Hi Maarten,

The files are correctly named, I write incorrectly
Finally, I could pre process all my subjects, you were right about the size of my files, something went wrong when I copied them. You will notice that I changed the names for all folders (anat, func, reg, segmented) in all .sh files, I add 1 or 2 and also for rest and mprage I add the respective numbers(I did the long way).

Now, I'm facing a new error trying to do the 2nd process (2 - single-subject RSFC (requires general preprocessing to be completed). I used the seeds from the fox folder in order to obtain the results. It seems thant It can't open a file that I see in the folder.

Thanks,
Carolina

cvalencia@cvalencia-Precision-WorkStation-T3400:~/Documentos/scripts$ ./batch_process.sh
/home/cvalencia/Documentos + /home/cvalencia/Documentos/scripts/subjects.txt + rest_res.nii.gz + rest + /home/cvalencia/Documentos/scripts/SEED_LIST.txt + /home/cvalencia/Documentos/scripts/templates/MNI152_T1_3mm_brain.nii.gz
--------------------------
running subject Subj001
--------------------------
------------------------
running seed Fox_tn_LP_3mm
------------------------
Extracting timeseries for seed Fox_tn_LP_3mm
Computing Correlation for seed Fox_tn_LP_3mm
++ 3dfim+: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: B. Douglas Ward
Wrote bucket dataset into /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_LP_3mm_corr.nii.gz
Z-transforming correlations for seed Fox_tn_LP_3mm
++ 3dcalc: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: A cast of thousands
** AFNI converts NIFTI_datatype=4 (INT16) in file /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_LP_3mm_corr.nii.gz to FLOAT32
++ Output dataset /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_LP_3mm_Z.nii.gz
Registering Z-transformed map to standard space
------------------------
running seed Fox_tn_MPF_3mm
------------------------
Extracting timeseries for seed Fox_tn_MPF_3mm
Computing Correlation for seed Fox_tn_MPF_3mm
++ 3dfim+: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: B. Douglas Ward
Wrote bucket dataset into /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_MPF_3mm_corr.nii.gz
Z-transforming correlations for seed Fox_tn_MPF_3mm
++ 3dcalc: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: A cast of thousands
** AFNI converts NIFTI_datatype=4 (INT16) in file /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_MPF_3mm_corr.nii.gz to FLOAT32
++ Output dataset /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_MPF_3mm_Z.nii.gz
Registering Z-transformed map to standard space
------------------------
running seed Fox_tn_PCC_3mm
------------------------
Extracting timeseries for seed Fox_tn_PCC_3mm
Computing Correlation for seed Fox_tn_PCC_3mm
++ 3dfim+: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: B. Douglas Ward
Wrote bucket dataset into /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_PCC_3mm_corr.nii.gz
Z-transforming correlations for seed Fox_tn_PCC_3mm
++ 3dcalc: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: A cast of thousands
** AFNI converts NIFTI_datatype=4 (INT16) in file /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_PCC_3mm_corr.nii.gz to FLOAT32
++ Output dataset /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_PCC_3mm_Z.nii.gz
Registering Z-transformed map to standard space
------------------------
running seed Fox_tn_FEF_3mm
------------------------
Extracting timeseries for seed Fox_tn_FEF_3mm
** FATAL ERROR: Can't open dataset '/home/cvalencia/Documentos/scripts/seeds/Fox_tn_FEF_3mm.nii.gz'
** Program compile date = Jan 7 2011
Computing Correlation for seed Fox_tn_FEF_3mm
++ 3dfim+: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: B. Douglas Ward
3dfim+ Error: Unable to read time series file: /home/cvalencia/Documentos/Subj001/func1/seed_ts/Fox_tn_FEF_3mm.1D
Z-transforming correlations for seed Fox_tn_FEF_3mm
++ 3dcalc: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_FEF_3mm_corr.nii.gz
** Program compile date = Jan 7 2011
Registering Z-transformed map to standard space
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_FEF_3mm_Z'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_FEF_3mm_Z): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_FEF_3mm_Z
ERROR: Could not open image /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_FEF_3mm_Z
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_FEF_3mm_Z.nii.gz
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/6_singlesubjectRSFC.sh: línea 63: 2884 Abortado flirt -in ${RSFC_dir}/${seed_name}_Z.nii.gz -ref ${standard} -applyxfm -init ${reg_dir}/example_func2standard.mat -out ${RSFC_dir}/${seed_name}_Z_2standard.nii.gz
------------------------
running seed Fox_tn_IPS_3mm
------------------------
Extracting timeseries for seed Fox_tn_IPS_3mm
** FATAL ERROR: Can't open dataset '/home/cvalencia/Documentos/scripts/seeds/Fox_tn_IPS_3mm.nii.gz'
** Program compile date = Jan 7 2011
Computing Correlation for seed Fox_tn_IPS_3mm
++ 3dfim+: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: B. Douglas Ward
3dfim+ Error: Unable to read time series file: /home/cvalencia/Documentos/Subj001/func1/seed_ts/Fox_tn_IPS_3mm.1D
Z-transforming correlations for seed Fox_tn_IPS_3mm
++ 3dcalc: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_IPS_3mm_corr.nii.gz
** Program compile date = Jan 7 2011
Registering Z-transformed map to standard space
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_IPS_3mm_Z'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_IPS_3mm_Z): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_IPS_3mm_Z
ERROR: Could not open image /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_IPS_3mm_Z
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_IPS_3mm_Z.nii.gz
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/6_singlesubjectRSFC.sh: línea 63: 2891 Abortado flirt -in ${RSFC_dir}/${seed_name}_Z.nii.gz -ref ${standard} -applyxfm -init ${reg_dir}/example_func2standard.mat -out ${RSFC_dir}/${seed_name}_Z_2standard.nii.gz
------------------------
running seed Fox_tn_MT_3mm
------------------------
Extracting timeseries for seed Fox_tn_MT_3mm
** FATAL ERROR: Can't open dataset '/home/cvalencia/Documentos/scripts/seeds/Fox_tn_MT_3mm.nii.gz'
** Program compile date = Jan 7 2011
Computing Correlation for seed Fox_tn_MT_3mm
++ 3dfim+: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: B. Douglas Ward
3dfim+ Error: Unable to read time series file: /home/cvalencia/Documentos/Subj001/func1/seed_ts/Fox_tn_MT_3mm.1D
Z-transforming correlations for seed Fox_tn_MT_3mm
++ 3dcalc: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_MT_3mm_corr.nii.gz
** Program compile date = Jan 7 2011
Registering Z-transformed map to standard space
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_MT_3mm_Z'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_MT_3mm_Z): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_MT_3mm_Z
ERROR: Could not open image /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_MT_3mm_Z
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj001/func1/RSFC/Fox_tn_MT_3mm_Z.nii.gz
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/6_singlesubjectRSFC.sh: línea 63: 2914 Abortado flirt -in ${RSFC_dir}/${seed_name}_Z.nii.gz -ref ${standard} -applyxfm -init ${reg_dir}/example_func2standard.mat -out ${RSFC_dir}/${seed_name}_Z_2standard.nii.gz
+ + rest_res.nii.gz + rest + /home/cvalencia/Documentos/scripts/SEED_LIST.txt + /home/cvalencia/Documentos/scripts/templates/MNI152_T1_3mm_brain.nii.gz
cat: rest: No existe el fichero o el directorio
cvalencia@cvalencia-Precision-WorkStation-T3400:~/Documentos/scripts$