Hi Donna,
thanks for your help. `ls /mrt/Visac/*Visac/stats/*Visac_fullGLM/c*.nii`
only specifies the conds =column names. The stat-values are stored in
$CURRDIR/deformed_RH_*.metric files, one for each subject. So my code
needs to take the names of the .nii files, find each of the so specified
columns in each of the two deformed.metrics files, and combine them into
one metric file. So I think what I need is 2 loops. I tried this:
OUTFILE=my_composite.metric
rm -rf $OUTFILE
COL_ENTRIES=""
MET_ENTRIES=""
for EACHCOL in `ls /mrt/Visac/*Visac/stats/*Visac_fullGLM/c*.nii`
do
COL_ENTRIES="$COL_ENTRIES `basename $EACHCOL` 1"
done
for EACHMETRIC in `ls
/mrt/Visac/group_metrics/Visac_fullGLM/deformed_RH_*Visac_beta.metric` do
MET_ENTRIES="$MET_ENTRIES $EACHMETRIC 1"
done
caret_command -metric-composite-identified-columns $OUTFILE $EACHMETRIC
$COL_ENTRIES
I get: METRIC COMPOSITE IDENTIFIED COLUMNS ERROR: ERROR column name/number
cCue_EndoLeft.nii not found in file deformed_RH_02Visac_beta.metric
deformed_RH_02Visac_beta.metric looks the same as the file for subj 01 and
is in the same folder. Any ideas what could be wrong?
Also, what is the "1" at the end of the line for?
Thanks a lot!!
Julia
> 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
>> _______________________________________________
>> caret-users mailing list
>> [email protected]
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
> _______________________________________________
> caret-users mailing list
> [email protected]
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
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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