Hi Maarten,

I run again with the correct names of the seeds and it was OK, for patient 1
Now I try to run the second subject only change the subjects.txt but again some problems presented in the logfile, I'm not sure of the problem this time
I already understand the seed method to process resting state MRI data, how I create my own seed, for example if I want to do the same seed listed with the coordinates in the paper "Mapping the functional connectivity of anterior cingulate cortex", I open in FSLview the template MNI152_T1_3mm_brain with the seed Fox_tn_LP_3mm and I see the voxels that represent the specific seed.How I create a similar file?

Thanks four your patience

Carolina




cvalencia@cvalencia-Precision-WorkStation-T3400:~/Documentos/scripts$ ./batch_process.sh
/home/cvalencia/Documentos + /home/cvalencia/Documentos/scripts/subjects.txt + rest_res.nii.gz + rest1 + /home/cvalencia/Documentos/scripts/SEED_LIST.txt + /home/cvalencia/Documentos/scripts/templates/MNI152_T1_3mm_brain.nii.gz
--------------------------
running subject Subj002
--------------------------
------------------------
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
3dfim+ Error: Unable to open data file: /home/cvalencia/Documentos/Subj002/func1/rest_res.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
** FATAL ERROR: can't open dataset /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tn_LP_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/Subj002/func1/RSFC/Fox_tn_LP_3mm_Z'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tn_LP_3mm_Z): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tn_LP_3mm_Z
ERROR: Could not open image /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tn_LP_3mm_Z
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tn_LP_3mm_Z.nii.gz
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/6_singlesubjectRSFC.sh: línea 63: 4886 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_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
3dfim+ Error: Unable to open data file: /home/cvalencia/Documentos/Subj002/func1/rest_res.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
** FATAL ERROR: can't open dataset /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tn_MPF_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/Subj002/func1/RSFC/Fox_tn_MPF_3mm_Z'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tn_MPF_3mm_Z): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tn_MPF_3mm_Z
ERROR: Could not open image /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tn_MPF_3mm_Z
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tn_MPF_3mm_Z.nii.gz
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/6_singlesubjectRSFC.sh: línea 63: 4893 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_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
3dfim+ Error: Unable to open data file: /home/cvalencia/Documentos/Subj002/func1/rest_res.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
** FATAL ERROR: can't open dataset /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tn_PCC_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/Subj002/func1/RSFC/Fox_tn_PCC_3mm_Z'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tn_PCC_3mm_Z): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tn_PCC_3mm_Z
ERROR: Could not open image /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tn_PCC_3mm_Z
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tn_PCC_3mm_Z.nii.gz
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/6_singlesubjectRSFC.sh: línea 63: 4900 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_tp_FEF_3mm
------------------------
Extracting timeseries for seed Fox_tp_FEF_3mm
Computing Correlation for seed Fox_tp_FEF_3mm
++ 3dfim+: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: B. Douglas Ward
3dfim+ Error: Unable to open data file: /home/cvalencia/Documentos/Subj002/func1/rest_res.nii.gz
Z-transforming correlations for seed Fox_tp_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/Subj002/func1/RSFC/Fox_tp_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/Subj002/func1/RSFC/Fox_tp_FEF_3mm_Z'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tp_FEF_3mm_Z): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tp_FEF_3mm_Z
ERROR: Could not open image /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tp_FEF_3mm_Z
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tp_FEF_3mm_Z.nii.gz
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/6_singlesubjectRSFC.sh: línea 63: 4907 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_tp_IPS_3mm
------------------------
Extracting timeseries for seed Fox_tp_IPS_3mm
Computing Correlation for seed Fox_tp_IPS_3mm
++ 3dfim+: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: B. Douglas Ward
3dfim+ Error: Unable to open data file: /home/cvalencia/Documentos/Subj002/func1/rest_res.nii.gz
Z-transforming correlations for seed Fox_tp_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/Subj002/func1/RSFC/Fox_tp_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/Subj002/func1/RSFC/Fox_tp_IPS_3mm_Z'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tp_IPS_3mm_Z): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tp_IPS_3mm_Z
ERROR: Could not open image /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tp_IPS_3mm_Z
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tp_IPS_3mm_Z.nii.gz
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/6_singlesubjectRSFC.sh: línea 63: 4914 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_tp_MT_3mm
------------------------
Extracting timeseries for seed Fox_tp_MT_3mm
Computing Correlation for seed Fox_tp_MT_3mm
++ 3dfim+: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: B. Douglas Ward
3dfim+ Error: Unable to open data file: /home/cvalencia/Documentos/Subj002/func1/rest_res.nii.gz
Z-transforming correlations for seed Fox_tp_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/Subj002/func1/RSFC/Fox_tp_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/Subj002/func1/RSFC/Fox_tp_MT_3mm_Z'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tp_MT_3mm_Z): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tp_MT_3mm_Z
ERROR: Could not open image /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tp_MT_3mm_Z
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj002/func1/RSFC/Fox_tp_MT_3mm_Z.nii.gz
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/6_singlesubjectRSFC.sh: línea 63: 4930 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 + rest1 + /home/cvalencia/Documentos/scripts/SEED_LIST.txt + /home/cvalencia/Documentos/scripts/templates/MNI152_T1_3mm_brain.nii.gz
cat: rest1: No existe el fichero o el directorio
cvalencia@cvalencia-Precision-WorkStation-T3400:~/Documentos/scripts$