 |
 |
Hi Matthew, Yes, the lower level contrasts appear (pasted below). However, we discovered that this 2nd level feat could run on another server - making us think that on one server, the process just kicks out. Have you heard of this before? Thank you and best wishes, Nim Higher-level FEAT results(one for each lower-level contrast) Lower-level contrast 1 (Go) Lower-level contrast 2 (Nogo) Lower-level contrast 3 (Go-Nogo) On Wed, Dec 6, 2017 at 10:30 AM, Matthew Webster < [log in to unmask]> wrote: > 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] > <[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/mo >> del/level1run1_gng+.feat >> > /usr/share/fsl/5.0/bin/featregapply /danl/LindaMayes/pb2234/emo/mo >> del/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/mo >> del/level1run1_gng+.feat/reg_standard/mask /danl/LindaMayes/pb2234/emo/mo >> del/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/mo >> del/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/mo >> del/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/mo >> del/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/mo >> del/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/mo >> del/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/mo >> del/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/mo >> del/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/mo >> del/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/mo >> del/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/mo >> del/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/mo >> del/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) > <https://maps.google.com/?q=Schermerhorn+Hall)+1190+Amsterdam+Avenue&entry=gmail&source=g> > 1190 Amsterdam Avenue > <https://maps.google.com/?q=Schermerhorn+Hall)+1190+Amsterdam+Avenue&entry=gmail&source=g>, > MC 5501 > New York, NY 10027 > 212-854-1925 <(212)%20854-1925> > [log in to unmask] > tottenhamlab.psych.columbia.edu > > > > -- 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