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help > RE: Loading conn files in SPM
Aug 6, 2015 05:08 PM | Alfonso Nieto-Castanon - Boston University
RE: Loading conn files in SPM
Hi Chaleece,
This indicates that SPM finds no significant "any condition/task effects" in your data. There are several potential reasons, my best guess is that this is related to the explicit masking of the analyses combined with the band-pass filtering of your original data (by default SPM will look for "in-brain" voxels by comparing their average BOLD signal to the average global BOLD signal; since your data is band-pass filtered the average BOLD signal is always 0). I would suggest to change in your script the line "spm.stats.fmri_spec.mthresh=.8" to ""spm.stats.fmri_spec.mthresh=-inf" in order to skip this implicit masking altogether. Please let me know if that does not seem to be the issue here.
Best
Alfonso
Originally posted by Chaleece Sandberg:
This indicates that SPM finds no significant "any condition/task effects" in your data. There are several potential reasons, my best guess is that this is related to the explicit masking of the analyses combined with the band-pass filtering of your original data (by default SPM will look for "in-brain" voxels by comparing their average BOLD signal to the average global BOLD signal; since your data is band-pass filtered the average BOLD signal is always 0). I would suggest to change in your script the line "spm.stats.fmri_spec.mthresh=.8" to ""spm.stats.fmri_spec.mthresh=-inf" in order to skip this implicit masking altogether. Please let me know if that does not seem to be the issue here.
Best
Alfonso
Originally posted by Chaleece Sandberg:
Hello again,
I hate to be a bother, but I have now run into another problem when I try to actually run the GLM in SPM:
Running 'Model estimation'
SPM12: spm_spm (v6015) 11:58:27 - 06/08/2015
========================================================================
SPM12: spm_est_non_sphericity (v6015) 11:58:30 - 06/08/2015
========================================================================
Chunk 97/97 : ...processing
Failed 'Model estimation'
Error using spm_est_non_sphericity (line 196)
Please check your data: There are no significant voxels.
In file "C:\Users\Public\Documents\spm12\spm_est_non_sphericity.m" (v6015), function "spm_est_non_sphericity" at line 196.
In file "C:\Users\Public\Documents\spm12\spm_spm.m" (v6015), function "spm_spm" at line 418.
In file "C:\Users\Public\Documents\spm12\config\spm_run_fmri_est.m" (v5809), function "spm_run_fmri_est" at line 33.
The following modules did not run:
Failed: Model estimation
Does this mean that the Denoising step somehow reduced any significance? I didn't include the conditions as confounds for denoising. I am attaching my my batch for spm, if that helps. Would you like the conn.mat file?
I hate to be a bother, but I have now run into another problem when I try to actually run the GLM in SPM:
Running 'Model estimation'
SPM12: spm_spm (v6015) 11:58:27 - 06/08/2015
========================================================================
SPM12: spm_est_non_sphericity (v6015) 11:58:30 - 06/08/2015
========================================================================
Chunk 97/97 : ...processing
Failed 'Model estimation'
Error using spm_est_non_sphericity (line 196)
Please check your data: There are no significant voxels.
In file "C:\Users\Public\Documents\spm12\spm_est_non_sphericity.m" (v6015), function "spm_est_non_sphericity" at line 196.
In file "C:\Users\Public\Documents\spm12\spm_spm.m" (v6015), function "spm_spm" at line 418.
In file "C:\Users\Public\Documents\spm12\config\spm_run_fmri_est.m" (v5809), function "spm_run_fmri_est" at line 33.
The following modules did not run:
Failed: Model estimation
Does this mean that the Denoising step somehow reduced any significance? I didn't include the conditions as confounds for denoising. I am attaching my my batch for spm, if that helps. Would you like the conn.mat file?
Threaded View
Title | Author | Date |
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Roger Beaty | Jun 12, 2014 | |
Leah Fleming | Nov 23, 2016 | |
kito24 | Feb 7, 2017 | |
Laila Franke | Dec 19, 2018 | |
Pravesh Parekh | Dec 19, 2018 | |
Leah Fleming | Feb 8, 2017 | |
Alfonso Nieto-Castanon | Jun 13, 2014 | |
Chaleece Sandberg | Jul 31, 2015 | |
Alfonso Nieto-Castanon | Aug 3, 2015 | |
Chaleece Sandberg | Aug 5, 2015 | |
Nole Hiebert | Aug 23, 2018 | |
Alfonso Nieto-Castanon | Aug 6, 2015 | |
Chaleece Sandberg | Aug 6, 2015 | |
Chaleece Sandberg | Aug 6, 2015 | |
Alfonso Nieto-Castanon | Aug 6, 2015 | |
laurentcohen | Sep 14, 2018 | |
Chaleece Sandberg | Oct 2, 2015 | |
Alfonso Nieto-Castanon | Oct 8, 2015 | |
kito24 | Feb 9, 2017 | |
Ines Del Cerro | Nov 9, 2017 | |
Patrick McConnell | Nov 3, 2017 | |
Roger Beaty | Jan 26, 2015 | |
Alfonso Nieto-Castanon | Jan 27, 2015 | |
Roger Beaty | Jan 27, 2015 | |
Alfonso Nieto-Castanon | Jan 29, 2015 | |
laurel morris | Mar 11, 2016 | |
Alfonso Nieto-Castanon | Mar 14, 2016 | |
Isabel Berwian | Nov 28, 2016 | |
Anila D'Mello | Nov 10, 2015 | |
Roger Beaty | Jun 14, 2014 | |