3dICC String Parsing error

Hi all.

Wanting to run 3dICC to check for differences in the average signal across 19 different pre-processing strategies and I’m running into some issues with string parsing.

I’m running it on my local machine with the following:

3dICC -prefix Warp_ICC3 -jobs 1
-mask ‘MaskofMasks.nii’
-model “1+initializer+target+(1|Subj)”
-InputFile ‘inputfile’
-dataTable ‘Inputfiles.txt’

But it keeps throwing errors like these:
** Error:
Expecting 1 parameters for option “-model”.
Have 3 parameter(s) in string “1+initializer+target+(1|Subj) -InputFile inputfile” instead.
NOTE that -InputFile in bad option above is not a recognized option.

** Error:
Error parsing arguments. See 3dICC -help for details

3dICC -prefix Warp_ICC3 -jobs 1 -mask ‘MaskofMasks.nii’ -InputFile ‘inputfile’ -model ‘1+initializer+target+(1|Subj)’ -dataTable ‘Inputfiles.txt’

** Error:
Expecting 1 parameters for option “-mask”.
Have 3 parameter(s) in string “MaskofMasks.nii -InputFile inputfile” instead.
NOTE that -InputFile in bad option above is not a recognized option.

** Error:
Error parsing arguments. See 3dICC -help for details.

Hoping it’s something simple I just missed.

AFNI version is Precompiled binary linux_ubuntu_16_64: Oct 19 2020 (Version AFNI_20.3.01 ‘Vespasian’), Inputfile.txt looks something like this, tab separated:

subject initializer target inputfile
sub-M68200328 EPI Kid_TPM MeanEPI_to_KIDSPMTPM_GM_M68200328.nii.gz
sub-M68200328 EPI MNI MeanEPI_to_MNI_Brain_Template_M68200328.nii.gz
sub-M68200328 EPI Avg_MNI MeanEPI_to_Post_MNI_Averaged_Brain_Template_M68200328.nii.gz
sub-M68200328 T1 Kid_TPM MeanEPI_to_T1_to_KIDSPMTPM_GM_M68200328.nii.gz
sub-M68200328 EPI MM_EPI MeanEPI_to_T1_to_Multimodal_Study_Specific_EPI_Template_M68200328.nii.gz
sub-M68200328 T1 Avg_MNI MeanEPI_to_T1_to_Post_MNI_Averaged_Brain_Template_M68200328.nii.gz
sub-M68200328 T1 UM_EPI MeanEPI_to_T1_to_Unimodal_EPI_Study_Specific_Template_M68200328.nii.gz
sub-M68200328 EPI MM_EPI MeanEPI_to_to_Multimodal_Study_Specific_EPI_Template_M68200328.nii.gz
sub-M68200328 EPI MM_T1 MeanEPI_to_to_Multimodal_Study_Specific_T1_Template_M68200328.nii.gz
sub-M68200328 EPI UM_EPI MeanEPI_to_Unimodal_Study_Specific_EPI_Template_M68200328.nii.gz
sub-M68200328 T1 TPM12 SPM12_Coreg_M68200328.nii.gz
sub-M68200328 EPI TPM12 SPM12_NoCoreg_M68200328.nii.gz
sub-M68200328 EPI Kid_TPM SPM12_TOM8_NoCoreg_M68200328.nii.gz
sub-M68200328 T1 Kid_TPM SPM12_TOM8_TPMs_Coreg_M68200328.nii.gz
sub-M68200328 EPI Kid_TPM SPM8_Kid_TPM_No_Coreg_M68200328.nii.gz
sub-M68200328 EPI TPM8 SPM8_No_Coreg_M68200328.nii.gz
sub-M68200328 T1 Kid_TPM T1_to_KIDSPMTPM_GM_M68200328.nii.gz
sub-M68200328 T1 MNI T1_to_MNI_Template_M68200328.nii.gz
sub-M68200328 T1 MM_T1 T1_to_Multimodal_Study_Specific_T1_Template_M68200328.nii.gz

Try this:

  1. remove

-InputFile ‘inputfile’ \

from your script,

  1. change the column label ‘inputfile’ in file ‘Inputfiles.txt’ to ‘InputFIle’,

  2. change

-dataTable ‘Inputfiles.txt’

to

-dataTable @Inputfiles.txt

That call resulted in the following:

3dICC -prefix Warp_ICC3 -jobs 1 \

-mask ‘MaskofMasks.nii’
-model “1+initializer+target+(1|Subj)”
-dataTable @Inputfiles.txt
Read 13000 items
Error in if (len%%wd != 0) errex.AFNI(paste(“The content under -dataTable is not rectangular !”, :
argument is of length zero
Calls: process.ICC.opts
Execution halted

It sounds like there is some issue with the table. It’s hard to guess without accessing to the table.

Tried to attached it but the forum wouldn’t accept anything that wasn’t an image.

The delimiter is a tab, should it be something else?