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help > RE: automated preprocessing steps
Nov 15, 2014 02:11 AM | Alfonso Nieto-Castanon - Boston University
RE: automated preprocessing steps
Hi Jisook,
All preprocessing steps in CONN use the default values set by SPM (typically specified in the file spm_defaults.m or user-defined through spm_get_defaults(...) commands). The simplest way to check which particular values/parameters are being used in CONN and depending on your current version of SPM is to go to the Setup.Structural or Setup.Functional tabs in CONN, then select Options.Preprocessing, select there the preprocessing step you want to inquire about, and select the option "interactive SPM batch editor only". This will launch the spm batch editor listing exactly how that preprocessing step would be performed and including all relevant parameters.
Hope this helps
Alfonso
Originally posted by Ji Sook Park:
All preprocessing steps in CONN use the default values set by SPM (typically specified in the file spm_defaults.m or user-defined through spm_get_defaults(...) commands). The simplest way to check which particular values/parameters are being used in CONN and depending on your current version of SPM is to go to the Setup.Structural or Setup.Functional tabs in CONN, then select Options.Preprocessing, select there the preprocessing step you want to inquire about, and select the option "interactive SPM batch editor only". This will launch the spm batch editor listing exactly how that preprocessing step would be performed and including all relevant parameters.
Hope this helps
Alfonso
Originally posted by Ji Sook Park:
Hi,
Preprocessing steps were done through Conn 14 for resting state functional connectivity analysis (pretraining vs. posttraining).
I chose the default preprocessing pipeline for volume-based analysis (to MNI-space).
It includes functional realignment & unwarp, functional slice-timing correction (descending),
structural segmentation & normalization, functional normalization, functional outlier detection (ART-based),
and functional smoothing (I changed to 4 mm).
The Conn went through preprocessing steps using SPM8.
Behind what I have chosen, I was not sure what parameters this default has selected for the default preprocessing steps.
I need specific details to report the preprocessing steps for publication.
If you know how I find this information, please let me know!
Thank you in advance!
Jisook
Preprocessing steps were done through Conn 14 for resting state functional connectivity analysis (pretraining vs. posttraining).
I chose the default preprocessing pipeline for volume-based analysis (to MNI-space).
It includes functional realignment & unwarp, functional slice-timing correction (descending),
structural segmentation & normalization, functional normalization, functional outlier detection (ART-based),
and functional smoothing (I changed to 4 mm).
The Conn went through preprocessing steps using SPM8.
Behind what I have chosen, I was not sure what parameters this default has selected for the default preprocessing steps.
I need specific details to report the preprocessing steps for publication.
If you know how I find this information, please let me know!
Thank you in advance!
Jisook
Threaded View
| Title | Author | Date |
|---|---|---|
| Ji Sook Park | Oct 28, 2014 | |
| Alfonso Nieto-Castanon | Nov 15, 2014 | |
| Juan Gea | Oct 28, 2014 | |