Hi guys,
when I use the batch_process.sh from fcon_1000,
I have a question about NUISANCE SIGNAL REGRESSION, there are some errors occurred.
I am a very beginner, looking forward to your help.
thank you so much.




--------------------------------------------
!!!! RUNNING NUISANCE SIGNAL REGRESSION !!!!
--------------------------------------------
Splitting up sub19738 motion parameters
Extracting global signal for sub19738
++ 3dmaskave: AFNI version=AFNI_2011_12_21_1014 (Apr 24 2014) [64-bit]
+++ 61534 voxels survive the mask
Extracting signal from csf for sub19738
++ 3dmaskave: AFNI version=AFNI_2011_12_21_1014 (Apr 24 2014) [64-bit]
+++ 160 voxels survive the mask
Extracting signal from white matter for sub19738
++ 3dmaskave: AFNI version=AFNI_2011_12_21_1014 (Apr 24 2014) [64-bit]
+++ 2628 voxels survive the mask
Modifying model file
Running feat model
Running film to get residuals
-r: Option doesn't exist!
try: film_gls --help
++ 3dTstat: AFNI version=AFNI_2011_12_21_1014 (Apr 24 2014) [64-bit]
++ Authored by: KR Hammett & RW Cox
** FATAL ERROR: Can't open dataset /home/peter/fcon_1000/Baltimore/sub19738/func/nuisance/stats/res4d.nii.gz
** Program compile date = Apr 24 2014
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (Apr 24 2014) [64-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset /home/peter/fcon_1000/Baltimore/sub19738/func/nuisance/stats/res4d.nii.gz
** Program compile date = Apr 24 2014
Image Exception : #22 :: ERROR: Could not open image /home/peter/fcon_1000/Baltimore/sub19738/func/rest_res
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/peter/fcon_1000/scripts/5_nuisance.sh: line 95:  5030 Aborted                 (core dumped) flirt -ref ${reg_dir}/standard -in ${func_dir}/${rest}_res -out ${func_dir}/${rest}_res2standard -applyxfm -init ${reg_dir}/example_func2standard.mat -interp trilinear

Hello Peter,

it turns out that the FSL-guys changed the options for film_gls. All options for that command are now -- instead of -.

You can adjust the line with film_gls in the 5_nuisance.sh script so all options have the --

Or alternatively replace that line by the line below

film_gls --rn ${nuisance_dir}/stats --noest --sa --ms 5 ${func_dir}/${rest}_pp.nii.gz ${nuisance_dir}/nuisance.mat ${minVal}

hope this helps,
Maarten

thank you, Maarten Mennes,
I have tried per your instruction, and get the following results.
the Baltimore data was used, two errors as following:

first one,
"--rn: Missing non-optional argument!"
second one,
and still the FATAL ERROR as last time, "FATAL ERROR: can't open dataset /home/peter/fcon_1000/Baltimore/sub17017/func/nuisance/stats/res4d.nii.gz"
in fact, I have checked the directories in my computer, there's no such directory existing, no ~/stats at all.
do you know what's wrong happened here?
thank you so much.
and then I NOTICED sth happened, I adjusted the script, finally, well done.

thanks.

I still have another question is that,
is there any new version of fcon_1000_scripts? that I don't have to change the code.

have a good day.

Peter

Hello Peter,

seems like more has changed

try this:

film_gls --rn=${nuisance_dir}/stats --noest --sa --ms=5 --in=${func_dir}/${rest}_pp.nii.gz --pd=${nuisance_dir}/nuisance.mat --thr=${minVal}


Furthermore we stopped support of the scripts as they are a reflection of the analyses as we did them in 2010. Now 4 years later standards have changed, e.g., we don't do global signal correction anymore, bandpass filtering is questioned etc. To accommodate these changes there is now C-PAC, which provides a full processing pipeline. You can find it here: http://fcp-indi.github.io/

Maarten

thank you so much, Maartenn.

I will try the new one.

Have a good day.

Peter