help
help > RE: Loading conn files in SPM
Jan 27, 2015 09:01 PM | Roger Beaty
RE: Loading conn files in SPM
Hi Alfonso,
Yes, I am trying to look at BOLD activation differences between conditions (i.e., standard SPM GLM analysis), not connectivity differences. The goal is basically to compare these univariate results from SPM with some multivariate connectivity results produced by CONN. If possible, I would like to use the preprocessed images from CONN. Any thoughts on how to do this?
Thanks,
Roger
Originally posted by Alfonso Nieto-Castanon:
Yes, I am trying to look at BOLD activation differences between conditions (i.e., standard SPM GLM analysis), not connectivity differences. The goal is basically to compare these univariate results from SPM with some multivariate connectivity results produced by CONN. If possible, I would like to use the preprocessed images from CONN. Any thoughts on how to do this?
Thanks,
Roger
Originally posted by Alfonso Nieto-Castanon:
Hi
Roger,
Sorry but CONN does not create first-level SPM.mat files that you could import into SPM. Could you please expand a bit on what exactly you are trying to do to see if there are some work-arounds that come to mind? (e.g. are you trying to use CONN preprocessed time-series to look at the "activation" -BOLD signal changes; not connectivity- associated with each condition; if that is the case you could have CONN generate those first-level estimates directly during the denoising step)
Thanks
Alfonso
Originally posted by Roger Beaty:
Sorry but CONN does not create first-level SPM.mat files that you could import into SPM. Could you please expand a bit on what exactly you are trying to do to see if there are some work-arounds that come to mind? (e.g. are you trying to use CONN preprocessed time-series to look at the "activation" -BOLD signal changes; not connectivity- associated with each condition; if that is the case you could have CONN generate those first-level estimates directly during the denoising step)
Thanks
Alfonso
Originally posted by Roger Beaty:
Hi Alfonso and
all,
Following up from my previous question, I'm now trying to load the preprocessed time series from Conn into SPM for first- and second-level analyses. The SPM batch editor requires an SPM.mat file with timing information and a time series in temporal order to specify a model. This information is already implied by the condition files produced by Conn. Is it possible to bypass these steps and simply upload the condition files from Conn to specify a model in SPM?
Thanks,
Roger
Originally posted by Alfonso Nieto-Castanon:
Following up from my previous question, I'm now trying to load the preprocessed time series from Conn into SPM for first- and second-level analyses. The SPM batch editor requires an SPM.mat file with timing information and a time series in temporal order to specify a model. This information is already implied by the condition files produced by Conn. Is it possible to bypass these steps and simply upload the condition files from Conn to specify a model in SPM?
Thanks,
Roger
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 | |