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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| February 18, 2017 11:55PM | |
Hi, all
I am new to AFNI and I am trying to perform some resting-fMRI functional connectivity analysis. I used uber_subject.py to process the data first, however it generated an error "0m total number of fixed regressors (166) is too many for 235 retained time points!" during the 3dTproject program.
In uber_subject.py, "analysis initialization" is checked, "type" is set to "rest", processing blocks is set to "tshift align tlrc volreg blur mask scale regress"; "stimulus timing files" is unchecked because I'm processing resting-state data, "expected options" are default except that the "volume registration base" is choosen to be the first one, "extra regress options" is unchecked, "extra align options is checked" and under it I also checked "align: use giant_move". I also choose the tlrc template to be "MNI_avg152T1+tlrc".
This is the error part of the output file:
3dREMLfit -matrix X.xmat.1D -input pb04.par2.r01.blur+tlrc.HEAD \
-fout -tout -Rbuck stats.par2_REML -Rvar stats.par2_REMLvar \
-Rfitts fitts.par2_REML -Rerrts errts.par2_REML -verb
++ N.B.: 3dREMLfit command above written to file stats.REML_cmd
++ (b) Visualization/analysis of the matrix via ExamineXmat.R
++ (c) Synthesis of sub-model datasets using 3dSynthesize
++ ==========================================================
++ Wrote matrix values to file X.nocensor.xmat.1D
++ ----- Signal+Baseline matrix condition [X] (166x165): 2650.6 ++ OK ++
++ ----- Baseline-only matrix condition [X] (166x165): 2650.6 ++ OK ++
++ ----- stim_base-only matrix condition [X] (166x160): 1967.76 ++ OK ++
++ ----- polort-only matrix condition [X] (166x5): 1.14995 ++ VERY GOOD ++
++ 3dDeconvolve exits: -x1D_stop option was invoked
3dTproject -polort 0 -input pb04.par2.r01.blur+tlrc.HEAD -censor motion_par2_censor.1D -cenmode ZERO -ort X.nocensor.xmat.1D -prefix errts.par2.tproject
++ 3dTproject: AFNI version=AFNI_17.0.07 (Feb 7 2017) [64-bit]
++ Authored by: Cox the Algebraic (Linear)
++ input time points = 235 ; censored = 69 ; remaining = 166
++ Setting up regressors
++ 1 Blocks * 1 polynomials -- 1 polort regressors
+ -- 165 other fixed ort regressors
[7m** ERROR:[0m total number of fixed regressors (166) is too many for 235 retained time points!
[7m** FATAL ERROR:[0m Cannot continue after above errors
!!
** Program compile date = Feb 7 2017
Anyone has some ideas of what is going on?
I can't put the entire output file here because it is too long, but I am happy to provide any further information if needed.
I am new to AFNI and I am trying to perform some resting-fMRI functional connectivity analysis. I used uber_subject.py to process the data first, however it generated an error "0m total number of fixed regressors (166) is too many for 235 retained time points!" during the 3dTproject program.
In uber_subject.py, "analysis initialization" is checked, "type" is set to "rest", processing blocks is set to "tshift align tlrc volreg blur mask scale regress"; "stimulus timing files" is unchecked because I'm processing resting-state data, "expected options" are default except that the "volume registration base" is choosen to be the first one, "extra regress options" is unchecked, "extra align options is checked" and under it I also checked "align: use giant_move". I also choose the tlrc template to be "MNI_avg152T1+tlrc".
This is the error part of the output file:
3dREMLfit -matrix X.xmat.1D -input pb04.par2.r01.blur+tlrc.HEAD \
-fout -tout -Rbuck stats.par2_REML -Rvar stats.par2_REMLvar \
-Rfitts fitts.par2_REML -Rerrts errts.par2_REML -verb
++ N.B.: 3dREMLfit command above written to file stats.REML_cmd
++ (b) Visualization/analysis of the matrix via ExamineXmat.R
++ (c) Synthesis of sub-model datasets using 3dSynthesize
++ ==========================================================
++ Wrote matrix values to file X.nocensor.xmat.1D
++ ----- Signal+Baseline matrix condition [X] (166x165): 2650.6 ++ OK ++
++ ----- Baseline-only matrix condition [X] (166x165): 2650.6 ++ OK ++
++ ----- stim_base-only matrix condition [X] (166x160): 1967.76 ++ OK ++
++ ----- polort-only matrix condition [X] (166x5): 1.14995 ++ VERY GOOD ++
++ 3dDeconvolve exits: -x1D_stop option was invoked
3dTproject -polort 0 -input pb04.par2.r01.blur+tlrc.HEAD -censor motion_par2_censor.1D -cenmode ZERO -ort X.nocensor.xmat.1D -prefix errts.par2.tproject
++ 3dTproject: AFNI version=AFNI_17.0.07 (Feb 7 2017) [64-bit]
++ Authored by: Cox the Algebraic (Linear)
++ input time points = 235 ; censored = 69 ; remaining = 166
++ Setting up regressors
++ 1 Blocks * 1 polynomials -- 1 polort regressors
+ -- 165 other fixed ort regressors
[7m** ERROR:[0m total number of fixed regressors (166) is too many for 235 retained time points!
[7m** FATAL ERROR:[0m Cannot continue after above errors
!!
** Program compile date = Feb 7 2017
Anyone has some ideas of what is going on?
I can't put the entire output file here because it is too long, but I am happy to provide any further information if needed.
| Subject | Author | Posted |
|---|---|---|
|
yunhui | February 18, 2017 11:55PM |
|
Bob Cox | February 19, 2017 04:23PM |
