Hello Matthew,

Thank you so much for your quick response.

The logs for level 1s seem to indicate successful completion.
Below is an example from Run1's log.
I appreciate your guidance and help.
Nim

Progress Report / Log

Started at Fri Dec 1 15:33:53 EST 2017

Feat main script

/bin/cp /danl/LindaMayes/pb2234/emo/model/level1run1_gng.feat/level1run1_gng.fsf
design.fsf

/usr/share/fsl/5.0/bin/feat_model design

mkdir .files;cp /usr/share/fsl/5.0/doc/fsl.css .files;cp -r
/usr/share/fsl/5.0/doc/images .files/images

/usr/share/fsl/5.0/bin/fsl_sub -T 10 -l logs -N feat0_init
/usr/share/fsl/5.0/bin/feat
/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/design.fsf -D
/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat -I 1 -init
25431

/usr/share/fsl/5.0/bin/fsl_sub -T 207 -l logs -N feat2_pre -j 25431
/usr/share/fsl/5.0/bin/feat
/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/design.fsf -D
/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat -I 1 -prestats
26865

/usr/share/fsl/5.0/bin/fsl_sub -T 68 -l logs -N feat3_film -j 26865
/usr/share/fsl/5.0/bin/feat
/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/design.fsf -D
/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat -I 1 -stats
22856

/usr/share/fsl/5.0/bin/fsl_sub -T 119 -l logs -N feat4_post -j 22856
/usr/share/fsl/5.0/bin/feat
/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/design.fsf -D
/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat -poststats 0
1033

/usr/share/fsl/5.0/bin/fsl_sub -T 1 -l logs -N feat5_stop -j
26865,22856,1033 /usr/share/fsl/5.0/bin/feat
/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/design.fsf -D
/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat -stop
1087

________________________________
Initialisation

/usr/share/fsl/5.0/bin/fslmaths
/danl/LindaMayes/pb2234/emo/BOLD/run1/bold prefiltered_func_data -odt
float
Total original volumes = 304

/usr/share/fsl/5.0/bin/fslroi prefiltered_func_data example_func 152 1

________________________________
Preprocessing:Stage 1

/usr/share/fsl/5.0/bin/mainfeatreg -F 6.00 -d
/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat -l
/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/logs/feat2_pre
-R /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/report_unwarp.html
-r /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/report_reg.html
-i /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/example_func.nii.gz
-n 10 -h /danl/LindaMayes/pb2234/anatomical/mprage_brain -w BBR -x
90 -s /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument
"/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat"
Option -l ( logfile )input with argument
"/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument
"/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument
"/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/report_reg.html"
Option -i ( main input ) input with argument
"/danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/example_func.nii.gz"
Option -n ( use nonlinear reg ) input with argument "10"
Option -h ( high-res structural image ) selected with argument
"/danl/LindaMayes/pb2234/anatomical/mprage_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument
"/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain"
Option -y ( standard dof ) selected with argument "12"
Option -z ( standard search ) selected with argument "90"

________________________________
Registration

/bin/mkdir -p /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg

/usr/share/fsl/5.0/bin/fslmaths
/danl/LindaMayes/pb2234/anatomical/mprage_brain highres

/usr/share/fsl/5.0/bin/fslmaths
/danl/LindaMayes/pb2234/anatomical/mprage highres_head

Checking for /danl/LindaMayes/pb2234/anatomical/mprage_brain2MNI152_T1_2mm_brain_warp
and /danl/LindaMayes/pb2234/anatomical/mprage_brain2MNI152_T1_2mm_brain.mat

/usr/share/fsl/5.0/bin/fslmaths
/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain standard

/usr/share/fsl/5.0/bin/fslmaths
/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm standard_head

/usr/share/fsl/5.0/bin/fslmaths
/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain_mask_dil
standard_mask

did not find file: example_func2highres.mat. Generating transform.

/usr/share/fsl/5.0/bin/epi_reg --epi=example_func --t1=highres_head
--t1brain=highres --out=example_func2highres
Running FAST segmentation FLIRT pre-alignment Running BBR 0.513011
0.999999 -0.000262 -0.001315 0.000000 0.000255 0.999983 -0.005792
0.000000 0.001317 0.005792 0.999982 0.000000 -1.407903 2.873569
1.441478 1.000000

/usr/share/fsl/5.0/bin/convert_xfm -inverse -omat
highres2example_func.mat example_func2highres.mat

/usr/share/fsl/5.0/bin/slicer example_func2highres highres -s 2 -x
0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35
sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35
sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ;
/usr/share/fsl/5.0/bin/pngappend sla.png + slb.png + slc.png + sld.png
+ sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png
+ sll.png example_func2highres1.png ; /usr/share/fsl/5.0/bin/slicer
highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x
0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55
slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55
slk.png -z 0.65 sll.png ; /usr/share/fsl/5.0/bin/pngappend sla.png +
slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png +
sli.png + slj.png + slk.png + sll.png example_func2highres2.png ;
/usr/share/fsl/5.0/bin/pngappend example_func2highres1.png -
example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png
example_func2highres2.png

/bin/rm example_func2highres1.png

did not find file: highres2standard.mat. Generating transform.

/usr/share/fsl/5.0/bin/flirt -in highres -ref standard -out
highres2standard -omat highres2standard.mat -cost corratio -dof 12
-searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear

/usr/share/fsl/5.0/bin/fnirt --iout=highres2standard_head
--in=highres_head --aff=highres2standard.mat
--cout=highres2standard_warp --iout=highres2standard
--jout=highres2highres_jac --config=T1_2_MNI152_2mm
--ref=standard_head --refmask=standard_mask --warpres=10,10,10

/usr/share/fsl/5.0/bin/applywarp -i highres -r standard -o
highres2standard -w highres2standard_warp

/usr/share/fsl/5.0/bin/convert_xfm -inverse -omat standard2highres.mat
highres2standard.mat

/usr/share/fsl/5.0/bin/slicer highres2standard standard -s 2 -x 0.35
sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35
sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35
sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ;
/usr/share/fsl/5.0/bin/pngappend sla.png + slb.png + slc.png + sld.png
+ sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png
+ sll.png highres2standard1.png ; /usr/share/fsl/5.0/bin/slicer
standard highres2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55
slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55
slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55
slk.png -z 0.65 sll.png ; /usr/share/fsl/5.0/bin/pngappend sla.png +
slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png +
sli.png + slj.png + slk.png + sll.png highres2standard2.png ;
/usr/share/fsl/5.0/bin/pngappend highres2standard1.png -
highres2standard2.png highres2standard.png; /bin/rm -f sl?.png
highres2standard2.png

/bin/rm highres2standard1.png

/usr/share/fsl/5.0/bin/convert_xfm -omat example_func2standard.mat
-concat highres2standard.mat example_func2highres.mat

/usr/share/fsl/5.0/bin/convertwarp --ref=standard
--premat=example_func2highres.mat --warp1=highres2standard_warp
--out=example_func2standard_warp

/usr/share/fsl/5.0/bin/applywarp --ref=standard --in=example_func
--out=example_func2standard --warp=example_func2standard_warp

/usr/share/fsl/5.0/bin/convert_xfm -inverse -omat
standard2example_func.mat example_func2standard.mat

/usr/share/fsl/5.0/bin/slicer example_func2standard standard -s 2 -x
0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35
sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35
sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ;
/usr/share/fsl/5.0/bin/pngappend sla.png + slb.png + slc.png + sld.png
+ sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png
+ sll.png example_func2standard1.png ; /usr/share/fsl/5.0/bin/slicer
standard example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x
0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55
slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55
slk.png -z 0.65 sll.png ; /usr/share/fsl/5.0/bin/pngappend sla.png +
slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png +
sli.png + slj.png + slk.png + sll.png example_func2standard2.png ;
/usr/share/fsl/5.0/bin/pngappend example_func2standard1.png -
example_func2standard2.png example_func2standard.png; /bin/rm -f
sl?.png example_func2standard2.png

________________________________
Preprocessing:Stage 2

/usr/share/fsl/5.0/bin/mcflirt -in prefiltered_func_data -out
prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel
-rmsabs -spline_final

/bin/mkdir -p mc ; /bin/mv -f prefiltered_func_data_mcf.mat
prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms
prefiltered_func_data_mcf_abs_mean.rms
prefiltered_func_data_mcf_rel.rms
prefiltered_func_data_mcf_rel_mean.rms mc

/usr/share/fsl/5.0/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t
'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a
x,y,z -w 640 -h 144 -o rot.png

/usr/share/fsl/5.0/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t
'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a
x,y,z -w 640 -h 144 -o trans.png

/usr/share/fsl/5.0/bin/fsl_tsplot -i
prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t
'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a
absolute,relative -o disp.png

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func

/usr/share/fsl/5.0/bin/bet2 mean_func mask -f 0.3 -n -m;
/usr/share/fsl/5.0/bin/immv mask_mask mask

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_mcf -mas mask
prefiltered_func_data_bet

/usr/share/fsl/5.0/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
0.000000 5770.526855

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_bet -thr
577.0526855 -Tmin -bin mask -odt char

/usr/share/fsl/5.0/bin/fslstats prefiltered_func_data_mcf -k mask -p 50
4826.570312

/usr/share/fsl/5.0/bin/fslmaths mask -dilF mask

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_mcf -mas mask
prefiltered_func_data_thresh

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func

/usr/share/fsl/5.0/bin/susan prefiltered_func_data_thresh 3619.927734
2.5477707006369426 3 1 1 mean_func 3619.927734
prefiltered_func_data_smooth

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_smooth -mas mask
prefiltered_func_data_smooth

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_smooth -mul
2.0718645650178606 prefiltered_func_data_intnorm

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_intnorm -bptf
45.0 -1 -add tempMean prefiltered_func_data_tempfilt

/usr/share/fsl/5.0/bin/imrm tempMean

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_tempfilt
filtered_func_data

/usr/share/fsl/5.0/bin/fslmaths filtered_func_data -Tmean mean_func

/bin/rm -rf prefiltered_func_data*

________________________________
Stats

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText
/danl/LindaMayes/pb2234/emo/model/onsets/go1.txt
custom_timing_files/ev1.txt

mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText
/danl/LindaMayes/pb2234/emo/model/onsets/nogo1.txt
custom_timing_files/ev2.txt

cp mc/prefiltered_func_data_mcf.par mc/prefiltered_func_data_mcf_final.par

paste -d ' ' mc/prefiltered_func_data_mcf_final.par > confoundevs.txt

/usr/share/fsl/5.0/bin/feat_model design confoundevs.txt

/usr/share/fsl/5.0/bin/film_gls --in=filtered_func_data --rn=stats
--pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con
Log directory is: stats
paradigm.getDesignMatrix().Nrows()=304
paradigm.getDesignMatrix().Ncols()=10
sizeTS=304
numTS=115085
Calculating residuals...
Completed
Estimating residual autocorrelation...
Calculating raw AutoCorrs... Completed
mode = 10205.5
sig = 528
Spatially smoothing auto corr estimates
................
Completed
Tukey M = 17
Tukey estimates... Completed
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

/usr/share/fsl/5.0/bin/smoothest -d 294 -m mask -r stats/res4d >
stats/smoothness

________________________________
Post-stats

On Wed, Dec 6, 2017 at 8:36 AM, Matthew Webster <[log in to unmask]> wrote:

Hello,
The log section looks like it is for the preparation of the gfeat sub-jobs ( the final command is consistent with the preparation ending succesfully ). Can you look at the reports for cope1.feat etc in the gfeat folder and see if there are any errors reported there?

Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford

> On 5 Dec 2017, at 20:33, Nim Tottenham <[log in to unmask]> wrote:
>
> Hello,
>
> I have a task with 2 runs. The level 1 processing has been run on these 2 runs. Now, at level 2 in Feat, the process crashes and I cannot figure out why. (stops at: /usr/share/fsl/5.0/bin/fslmaths tdof_t3 -mas mask tdof_t3)
>
> Could you help me understand what I need to do to fix this?
>
> Here is the log output:
>
> Progress Report / Log
> Started at Sat Dec 2 06:52:58 EST 2017
> Feat main script
> /bin/cp /danl/LindaMayes/pb2234/emo/model_gng.gfeat/design.fsf design.fsf
> /usr/share/fsl/5.0/bin/feat_model design
> mkdir .files;cp /usr/share/fsl/5.0/doc/fsl.css .files;cp -r /usr/share/fsl/5.0/doc/images .files/images
> /usr/share/fsl/5.0/bin/fsl_sub -T 60 -l logs -N feat2_pre /usr/share/fsl/5.0/bin/feat /danl/LindaMayes/pb2234/emo/model_gng+.gfeat/design.fsf -D /danl/LindaMayes/pb2234/emo/model_gng+.gfeat -gfeatprep
> Higher-level input files preparation
> /usr/share/fsl/5.0/bin/featregapply /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat
> /usr/share/fsl/5.0/bin/featregapply /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat
> /usr/share/fsl/5.0/bin/fslmerge -t bg_image /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/reg/highres /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/reg/highres
> /usr/share/fsl/5.0/bin/fslmaths bg_image -inm 1000 -Tmean bg_image -odt float
> /usr/share/fsl/5.0/bin/fslmerge -t mask /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/mask /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/mask
> mkdir -p inputreg
> /usr/share/fsl/5.0/bin/fslmaths ../mask -mul 2 -Tmean masksum -odt short
> /usr/share/fsl/5.0/bin/fslmaths masksum -thr 2 -add masksum masksum
> /usr/share/fsl/5.0/bin/overlay 0 0 -c ../bg_image -a masksum 0.9 4 masksum_overlay
> /usr/share/fsl/5.0/bin/slicer masksum_overlay -S 2 750 masksum_overlay.png
> /usr/share/fsl/5.0/bin/fslmaths masksum -mul 0 maskunique
> /usr/share/fsl/5.0/bin/fslmaths /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/mask -mul -1 -add 1 -mul 1 -add maskunique maskunique
> /usr/share/fsl/5.0/bin/fslmaths /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/mask -mul -1 -add 1 -mul 2 -add maskunique maskunique
> /usr/share/fsl/5.0/bin/fslmaths masksum -thr 1 -uthr 1 -bin -mul maskunique maskunique
> /usr/share/fsl/5.0/bin/overlay 0 0 ../bg_image -a maskunique 0.9 2 maskunique_overlay
> /usr/share/fsl/5.0/bin/slicer maskunique_overlay -S 2 750 maskunique_overlay.png
> /bin/cp /usr/share/fsl/5.0/etc/luts/ramp.gif .ramp.gif
> /usr/share/fsl/5.0/bin/fslmaths mask -Tmin mask
> /usr/share/fsl/5.0/bin/fslmerge -t mean_func /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/mean_func /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/mean_func
> /usr/share/fsl/5.0/bin/fslmaths mean_func -Tmean mean_func
> /usr/share/fsl/5.0/bin/fslmerge -t cope1 /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/stats/cope1 /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/stats/cope1
> /usr/share/fsl/5.0/bin/fslmaths cope1 -mas mask cope1
> printf '0.24688815000000003 ' >> design.lcon
> /usr/share/fsl/5.0/bin/fslmerge -t varcope1 /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/stats/varcope1 /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/stats/varcope1
> /usr/share/fsl/5.0/bin/fslmaths varcope1 -mas mask varcope1
> /usr/share/fsl/5.0/bin/fslmaths /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/stats/cope1 -mul 0 -add 294 /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/stats/FEtdof_t1
> /usr/share/fsl/5.0/bin/fslmaths /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/stats/cope1 -mul 0 -add 294 /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/stats/FEtdof_t1
> /usr/share/fsl/5.0/bin/fslmerge -t tdof_t1 /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/stats/FEtdof_t1 /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/stats/FEtdof_t1
> /usr/share/fsl/5.0/bin/fslmaths tdof_t1 -mas mask tdof_t1
> /usr/share/fsl/5.0/bin/fslmerge -t cope2 /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/stats/cope2 /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/stats/cope2
> /usr/share/fsl/5.0/bin/fslmaths cope2 -mas mask cope2
> printf '0.17108145 ' >> design.lcon
> /usr/share/fsl/5.0/bin/fslmerge -t varcope2 /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/stats/varcope2 /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/stats/varcope2
> /usr/share/fsl/5.0/bin/fslmaths varcope2 -mas mask varcope2
> /usr/share/fsl/5.0/bin/fslmaths /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/stats/cope2 -mul 0 -add 294 /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/stats/FEtdof_t2
> /usr/share/fsl/5.0/bin/fslmaths /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/stats/cope2 -mul 0 -add 294 /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/stats/FEtdof_t2
> /usr/share/fsl/5.0/bin/fslmerge -t tdof_t2 /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/stats/FEtdof_t2 /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/stats/FEtdof_t2
> /usr/share/fsl/5.0/bin/fslmaths tdof_t2 -mas mask tdof_t2
> /usr/share/fsl/5.0/bin/fslmerge -t cope3 /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/stats/cope3 /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/stats/cope3
> /usr/share/fsl/5.0/bin/fslmaths cope3 -mas mask cope3
> printf '0.16967985 ' >> design.lcon
> /usr/share/fsl/5.0/bin/fslmerge -t varcope3 /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/stats/varcope3 /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/stats/varcope3
> /usr/share/fsl/5.0/bin/fslmaths varcope3 -mas mask varcope3
> /usr/share/fsl/5.0/bin/fslmaths /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/stats/cope3 -mul 0 -add 294 /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/stats/FEtdof_t3
> /usr/share/fsl/5.0/bin/fslmaths /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/stats/cope3 -mul 0 -add 294 /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/stats/FEtdof_t3
> /usr/share/fsl/5.0/bin/fslmerge -t tdof_t3 /danl/LindaMayes/pb2234/emo/model/level1run1_gng+.feat/reg_standard/stats/FEtdof_t3 /danl/LindaMayes/pb2234/emo/model/level1run2_gng+.feat/reg_standard/stats/FEtdof_t3
> /usr/share/fsl/5.0/bin/fslmaths tdof_t3 -mas mask tdof_t3
>
> Thank you so much.
> Warmly,
> Nim

Nim Tottenham, Ph.D.
Associate Professor of Psychology
Columbia University
Department of Psychology (355D Schermerhorn Hall)
1190 Amsterdam Avenue, MC 5501
New York, NY 10027
212-854-1925
[log in to unmask]
tottenhamlab.psych.columbia.edu