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help > RE: Setup Pipeline error: "mismatched dimensions"
Apr 5, 2017 09:04 PM | Alfonso Nieto-Castanon - Boston University
RE: Setup Pipeline error: "mismatched dimensions"
Hi Sascha
Simply placing the "functional removal of initial scans" step at the beginning of your pipeline (instead of at the end) should work without a problem. The error that you describe is arising because your first-level covariates are being created during the "realignment" and the "outlier detection" steps (before the initial five scans are being removed) so they end up having different lengths / number of timepoints than your functional data (which is not cropped until later in that pipeline). Moving the "functional removal" step before realignment will fix this issue (and yes, I will see if I can make CONN a bit smarter and have it crop the first-level covariates automatically when using the "functional removal of initial scans" step in order to avoid this issue in the future, thanks for pointing this issue out)
Hope this helps
Alfonso
Originally posted by Sascha Froelich:
Simply placing the "functional removal of initial scans" step at the beginning of your pipeline (instead of at the end) should work without a problem. The error that you describe is arising because your first-level covariates are being created during the "realignment" and the "outlier detection" steps (before the initial five scans are being removed) so they end up having different lengths / number of timepoints than your functional data (which is not cropped until later in that pipeline). Moving the "functional removal" step before realignment will fix this issue (and yes, I will see if I can make CONN a bit smarter and have it crop the first-level covariates automatically when using the "functional removal of initial scans" step in order to avoid this issue in the future, thanks for pointing this issue out)
Hope this helps
Alfonso
Originally posted by Sascha Froelich:
Hello,
I preprocessed my data with conn successfully. Then I wanted to proceed to the "Setup" step: I clicked "Done", then tried to run the default Setup pipeline, upon which I received the following two error messages for every subject:
This is my preprocessing pipeline (in order):
Due to the apparent lack of 5 scans I thought the problem might be due to my last preprocessing step (removal of first 5 functional scans). But then why would conn offer this preprocessing option if it were not able to further process the resulting data?
I am using CONN v.16.b
What is the problem here?
Thanks!
Best,
Sascha
I preprocessed my data with conn successfully. Then I wanted to proceed to the "Setup" step: I clicked "Done", then tried to run the default Setup pipeline, upon which I received the following two error messages for every subject:
ERROR: Subject XXX Session 1 first-level
covariate realignment mismatched dimensions (250 rows, while
functional data has 245 scans; the number of rows of a first-level
covariate should equal the number of scans for this
subject/session)
ERROR: Subject XXX Session 1 first-level covariate scrubbing mismatched dimensions (250 rows, while functional data has 245 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject XXX Session 1 first-level covariate scrubbing mismatched dimensions (250 rows, while functional data has 245 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
This is my preprocessing pipeline (in order):
-functional Slice-time correction
-functional Realignment&Unwarp
-functional Center to (0,0,0) coordinates
-structural Center to (0,0,0) coordinates
-functional coregistration to structural
-structural segmentation&normalization
-functional normalization
-functional outlier detection (ART-based scrubbing)
-functional smoothing
-functional removal of initial scans (first 5 scans)
-functional Realignment&Unwarp
-functional Center to (0,0,0) coordinates
-structural Center to (0,0,0) coordinates
-functional coregistration to structural
-structural segmentation&normalization
-functional normalization
-functional outlier detection (ART-based scrubbing)
-functional smoothing
-functional removal of initial scans (first 5 scans)
Due to the apparent lack of 5 scans I thought the problem might be due to my last preprocessing step (removal of first 5 functional scans). But then why would conn offer this preprocessing option if it were not able to further process the resulting data?
I am using CONN v.16.b
What is the problem here?
Thanks!
Best,
Sascha
Threaded View
| Title | Author | Date |
|---|---|---|
| Sascha Froelich | Apr 5, 2017 | |
| Alfonso Nieto-Castanon | Apr 5, 2017 | |
| Raoul Hernandez | Jul 28, 2022 | |
| Alfonso Nieto-Castanon | Aug 1, 2022 | |
| Raoul Hernandez | Aug 3, 2022 | |
| Raoul Hernandez | Aug 20, 2022 | |
| Alfonso Nieto-Castanon | Aug 29, 2022 | |
| Matti Gärtner | Apr 28, 2017 | |
| Sascha Froelich | Apr 11, 2017 | |