Dear Expert,

I am using default pipeline for preprocessing. Recently I am facing an issue which I pasted below. Later I deleted all the files generated and restarted freshly, but it didn't recognise my structural file instead it has loaded reference file. Now I am doing structural segmentation separately. How to add the GM, WM and CSF images after segmentation? Please provide a solution.

Thanks
Ramesh

Earlier preprocessing - segmentation failed
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07-Mar-2020 01:39:32 - Running job #1
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07-Mar-2020 01:39:32 - Running 'Segment'

SPM12: spm_preproc_run (v7670) 01:39:32 - 07/03/2020
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Segment /mnt/research/conn_analysis/rs_fc_nm_rm/rs_fmri/augrp101_rs.nii,6
07-Mar-2020 01:40:18 - Failed 'Segment'
Error using mat2file
Index exceeds matrix dimensions.
In file "/mnt/professional/matlabpath/spm12/@file_array/subsasgn.m" (v7147), function "subfun" at line 164.
In file "/mnt/professional/matlabpath/spm12/@file_array/subsasgn.m" (v7147), function "subsasgn" at line 85.
In file "/mnt/professional/matlabpath/spm12/@nifti/subsasgn.m" (v7744), function "fun" at line 74.
In file "/mnt/professional/matlabpath/spm12/@nifti/subsasgn.m" (v7744), function "subsasgn" at line 20.
In file "/mnt/professional/matlabpath/spm12/spm_preproc_write8.m" (v7415), function "spm_preproc_write8" at line 306.
In file "/mnt/professional/matlabpath/spm12/spm_preproc_run.m" (v7670), function "run_job" at line 171.
In file "/mnt/professional/matlabpath/spm12/spm_preproc_run.m" (v7670), function "spm_preproc_run" at line 41.
In file "/mnt/professional/matlabpath/spm12/config/spm_cfg_preproc8.m" (v7629), function "spm_local_preproc_run" at line 474.
07-Mar-2020 01:40:18 - Running 'Normalise: Write'
07-Mar-2020 01:40:18 - Failed 'Normalise: Write'
Error using read_hdr (line 39)
Error reading header file "/mnt/research/conn_analysis/rs_fc_nm_rm/rs_fmri/y_augrp101_rs.nii".
In file "/mnt/professional/matlabpath/spm12/@nifti/private/read_hdr.m" (v7504), function "read_hdr" at line 39.
In file "/mnt/professional/matlabpath/spm12/@nifti/nifti.m" (v7758), function "nifti" at line 26.
In file "/mnt/professional/matlabpath/spm12/@nifti/nifti.m" (v7758), function "nifti" at line 97.
In file "/mnt/professional/matlabpath/spm12/config/spm_run_norm.m" (v7406), function "write_norm" at line 98.
In file "/mnt/professional/matlabpath/spm12/config/spm_run_norm.m" (v7406), function "spm_run_norm" at line 29.
The following modules did not run:
Failed: Segment
Failed: Normalise: Write
/mnt/research/conn_analysis/rs_fc_nm_rm/rs_fc_nm_rm.qlog/200307010711434/node.0001200307010711434.sh error
ERROR DESCRIPTION:
Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact #job as displayed in this error message)


Fresh preprocessing - completed with reference images


07-Mar-2020 10:15:39 - Running job #1
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07-Mar-2020 10:15:40 - Running 'Segment'

SPM12: spm_preproc_run (v7670) 10:15:40 - 07/03/2020
========================================================================
Segment /mnt/professional/matlabpath/conn/utils/surf/creferenceT1.nii
Segment /mnt/professional/matlabpath/conn/utils/surf/creferenceT1.nii
Segment /mnt/professional/matlabpath/conn/utils/surf/creferenceT1.nii
Segment /mnt/professional/matlabpath/conn/utils/surf/creferenceT1.nii
Segment /mnt/professional/matlabpath/conn/utils/surf/creferenceT1.nii
Segment /mnt/professional/matlabpath/conn/utils/surf/creferenceT1.nii
Segment /mnt/professional/matlabpath/conn/utils/surf/creferenceT1.nii
Segment /mnt/professional/matlabpath/conn/utils/surf/creferenceT1.nii
Segment /mnt/professional/matlabpath/conn/utils/surf/creferenceT1.nii
Segment /mnt/professional/matlabpath/conn/utils/surf/creferenceT1.nii
Segment /mnt/professional/matlabpath/conn/utils/surf/creferenceT1.nii