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help > RE: Importing realignment parameters
Apr 2, 2022 09:04 PM | Alfonso Nieto-Castanon - Boston University
RE: Importing realignment parameters
Dear Pavel,
You are doing everything correctly so my guess is that perhaps the realignment files do not follow the standard SPM convention (e.g. perhaps angles are in degrees units and/or the order of the 6 parameters differs so ART is interpreting the total amount of motion incorrectly)? For reference, the way CONN/ART will interpret the contents of your realignment files is based on the names/extensions of the files (from "help conn_batch"):
subject-motion files can be in any of the following formats: a) *.txt file (SPM
format; three translation parameters in mm followed by pitch/roll/yaw in radians);
b) *.par (FSL format; three Euler angles in radians followed by translation parameters
in mm); c) *.siemens.txt (Siemens MotionDetectionParameter.txt format); d) *.deg.txt (same
as SPM format but rotations in degrees instead of radians)
Hope this helps
Alfonso
Originally posted by Pavel Hok:
You are doing everything correctly so my guess is that perhaps the realignment files do not follow the standard SPM convention (e.g. perhaps angles are in degrees units and/or the order of the 6 parameters differs so ART is interpreting the total amount of motion incorrectly)? For reference, the way CONN/ART will interpret the contents of your realignment files is based on the names/extensions of the files (from "help conn_batch"):
subject-motion files can be in any of the following formats: a) *.txt file (SPM
format; three translation parameters in mm followed by pitch/roll/yaw in radians);
b) *.par (FSL format; three Euler angles in radians followed by translation parameters
in mm); c) *.siemens.txt (Siemens MotionDetectionParameter.txt format); d) *.deg.txt (same
as SPM format but rotations in degrees instead of radians)
Hope this helps
Alfonso
Originally posted by Pavel Hok:
Dear all,
I have been trying to import already pre-processed (i.e., realigned and normalized) data into CONN (21a). However, I would like to run the complete denoising procedure including scrubbing. The data was preprocessed using custom scripts, so I had to open a new (blank) project. I have successfully imported the functional and structural data and assigned realignment text files (each containing 6 vectors) to each subject as the first-level covariates. I have labelled this covariate as "realignment", hoping ART would recognise it as realignment parameters. Unfortunately, using otherwise default settings, ART identified as outliers almost all volumes, so I assume it not recognise the realignment covariates.
I have searched the forum, but could not find how exactly the external realignment files should be imported (i.e., labelled) to make ART work properly.
Thanks for any comments
Kind regards
Pavel Hok
I have been trying to import already pre-processed (i.e., realigned and normalized) data into CONN (21a). However, I would like to run the complete denoising procedure including scrubbing. The data was preprocessed using custom scripts, so I had to open a new (blank) project. I have successfully imported the functional and structural data and assigned realignment text files (each containing 6 vectors) to each subject as the first-level covariates. I have labelled this covariate as "realignment", hoping ART would recognise it as realignment parameters. Unfortunately, using otherwise default settings, ART identified as outliers almost all volumes, so I assume it not recognise the realignment covariates.
I have searched the forum, but could not find how exactly the external realignment files should be imported (i.e., labelled) to make ART work properly.
Thanks for any comments
Kind regards
Pavel Hok
Threaded View
| Title | Author | Date |
|---|---|---|
| Pavel Hok | Mar 30, 2022 | |
| Alfonso Nieto-Castanon | Apr 2, 2022 | |
| Pavel Hok | Apr 4, 2022 | |