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help > RE: Loading conn files in SPM
Oct 2, 2015 07:10 PM | Chaleece Sandberg
RE: Loading conn files in SPM
Hi Alfonso!
I have bad news. I am getting the same error with the threshold change you suggested. Do you know what else the problem may be? Could it be something in the way I'm setting up the Denoising step? I believe I verified all that during the conference call, but I could be missing something.
Thanks!
Chaleece
Originally posted by Alfonso Nieto-Castanon:
I have bad news. I am getting the same error with the threshold change you suggested. Do you know what else the problem may be? Could it be something in the way I'm setting up the Denoising step? I believe I verified all that during the conference call, but I could be missing something.
Thanks!
Chaleece
Originally posted by Alfonso Nieto-Castanon:
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 |
|---|---|---|
| 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 | |