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help > RE: Loading conn files in SPM
Aug 3, 2015 05:08 AM | Alfonso Nieto-Castanon - Boston University
RE: Loading conn files in SPM
Hi Chaleece,
Your hunch is correct, the BOLD signal will already be orthogonal to any effects entered in the 'Denoising' step so there is no need to add those covariates again in your SPM model when exporting these data. And regarding the "separated by condition" nii files, if you are using a relatively recent release of CONN you will get a series of files associated with "condition 0" named niftiSubject*_Condition0000.nii which contain all of your data (no separation by condition), so if using these data you may enter the same GLM design you would normally do in SPM (if you are instead entering the condition-specific timeseries into a first-level SPM GLM, then yes, you would typically need to permute your design matrix rows to follow the same order as in your functional data)
Hope this helps
Alfonso
Originally posted by Chaleece Sandberg:
Your hunch is correct, the BOLD signal will already be orthogonal to any effects entered in the 'Denoising' step so there is no need to add those covariates again in your SPM model when exporting these data. And regarding the "separated by condition" nii files, if you are using a relatively recent release of CONN you will get a series of files associated with "condition 0" named niftiSubject*_Condition0000.nii which contain all of your data (no separation by condition), so if using these data you may enter the same GLM design you would normally do in SPM (if you are instead entering the condition-specific timeseries into a first-level SPM GLM, then yes, you would typically need to permute your design matrix rows to follow the same order as in your functional data)
Hope this helps
Alfonso
Originally posted by Chaleece Sandberg:
Hi
Alfonso,
If you use the confound-corrected time-series .nii files created by CONN after the denoising step in the SPM GLM for a first level analysis, do you still need to include the "outliers and movement".mat file from art as a regressor in SPM if it was entered as a first-level covariate in CONN? My hunch is no, but I just want to verify. Also, if the .nii files are separated by condition, rather than run/session, do I need to set up the SPM GLM differently?
Thanks!
Chaleece
Originally posted by Alfonso Nieto-Castanon:
If you use the confound-corrected time-series .nii files created by CONN after the denoising step in the SPM GLM for a first level analysis, do you still need to include the "outliers and movement".mat file from art as a regressor in SPM if it was entered as a first-level covariate in CONN? My hunch is no, but I just want to verify. Also, if the .nii files are separated by condition, rather than run/session, do I need to set up the SPM GLM differently?
Thanks!
Chaleece
Originally posted by Alfonso Nieto-Castanon:
Hi
Roger,
If you want to use in SPM the BOLD timeseries after removal of confounding effects, you may simply select in Setup->Options the checkbox labeled 'Create confound-corrected time-series'. and that will create as part of the Preprocessing step a series of .nii files with these BOLD timeseries which you may then enter into SPM for further analyses (these will appear in your conn_*/results/preprocessing/ folder and the files will be named niftiDATA_Subject###_Condition###.nii).
If you have already run your preprocessing step and want to avoid having to repeat it, you may also simply type in the command window:
and that will create these same files from the already computed preprocessing-step results.
Hope this helps
Alfonso
Originally posted by Roger Beaty:
If you want to use in SPM the BOLD timeseries after removal of confounding effects, you may simply select in Setup->Options the checkbox labeled 'Create confound-corrected time-series'. and that will create as part of the Preprocessing step a series of .nii files with these BOLD timeseries which you may then enter into SPM for further analyses (these will appear in your conn_*/results/preprocessing/ folder and the files will be named niftiDATA_Subject###_Condition###.nii).
If you have already run your preprocessing step and want to avoid having to repeat it, you may also simply type in the command window:
conn_matc2nii;
and that will create these same files from the already computed preprocessing-step results.
Hope this helps
Alfonso
Originally posted by Roger Beaty:
Hi everyone,
I'm trying to load .mat files that were preprocessed in CONN back to SPM to perform a GLM analysis. In other words, I ran the preprocessing pipeline using the CONN gui and would like to import the files produced by CONN back to SPM. My guess is that CONN formats .mat files specific to the toolbox, and that these files are not easily loadable into the SPM GUI. Is it possible to import CONN files back to SPM and run a traditional GLM?
Many thanks,
Roger
I'm trying to load .mat files that were preprocessed in CONN back to SPM to perform a GLM analysis. In other words, I ran the preprocessing pipeline using the CONN gui and would like to import the files produced by CONN back to SPM. My guess is that CONN formats .mat files specific to the toolbox, and that these files are not easily loadable into the SPM GUI. Is it possible to import CONN files back to SPM and run a traditional GLM?
Many thanks,
Roger
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 | |