> OK - I think I know what's going on. For some reason (we'll look into why)
> when you use the -noest option FILM is not saving the res4d residuals
> file which is read by smoothest to estimate data smoothness. If you add
> the following lines around the relevant smoothest call then it won't get
> called in your case and instead the smoothness gets estimated from the
> stats images so hopefully all will be well.
>
> if { [ file exists stats/res4d.hdr ] {
> feat4:exec "$FSLDIR/bin/smoothest -d [ exec cat ${FD}/stats/dof ] -m
> ${FD}/mask -r ${FD}/stats/res4d > ${FD}/stats/smoothness" }
This works! Thanks,
Erik-Jan
> On Wed, 18 Sep 2002, Erik-Jan Vlieger wrote:
> > > > > Hi - this may be because you have so few time points - you can't
> > > > > really do prewhitening in this case. The next version will have a
> > > > > button to turn this off in such cases, but for the moment, you
> > > > > could try editing $FSLDIR/tcl/feat.tcl and change the film_gls
> > > > > call:
> > > > > replace "-sa -ms 5 -sp $FSLDIR/bin/susan_smooth"
> > > > > with "-noest"
> > > > > (but DON'T forget to put it back afterwards!!)
> > > >
> > > > OK,
> > > >
> > > > did this, and now Feat runs into another error. Is that because of
> > > > the change to $FSLDIR/tcl/feat.tcl? I would love to see the cluster
> > > > report, but perhaps this simply is not possible?
> > >
> > > Hi - not sure....hard to say from this. if you email me directly the
> > > report.log and a listing of the resulting .feat and .feat/stats
> > > directories that may tell us more...otherwise feel free to prepare the
> > > data on a web/ftp site and we'll take a look.
> >
> > Allright, here is the requested information, thanks again! If this is not
> > sufficient, I'll prepare the data somewhere.
> >
> > Erik-Jan Vlieger
> >
> >
> > This is what is printed on the command line:
> > --------------------------------------
> > child process exited abnormally
> > while executing
> > "exec grep DLH ${FD}/stats/smoothness | awk {{ print $2 }} - "
> > (procedure "feat4:poststats" line 54)
> > invoked from within
> > "feat4:poststats 0"
> > (procedure "feat4:proc" line 329)
> > invoked from within
> > "feat4:proc [ file rootname [ lindex $argv 0 ] ]"
> > (file "/usr/local//bin/feat" line 17)
> > --------------------------------------------
> >
> >
> >
> > This is the contents of the .feat directory:
> > -------------------------------------------------
> > design.con design.mat example_func.img mask.hdr
> > report.log thresh_zstat1.img
> > design.fsf design.ppm filtered_func_data.hdr mask.img stats/
> > design.gif example_func.hdr filtered_func_data.img report.html
> > thresh_zstat1.hdr
> > --------------------------------------------------
> > The last file created is report.log, the one before that was
> > thresh_zstat1.img/hdr
> >
> >
> >
> >
> > This is the content of the stats directory:
> > -------------------------------------------------
> > cmlogfile corrections.hdr logfile pe1.hdr ratios
> > smoothness varcope1.hdr zstat1.img cope1.hdr corrections.img neff1.hdr
> > pe1.img sigmasquareds.hdr tstat1.hdr varcope1.img cope1.img dof
> > neff1.img probs sigmasquareds.img tstat1.img zstat1.hdr
> > -------------------------------------------------
> > The last files created are zstat.img/hdr and tstat.img/hdr
> >
> >
> >
> >
> > This is the content of the report.log file:
> > ----------------------------------------------------
> > Started FEAT at wo sep 18 09:56:36 CEST 2002 on geertgroote.amc.uva.nl
> > Total original volumes = 22
> > /usr/local//bin/avwroi /Proj/FA/S1_12_N2_10_fa2tal2
> > /Proj/FA/S1_12_N2_10_fa2tal2.feat/example_func 11 1
> >
> > /usr/local//bin/ip /Proj/FA/S1_12_N2_10_fa2tal2
> > /Proj/FA/S1_12_N2_10_fa2tal2.feat/filtered_func_data 10 -s 2.12314225053
> > -m /Proj/FA/S1_12_N2_10_fa2tal2.feat/mask -I 10000
> > rm -rf /Proj/FA/S1_12_N2_10_fa2tal2.feat/prefiltered_func_data*
> >
> > /usr/local//bin/film_gls -rn /Proj/FA/S1_12_N2_10_fa2tal2.feat/stats
> > -noest -sp /usr/local//bin/susan_smooth
> > /Proj/FA/S1_12_N2_10_fa2tal2.feat/filtered_func_data
> > /Proj/FA/S1_12_N2_10_fa2tal2.feat/design.mat 51.918300
> > Log directory is: /Proj/FA/S1_12_N2_10_fa2tal2.feat/stats
> > Loading image... Completed
> > Applying threshold to Series... Completed
> > Completed
> > Prewhitening and Computing PEs...
> > 0.0047693,0.0095386,0.0143079,0.0190772,0.0238465,0.0286158,0.0333851,0.0
> >381544,0.0429237,0.047693,0.0524623,0.0572316,0.0620009,0.0667702,0.071539
> >5,0.0763088,0.0810781,0.0858474,0.0906167,0.095386,0.100155,0.104925,0.109
> >694,0.114463,0.119233,0.124002,0.128771,0.13354,0.13831,0.143079,0.147848,
> >0.152618,0.157387,0.162156,0.166926,0.171695,0.176464,0.181233,0.186003,0.
> >190772,0.195541,0.200311,0.20508,0.209849,0.214619,0.219388,0.224157,0.228
> >926,0.233696,0.238465,0.243234,0.248004,0.252773,0.257542,0.262312,0.26708
> >1,0.27185,0.276619,0.281389,0.286158,0.290927,0.295697,0.300466,0.305235,0
> >.310005,0.314774,0.319543,0.324312,0.329082,0.333851,0.33862,0.34339,0.348
> >159,0.352928,0.357698,0.362467,0.367236,0.372005,0.376775,0.381544,0.38631
> >3,0.391083,0.395852,0.400621,0.405391,0.41016,0.414929,0.419699,0.424468,0
> >.429237,0.434006,0.438776,0.443545,0.448314,0.453084,0.457853,0.462622,0.4
> >67392,0.472161,0.47693,0.481699,0.486469,0.491238,0.496007,0.500777,0.5055
> >46,0.510315,0.515085,0.519854,0.524623,0.529392,0.534162,0.538931,0.5437,0
> >.54847,0.553239,0.558008,0.562778,0.567547,0.572316,0.577085,0.581855,0.58
> >6624,0.591393,0.596163,0.600932,0.605701,0.610471,0.61524,0.620009,0.62477
> >8,0.629548,0.634317,0.639086,0.643856,0.648625,0.653394,0.658164,0.662933,
> >0.667702,0.672471,0.677241,0.68201,0.686779,0.691549,0.696318,0.701087,0.7
> >05857,0.710626,0.715395,0.720164,0.724934,0.729703,0.734472,0.739242,0.744
> >011,0.74878,0.75355,0.758319,0.763088,0.767857,0.772627,0.777396,0.782165,
> >0.786935,0.791704,0.796473,0.801243,0.806012,0.810781,0.81555,0.82032,0.82
> >5089,0.829858,0.834628,0.839397,0.844166,0.848936,0.853705,0.858474,0.8632
> >44,0.868013,0.872782,0.877551,0.882321,0.88709,0.891859,0.896629,0.901398,
> >0.906167,0.910937,0.915706,0.920475,0.925244,0.930014,0.934783,0.939552,0.
> >944322,0.949091,0.95386,0.95863,0.963399,0.968168,0.972937,0.977707,0.9824
> >76,0.987245,0.992015,0.996784,Completed Saving results...
> > Unthresholding Series... Completed
> > Saving image... Completed
> > Completed
> > /usr/local//bin/smoothest -d 2.100000e+01 -m
> > /Proj/FA/S1_12_N2_10_fa2tal2.feat/mask -r
> > /Proj/FA/S1_12_N2_10_fa2tal2.feat/stats/res4d >
> > /Proj/FA/S1_12_N2_10_fa2tal2.feat/stats/smoothness
> > AvwOpen: Error while opening header!: No such file or directory
> > rm -f /Proj/FA/S1_12_N2_10_fa2tal2.feat/stats/res4d*
> >
> > /usr/local//bin/contrast_mgr /Proj/FA/S1_12_N2_10_fa2tal2.feat/stats
> > /Proj/FA/S1_12_N2_10_fa2tal2.feat/design.con
> > Loading image... Completed
> > Thresholding Series... Completed
> > /usr/local//bin/avwmaths /Proj/FA/S1_12_N2_10_fa2tal2.feat/stats/zstat1
> > -mul /Proj/FA/S1_12_N2_10_fa2tal2.feat/mask
> > /Proj/FA/S1_12_N2_10_fa2tal2.feat/thresh_zstat1
> >
> > MaximumZ(1)=3.721206
> > -------------------------------------------------------------------
>
> Stephen M. Smith
> Head of Image Analysis, FMRIB
>
> Oxford University Centre for Functional MRI of the Brain
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
>
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
--
Erik-Jan Vlieger
Academic Medical Center
Dept. of Radiology, G1-209
P.O. Box 22660
1100 DD Amsterdam
The Netherlands
email: [log in to unmask]
Phone: +31 20 5664975
Fax: +31 20 5669753
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