Hello,

I am using fcon_1000 for rsfMRI processing for the first time.
My environment is Mac OSX10.7.

I ran the batch_process.sh script, but it ended with errors as below. I cannot figure out how to solve these errors.
Could you please help me out?

Makiko


[macpro101208:~/fcon_1000/scripts] yamadamakiko% ./batch_process.sh
/Users/yamadamakiko/fcon_1000/EXP02 + /Users/yamadamakiko/fcon_1000/EXP02/EXP02_subjects.txt + 4 + 203 + 200 + 2
preprocessing sub001
--------------------------------------
!!!! PREPROCESSING ANATOMICAL SCAN!!!!
--------------------------------------
deobliquing sub001 anatomical
++ 3drefit: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-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 sub001 anatomical
skull stripping sub001 anatomical
dyld: Library not loaded: /sw/lib/libglib-1.2.0.dylib
  Referenced from: /Users/yamadamakiko/abin/3dSkullStrip
  Reason: image not found
/Users/yamadamakiko/fcon_1000/scripts/1_anatpreproc.sh: line 45: 52304 Trace/BPT trap: 5       3dSkullStrip -input ${anat}_RPI.nii.gz -o_ply ${anat}_surf.nii.gz
++ 3dcalc: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset mprage_surf.nii.gz
** Program compile date = Aug 12 2011
---------------------------------------
!!!! PREPROCESSING FUNCTIONAL SCAN !!!!
---------------------------------------
Dropping first TRs
++ 3dcalc: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./rest_dr.nii.gz
Deobliquing sub001
++ 3drefit: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-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 sub001
Motion correcting sub001
++ 3dTstat: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rest_ro_mean.nii.gz
++ 3dvolreg: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
++ Authored by: RW Cox
++ Coarse del was 10, replaced with 3
++ Max displacement in automask = 1.11 (mm) at sub-brick 0
Skull stripping sub001
++ 3dAutomask: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset rest_mc.nii.gz
++ Forming automask
 + Fixed clip level = 1825.005005
 + Used gradual clip level = 1599.834961 .. 2094.415283
 + Number voxels above clip level = 25734
 + Clustering voxels ...
 + Largest cluster has 25586 voxels
 + Clustering voxels ...
 + Largest cluster has 24864 voxels
 + Filled   187 voxels in small holes; now have 25051 voxels
 + Clustering voxels ...
 + Largest cluster has 25051 voxels
 + Clustering non-brain voxels ...
 + Clustering voxels ...
 + Largest cluster has 118309 voxels
 + Mask now has 25051 voxels
++ Dilating automask
 + Clustering voxels ...
 + Largest cluster has 113653 voxels
++ 29707 voxels in the mask [out of 143360: 20.72%]
++ first  14 x-planes are zero [from R]
++ last   13 x-planes are zero [from L]
++ first   6 y-planes are zero [from P]
++ last    8 y-planes are zero [from A]
++ first   0 z-planes are zero [from I]
++ last    2 z-planes are zero [from S]
++ Output dataset ./rest_mask.nii.gz
++ CPU time = 0.800000 sec
++ 3dcalc: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./rest_ss.nii.gz
Getting example_func for registration for sub001
++ 3dcalc: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./example_func.nii.gz
Smoothing sub001
/Users/yamadamakiko/fcon_1000/scripts/2_funcpreproc.sh: line 75: fslmaths: command not found
Grand-mean scaling sub001
/Users/yamadamakiko/fcon_1000/scripts/2_funcpreproc.sh: line 79: fslmaths: command not found
Band-pass filtering sub001
++ 3dFourier: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
** FATAL ERROR: Can't open dataset 'rest_gms.nii.gz'
** Program compile date = Aug 12 2011
Removing linear and quadratic trends for sub001
++ 3dTstat: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
++ Authored by: KR Hammett & RW Cox
** FATAL ERROR: Can't open dataset rest_filt.nii.gz
** Program compile date = Aug 12 2011
++ 3dDetrend: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
** FATAL ERROR: Can't open dataset 'rest_filt.nii.gz'
** Program compile date = Aug 12 2011
++ 3dcalc: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset rest_filt_mean.nii.gz
** Program compile date = Aug 12 2011
Generating mask of preprocessed data for sub001
/Users/yamadamakiko/fcon_1000/scripts/2_funcpreproc.sh: line 93: fslmaths: command not found
------------------------------
!!!! RUNNING REGISTRATION !!!!
------------------------------
cp: /Users/yamadamakiko/fcon_1000/EXP02/sub001/anat/mprage_brain.nii.gz: No such file or directory
/Users/yamadamakiko/fcon_1000/scripts/3_registration.sh: line 57: flirt: command not found
/Users/yamadamakiko/fcon_1000/scripts/3_registration.sh: line 59: convert_xfm: command not found
/Users/yamadamakiko/fcon_1000/scripts/3_registration.sh: line 63: flirt: command not found
/Users/yamadamakiko/fcon_1000/scripts/3_registration.sh: line 65: convert_xfm: command not found
/Users/yamadamakiko/fcon_1000/scripts/3_registration.sh: line 69: convert_xfm: command not found
/Users/yamadamakiko/fcon_1000/scripts/3_registration.sh: line 71: flirt: command not found
/Users/yamadamakiko/fcon_1000/scripts/3_registration.sh: line 73: convert_xfm: command not found
/Users/yamadamakiko/fcon_1000/scripts/tissuepriors/3mm/
------------------------------
!!!! RUNNING SEGMENTATION !!!!
------------------------------
Segmenting brain for sub001
/Users/yamadamakiko/fcon_1000/scripts/4_segment.sh: line 55: fast: command not found
Creating global mask
++ 3dcopy: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
** failed to open input '/Users/yamadamakiko/fcon_1000/EXP02/sub001/func/rest_pp_mask.nii.gz' on non-AFNI write
Try including the view of the input dataset /Users/yamadamakiko/fcon_1000/EXP02/sub001/func/rest_pp_mask.nii.gz
or use its fullname. That might take care of the error.
Registering sub001 csf to native (functional) space
/Users/yamadamakiko/fcon_1000/scripts/4_segment.sh: line 64: flirt: command not found
Smoothing sub001 csf
/Users/yamadamakiko/fcon_1000/scripts/4_segment.sh: line 67: fslmaths: command not found
Registering sub001 csf to standard space
/Users/yamadamakiko/fcon_1000/scripts/4_segment.sh: line 70: flirt: command not found
Finding overlap between sub001 csf and prior
/Users/yamadamakiko/fcon_1000/scripts/4_segment.sh: line 73: fslmaths: command not found
Registering sub001 csf back to native space
/Users/yamadamakiko/fcon_1000/scripts/4_segment.sh: line 76: flirt: command not found
Threshold and binarize sub001 csf probability map
/Users/yamadamakiko/fcon_1000/scripts/4_segment.sh: line 79: fslmaths: command not found
Mask csf image by sub001 functional
/Users/yamadamakiko/fcon_1000/scripts/4_segment.sh: line 82: fslmaths: command not found
Registering sub001 wm to native (functional) space
/Users/yamadamakiko/fcon_1000/scripts/4_segment.sh: line 87: flirt: command not found
Smoothing sub001 wm
/Users/yamadamakiko/fcon_1000/scripts/4_segment.sh: line 90: fslmaths: command not found
Registering sub001 wm to standard space
/Users/yamadamakiko/fcon_1000/scripts/4_segment.sh: line 93: flirt: command not found
Finding overlap between sub001 wm and prior
/Users/yamadamakiko/fcon_1000/scripts/4_segment.sh: line 96: fslmaths: command not found
Registering sub001 wm back to native space
/Users/yamadamakiko/fcon_1000/scripts/4_segment.sh: line 99: flirt: command not found
Threshold and binarize sub001 wm probability map
/Users/yamadamakiko/fcon_1000/scripts/4_segment.sh: line 102: fslmaths: command not found
Mask wm image by sub001 functional
/Users/yamadamakiko/fcon_1000/scripts/4_segment.sh: line 105: fslmaths: command not found
--------------------------------------------
!!!! RUNNING NUISANCE SIGNAL REGRESSION !!!!
--------------------------------------------
Splitting up sub001 motion parameters
Extracting global signal for sub001
++ 3dmaskave: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
*** Cannot open mask dataset!
Extracting signal from csf for sub001
++ 3dmaskave: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
*** Cannot open mask dataset!
Extracting signal from white matter for sub001
++ 3dmaskave: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
*** Cannot open mask dataset!
Modifying model file
Running feat model
/Users/yamadamakiko/fcon_1000/scripts/5_nuisance.sh: line 82: feat_model: command not found
** FATAL ERROR: Can't open dataset '/Users/yamadamakiko/fcon_1000/EXP02/sub001/func/rest_pp_mask.nii.gz'
** Program compile date = Aug 12 2011
Running film to get residuals
/Users/yamadamakiko/fcon_1000/scripts/5_nuisance.sh: line 88: film_gls: command not found
++ 3dTstat: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
++ Authored by: KR Hammett & RW Cox
** FATAL ERROR: Can't open dataset /Users/yamadamakiko/fcon_1000/EXP02/sub001/func/nuisance/stats/res4d.nii.gz
** Program compile date = Aug 12 2011
++ 3dcalc: AFNI version=AFNI_2011_05_26_1457 (Aug 12 2011) [64-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset /Users/yamadamakiko/fcon_1000/EXP02/sub001/func/nuisance/stats/res4d.nii.gz
** Program compile date = Aug 12 2011
/Users/yamadamakiko/fcon_1000/scripts/5_nuisance.sh: line 95: flirt: command not found