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"
}
Thanks, Steve.
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...
> 0.0047693,0.0095386,0.0143079,0.0190772,0.0238465,0.0286158,0.0333851,0.0381544,0.0429237,0.047693,0.0524623,0.0572316,0.0620009,0.0667702,0.0715395,0.0763088,0.0810781,0.0858474,0.0906167,0.095386,0.100155,0.104925,0.109694,0.114463,0.119233,0.124002,0.128771,0.13354,0.13831,0.143079,0.147848,0.152618,0.157387,0.162156,0.166926,0.171695,0.176464,0.181233,0.186003,0.190772,0.195541,0.200311,0.20508,0.209849,0.214619,0.219388,0.224157,0.228926,0.233696,0.238465,0.243234,0.248004,0.252773,0.257542,0.262312,0.267081,0.27185,0.276619,0.281389,0.286158,0.290927,0.295697,0.300466,0.305235,0.310005,0.314774,0.319543,0.324312,0.329082,0.333851,0.33862,0.34339,0.348159,0.352928,0.357698,0.362467,0.367236,0.372005,0.376775,0.381544,0.386313,0.391083,0.395852,0.400621,0.405391,0.41016,0.414929,0.419699,0.424468,0.429237,0.434006,0.438776,0.443545,0.448314,0.453084,0.457853,0.462622,0.467392,0.472161,0.47693,0.481699,0.486469,0.491238,0.496007,0.500777,0.505546,0.510315,0.515085,0.519854,0.524623,0.529392,0.534162,0.538931,0.5437,0.54847,0.553239,0.558008,0.562778,0.567547,0.572316,0.577085,0.581855,0.586624,0.591393,0.596163,0.600932,0.605701,0.610471,0.61524,0.620009,0.624778,0.629548,0.634317,0.639086,0.643856,0.648625,0.653394,0.658164,0.662933,0.667702,0.672471,0.677241,0.68201,0.686779,0.691549,0.696318,0.701087,0.705857,0.710626,0.715395,0.720164,0.724934,0.729703,0.734472,0.739242,0.744011,0.74878,0.75355,0.758319,0.763088,0.767857,0.772627,0.777396,0.782165,0.786935,0.791704,0.796473,0.801243,0.806012,0.810781,0.81555,0.82032,0.825089,0.829858,0.834628,0.839397,0.844166,0.848936,0.853705,0.858474,0.863244,0.868013,0.872782,0.877551,0.882321,0.88709,0.891859,0.896629,0.901398,0.906167,0.910937,0.915706,0.920475,0.925244,0.930014,0.934783,0.939552,0.944322,0.949091,0.95386,0.95863,0.963399,0.968168,0.972937,0.977707,0.982476,0.987245,0.992015,0.996784,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
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