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help > RE: Missing confound-corrected time-series (dsw*.nii) in subject folder
Oct 11, 2021 01:10 AM | Yann Quide
RE: Missing confound-corrected time-series (dsw*.nii) in subject folder
Dear Alfonso,
I am still having this issue.
I checked all the points you previously raised, but no luck.
I tried to re-install the toolbox etc. still no luck.
Is there a way to re-create these files a posteriori?
Thanks for your help on this.
Best regards,
Yann
Originally posted by Yann Quide:
I am still having this issue.
I checked all the points you previously raised, but no luck.
I tried to re-install the toolbox etc. still no luck.
Is there a way to re-create these files a posteriori?
Thanks for your help on this.
Best regards,
Yann
Originally posted by Yann Quide:
Thanks Alfonso for
your feedback.
I tried to restart the denoising of my data again, making sure all boxes are ticked, checked the conn_process DONEW is set to 1 and overwrite the old data.
But no luck.
Do you think I should try and re-install the toolbox from fresh and re-process my data from scratch?
Or is there an alternative way to create these files?
Thanks again for your help.
Yann
Originally posted by Alfonso Nieto-Castanon:
I tried to restart the denoising of my data again, making sure all boxes are ticked, checked the conn_process DONEW is set to 1 and overwrite the old data.
But no luck.
Do you think I should try and re-install the toolbox from fresh and re-process my data from scratch?
Or is there an alternative way to create these files?
Thanks again for your help.
Yann
Originally posted by Alfonso Nieto-Castanon:
Dear
Yann
That's strange, I would probably suggest double-checking the following:
a) that the 'create cofound-corrected timeseries' option is still checked in the Setup.Options tab
b) that the file conn_process.m in line #1186 has not been modified and the variable DONEW... is set to 1 (it should read:
DONEWOUTPUTCONFCORR=1; % create confound-corrected timeseries option (0: old format -one file per condition-; 1: new format -one file per session-; 2: both)
and c) that when re-running the denoising step you are selecting the option that reads 'overwrite existing results'
With those options the denoised files named d*.nii "should" appear in your subject folders (the file names will only be dsw*.nii if your data was preprocessed in CONN using the default pipeline, otherwise they will simply be named by prepending the letter 'd' to the data in Setup.Functionals (primary dataset)
Hope this helps
Alfonso
Originally posted by Yann Quide:
That's strange, I would probably suggest double-checking the following:
a) that the 'create cofound-corrected timeseries' option is still checked in the Setup.Options tab
b) that the file conn_process.m in line #1186 has not been modified and the variable DONEW... is set to 1 (it should read:
DONEWOUTPUTCONFCORR=1; % create confound-corrected timeseries option (0: old format -one file per condition-; 1: new format -one file per session-; 2: both)
and c) that when re-running the denoising step you are selecting the option that reads 'overwrite existing results'
With those options the denoised files named d*.nii "should" appear in your subject folders (the file names will only be dsw*.nii if your data was preprocessed in CONN using the default pipeline, otherwise they will simply be named by prepending the letter 'd' to the data in Setup.Functionals (primary dataset)
Hope this helps
Alfonso
Originally posted by Yann Quide:
Dear Alfonso and other CONN users,
Although I selected the option to write the confound-corrected time-series in the Setup window, the dsw*.nii files do not appear in my subject folders.
I tried to rerun everything from scratch (including all preprocessing steps just in case), but no luck.
I am using CONN v20b in Matlab 2021a for Windows 10.
Did I miss something?
Is there a way to compute these files a posteriori?
Thanks in advance.
Yann
Although I selected the option to write the confound-corrected time-series in the Setup window, the dsw*.nii files do not appear in my subject folders.
I tried to rerun everything from scratch (including all preprocessing steps just in case), but no luck.
I am using CONN v20b in Matlab 2021a for Windows 10.
Did I miss something?
Is there a way to compute these files a posteriori?
Thanks in advance.
Yann
Threaded View
| Title | Author | Date |
|---|---|---|
| Yann Quide | Aug 31, 2021 | |
| Alfonso Nieto-Castanon | Sep 15, 2021 | |
| Yann Quide | Sep 16, 2021 | |
| Yann Quide | Oct 11, 2021 | |
| Yann Quide | Oct 13, 2021 | |
| Alfonso Nieto-Castanon | Oct 13, 2021 | |
| Yann Quide | Oct 13, 2021 | |
| Alfonso Nieto-Castanon | Oct 13, 2021 | |
| Yann Quide | Oct 14, 2021 | |
| Alfonso Nieto-Castanon | Oct 14, 2021 | |
| Yann Quide | Sep 13, 2021 | |