The logfile copy paste below


cvalencia@cvalencia-Precision-WorkStation-T3400:~/Documentos/scripts$ ./batch_process.sh
/home/cvalencia/Documentos + /home/cvalencia/Documentos/scripts/subjects.txt + 0 + 196 + 197 + 2.7
preprocessing Subj001
--------------------------------------
!!!! PREPROCESSING ANATOMICAL SCAN!!!!
--------------------------------------
deobliquing Subj001 anatomical
/home/cvalencia/Documentos/scripts/1_anatpreproc.sh: línea 36: 3drefit: orden no encontrada
Reorienting Subj001 anatomical
/home/cvalencia/Documentos/scripts/1_anatpreproc.sh: línea 40: 3dresample: orden no encontrada
skull stripping Subj001 anatomical
/home/cvalencia/Documentos/scripts/1_anatpreproc.sh: línea 45: 3dSkullStrip: orden no encontrada
/home/cvalencia/Documentos/scripts/1_anatpreproc.sh: línea 46: 3dcalc: orden no encontrada
---------------------------------------
!!!! PREPROCESSING FUNCTIONAL SCAN !!!!
---------------------------------------
Dropping first TRs
/home/cvalencia/Documentos/scripts/2_funcpreproc.sh: línea 49: 3dcalc: orden no encontrada
Deobliquing Subj001
/home/cvalencia/Documentos/scripts/2_funcpreproc.sh: línea 53: 3drefit: orden no encontrada
Reorienting Subj001
/home/cvalencia/Documentos/scripts/2_funcpreproc.sh: línea 57: 3dresample: orden no encontrada
Motion correcting Subj001
/home/cvalencia/Documentos/scripts/2_funcpreproc.sh: línea 61: 3dTstat: orden no encontrada
/home/cvalencia/Documentos/scripts/2_funcpreproc.sh: línea 62: 3dvolreg: orden no encontrada
Skull stripping Subj001
/home/cvalencia/Documentos/scripts/2_funcpreproc.sh: línea 66: 3dAutomask: orden no encontrada
/home/cvalencia/Documentos/scripts/2_funcpreproc.sh: línea 67: 3dcalc: orden no encontrada
Getting example_func for registration for Subj001
/home/cvalencia/Documentos/scripts/2_funcpreproc.sh: línea 71: 3dcalc: orden no encontrada
Smoothing Subj001
** ERROR (nifti_image_read): failed to find header file for 'rest_ss'
** ERROR: nifti_image_open(rest_ss): bad header info
Error: failed to open file rest_ss
Cannot open volume rest_ss for reading!
Grand-mean scaling Subj001
** ERROR (nifti_image_read): failed to find header file for 'rest_sm'
** ERROR: nifti_image_open(rest_sm): bad header info
Error: failed to open file rest_sm
Cannot open volume rest_sm for reading!
Band-pass filtering Subj001
/home/cvalencia/Documentos/scripts/2_funcpreproc.sh: línea 83: 3dFourier: orden no encontrada
Removing linear and quadratic trends for Subj001
/home/cvalencia/Documentos/scripts/2_funcpreproc.sh: línea 87: 3dTstat: orden no encontrada
/home/cvalencia/Documentos/scripts/2_funcpreproc.sh: línea 88: 3dDetrend: orden no encontrada
/home/cvalencia/Documentos/scripts/2_funcpreproc.sh: línea 89: 3dcalc: orden no encontrada
Generating mask of preprocessed data for Subj001
** ERROR (nifti_image_read): failed to find header file for 'rest_pp'
** ERROR: nifti_image_open(rest_pp): bad header info
Error: failed to open file rest_pp
Cannot open volume rest_pp for reading!
------------------------------
!!!! RUNNING REGISTRATION !!!!
------------------------------
mkdir: no se puede crear el directorio «/home/cvalencia/Documentos/Subj001/reg»: El archivo ya existe
cp: no se puede efectuar «stat» sobre «/home/cvalencia/Documentos/Subj001/anat/mprage_brain.nii.gz»: No existe el fichero o el directorio
cp: no se puede efectuar «stat» sobre «/home/cvalencia/Documentos/Subj001/func/example_func.nii.gz»: No existe el fichero o el directorio
** ERROR (nifti_image_read): failed to find header file for 'highres'
** ERROR: nifti_image_open(highres): bad header info
Error: failed to open file highres
ERROR: Could not open image highres
Image Exception : #22 :: Failed to read volume highres
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/3_registration.sh: línea 57: 5581 Abortado flirt -ref highres -in example_func -out example_func2highres -omat example_func2highres.mat -cost corratio -dof 6 -interp trilinear
Could not open matrix file example_func2highres.mat
Cannot read input-matrix
** ERROR (nifti_image_read): failed to find header file for 'highres'
** ERROR: nifti_image_open(highres): bad header info
Error: failed to open file highres
ERROR: Could not open image highres
Image Exception : #22 :: Failed to read volume highres
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/3_registration.sh: línea 63: 5583 Abortado flirt -ref standard -in highres -out highres2standard -omat highres2standard.mat -cost corratio -searchcost corratio -dof 12 -interp trilinear
Could not open matrix file highres2standard.mat
Cannot read input-matrix
Could not open matrix file example_func2highres.mat
Cannot read input-matrix
** ERROR (nifti_image_read): failed to find header file for 'example_func'
** ERROR: nifti_image_open(example_func): bad header info
Error: failed to open file example_func
ERROR: Could not open image example_func
Image Exception : #22 :: Failed to read volume example_func
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/3_registration.sh: línea 71: 5586 Abortado flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear
Could not open matrix file example_func2standard.mat
Cannot read input-matrix
/home/cvalencia/Documentos/scripts/tissuepriors/3mm/
------------------------------
!!!! RUNNING SEGMENTATION !!!!
------------------------------
mkdir: no se puede crear el directorio «/home/cvalencia/Documentos/Subj001/segment»: El archivo ya existe
Segmenting brain for Subj001
** ERROR (nifti_image_read): failed to find header file for 'mprage_brain'
** ERROR: nifti_image_open(mprage_brain): bad header info
Error: failed to open file mprage_brain
ERROR: Could not open image mprage_brain
Image Exception : #22 :: Failed to read volume mprage_brain.nii.gz
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/4_segment.sh: línea 55: 5594 Abortado fast -t 1 -g -p -o segment ${anat}_brain.nii.gz
Creating global mask
/home/cvalencia/Documentos/scripts/4_segment.sh: línea 59: 3dcopy: orden no encontrada
Registering Subj001 csf to native (functional) space
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/reg/example_func'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/reg/example_func): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/reg/example_func
ERROR: Could not open image /home/cvalencia/Documentos/Subj001/reg/example_func
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj001/reg/example_func
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/4_segment.sh: línea 64: 5596 Abortado flirt -in ${anat_dir}/segment_prob_0 -ref ${reg_dir}/example_func -applyxfm -init ${reg_dir}/highres2example_func.mat -out ${segment_dir}/csf2func
Smoothing Subj001 csf
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/segment/csf2func'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/segment/csf2func): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/segment/csf2func
Cannot open volume /home/cvalencia/Documentos/Subj001/segment/csf2func for reading!
Registering Subj001 csf to standard space
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/segment/csf_sm'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/segment/csf_sm): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/segment/csf_sm
ERROR: Could not open image /home/cvalencia/Documentos/Subj001/segment/csf_sm
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj001/segment/csf_sm
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/4_segment.sh: línea 70: 5598 Abortado flirt -in ${segment_dir}/csf_sm -ref ${reg_dir}/standard -applyxfm -init ${reg_dir}/example_func2standard.mat -out ${segment_dir}/csf2standard
Finding overlap between Subj001 csf and prior
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/segment/csf2standard'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/segment/csf2standard): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/segment/csf2standard
Cannot open volume /home/cvalencia/Documentos/Subj001/segment/csf2standard for reading!
Registering Subj001 csf back to native space
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/reg/example_func'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/reg/example_func): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/reg/example_func
ERROR: Could not open image /home/cvalencia/Documentos/Subj001/reg/example_func
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj001/reg/example_func
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/4_segment.sh: línea 76: 5600 Abortado flirt -in ${segment_dir}/csf_masked -ref ${reg_dir}/example_func -applyxfm -init ${reg_dir}/standard2example_func.mat -out ${segment_dir}/csf_native
Threshold and binarize Subj001 csf probability map
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/segment/csf_native'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/segment/csf_native): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/segment/csf_native
Cannot open volume /home/cvalencia/Documentos/Subj001/segment/csf_native for reading!
Mask csf image by Subj001 functional
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/segment/csf_bin'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/segment/csf_bin): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/segment/csf_bin
Cannot open volume /home/cvalencia/Documentos/Subj001/segment/csf_bin for reading!
Registering Subj001 wm to native (functional) space
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/reg/example_func'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/reg/example_func): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/reg/example_func
ERROR: Could not open image /home/cvalencia/Documentos/Subj001/reg/example_func
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj001/reg/example_func
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/4_segment.sh: línea 87: 5603 Abortado flirt -in ${anat_dir}/segment_prob_2 -ref ${reg_dir}/example_func -applyxfm -init ${reg_dir}/highres2example_func.mat -out ${segment_dir}/wm2func
Smoothing Subj001 wm
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/segment/wm2func'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/segment/wm2func): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/segment/wm2func
Cannot open volume /home/cvalencia/Documentos/Subj001/segment/wm2func for reading!
Registering Subj001 wm to standard space
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/segment/wm_sm'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/segment/wm_sm): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/segment/wm_sm
ERROR: Could not open image /home/cvalencia/Documentos/Subj001/segment/wm_sm
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj001/segment/wm_sm
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/4_segment.sh: línea 93: 5605 Abortado flirt -in ${segment_dir}/wm_sm -ref ${reg_dir}/standard -applyxfm -init ${reg_dir}/example_func2standard.mat -out ${segment_dir}/wm2standard
Finding overlap between Subj001 wm and prior
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/segment/wm2standard'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/segment/wm2standard): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/segment/wm2standard
Cannot open volume /home/cvalencia/Documentos/Subj001/segment/wm2standard for reading!
Registering Subj001 wm back to native space
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/reg/example_func'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/reg/example_func): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/reg/example_func
ERROR: Could not open image /home/cvalencia/Documentos/Subj001/reg/example_func
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj001/reg/example_func
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/4_segment.sh: línea 99: 5607 Abortado flirt -in ${segment_dir}/wm_masked -ref ${reg_dir}/example_func -applyxfm -init ${reg_dir}/standard2example_func.mat -out ${segment_dir}/wm_native
Threshold and binarize Subj001 wm probability map
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/segment/wm_native'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/segment/wm_native): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/segment/wm_native
Cannot open volume /home/cvalencia/Documentos/Subj001/segment/wm_native for reading!
Mask wm image by Subj001 functional
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/segment/wm_bin'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/segment/wm_bin): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/segment/wm_bin
Cannot open volume /home/cvalencia/Documentos/Subj001/segment/wm_bin for reading!
--------------------------------------------
!!!! RUNNING NUISANCE SIGNAL REGRESSION !!!!
--------------------------------------------
Splitting up Subj001 motion parameters
awk: cannot open /home/cvalencia/Documentos/Subj001/func/rest_mc.1D (No such file or directory)
awk: cannot open /home/cvalencia/Documentos/Subj001/func/rest_mc.1D (No such file or directory)
awk: cannot open /home/cvalencia/Documentos/Subj001/func/rest_mc.1D (No such file or directory)
awk: cannot open /home/cvalencia/Documentos/Subj001/func/rest_mc.1D (No such file or directory)
awk: cannot open /home/cvalencia/Documentos/Subj001/func/rest_mc.1D (No such file or directory)
awk: cannot open /home/cvalencia/Documentos/Subj001/func/rest_mc.1D (No such file or directory)
Extracting global signal for Subj001
/home/cvalencia/Documentos/scripts/5_nuisance.sh: línea 60: 3dmaskave: orden no encontrada
Extracting signal from csf for Subj001
/home/cvalencia/Documentos/scripts/5_nuisance.sh: línea 64: 3dmaskave: orden no encontrada
Extracting signal from white matter for Subj001
/home/cvalencia/Documentos/scripts/5_nuisance.sh: línea 68: 3dmaskave: orden no encontrada
Modifying model file
Running feat model
Not enough data in /home/cvalencia/Documentos/Subj001/func/nuisance/global.1D
/home/cvalencia/Documentos/scripts/5_nuisance.sh: línea 84: 3dBrickStat: orden no encontrada
Running film to get residuals
Log directory is: /home/cvalencia/Documentos/Subj001/func/nuisance/stats+++
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/func/rest_pp'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/func/rest_pp): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/func/rest_pp
ERROR: Could not open image /home/cvalencia/Documentos/Subj001/func/rest_pp
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj001/func/rest_pp.nii.gz


An exception has been thrown
Failed to read volume /home/cvalencia/Documentos/Subj001/func/rest_pp.nii.gzTrace: read_volume4DROI.

/home/cvalencia/Documentos/scripts/5_nuisance.sh: línea 91: 3dTstat: orden no encontrada
/home/cvalencia/Documentos/scripts/5_nuisance.sh: línea 92: 3dcalc: orden no encontrada
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj001/func/rest_res'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj001/func/rest_res): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj001/func/rest_res
ERROR: Could not open image /home/cvalencia/Documentos/Subj001/func/rest_res
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj001/func/rest_res
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/5_nuisance.sh: línea 95: 5644 Abortado flirt -ref ${reg_dir}/standard -in ${func_dir}/${rest}_res -out ${func_dir}/${rest}_res2standard -applyxfm -init ${reg_dir}/example_func2standard.mat -interp trilinear
+ + + + +
cat: rest: No existe el fichero o el directorio