Hi,
  I am new here. I have read the fcon_1000 ScriptUse, but i also have some problems about steps of functional image preprocessing.
first, if i only do general functional image preprocessing,could i only use the 2_funcpreproc.sh, 3_registration.sh, 4_segmentation.sh and 5_nuisance.sh scripts?
second, does batch_process.sh contains all preprocessing steps for directly using?
  Please give me some suggestion about functional image preprocessing.Thanks.

Hi Elina,

if you only want to process the functional image, you should only use 2_funcpreproc. All other steps require you to also include and preprocess the anatomical scan.

Yes, you can use batch_preprocess.sh to set up your preprocessing to run across all sites. It will then do all the preprocessing steps.

Hope this helps,
Maarten

 Hi Maarten, many thanks for your help!
After modifying the script-- batch_process.sh(only calls 0_preprocess.sh and 2_funcpreproc.sh), i met some questions.
like this:
root@ubuntu:/media/Work/zlm_test/con# ./batch_process.sh
/media/Work/zlm_test/con/con_duyu + /media/Work/zlm_test/con/con_duyu/con_duyu_subjects.txt + 0 + 204 + 205 + 2
---------------------------------------
!!!! PREPROCESSING FUNCTIONAL SCAN !!!!
---------------------------------------
Dropping first TRs
++ 3dcalc: AFNI version=AFNI_2011_05_26_1457 (Oct 15 2011) [32-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset con_duyu.nii.gz[0..204]
Deobliquing con_duyu
++ 3drefit: AFNI version=AFNI_2011_05_26_1457 (Oct 15 2011) [32-bit]
++ Authored by: RW Cox
** ERROR: Can't open dataset con_duyu_dr.nii.gz
meanwhile,generated a "func" document, which contains start ,start++ and start++++ documents etc.
Maarten,i am a beginner.These days, i have been learning these by myself. Please help me find my errors.
Thanks in forward for any help!

hi elina,

let's start from the beginning.

What is your directory structure?

/home/work/project/subject/anat/mprage.nii.gz
/home/work/project/subject/rest/rest.nii.gz

Is your setup like this? To start you could also download one of the datasets and test the processing on those. The make you data look like that dataset and apply the scripts there.

This earlier thread might also have some useful information for you.
http://www.nitrc.org/forum/message.php?m... 

Hang in there!
Maarten

Hi Maarten,

Thank you very much! With your help i had successfully run the scripts---2_funcpreproc.sh,and 3_registration.sh.
But when i ran the 5_nuisance.sh, a lot of errors appears in the terminal.
I don't do the scripts 4_segmentation.sh, because i think it is used for processing the anat data. 
so, how can i chang the dimensions of input or mask datasets? The global,csf and wm mask i used were come from the fcon_1000 scripts  file (in tissuepriors file ). 
  
  [url=mailto:root@ubuntu:/home/fcon_1000/my_data/scripts]root@ubuntu:/home/fcon_1000/my_data/scripts[/url]# ./5_nuisance.sh
--------------------------------------------
!!!! RUNNING NUISANCE SIGNAL REGRESSION !!!!
--------------------------------------------
Splitting up con_duyu motion parameters
Extracting global signal for con_duyu
++ 3dmaskave: AFNI version=AFNI_2011_05_26_1457 (Oct 15 2011) [32-bit]
*** Input and mask datasets are not same dimensions!
Extracting signal from csf for con_duyu
++ 3dmaskave: AFNI version=AFNI_2011_05_26_1457 (Oct 15 2011) [32-bit]
*** Input and mask datasets are not same dimensions!
Extracting signal from white matter for con_duyu
++ 3dmaskave: AFNI version=AFNI_2011_05_26_1457 (Oct 15 2011) [32-bit]
*** Cannot open mask dataset!
Modifying model file
Running feat model
Not enough data in /home/fcon_1000/my_data/con_duyu/func/nuisance/global.1D
++ 21230 voxels in mask
Running film to get residuals
Log directory is: /home/fcon_1000/my_data/con_duyu/func/nuisance/stats

An exception has been thrown
Unable to open /home/fcon_1000/my_data/con_duyu/func/nuisance/nuisance.mat
++ 3dTstat: AFNI version=AFNI_2011_05_26_1457 (Oct 15 2011) [32-bit]
++ Authored by: KR Hammett & RW Cox
** FATAL ERROR: Can't open dataset /home/fcon_1000/my_data/con_duyu/func/nuisance/stats/res4d.nii.gz
** Program compile date = Oct 15 2011
++ 3dcalc: AFNI version=AFNI_2011_05_26_1457 (Oct 15 2011) [32-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset /home/fcon_1000/my_data/con_duyu/func/nuisance/stats/res4d.nii.gz
** Program compile date = Oct 15 2011
** ERROR (nifti_image_read): failed to find header file for '/home/fcon_1000/my_data/con_duyu/func/con_duyu_res'
** ERROR: nifti_image_open(/home/fcon_1000/my_data/con_duyu/func/con_duyu_res): bad header info
ERROR: failed to open file /home/fcon_1000/my_data/con_duyu/func/con_duyu_res
ERROR: Could not open image /home/fcon_1000/my_data/con_duyu/func/con_duyu_res
Image Exception : #22 :: Failed to read volume /home/fcon_1000/my_data/con_duyu/func/con_duyu_res
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
./5_nuisance.sh: line 95:  2005 Aborted                 flirt -ref ${reg_dir}/standard -in ${func_dir}/${rest}_res -out ${func_dir}/${rest}_res2standard -applyxfm -init ${reg_dir}/example_func2standard.mat -interp trilinear

Thanks in forward for your help!
Best wishes!
 
  elina

Hi Elina,

if you don't do 4_segmentation you'll indeed get these errors, as the white matter, CSF and global signal masks will not have been created. I would not use the standard tissuepriors as masks for all subjects, you'll get inaccuracies in estimating that signal from the different tissue types.

That said, you can change resample an image to a different voxelsize using the AFNI command 3dresample, if you're images are in standard space and you already calculated the transformation matrices you should be able to register them a standard brain with a different voxelsize.

Maarten