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help > RE: Changing ART presets in batch preprocessing
Sep 3, 2015 12:09 AM | Alfonso Nieto-Castanon - Boston University
RE: Changing ART presets in batch preprocessing
Hi Ruth,
Yes, you may define that information as part of the 'art_thresholds' vector, in particular your settings would look like:
conn_setup_threshold(... 'art_thresholds', [value1, value2, 0, 0, 1], ...);
These are the same options as the 'art_thresholds' field part of the batch.New command, and are explained in help conn_batch. Please double-check that you have a sufficiently recent version of CONN, since the option to specify all these additional values was added somewhat recently. You should see there something like:
art_thresholds : (functional_art) ART thresholds for identifying outlier scans
art_thresholds(1): threshold value for global-signal (z-value; default 9)
art_thresholds(2): threshold value for subject-motion (mm; default 2)
additional options: art_thresholds(3): 1/0 global-signal threshold based on scan-to-scan changes in global-BOLD measure (default 1)
art_thresholds(4): 1/0 subject-motion threshold based on scan-to-scan changes in subject-motion measure (default 1)
art_thresholds(5): 1/0 subject-motion threhsold based on composite-movement measure (default 1)
art_thresholds(6): 1/0 force interactive mode (ART gui) (default 0)
art_thresholds(7): [only when art_threshold(5)=0] subject-motion threshold based on rotation measure
Hope this helps
Alfonso
Originally posted by Ruth Shaffer:
Yes, you may define that information as part of the 'art_thresholds' vector, in particular your settings would look like:
conn_setup_threshold(... 'art_thresholds', [value1, value2, 0, 0, 1], ...);
These are the same options as the 'art_thresholds' field part of the batch.New command, and are explained in help conn_batch. Please double-check that you have a sufficiently recent version of CONN, since the option to specify all these additional values was added somewhat recently. You should see there something like:
art_thresholds : (functional_art) ART thresholds for identifying outlier scans
art_thresholds(1): threshold value for global-signal (z-value; default 9)
art_thresholds(2): threshold value for subject-motion (mm; default 2)
additional options: art_thresholds(3): 1/0 global-signal threshold based on scan-to-scan changes in global-BOLD measure (default 1)
art_thresholds(4): 1/0 subject-motion threshold based on scan-to-scan changes in subject-motion measure (default 1)
art_thresholds(5): 1/0 subject-motion threhsold based on composite-movement measure (default 1)
art_thresholds(6): 1/0 force interactive mode (ART gui) (default 0)
art_thresholds(7): [only when art_threshold(5)=0] subject-motion threshold based on rotation measure
Hope this helps
Alfonso
Originally posted by Ruth Shaffer:
Hello,
I am trying to batch preprocess resting state data and am using the following step to start ART motion scrubbing and smoothing:
conn_setup_preproc({'functional_art','functional_smooth'},'art_thresholds',[value1 value2],'fwhm',value3);
I am trying to change the following presets within functional_art:
use diff global: yes
use abs global: no
use diff motion: yes
use abs motion: no
use comp motion: yes
to be this instead:
use diff global: no
use abs global: yes
use diff motion: no
use abs motion: yes
use comp motion: yes
But am running into difficulty and couldn't find this in the manual. Is there a name for these specifications that we could follow with 1's and 0's and insert into the code above to indicate the options we select (sort of like the 'art_thresholds',[value1 value2] part of the code above)?
Thank you in advance for any help on this you can give me!
Best,
Ruth Shaffer
I am trying to batch preprocess resting state data and am using the following step to start ART motion scrubbing and smoothing:
conn_setup_preproc({'functional_art','functional_smooth'},'art_thresholds',[value1 value2],'fwhm',value3);
I am trying to change the following presets within functional_art:
use diff global: yes
use abs global: no
use diff motion: yes
use abs motion: no
use comp motion: yes
to be this instead:
use diff global: no
use abs global: yes
use diff motion: no
use abs motion: yes
use comp motion: yes
But am running into difficulty and couldn't find this in the manual. Is there a name for these specifications that we could follow with 1's and 0's and insert into the code above to indicate the options we select (sort of like the 'art_thresholds',[value1 value2] part of the code above)?
Thank you in advance for any help on this you can give me!
Best,
Ruth Shaffer
Threaded View
| Title | Author | Date |
|---|---|---|
| Ruth Shaffer | Sep 2, 2015 | |
| Alfonso Nieto-Castanon | Sep 3, 2015 | |
| Ruth Shaffer | Sep 4, 2015 | |