Hello AFNI experts, this is the first time I am running 3dLME. Any help or redirection to another post (have not found a similar question) will be very appreciated. When I try running my 3dLME script I am encountering the following error (towards bottom):
tcsh -x testing_3dLME &
[2] 18666
jazmin@jazmin-desktop:/media/jazmin/parta/scripts$ 3dLME -prefix Test3dLME -jobs 1 -model cond*group -ranEff ~1 -SS_type 3 -num_glt 4 -gltLabel 1 Time2-Time1 -gltCode 1 cond : 1*Time2 -1*Time1 -gltLabel 2 Time1-Time2 -gltCode 2 cond : 1*Time1 -1*Time2 -gltLabel 3 Time2 -gltCode 3 cond : 1*Time2 -gltLabel 4 Time1 -gltCode 4 cond : 1*Time1 -num_glf 1 -glfLabel 1 Time2-Time1 -glfCode 1 group : 1*ctr & 1*pat cond : 1*Time2 -1*Time1 -dataTable Subj cond group InputFile s1 Time2 ctr /media/jazmin/parta/175_THC_Kumra/23078/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz s1 Time1 ctr /media/jazmin/parta/175_THC_Kumra/18806/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz s2 Time2 ctr /media/jazmin/parta/175_THC_Kumra/23165/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz s2 Time1 ctr /media/jazmin/parta/175_THC_Kumra/18930/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz s3 Time2 pat /media/jazmin/parta/175_THC_Kumra/22978/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz s3 Time1 pat /media/jazmin/parta/175_THC_Kumra/19403/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz s4 Time2 pat /media/jazmin/parta/175_THC_Kumra/23255/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz s4 Time1 pat /media/jazmin/parta/175_THC_Kumra/19612/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz
Loading required package: nlme
Package nlme loaded successfully!
Loading required package: phia
Loading required package: car
Package phia loaded successfully!
++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
4 subjects : s1 s2 s3 s4
8 response values
2 levels for factor cond : Time1 Time2
2 levels for factor group : ctr pat
4 post hoc tests
Contingency tables of subject distributions among the categorical variables:
Tabulation of subjects against all categorical variables
~~~~~~~~~~~~~~
Subj vs cond:
Time1 Time2
s1 1 1
s2 1 1
s3 1 1
s4 1 1
~~~~~~~~~~~~~~
Subj vs group:
ctr pat
s1 2 0
s2 2 0
s3 0 2
s4 0 2
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++
Reading input files now...
Reading input files: Done!
If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or the GLT coding
is likely inappropriate.
[1] "Great, test run passed at voxel (30, 54, 45)!"
[1] "Start to compute 91 slices along Z axis. You can monitor the progress"
[1] "and estimate the total run time as shown below."
[1] "11/06/15 15:28:29.948"
Error in Stat[lop$nF[1] + 2 * lop$num_glt + ii] <- glfRes[2, 2] :
replacement has length zero
Calls: aperm -> apply -> FUN
...........................................................................................................................................................................................
This is the script that examines 2 (group) x 2 (time, within subjects variable) interaction. (Small n because this is just a test):
3dLME -prefix Test3dLME -jobs 1\
-model 'cond*group'\
-ranEff '~1'\
-SS_type 3\
-num_glt 4\
-gltLabel 1 'Time2-Time1' -gltCode 1 'cond : 1*Time2 -1*Time1'\
-gltLabel 2 'Time1-Time2' -gltCode 2 'cond : 1*Time1 -1*Time2'\
-gltLabel 3 'Time2' -gltCode 3 'cond : 1*Time2'\
-gltLabel 4 'Time1' -gltCode 4 'cond : 1*Time1'\
-num_glf 1\
-glfLabel 1 'Time2-Time1' -glfCode 1 'group : 1*ctr & 1*pat cond : 1*Time2 -1*Time1'\
-dataTable\
Subj cond group InputFile\
s1 Time2 ctr /media/jazmin/parta/175_THC_Kumra/23078/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz\
s1 Time1 ctr /media/jazmin/parta/175_THC_Kumra/18806/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz\
s2 Time2 ctr /media/jazmin/parta/175_THC_Kumra/23165/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz\
s2 Time1 ctr /media/jazmin/parta/175_THC_Kumra/18930/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz\
s3 Time2 pat /media/jazmin/parta/175_THC_Kumra/22978/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz\
s3 Time1 pat /media/jazmin/parta/175_THC_Kumra/19403/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz\
s4 Time2 pat /media/jazmin/parta/175_THC_Kumra/23255/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz\
s4 Time1 pat /media/jazmin/parta/175_THC_Kumra/19612/func/RSFC/S1_ACGcaudal_motor_lowres_Z.nii.gz
Thank you.
