Hi Maarten,

I would like to know if I have the correct output files and folders from the pre processing run:
Subj/0001
Subj/0001/anat
mprage.nii.gz (ORIG), mprage_brain.nii.gz, mprage_RPI.nii.gz, mprage_surf.nii.gz.ply, segment_mixeltype.nii.gz, segment_prob_0.nii.gz, segment_prob_1.nii.gz, segment_prob_2.nii.gz, segment_pve_0.nii.gz, segment_pve_1.nii.gz, segment_pve_2.nii.gz, segment_pveseg.nii.gz,segment_seg.nii.gz, segment_seg_0.nii.gz, segment_seg_1.nii.gz, segment_seg_2.nii.gz
Subj/0001/func
rest.nii.gz, example_func.nii.gz,rest_dr.nii.gz, rest_dt.nii.gz, rest_filt.nii.gz, rest_filt_mean.nii.gz, rest_gms.nii.gz, rest_mask.nii.gz, rest_mc.1D, rest_mc.nii.gz, rest_pp.nii.gz, rest_pp_mask.nii.gz, rest-res.nii.gz, rest1_res2standard.nii.gz, rest_ro.nii.gz, rest_ro_mean.nii.gz, rest_sm.nii.gz, rest_ss.nii.gz
Subj/0001/func/nuisance
csf.1D, global.1D, mc1.1D, mc2.1D, mc3.1D, mc4.1D, mc5.1D, mc6.1D, nuisance.con, nuisance.frf, nuisance.fsf, nuisance.mat, nuisance.min, nuisance.png, nuisance.ppm, nuisance.trg, nuisance_cov.png, nuisance_cov.ppm, wm.1D
Subj/0001/func/nuisance/stats
corrections.nii.gz, dof, logfile, pe1.nii.gz, pe2.nii.gz, pe3.nii.gz, pe4.nii.gz, pe5.nii.gz, pe6.nii.gz, pe7.nii.gz, pe8.nii.gz, pe9.nii.gz, res4d.nii.gz, res4d_mean.nii.gz, sigmasquareds.nii.gz, threshac1.nii.gz
Subj/0001/reg
example_func.nii.gz, example_func2highres.nii.gz, example_func2highres.mat, example_func2standard.mat, example_func2standard.nii.gz, highres.nii.gz, highres2exampple_func.mat, highres2standard_func.mat, highres2standard.nii.gz, standard.nii.gz, standard2example_func.mat, standard2highres_func.mat
Subj/0001/segment
csf2func.nii.gz, csf2standard.nii.gz, csf_bin.nii.gz, csf_mask.nii.gz, csf_masked.nii.gz, csf_native.nii.gz, csf_sm.nii.gz, global_mask.nii.gz, wm2func.nii.gz, wm2standard.nii.gz, wm_bin.nii.gz, wm_mask.nii.gz, wm_masked.nii.gz, wm_native.nii.gz, wm_sm.nii.gz


Moreover I tried to run with other subjects and other scans, I have to change all the scripts to read other functional volume, I add rest2 and edited also the creation of folders ie: reg2, segment2
I don have problems with a few subjects but with somes I have this problem (below the log file)

Also, I would like to know, if to run the other steps (2, 3 and 4) if I should have other files differents of the listed above

Thanks alot,
Best regards,
Carolina

/home/cvalencia/Documentos + /home/cvalencia/Documentos/scripts/subjects.txt + 0 + 196 + 197 + 2.7
preprocessing Subj013
--------------------------------------
!!!! PREPROCESSING ANATOMICAL SCAN!!!!
--------------------------------------
deobliquing Subj013 anatomical
++ 3drefit: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset mprage.nii.gz
+ loading and re-writing entire dataset mprage.nii.gz
++ WARNING: nifti_read_buffer(mprage.nii.gz):
data bytes needed = 20185088
data bytes input = 20122458
number missing = 62630 (set to 0)
** load bricks: cannot read brick 0 from 'mprage.nii.gz'
** ERROR: Can't write NIfTI file since dataset isn't loaded: ./mprage.nii.gz
++ 3drefit processed 1 datasets
Reorienting Subj013 anatomical
++ WARNING: nifti_read_buffer(mprage.nii.gz):
data bytes needed = 20185088
data bytes input = 20122458
number missing = 62630 (set to 0)
** load bricks: cannot read brick 0 from 'mprage.nii.gz'
++ WARNING: nifti_read_buffer(mprage.nii.gz):
data bytes needed = 20185088
data bytes input = 20122458
number missing = 62630 (set to 0)
** load bricks: cannot read brick 0 from 'mprage.nii.gz'
r_fill_resampled_data_brick: failure to compute dataset slice 0
failure to resample dataset, exiting...
skull stripping Subj013 anatomical
**ERROR: can't open dataset mprage_RPI.nii.gz
++ 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 mprage_RPI.nii.gz
** Program compile date = Jan 7 2011
---------------------------------------
!!!! PREPROCESSING FUNCTIONAL SCAN !!!!
---------------------------------------
Dropping first TRs
++ 3dcalc: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: A cast of thousands
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as rest2.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:rest2.nii.gz is 10.166433 degrees from plumb.
** ERROR: output dataset name 'rest2_dr.nii.gz' conflicts with existing file
** ERROR: dataset NOT written to disk!
Deobliquing Subj013
++ 3drefit: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset rest2_dr.nii.gz
+ loading and re-writing entire dataset rest2_dr.nii.gz
++ WARNING: nifti_read_buffer(rest2_dr.nii.gz):
data bytes needed = 262144
data bytes input = 193507
number missing = 68637 (set to 0)
** load bricks: cannot read brick 0 from 'rest2_dr.nii.gz'
** ERROR: Can't write NIfTI file since dataset isn't loaded: ./rest2_dr.nii.gz
++ 3drefit processed 1 datasets
Reorienting Subj013
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as rest2_dr.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:rest2_dr.nii.gz is 10.166433 degrees from plumb.
++ WARNING: nifti_read_buffer(rest2_dr.nii.gz):
data bytes needed = 262144
data bytes input = 193507
number missing = 68637 (set to 0)
** load bricks: cannot read brick 0 from 'rest2_dr.nii.gz'
++ WARNING: nifti_read_buffer(rest2_dr.nii.gz):
data bytes needed = 262144
data bytes input = 193507
number missing = 68637 (set to 0)
** load bricks: cannot read brick 0 from 'rest2_dr.nii.gz'
r_fill_resampled_data_brick: failure to compute dataset slice 0
failure to resample dataset, exiting...
Motion correcting Subj013
++ 3dTstat: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: KR Hammett & RW Cox
** FATAL ERROR: Can't open dataset rest2_ro.nii.gz
** Program compile date = Jan 7 2011
++ 3dvolreg: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: RW Cox
** FATAL ERROR: Couldn't open -base dataset rest2_ro_mean.nii.gz
** Program compile date = Jan 7 2011
Skull stripping Subj013
++ 3dAutomask: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: Emperor Zhark
** FATAL ERROR: Can't open dataset 'rest2_mc.nii.gz'
** Program compile date = Jan 7 2011
++ 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 rest2_mc.nii.gz
** Program compile date = Jan 7 2011
Getting example_func for registration for Subj013
++ 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 rest2_ss.nii.gz[7]
** Program compile date = Jan 7 2011
Smoothing Subj013
** ERROR (nifti_image_read): failed to find header file for 'rest2_ss'
** ERROR: nifti_image_open(rest2_ss): bad header info
Error: failed to open file rest2_ss
Cannot open volume rest2_ss for reading!
Grand-mean scaling Subj013
** ERROR (nifti_image_read): failed to find header file for 'rest2_sm'
** ERROR: nifti_image_open(rest2_sm): bad header info
Error: failed to open file rest2_sm
Cannot open volume rest2_sm for reading!
Band-pass filtering Subj013
++ 3dFourier: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
** FATAL ERROR: Can't open dataset 'rest2_gms.nii.gz'
** Program compile date = Jan 7 2011
Removing linear and quadratic trends for Subj013
++ 3dTstat: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: KR Hammett & RW Cox
** FATAL ERROR: Can't open dataset rest2_filt.nii.gz
** Program compile date = Jan 7 2011
++ 3dDetrend: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
** FATAL ERROR: Can't open dataset 'rest2_filt.nii.gz'
** Program compile date = Jan 7 2011
++ 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 rest2_filt_mean.nii.gz
** Program compile date = Jan 7 2011
Generating mask of preprocessed data for Subj013
** ERROR (nifti_image_read): failed to find header file for 'rest2_pp'
** ERROR: nifti_image_open(rest2_pp): bad header info
Error: failed to open file rest2_pp
Cannot open volume rest2_pp for reading!
------------------------------
!!!! RUNNING REGISTRATION !!!!
------------------------------
mkdir: no se puede crear el directorio «/home/cvalencia/Documentos/Subj013/reg2»: El archivo ya existe
cp: no se puede efectuar «stat» sobre «/home/cvalencia/Documentos/Subj013/anat2/mprage_brain.nii.gz»: No existe el fichero o el directorio
cp: no se puede efectuar «stat» sobre «/home/cvalencia/Documentos/Subj013/func2/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: 4848 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: 4850 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: 4853 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/Subj013/segment2»: El archivo ya existe
Segmenting brain for Subj013
** 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: 4861 Abortado fast -t 1 -g -p -o segment ${anat}_brain.nii.gz
Creating global mask
++ 3dcopy: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
** failed to open input '/home/cvalencia/Documentos/Subj013/func2/rest2_pp_mask.nii.gz' on non-AFNI write
Try including the view of the input dataset /home/cvalencia/Documentos/Subj013/func2/rest2_pp_mask.nii.gz
or use its fullname. That might take care of the error.
Registering Subj013 csf to native (functional) space
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/reg2/example_func'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/reg2/example_func): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/reg2/example_func
ERROR: Could not open image /home/cvalencia/Documentos/Subj013/reg2/example_func
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj013/reg2/example_func
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/4_segment.sh: línea 64: 4863 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 Subj013 csf
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/segment2/csf2func'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/segment2/csf2func): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/segment2/csf2func
Cannot open volume /home/cvalencia/Documentos/Subj013/segment2/csf2func for reading!
Registering Subj013 csf to standard space
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/segment2/csf_sm'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/segment2/csf_sm): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/segment2/csf_sm
ERROR: Could not open image /home/cvalencia/Documentos/Subj013/segment2/csf_sm
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj013/segment2/csf_sm
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/4_segment.sh: línea 70: 4865 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 Subj013 csf and prior
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/segment2/csf2standard'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/segment2/csf2standard): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/segment2/csf2standard
Cannot open volume /home/cvalencia/Documentos/Subj013/segment2/csf2standard for reading!
Registering Subj013 csf back to native space
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/reg2/example_func'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/reg2/example_func): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/reg2/example_func
ERROR: Could not open image /home/cvalencia/Documentos/Subj013/reg2/example_func
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj013/reg2/example_func
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/4_segment.sh: línea 76: 4867 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 Subj013 csf probability map
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/segment2/csf_native'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/segment2/csf_native): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/segment2/csf_native
Cannot open volume /home/cvalencia/Documentos/Subj013/segment2/csf_native for reading!
Mask csf image by Subj013 functional
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/segment2/csf_bin'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/segment2/csf_bin): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/segment2/csf_bin
Cannot open volume /home/cvalencia/Documentos/Subj013/segment2/csf_bin for reading!
Registering Subj013 wm to native (functional) space
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/reg2/example_func'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/reg2/example_func): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/reg2/example_func
ERROR: Could not open image /home/cvalencia/Documentos/Subj013/reg2/example_func
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj013/reg2/example_func
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/4_segment.sh: línea 87: 4870 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 Subj013 wm
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/segment2/wm2func'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/segment2/wm2func): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/segment2/wm2func
Cannot open volume /home/cvalencia/Documentos/Subj013/segment2/wm2func for reading!
Registering Subj013 wm to standard space
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/segment2/wm_sm'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/segment2/wm_sm): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/segment2/wm_sm
ERROR: Could not open image /home/cvalencia/Documentos/Subj013/segment2/wm_sm
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj013/segment2/wm_sm
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/4_segment.sh: línea 93: 4872 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 Subj013 wm and prior
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/segment2/wm2standard'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/segment2/wm2standard): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/segment2/wm2standard
Cannot open volume /home/cvalencia/Documentos/Subj013/segment2/wm2standard for reading!
Registering Subj013 wm back to native space
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/reg2/example_func'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/reg2/example_func): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/reg2/example_func
ERROR: Could not open image /home/cvalencia/Documentos/Subj013/reg2/example_func
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj013/reg2/example_func
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/4_segment.sh: línea 99: 4874 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 Subj013 wm probability map
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/segment2/wm_native'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/segment2/wm_native): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/segment2/wm_native
Cannot open volume /home/cvalencia/Documentos/Subj013/segment2/wm_native for reading!
Mask wm image by Subj013 functional
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/segment2/wm_bin'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/segment2/wm_bin): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/segment2/wm_bin
Cannot open volume /home/cvalencia/Documentos/Subj013/segment2/wm_bin for reading!
--------------------------------------------
!!!! RUNNING NUISANCE SIGNAL REGRESSION !!!!
--------------------------------------------
Splitting up Subj013 motion parameters
awk: cannot open /home/cvalencia/Documentos/Subj013/func2/rest2_mc.1D (No such file or directory)
awk: cannot open /home/cvalencia/Documentos/Subj013/func2/rest2_mc.1D (No such file or directory)
awk: cannot open /home/cvalencia/Documentos/Subj013/func2/rest2_mc.1D (No such file or directory)
awk: cannot open /home/cvalencia/Documentos/Subj013/func2/rest2_mc.1D (No such file or directory)
awk: cannot open /home/cvalencia/Documentos/Subj013/func2/rest2_mc.1D (No such file or directory)
awk: cannot open /home/cvalencia/Documentos/Subj013/func2/rest2_mc.1D (No such file or directory)
Extracting global signal for Subj013
++ 3dmaskave: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
*** Cannot open mask dataset!
Extracting signal from csf for Subj013
++ 3dmaskave: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
*** Cannot open mask dataset!
Extracting signal from white matter for Subj013
++ 3dmaskave: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
*** Cannot open mask dataset!
Modifying model file
Running feat model
Not enough data in /home/cvalencia/Documentos/Subj013/func2/nuisance2/global.1D
** FATAL ERROR: Can't open dataset '/home/cvalencia/Documentos/Subj013/func2/rest2_pp_mask.nii.gz'
** Program compile date = Jan 7 2011
Running film to get residuals
Log directory is: /home/cvalencia/Documentos/Subj013/func2/nuisance2/stats++
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/func2/rest2_pp'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/func2/rest2_pp): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/func2/rest2_pp
ERROR: Could not open image /home/cvalencia/Documentos/Subj013/func2/rest2_pp
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj013/func2/rest2_pp.nii.gz


An exception has been thrown
Failed to read volume /home/cvalencia/Documentos/Subj013/func2/rest2_pp.nii.gzTrace: read_volume4DROI.

++ 3dTstat: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: KR Hammett & RW Cox
** FATAL ERROR: Can't open dataset /home/cvalencia/Documentos/Subj013/func2/nuisance2/stats/res4d.nii.gz
** Program compile date = Jan 7 2011
++ 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/Subj013/func2/nuisance2/stats/res4d.nii.gz
** Program compile date = Jan 7 2011
** ERROR (nifti_image_read): failed to find header file for '/home/cvalencia/Documentos/Subj013/func2/rest2_res'
** ERROR: nifti_image_open(/home/cvalencia/Documentos/Subj013/func2/rest2_res): bad header info
Error: failed to open file /home/cvalencia/Documentos/Subj013/func2/rest2_res
ERROR: Could not open image /home/cvalencia/Documentos/Subj013/func2/rest2_res
Image Exception : #22 :: Failed to read volume /home/cvalencia/Documentos/Subj013/func2/rest2_res
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/cvalencia/Documentos/scripts/5_nuisance.sh: línea 95: 4935 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: rest2: No existe el fichero o el directorio