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Subject:

Re: how to set options not available in FEAT GUI?

From:

Bettyann Chodkowski <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 17 Nov 2004 18:19:50 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (66 lines)

>Hi - yes, that's easy. If you take a local copy of feat.tcl, then do:
>cd $FSLDIR/bin
>cp feat my_feat
>and edit that to point to the local copy of feat.tcl, all should be well.

thanks for pointing me in the right direction so i could add options to FEAT's
mcflirt.  since i am not able to write to $FSLDIR (i would assume this is true
of most users), i copied and modified two files, created a symbolic link to a
third, and created environment variable FSLTEST:

% echo $FSLTEST
/home/bettyann/Development/fsl

% ll
total 406
-rwxrwxr-x   1 bettyann fmri        1079 Nov 16 15:06 feat
-rwxrwxr-x   1 bettyann fmri      192594 Nov 17 12:38 feat.tcl
lrwxrwxrwx   1 bettyann fmri          31 Nov 15 20:33 fslstart.tcl -> /usr/local/fsl/tcl/fslstart.tcl

% diff feat $FSLDIR/bin
< set FSLDIR  $env(FSLDIR)
< set FSLTEST $env(FSLTEST)
---
> set FSLDIR $env(FSLDIR)
45,46c15
< # source ${FSLDIR}/tcl/feat.tcl
< source ${FSLTEST}/feat.tcl
---
> source ${FSLDIR}/tcl/feat.tcl

% diff feat.tcl $FSLDIR/tcl
4802,4806d4793
< # tell me what fmri(opts__*) array elements are defined
< foreach opt [ lsort [ array names fmri "opts__*" ]] {
<    puts "fmri($opt) : $fmri($opt)"
< }
<
5368,5370c5355
<     set opts ""
<     if [ info exists fmri(opts__mcflirt) ] { set opts $fmri(opts__mcflirt) }
<     fsl:exec "${FSLDIR}/bin/mcflirt -in $funcdata -out prefiltered_func_data_mcf -plots -refvol
$target_vol_number -rmsrel -rmsabs $opts" -r
---
>     fsl:exec "${FSLDIR}/bin/mcflirt -in $funcdata -out prefiltered_func_data_mcf -plots -refvol
$target_vol_number -rmsrel -rmsabs" -r
5374,5376d5358
<     if [ regexp -- "\-mats" $opts ] {
<       fsl:exec "/bin/mv -f prefiltered_func_data_mcf.mat mc/mat"
<     }

i decided to add elements opts__* to global variable fmri to make this feature
more flexible.  and i'll continue to use the same logic to add non-GUI-specified
options for other programs.

i thought i'd pass this along in case anyone wishes to incorporate the same logic
into their code.

thanks for the help.
best regards,
- bettyann
_____________________________________
BettyAnn Chodkowski                       F.M. Kirby Center
e: [log in to unmask]          Kennedy Krieger Institute
v: 443.923.9524                           707 N. Broadway
f: 443.923.9279                           Baltimore, MD, USA  21205

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