Hi Marteen,

I have AFNI installed but not accessible in the path, I edited the .bashrc
Then I run the batch_process.sh and it starts to process... but it stops in the nuisance step, I understand there is a file missed...

Thanks!


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
++ 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
++ 3drefit processed 1 datasets
Reorienting Subj001 anatomical
skull stripping Subj001 anatomical
The intensity in the output dataset is a modified version
of the intensity in the input volume.
To obtain a masked version of the input with identical values inside
the brain, you can either use 3dSkullStrip's -orig_vol option
or run the following command:
3dcalc -a mprage_RPI.nii.gz -b mprage_surf.nii.gz+orig -expr 'a*step(b)' \
-prefix mprage_surf.nii.gz_orig_vol
to generate a new masked version of the input.
++ 3dcalc: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: A cast of thousands
++ Output dataset ./mprage_brain.nii.gz
---------------------------------------
!!!! 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 rest.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:rest.nii.gz is 5.179751 degrees from plumb.
++ Output dataset ./rest_dr.nii.gz
Deobliquing Subj001
++ 3drefit: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset rest_dr.nii.gz
+ loading and re-writing entire dataset rest_dr.nii.gz
++ 3drefit processed 1 datasets
Reorienting Subj001
Motion correcting Subj001
++ 3dTstat: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rest_ro_mean.nii.gz
++ 3dvolreg: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: RW Cox
++ Coarse del was 10, replaced with 3
++ Max displacement in automask = 0.40 (mm) at sub-brick 0
Skull stripping Subj001
++ 3dAutomask: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: Emperor Zhark
++ Loading dataset rest_mc.nii.gz
++ Forming automask
+ Fixed clip level = 414.830291
+ Used gradual clip level = 370.560822 .. 455.330688
+ Number voxels above clip level = 31506
+ Clustering voxels ...
+ Largest cluster has 30753 voxels
+ Clustering voxels ...
+ Largest cluster has 30208 voxels
+ Filled 196 voxels in small holes; now have 30404 voxels
+ Clustering voxels ...
+ Largest cluster has 30404 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 100668 voxels
+ Mask now has 30404 voxels
++ Dilating automask
+ Clustering voxels ...
+ Largest cluster has 96134 voxels
++ 34938 voxels in the mask [out of 131072: 26.66%]
++ first 13 x-planes are zero [from R]
++ last 12 x-planes are zero [from L]
++ first 7 y-planes are zero [from P]
++ last 7 y-planes are zero [from A]
++ first 0 z-planes are zero [from I]
++ last 0 z-planes are zero [from S]
++ Output dataset ./rest_mask.nii.gz
++ CPU time = 1.060000 sec
++ 3dcalc: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: A cast of thousands
++ Output dataset ./rest_ss.nii.gz
Getting example_func for registration for Subj001
++ 3dcalc: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: A cast of thousands
++ Output dataset ./example_func.nii.gz
Smoothing Subj001
Grand-mean scaling Subj001
Band-pass filtering Subj001
++ 3dFourier: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
Removing linear and quadratic trends for Subj001
++ 3dTstat: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rest_filt_mean.nii.gz
++ 3dDetrend: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ 3dcalc: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
++ Authored by: A cast of thousands
++ Output dataset ./rest_pp.nii.gz
Generating mask of preprocessed data for Subj001
------------------------------
!!!! RUNNING REGISTRATION !!!!
------------------------------
mkdir: no se puede crear el directorio «/home/cvalencia/Documentos/Subj001/reg»: El archivo ya existe
/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
Creating global mask
++ 3dcopy: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
Registering Subj001 csf to native (functional) space
Smoothing Subj001 csf
Registering Subj001 csf to standard space
Finding overlap between Subj001 csf and prior
Registering Subj001 csf back to native space
Threshold and binarize Subj001 csf probability map
Mask csf image by Subj001 functional
Registering Subj001 wm to native (functional) space
Smoothing Subj001 wm
Registering Subj001 wm to standard space
Finding overlap between Subj001 wm and prior
Registering Subj001 wm back to native space
Threshold and binarize Subj001 wm probability map
Mask wm image by Subj001 functional
--------------------------------------------
!!!! RUNNING NUISANCE SIGNAL REGRESSION !!!!
--------------------------------------------
Splitting up Subj001 motion parameters
Extracting global signal for Subj001
++ 3dmaskave: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
+++ 34938 voxels survive the mask
Extracting signal from csf for Subj001
++ 3dmaskave: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
+++ 173 voxels survive the mask
Extracting signal from white matter for Subj001
++ 3dmaskave: AFNI version=AFNI_2010_10_19_1028 (Jan 7 2011) [32-bit]
+++ 1440 voxels survive the mask
Modifying model file
Running feat model
++ 34938 voxels in mask
Running film to get residuals
Log directory is: /home/cvalencia/Documentos/Subj001/func/nuisance/stats++++
paradigm.getDesignMatrix().Nrows()=197
paradigm.getDesignMatrix().Ncols()=9
sizeTS=197
numTS=34938
Completed
Prewhitening and Computing PEs...
Percentage done:
1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed
Saving results...
Completed
++ 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/Subj001/func/nuisance/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/Subj001/func/nuisance/stats/res4d.nii.gz
** Program compile date = Jan 7 2011
** 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: 24898 Abortado flirt -ref ${reg_dir}/standard -in ${func_dir}/${rest}_res -out ${func_dir}/${rest}_res2standard -applyxfm -init ${reg_dir}/example_func2standard.mat -interp trilinear
+ + + + +
cat: rest: No existe el fichero o el directorio
cvalencia@cvalencia-Precision-WorkStation-T3400:~/Documentos/scripts$