Dear Chris,
I would be grateful for your help with the following error.
I am trying to use your MR Clinical Toolbox in SPM 12 to perform
Enantiomorphic normalisation on a T1 scan prior to using Freesurfer
recon all.
The scan contains a large brain tumour which I manually segmented
and binarised using FSLeyes on the T1 scan. I then supplied the T1
image with the binarised lesion segmentation as the 'Lesion Map'.
My T1 and lesion image dimensions are 0.5 mm x 0.5 mm x 1mm. Both
images are world orientated Radiological RAS.
Unfortunately, I am unable to run the toolbox as it throws the
following error:
31-Mar-2021 16:19:35 - Failed 'MR segment-normalize'
Index exceeds the number of array elements (8).
In file "/Users/MATLAB/spm12/@nifti/nifti.m" (v7758), function
"nifti" at line 59.
In file "/Users/yizhouwan/MATLAB/spm12/spm_vol_nifti.m" (v6079),
function "spm_vol_nifti" at line 19.
In file "/Users/yizhouwan/MATLAB/spm12/spm_vol.m" (v5958), function
"spm_vol_hdr" at line 128.
In file "/Users/yizhouwan/MATLAB/spm12/spm_vol.m" (v5958), function
"spm_vol" at line 61.
In file
"/Users/yizhouwan/MATLAB/spm12/toolbox/Clinical-master/clinical_mrnormseg_job.m"
(???), function "clinical_mrnormseg_job" at line 14.
In file
"/Users/yizhouwan/MATLAB/spm12/toolbox/Clinical-master/tbx_cfg_clinical.m"
(???), function "clinical_local_mrnormseg" at line 319.
The following modules did not run:
Failed: MR segment-normalize
At first I thought this was due to my voxel dimensions not being 1
x 1 x1 but after changing the voxel option to 0.5 0.5 1, I get the
same error.
I have also run the toolbox using your tutorial T1 and lesionT1
images and there is no problem.
I would be grateful for any assistance you can provide.
Many thanks,
Kind regards
Yizhou
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