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Robin

January 07, 2019 09:31AM

Registered: 9 years ago
Posts: 202

Hello Bob and thanks for such a detailed reply!

1+2) On that you would not recommend 3dFWHMx -detrende for already processed data:
That is interesting since afni-proc seems to preform smoothness estimates with the -detrend option per default.
My afni version is brand new:

afni -ver
Precompiled binary linux_ubuntu_16_64: Dec  4 2018 (Version AFNI_18.3.13 'Augustus')

In my afni-proc I have:

...
-regress_est_blur_errts \
    -mask_epi_anat yes \
...

That generates this .proc code:

3dFWHMx -detrend -mask mask_epi_anat.$subj+tlrc                           \
            -ACF files_ACF/out.3dFWHMx.ACF.errts.r$run.1D                     \
            errts.${subj}+tlrc"[$trs]" >> blur.errts.1D

Which apparently uses -detrend on the errts data which you did not recommend! It's because I just recently found out that afni-proc could give me the smoothness automatically I had to think of -detrend vs no -detrend. Any comments on that?
Also, sorry for being unclear. With average acf parameters I meant average across subjects for each a b c parameter! But OK, that means that it's not that strange that the cluster-size tables differ, since the a,b,c params differ for detend and no detrend (which I guess they "should" even though the data is already detrended at the errts stage?). And the results for -detrend vs -no-detrend does not differ THAT much. Still annoying ;). We will just stop using -detrend then.

3). Since my afni version is new (Precompiled binary linux_ubuntu_16_64: Dec 4 2018 (Version AFNI_18.3.13 'Augustus') I don't know why I don't get the Px files. But the ones I have, are they the correct files but with the wrong name? Or am I missing some files?

This is the 3dttest command (currently used on the coef from seed based resting state analysis):

3dttest++ -paired -prefix AvP_opt_anaticor -mask $mask_anat -ETAC -ETAC_blur 4 6 -ETAC_opt NN=1:hpow=0:sid=1:pthr=0.01,0.05,0.002,0.01:name=robin \
-setA ALC \
1	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA01_ALC+tlrc'[2]' \
3	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA03_ALC+tlrc'[2]' \
4	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA04_ALC+tlrc'[2]' \
6	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA06_ALC+tlrc'[2]' \
8	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA08_ALC+tlrc'[2]' \
9	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA09_ALC+tlrc'[2]' \
10	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA10_ALC+tlrc'[2]' \
11	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA11_ALC+tlrc'[2]' \
12	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA12_ALC+tlrc'[2]' \
14	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA14_ALC+tlrc'[2]' \
15	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA15_ALC+tlrc'[2]' \
18	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA18_ALC+tlrc'[2]' \
19	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA19_ALC+tlrc'[2]' \
20	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA20_ALC+tlrc'[2]' \
21	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA21_ALC+tlrc'[2]' \
23	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA23_ALC+tlrc'[2]' \
25	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA25_ALC+tlrc'[2]' \
27	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA27_ALC+tlrc'[2]' \
28	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA28_ALC+tlrc'[2]' \
29	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA29_ALC+tlrc'[2]' \
30	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA30_ALC+tlrc'[2]' \
31	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA31_ALC+tlrc'[2]' \
32	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA32_ALC+tlrc'[2]' \
33	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA33_ALC+tlrc'[2]' \
34	/home/robka/faah/rest/analysis/group/alc/DMN_RR_D/RRmap_FA34_ALC+tlrc'[2]' \
-setB PBO \
1	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA01_PBO+tlrc'[2]' \
3	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA03_PBO+tlrc'[2]' \
4	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA04_PBO+tlrc'[2]' \
6	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA06_PBO+tlrc'[2]' \
8	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA08_PBO+tlrc'[2]' \
9	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA09_PBO+tlrc'[2]' \
10	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA10_PBO+tlrc'[2]' \
11	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA11_PBO+tlrc'[2]' \
12	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA12_PBO+tlrc'[2]' \
14	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA14_PBO+tlrc'[2]' \
15	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA15_PBO+tlrc'[2]' \
18	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA18_PBO+tlrc'[2]' \
19	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA19_PBO+tlrc'[2]' \
20	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA20_PBO+tlrc'[2]' \
21	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA21_PBO+tlrc'[2]' \
23	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA23_PBO+tlrc'[2]' \
25	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA25_PBO+tlrc'[2]' \
27	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA27_PBO+tlrc'[2]' \
28	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA28_PBO+tlrc'[2]' \
29	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA29_PBO+tlrc'[2]' \
30	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA30_PBO+tlrc'[2]' \
31	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA31_PBO+tlrc'[2]' \
32	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA32_PBO+tlrc'[2]' \
33	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA33_PBO+tlrc'[2]' \
34	/home/robka/faah/rest/analysis/group/pbo/DMN_RR_D/RRmap_FA34_PBO+tlrc'[2]' \

These are the output files:

3dttest.sh                     TT.gsJ2pkIRgFF.0009.minmax.1D  TT.gsJ2pkIRgFF.0024.minmax.1D  TT.gsJ2pkIRgFF.0039.minmax.1D  TT.gsJ2pkIRgFF.0054.minmax.1D  TT.gsJ2pkIRgFF.0069.minmax.1D
AvP_opt_anaticor.B4.0.nii      TT.gsJ2pkIRgFF.0010.minmax.1D  TT.gsJ2pkIRgFF.0025.minmax.1D  TT.gsJ2pkIRgFF.0040.minmax.1D  TT.gsJ2pkIRgFF.0055.minmax.1D  TT.gsJ2pkIRgFF.0070.minmax.1D
AvP_opt_anaticor.B6.0.nii      TT.gsJ2pkIRgFF.0011.minmax.1D  TT.gsJ2pkIRgFF.0026.minmax.1D  TT.gsJ2pkIRgFF.0041.minmax.1D  TT.gsJ2pkIRgFF.0056.minmax.1D  TT.gsJ2pkIRgFF.0071.minmax.1D
AvP_opt_anaticor+tlrc.BRIK     TT.gsJ2pkIRgFF.0012.minmax.1D  TT.gsJ2pkIRgFF.0027.minmax.1D  TT.gsJ2pkIRgFF.0042.minmax.1D  TT.gsJ2pkIRgFF.0057.minmax.1D  TT.gsJ2pkIRgFF.0072.minmax.1D
AvP_opt_anaticor+tlrc.HEAD     TT.gsJ2pkIRgFF.0013.minmax.1D  TT.gsJ2pkIRgFF.0028.minmax.1D  TT.gsJ2pkIRgFF.0043.minmax.1D  TT.gsJ2pkIRgFF.0058.minmax.1D  TT.gsJ2pkIRgFF.0073.minmax.1D
MNI152_2009_template.nii.gz    TT.gsJ2pkIRgFF.0014.minmax.1D  TT.gsJ2pkIRgFF.0029.minmax.1D  TT.gsJ2pkIRgFF.0044.minmax.1D  TT.gsJ2pkIRgFF.0059.minmax.1D  TT.gsJ2pkIRgFF.0074.minmax.1D
TT.gsJ2pkIRgFF.0000.minmax.1D  TT.gsJ2pkIRgFF.0015.minmax.1D  TT.gsJ2pkIRgFF.0030.minmax.1D  TT.gsJ2pkIRgFF.0045.minmax.1D  TT.gsJ2pkIRgFF.0060.minmax.1D  TT.gsJ2pkIRgFF.0075.minmax.1D
TT.gsJ2pkIRgFF.0001.minmax.1D  TT.gsJ2pkIRgFF.0016.minmax.1D  TT.gsJ2pkIRgFF.0031.minmax.1D  TT.gsJ2pkIRgFF.0046.minmax.1D  TT.gsJ2pkIRgFF.0061.minmax.1D  TT.gsJ2pkIRgFF.0076.minmax.1D
TT.gsJ2pkIRgFF.0002.minmax.1D  TT.gsJ2pkIRgFF.0017.minmax.1D  TT.gsJ2pkIRgFF.0032.minmax.1D  TT.gsJ2pkIRgFF.0047.minmax.1D  TT.gsJ2pkIRgFF.0062.minmax.1D  TT.gsJ2pkIRgFF.0077.minmax.1D
TT.gsJ2pkIRgFF.0003.minmax.1D  TT.gsJ2pkIRgFF.0018.minmax.1D  TT.gsJ2pkIRgFF.0033.minmax.1D  TT.gsJ2pkIRgFF.0048.minmax.1D  TT.gsJ2pkIRgFF.0063.minmax.1D  TT.gsJ2pkIRgFF.0078.minmax.1D
TT.gsJ2pkIRgFF.0004.minmax.1D  TT.gsJ2pkIRgFF.0019.minmax.1D  TT.gsJ2pkIRgFF.0034.minmax.1D  TT.gsJ2pkIRgFF.0049.minmax.1D  TT.gsJ2pkIRgFF.0064.minmax.1D  TT.gsJ2pkIRgFF.0079.minmax.1D
TT.gsJ2pkIRgFF.0005.minmax.1D  TT.gsJ2pkIRgFF.0020.minmax.1D  TT.gsJ2pkIRgFF.0035.minmax.1D  TT.gsJ2pkIRgFF.0050.minmax.1D  TT.gsJ2pkIRgFF.0065.minmax.1D
TT.gsJ2pkIRgFF.0006.minmax.1D  TT.gsJ2pkIRgFF.0021.minmax.1D  TT.gsJ2pkIRgFF.0036.minmax.1D  TT.gsJ2pkIRgFF.0051.minmax.1D  TT.gsJ2pkIRgFF.0066.minmax.1D
TT.gsJ2pkIRgFF.0007.minmax.1D  TT.gsJ2pkIRgFF.0022.minmax.1D  TT.gsJ2pkIRgFF.0037.minmax.1D  TT.gsJ2pkIRgFF.0052.minmax.1D  TT.gsJ2pkIRgFF.0067.minmax.1D
TT.gsJ2pkIRgFF.0008.minmax.1D  TT.gsJ2pkIRgFF.0023.minmax.1D  TT.gsJ2pkIRgFF.0038.minmax.1D  TT.gsJ2pkIRgFF.0053.minmax.1D  TT.gsJ2pkIRgFF.0068.minmax.1D

Thanks a lot Bob!

Edited 1 time(s). Last edit at 01/08/2019 07:28AM by Robin.

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Subject	Author	Posted
3dttest++: Clustsim and ETAC questions	Robin	December 05, 2018 08:53AM
Re: 3dttest++: Clustsim and ETAC questions	RWCox	December 14, 2018 10:17AM
Re: 3dttest++: Clustsim and ETAC questions	Robin	January 07, 2019 09:31AM
Re: 3dttest++: Clustsim and ETAC questions	Robin	January 21, 2019 02:56PM
Re: 3dttest++: Clustsim and ETAC questions	rick reynolds	January 28, 2019 01:15PM
Re: 3dttest++: Clustsim and ETAC questions	Robin	February 04, 2019 09:07AM
Re: 3dttest++: Clustsim and ETAC questions	rick reynolds	February 05, 2019 11:04AM
Re: 3dttest++: Clustsim and ETAC questions	Robin	February 05, 2019 12:22PM
Re: 3dttest++: Clustsim and ETAC questions	rick reynolds	February 05, 2019 12:42PM