![]() The final data used for registration after processing/ Step 1 I used dcm2niix output for post-processing… filename dwi_T0000_straight_resa_ Sct_image -set-sform-to-qform data_Īfter I’ve done it also for other inputs labels and segmentation, I re-ran the registration on the corrected one. Then I ran the following syntax to set sform and qform on my input data,seg and labels. **ValueError: Image sform does not match qform** Raise ValueError("Image sform does not match qform") Image(self.centerline_reference_filename, check_sform=True).save(os.path.join(path_tmp, "centerline_"))įile "/data/home/s4333238/.ssh/spinalcordtoolbox/spinalcordtoolbox/image.py", line 311, in _init_ Sct_image -i /tmp/sct-20210306153353.274717-register_to_template-3ql8kvwm/template_ -set-sform-to-qform -o /tmp/sct-20210306153353_same-affine.274717-register_to_template-3ql8kvwm/template_.įile "/data/home/s4333238/.ssh/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_register_to_template.py", line 1281, in įile "/data/home/s4333238/.ssh/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_register_to_template.py", line 533, in mainįile "/data/home/s4333238/.ssh/spinalcordtoolbox/spinalcordtoolbox/straightening.py", line 111, in straighten Consider setting the two matrices to be equal by running:** **Image /tmp/sct-20210306153353.274717-register_to_template-3ql8kvwm/template_ has different qform and sform matrices. Straighten the spinal cord using centerline/segmentation.Ĭreating temporary folder (/tmp/sct-20210306153822.455291-straighten_spinalcord-p1h_7a5e) To avoid intensity overflow due to convertion to +uint8+, intensity will be rescaled to the maximum quantization scaleĬhange orientation of input images to RPI. Segmentation: dwi_mean_seg_res_reg_Ĭreating temporary folder (/tmp/sct-20210306153353.274717-register_to_template-3ql8kvwm)Ĭopying input data to tmp folder and convert to nii.Ĭheck if provided labels are available in the template Sct_register_to_template -i dwi_stra_ -s dwi_mean_seg_res_reg_ -lspinal sc_ -t exvivo-template/ -c t1 resampled,straightened,labeled, I ran the following command for registration… Then I re-ran the syntax using dwi_res_straight_ as input…įsleyes dwi_1500_T0000_res_straight_ sc_ &Ĩ-After I had the data and cord seg. So, I tried to swapdim to get the labels correctly pointed in the right axis I used the following syntaxįslswapdim dwi_res_ x z y dwi_res_straight_ **Inde圎rror: index 935 is out of bounds for axis 1 with size 195** Out = _add_labels(zeros_like(img), coordinates)įile "/data/home/s4333238/.ssh/spinalcordtoolbox/spinalcordtoolbox/labels.py", line 84, in _add_labels Out = sct_labels.create_labels_empty(img, labels)įile "/data/home/s4333238/.ssh/spinalcordtoolbox/spinalcordtoolbox/labels.py", line 53, in create_labels_empty Terminal output error… Traceback (most recent call last):įile "/data/home/s4333238/.ssh/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_label_utils.py", line 413, in įile "/data/home/s4333238/.ssh/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_label_utils.py", line 261, in main **dwi mean was computed and cord segmentation produced using sct_propsegħ-Now, I tried to create the segments labels using the following syntax along Z direction… Please note, I used dcm2niix nifty output for first registration and mrconvert output for second attempt. I provided these information to make sure which software should be used to handle the post-processing in correct way when using SCT. The fslhd output using ***mrconvert*** converter is below The fslhd output using dcm2niix converter is below filename dwi_b0_b1500_ Converted to nifty using mrconvert as package from MRtrix dcm to nifty and also used dcm2niix software for comparison… I did the following steps but ended up with an error in template registration…ġ-Dicom data imported from Bruker animal MRI system. I’m trying to register my high resolution Ex vivo human dwi data into T1 template here.
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