Hi Maarten,

Sorry but I don't understand your last email, I edited the batch_process.sh (copy paste below) according to my data, but I don't find where to edit my func folder.
About the error when trying to execute the batch_process.sh
cvalencia@cvalencia-Precision-WorkStation-T3400:~/Documentos/scripts$ batch_process.sh
batch_process.sh: orden no encontrada
In English I thing is order not found
I know it sounds weird, and I have no idea, moreover I'm begging user of ubuntu too.


####################
## scripts directory
####################
## directory where you put the scripts downloaded from http://www.nitrc.org/projects/fcon_1000
## e.g. /home/fcon_1000/scripts
scripts_dir=/home/cvalencia/Documentos/scripts


###########################
## what do you want to run?
###########################
## 1 - general RSFC preprocessing
## 2 - single-subject RSFC (requires general preprocessing to be completed)
## 3 - ALFF/fALFF (default frequency band of interest is 0.01-0.1Hz)
## 4 - Dual Regression
what_to_do=1


#######################
## some important names
#######################
## anatomical scan you want to use (no extension)
anat_name=20100710_12333209971816fl3D1x1x1sagSUBJECTNC0001s003a001
## resting-state scan you want to use (no extension)
rest_name=20100710_12333209968684ep2dboldDRAANA2700SUBJECTNC0001s004a001


################################################
## Extra parameters needed to run postprocessing
################################################
## image you want to use to calculate RSFC for.
## This is usually the image containing resting-state scan after regressing out the nuisance parameters
postprocessing_image=rest_res.nii.gz
## path to list of seeds you want to calculate RSFC for e.g. /home/fcon_1000/scripts/my_seeds.txt
## DEFAULT path = within the scripts directory specified above
## the list includes the full path for each seed e.g. /home/my_seeds/connectomes_seed_3mm.nii.gz
seed_list=${scripts_dir}/SEED_LIST.txt
## image you want to use for postprocessing in MNI space
## This image is used in the dual regression step. Dual regression is applied to this image.
postprocessing_mni_image=rest_res2standard.nii.gz
## mask used for Dual Regression; default = MNI based mask
## the resolution has to be consistent with the DR templates
mask=${FSLDIR}/data/standard/MNI152_T1_3mm_brain_mask.nii.gz
## template used for Dual Regression
## default = the metaICA image, including 20 ICA components as derived in Biswal et al. 2010, PNAS
## running Dual Regression is tuned to run for 20 components you will have to edit 8_singlesubjectDR.sh if you want to use a different template
DR_template=${scripts_dir}/templates/metaICA.nii.gz


#######################################
## Standard brain used for registration
## include the /full/path/to/it
#######################################
standard_brain=${FSLDIR}/data/standard/MNI152_T1_3mm_brain.nii.gz


#####################################################################################
## batch processing parameter list
## DO NOT FORGET TO EDIT batch_list.txt itself to include the appropriate directories
#####################################################################################
## path to batch_list.txt, e.g., /home/fcon_1000/scripts/my_batch_list.txt.
## DEFAULT = within the scripts directory specified above
## This file contains the sites (and their parameters) you want to process.
## batch_list.txt contains 1 line per site listing:
## - analysis directory, i.e. full/path/to/site
## - subjectlist, i.e. full/path/to/site/site_subjects.txt
## - first timepoint, default = 0 (start with the 1st volume)
## - last timepoint = number of timepoints - 1 (since count starts at 0)
## - number of timepoints in the timeseries
## - TR
batch_list=${scripts_dir}/batch_list_cv.txt