Hi Anders,
There are a small number of "simple" commands that indeed don't get
captured in the logs, in which case you can take a look at
$FSLDIR/tcl/featlib.tcl to fill in the blanks.
In this particular case, I believe it is the following 'immv' that gets
the cope1 and varcope1 files created by 'fslmerge' (commands captured in
the .gfeat/report_log.html) into the cope1.feat directory and ready for
flameo (command captured in .gfeat/cope1.feat/report_log.html)
#}}}
#{{{ FLAME1
fsl:exec "cat ../design.lcon | awk '{ print \$$session }' > design.lcon"
imcp ../bg_image example_func
imcp ../mean_func mean_func
imcp ../mask mask
set funcdata [ feat5:strip [ file tail $FD ] ]
immv ../$funcdata filtered_func_data
immv ../var$funcdata var_filtered_func_data
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: [log in to unmask]
On 1/22/13 4:54 PM, "Anders Eklund" <[log in to unmask]> wrote:
>Dear FSL experts,
>
>through the FSL logs I have managed to write a bash script that runs the
>first level analysis. However, for the higher level analysis it seems
>like some commands are missing in the logs. I understand that the results
>from the first level analysis are transformed into MNI space and
>concatenated into one cope and varcope file for each contrast, but I
>can't see the actual call to flame. In another log file I found the
>following command,
>
>flameo --cope=filtered_func_data --vc=var_filtered_func_data
>--dvc=tdof_filtered_func_data --mask=mask --ld=stats --dm=design.mat
>--cs=design.grp --tc=design.con --runmode=fe
>
>but I can't find how filtered_func_data and var_filtered_func_data are
>calculated, are these simply equal to the cope and varcope files?
>
>It would be great if anyone could tell me which source file to look into.
>
>Cheers,
>Anders
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