Hello,

         Thanks for the report - everything looks OK in the lower-level so that’s fine. In the gfeat report, you should have something like this in the results section ( the contrast names will vary ). Clicking on one of the “Lower-level contrasts” pages should go to a sub-report with its own report log - can you check those as well?

Kind Regards

Matthew

--------------------------------

Dr Matthew Webster

FMRIB Centre 

John Radcliffe Hospital

University of Oxford

On 6 Dec 2017, at 13:50, nim tottenham - Columbia <[log in to unmask]> wrote:

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


<snip>
________________________________
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