Hello,
I am trying to perform preprocessing of resting state data (with conn 18b) after performing motion correction and unwarping with fsl mcflirt and topup, respectively. I have imported the motion corrected/unwarped data into conn as the primary dataset. I have also imported the motion parameters as a 1st level covariate labelled 'realignment'.
These are the preprocessing steps I am trying to run (basically the default pipeline starting at the functional Outlier detection step):
functional Outlier detection (ART-based identification of outlier scans for scrubbing)
functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
functional Smoothing (spatial convolution with Gaussian kernel)
functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
However, I am getting the following error during preprocessing (at functional Direct Segmentation & Normalization):
[code]SPM preprocessing job
(1).spm.spatial.preproc.channel.vols = /Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/art_mean_fmri.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [2 2 2]
(2).spm.spatial.normalise.write.subj.def = /Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/y_art_mean_fmri.nii
(2).spm.spatial.normalise.write.subj.resample(1) = /Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/art_mean_fmri.nii
(2).spm.spatial.normalise.write.subj.resample(2) = /Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/c1art_mean_fmri.nii
(2).spm.spatial.normalise.write.subj.resample(453) = /Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/fmri.nii,449
(2).spm.spatial.normalise.write.subj.resample(454) = /Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/fmri.nii,450[/code][code]------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Segment'[/code][code]SPM12: spm_preproc_run (v6365) 23:36:48 - 09/03/2019
========================================================================
Segment /Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/art_mean_fmri.nii
Failed 'Segment'
Index exceeds matrix dimensions.
In file "/usr/local/spm12/spm_maff8.m" (v7202), function "loadbuf" at line 94.
In file "/usr/local/spm12/spm_maff8.m" (v7202), function "spm_maff8" at line 25.
In file "/usr/local/spm12/spm_preproc_run.m" (v6365), function "run_job" at line 107.
In file "/usr/local/spm12/spm_preproc_run.m" (v6365), function "spm_preproc_run" at line 41.
In file "/usr/local/spm12/config/spm_cfg_preproc8.m" (v6952), function "spm_local_preproc_run" at line 450.[/code][code]Running 'Normalise: Write'
Failed 'Normalise: Write'
Error using read_hdr (line 32)
Error reading header file "/Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/y_art_mean_fmri.nii".
In file "/usr/local/spm12/@nifti/private/read_hdr.m" (v7147), function "read_hdr" at line 32.
In file "/usr/local/spm12/@nifti/nifti.m" (v7147), function "nifti" at line 26.
In file "/usr/local/spm12/@nifti/nifti.m" (v7147), function "nifti" at line 81.
In file "/usr/local/spm12/config/spm_run_norm.m" (v6578), function "write_norm" at line 98.
In file "/usr/local/spm12/config/spm_run_norm.m" (v6578), function "spm_run_norm" at line 29.[/code][code]The following modules did not run:
Failed: Segment
Failed: Normalise: Write[/code][code]ERROR DESCRIPTION:[/code][code]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)
------------------
Running job #1
------------------
CONN18.b
SPM12 + ALI Anatomy DEM FieldMap MEEGtools Masking com conn
Matlab v.2017b
project: CONN18.b
storage: 14296.5Gb available[/code][code]spm @ /usr/local/spm12
conn @ /usr/local/spm12/toolbox/conn[/code]
The image sizes and resolution are the same across images, including the unwarped fmri data and the art_mean_fmri (96 96 66, 2 x 2 x 2).
In addition, the scrubbing covariate appears with a diagonal of dots (see attachment) and the functional data are being reoriented by tilting the head up (see attachment).
I appreciate any help solving these issues.
Regards,
Juan
I am trying to perform preprocessing of resting state data (with conn 18b) after performing motion correction and unwarping with fsl mcflirt and topup, respectively. I have imported the motion corrected/unwarped data into conn as the primary dataset. I have also imported the motion parameters as a 1st level covariate labelled 'realignment'.
These are the preprocessing steps I am trying to run (basically the default pipeline starting at the functional Outlier detection step):
functional Outlier detection (ART-based identification of outlier scans for scrubbing)
functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
functional Smoothing (spatial convolution with Gaussian kernel)
functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
However, I am getting the following error during preprocessing (at functional Direct Segmentation & Normalization):
[code]SPM preprocessing job
(1).spm.spatial.preproc.channel.vols = /Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/art_mean_fmri.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [2 2 2]
(2).spm.spatial.normalise.write.subj.def = /Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/y_art_mean_fmri.nii
(2).spm.spatial.normalise.write.subj.resample(1) = /Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/art_mean_fmri.nii
(2).spm.spatial.normalise.write.subj.resample(2) = /Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/c1art_mean_fmri.nii
(2).spm.spatial.normalise.write.subj.resample(453) = /Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/fmri.nii,449
(2).spm.spatial.normalise.write.subj.resample(454) = /Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/fmri.nii,450[/code][code]------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Segment'[/code][code]SPM12: spm_preproc_run (v6365) 23:36:48 - 09/03/2019
========================================================================
Segment /Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/art_mean_fmri.nii
Failed 'Segment'
Index exceeds matrix dimensions.
In file "/usr/local/spm12/spm_maff8.m" (v7202), function "loadbuf" at line 94.
In file "/usr/local/spm12/spm_maff8.m" (v7202), function "spm_maff8" at line 25.
In file "/usr/local/spm12/spm_preproc_run.m" (v6365), function "run_job" at line 107.
In file "/usr/local/spm12/spm_preproc_run.m" (v6365), function "spm_preproc_run" at line 41.
In file "/usr/local/spm12/config/spm_cfg_preproc8.m" (v6952), function "spm_local_preproc_run" at line 450.[/code][code]Running 'Normalise: Write'
Failed 'Normalise: Write'
Error using read_hdr (line 32)
Error reading header file "/Volumes/My_Book_Pro/BDD-OCD/Analysis/fMRI/REST/spm/115a/y_art_mean_fmri.nii".
In file "/usr/local/spm12/@nifti/private/read_hdr.m" (v7147), function "read_hdr" at line 32.
In file "/usr/local/spm12/@nifti/nifti.m" (v7147), function "nifti" at line 26.
In file "/usr/local/spm12/@nifti/nifti.m" (v7147), function "nifti" at line 81.
In file "/usr/local/spm12/config/spm_run_norm.m" (v6578), function "write_norm" at line 98.
In file "/usr/local/spm12/config/spm_run_norm.m" (v6578), function "spm_run_norm" at line 29.[/code][code]The following modules did not run:
Failed: Segment
Failed: Normalise: Write[/code][code]ERROR DESCRIPTION:[/code][code]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)
------------------
Running job #1
------------------
CONN18.b
SPM12 + ALI Anatomy DEM FieldMap MEEGtools Masking com conn
Matlab v.2017b
project: CONN18.b
storage: 14296.5Gb available[/code][code]spm @ /usr/local/spm12
conn @ /usr/local/spm12/toolbox/conn[/code]
The image sizes and resolution are the same across images, including the unwarped fmri data and the art_mean_fmri (96 96 66, 2 x 2 x 2).
In addition, the scrubbing covariate appears with a diagonal of dots (see attachment) and the functional data are being reoriented by tilting the head up (see attachment).
I appreciate any help solving these issues.
Regards,
Juan