AFNI Message Board

Dear AFNI users-

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

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nhannawa
June 14, 2018 07:19AM
Hi Gang,

Thank you for your quick and very helpful reply!
As you suggested, I have changed the model and centred 'Time_dif' within each visit, before running the model on 10 subjects
However I am still running into problems and am unsure what I'm doing wrong -

My model specification now reads:

3dLME -prefix LME_fMRI_fsl -jobs 2 \
-model 'Visit*Time_dif+Base_DD+Base_Age' \
-qVars 'Time_dif,Base_DD,Base_Age' \
-num_glt 3 \
-gltLabel 1 'Visit_1_2' -gltCode 1 'Visit : 1*v1 -1*v2' \
-gltLabel 2 'Visit_2_3' -gltCode 2 'Visit : 1*v2 -1*v3' \
-gltLabel 3 'Effect_of_time' -gltCode 3 'Time_dif :' \
-ranEff '~1+Time_dif' -SS_type 3 \
-dbgArgs \
-dataTable @10_subs.txt

And the data table :
Subj Visit Time_dif Base_DD Base_Age InputFile \
s01 v1 0 4.71 56.15 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V1/001_V1/1_run_Naomi.feat/reg_standard/stats/cope8.nii.gz \
s01 v1 0 4.71 56.15 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V1/001_V1/2_run_Naomi.feat/reg_standard/stats/cope8.nii.gz \
s01 v2 -9.5 4.71 56.15 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V2/001_V2/1_run_Naomi++.feat/reg_standard/stats/cope8.nii.gz \
s01 v2 -9.5 4.71 56.15 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V2/001_V2/2_run_Naomi+.feat/reg_standard/stats/cope8.nii.gz \
s01 v3 -85.1 4.71 56.15 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V3/001_V3/1_run_Naomi.feat/reg_standard/stats/cope8.nii.gz \
...
s14 v2 -79.5 2.82 50.22 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V2/014_V2/2_run_Naomi.feat/reg_standard/stats/cope8.nii.gz \
s14 v3 -179.1 2.82 50.22 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V3/014_V3/1_run_Naomi+++.feat/reg_standard/stats/cope8.nii.gz \
s14 v3 -179.1 2.82 50.22 /media/nhannawa/NIU3/Motor_task_TRANSEURO_FSL/PD_V3/014_V3/2_run_Naomi++.feat/reg_standard/stats/cope8.nii.gz

I also checked the both the specification and table using the file tool, which showed no problems:
file_tool -infiles test.txt -test
test.txt has 0 bad characters
test.txt file type: UNIX

Any ideas what the remaining problem might be?
Thanks again,
Naomi
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Subject Author Posted

3dLME inputs

nhannawa June 13, 2018 09:14AM

Re: 3dLME inputs

gang June 13, 2018 11:51AM

Re: 3dLME inputs

nhannawa June 14, 2018 07:19AM