Julia,
Here is the usage for this command:
caret_command -metric-composite-identified-columns
<output-metric-file-name>
[input-metric-file-1 file-1-column]
...
[input-metric-file-N file-2-column]
Composite the selected columns from the input metric
files and place them into the output metric file.
"column" is either the number of the column, which
starts at one, or the name of the column. If a
a name contains spaces, it must be enclosed in double
quotes. Name has priority over number.
I'm not 100% certain, but I think file-1-column refers to what the
column is named in the input file, rather than what you want it to be
named in the output file. So if there is just a single column in
$EACHCOL, the simplest thing is to just specify 1 there, to indicate the
first (and only) column.
I think I would do this, instead of what you have:
OUTFILE=my_composite.metric
rm -rf $OUTFILE
COL_ENTRIES=""
for EACHCOL in `ls /mrt/Visac/*Visac/stats/*Visac_fullGLM/c*.nii`
do
COL_ENTRIES="$COL_ENTRIES $EACHCOL 1"
done
caret_command -metric-composite-identified-columns $OUTFILE $COL_ENTRIES
Note that there should be only one caret_command, but it should specify
all four cols. All you need the loop for is to generate this part of
the command:
[input-metric-file-1 file-1-column]
...
[input-metric-file-N file-2-column]
Donna
On 03/30/2010 10:19 AM, Julia Bender wrote:
> Hi,
>
> thanks for your help. I'm trying to composite four conds columns from two
> subjects' deformed-metric-files into one combined metric file:
>
> for EACHCOL in `ls /mrt/Visac/*Visac/stats/*Visac_fullGLM/c*.nii` (= my
> four conds files)
> do
> caret_command -metric-composite-identified-columns $CURRDIR/RH_`basename
> $EACHCOL .nii`.metric $CURRDIR/deformed_RH_*.metric `basename $EACHCOL
> .nii`
> done
>
> I get: "METRIC COMPOSITE IDENTIFIED COLUMNS ERROR: ERROR column
> name/number cCue_EndoLeft (=my first conds column) not found in file
> deformed_RH_01Visac_beta.metric"
>
> CURRDIR is the directory were the deformed-metric-files are. I have full
> permission on all files. In the deformed-metric-files the columns are
> named like this: tag-column-name 0 cCue_EndoLeft.nii[1]
>
> I understand that I need to specify either column name or number so that
> columns are combined correctly. I tried to do that with `basename $EACHCOL
> .nii` , which obviously doesn't work. Do you know how I can assign
> name/number in the loop?
>
> Thanks a lot!
>
> Julia
>
> Dipl. Psych. Julia Bender
> Humboldt Universität zu Berlin
> Mathematisch - Naturwissenschaftliche Fakultät II
> Institut für Psychologie, Abt. Klinische Psychologie
> Unter den Linden 6
> D-10099 Berlin
>
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