open-discussion
open-discussion > RE: Including CompCor(CONN toolbox) into SPM batch
Mar 1, 2019 11:03 AM | Lars Kasper - Translational Neuromodeling Unit, IBT, University of Zurich and ETH Zurich
RE: Including CompCor(CONN toolbox) into SPM batch
Dear Ralf,
thank you for trying out the development version!
Originally posted by Ralf Veit:
Now, this is really weird. I just tried out your attached batch, and it runs all the way into the tapas_physio_create_noise_rois_regressors function for me. You still seem to be stuck at tapas_physio_read_physlogfiles, am I right? Could it be that the other version of PhysIO is still on the path and is accidentally called? Maybe you could set a breakpoint in tapas_physio_main_create_regressors (of the development version) just before the read_physlogfiles (about line 100) and see whether it indeed uses this version of the main function?
This is a good suggestion, to be able to unmark the vendor, I will include that in a future version. Since Physio was originally developed for model-based noise correction using peripheral recordings, having no recordings wasn't anticipated originally. So as it stands, this is expected behavior and leaving any vendor (as e.g., Philips in your batch) should work.
I am using spm12 (v7129) with matlab 2016b. I have one more question regarding your batch you provided in your response to Sara. There seems to be only one file in the fmri time series option (wuafmri01.nii). Why not the whole series?
In my example, 01 refers to the run, so this is indeed a 4D-nifti file. If you have 1 nifti file per volume, you should include all files of the series, as you did correctly in your batch. Both ways should work with the development version (R2018.1 had a bug for 3D files, I think).
All the best,
Lars
thank you for trying out the development version!
Originally posted by Ralf Veit:
Dear Lars,
I downloaded your development version (tapas version is R2018.2.0) and now there is an example file tapas_physio_example_philips_ecg3t_spm_job.m. After modification of the file according to your suggestions, the error is still the same
Running 'TAPAS PhysIO Toolbox'
Failed 'TAPAS PhysIO Toolbox'
Error using textread (line 165)
File not found.
I downloaded your development version (tapas version is R2018.2.0) and now there is an example file tapas_physio_example_philips_ecg3t_spm_job.m. After modification of the file according to your suggestions, the error is still the same
Running 'TAPAS PhysIO Toolbox'
Failed 'TAPAS PhysIO Toolbox'
Error using textread (line 165)
File not found.
Now, this is really weird. I just tried out your attached batch, and it runs all the way into the tapas_physio_create_noise_rois_regressors function for me. You still seem to be stuck at tapas_physio_read_physlogfiles, am I right? Could it be that the other version of PhysIO is still on the path and is accidentally called? Maybe you could set a breakpoint in tapas_physio_main_create_regressors (of the development version) just before the read_physlogfiles (about line 100) and see whether it indeed uses this version of the main function?
and I have again different errors using
different vendors. There is no option to unmark vendor. Thereafter
I tried the following in the script
matlabbatch{1}.spm.tools.physio.log_files.vendor = {''};
but the program stopped
SWITCH expression must be a scalar or character vector constant and refered to tapas_physio_fill_empty_parameters.m
matlabbatch{1}.spm.tools.physio.log_files.vendor = {''};
but the program stopped
SWITCH expression must be a scalar or character vector constant and refered to tapas_physio_fill_empty_parameters.m
This is a good suggestion, to be able to unmark the vendor, I will include that in a future version. Since Physio was originally developed for model-based noise correction using peripheral recordings, having no recordings wasn't anticipated originally. So as it stands, this is expected behavior and leaving any vendor (as e.g., Philips in your batch) should work.
I am using spm12 (v7129) with matlab 2016b. I have one more question regarding your batch you provided in your response to Sara. There seems to be only one file in the fmri time series option (wuafmri01.nii). Why not the whole series?
In my example, 01 refers to the run, so this is indeed a 4D-nifti file. If you have 1 nifti file per volume, you should include all files of the series, as you did correctly in your batch. Both ways should work with the development version (R2018.1 had a bug for 3D files, I think).
All the best,
Lars
Threaded View
Title | Author | Date |
---|---|---|
Sara Calzolari | Jan 30, 2019 | |
Lars Kasper | Jan 31, 2019 | |
Sara Calzolari | Feb 11, 2019 | |
Lars Kasper | Feb 13, 2019 | |
Ralf Veit | Feb 28, 2019 | |
Lars Kasper | Feb 28, 2019 | |
Ralf Veit | Mar 1, 2019 | |
Lars Kasper | Mar 1, 2019 | |
Ralf Veit | Mar 1, 2019 | |
Lars Kasper | Mar 1, 2019 | |
Ralf Veit | Mar 4, 2019 | |
Ralf Veit | Mar 5, 2019 | |
Lars Kasper | Mar 5, 2019 | |
Ralf Veit | Mar 5, 2019 | |
Lars Kasper | Mar 9, 2019 | |
Ralf Veit | Mar 11, 2019 | |