmp.CAniyjLkgw/epi_reg_d Running FAST segmentation FLIRT pre-alignment Running BBR Image Exception : #75 :: 3D only method called by higher-dimensional volume. 3D only method called by higher-dimensional volume. Could not open matrix file /tmp/tmp.CAniyjLkgw/epi_reg_d.mat /extra/fsl/bin/epi_reg: line 399: 958 Segmentation fault (core dumped) $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout} --premat=${vout}.mat --interp=spline

Whether I provide a T1 mask or not, I get the same error. I am using Doker container. Could you please help me with this issue ?

Thank you very much, MM

schillkg commented 3 months ago

Can you verify that both the b0.nii.gz and T1.nii.gz are 3D volumes only? A common mistake is giving all b=0 images as inputs as a 4D volume.

schillkg commented 2 months ago

We are marking this as complete. Allowing multiple b=0 images is a feature to include in future updates.