[caret-users] -metric-composite-identified-columns

Julia Bender julia.bender.1 at cms.hu-berlin.de
Thu Apr 1 06:20:25 CDT 2010


Hi Donna,

yes, you're right, that's exactly what I want. Unfortunately the script
you've sent me doesnt' go through and I don't know why. I did:

for CONDITION in `ls /mrt/Visac/*Visac/stats/*Visac_fullGLM/c*.nii`
do
    OUTFILE=RH_$CONDITION.metric
    CONDITION=`basename $CONDITION`
    ENTRIES=""
    for METRIC in `ls
/mrt/Visac/group_metrics/Visac_fullGLM/deformed_RH_*Visac_beta.metric`
    do
        ENTRIES="$METRIC $CONDITION"
    done

    caret_command -metric-composite-identified-columns $OUTFILE $ENTRIES
done

I get:

METRIC COMPOSITE IDENTIFIED COLUMNS ERROR: ERROR column name/number
cCue_EndoLeft.nii not found in file deformed_RH_02Visac_beta.metric


METRIC COMPOSITE IDENTIFIED COLUMNS ERROR: ERROR column name/number
cCue_EndoRight.nii not found in file deformed_RH_02Visac_beta.metric


METRIC COMPOSITE IDENTIFIED COLUMNS ERROR: ERROR column name/number
cCue_ExoLeft.nii not found in file deformed_RH_02Visac_beta.metric


METRIC COMPOSITE IDENTIFIED COLUMNS ERROR: ERROR column name/number
cCue_ExoRight.nii not found in file deformed_RH_02Visac_beta.metric


METRIC COMPOSITE IDENTIFIED COLUMNS ERROR: ERROR column name/number
cCue_EndoLeft.nii not found in file deformed_RH_02Visac_beta.metric


METRIC COMPOSITE IDENTIFIED COLUMNS ERROR: ERROR column name/number
cCue_EndoRight.nii not found in file deformed_RH_02Visac_beta.metric


METRIC COMPOSITE IDENTIFIED COLUMNS ERROR: ERROR column name/number
cCue_ExoLeft.nii not found in file deformed_RH_02Visac_beta.metric


METRIC COMPOSITE IDENTIFIED COLUMNS ERROR: ERROR column name/number
cCue_ExoRight.nii not found in file deformed_RH_02Visac_beta.metric


This is weird because both deformed_RH_01Visac* and deformed_RH_02Visac*
are in the same folder, have the same permissions and the header info is
the same (despite the sub# of course):
                                          :
BeginHeader
Caret-Version 5.613
Date 2010-03-30T14:22:43
comment Deformed from: RH_02Visac_beta.metric	Deformed with:
deformed_Human.02Visac.R.73730.deform_map
encoding BINARY
EndHeader
tag-version 2
tag-number-of-nodes 73730
tag-number-of-columns 4
tag-title
tag-column-name 0  cCue_EndoLeft.nii[1]
tag-column-name 1  cCue_EndoRight.nii[1]
tag-column-name 2  cCue_ExoLeft.nii[1]
tag-column-name 3  cCue_ExoRight.nii[1]
tag-column-comment 0 CARET v5.613	Mapped to surface:
Human.02Visac.R.Fiducial.65561.coord	Mapped from volume:
cCue_EndoLeft.nii	Subvolume: 0	Algorithm: Metric Enclosing Voxel	intent:
None	intent_code: 0	intent_p1: 0.000	intent_p2: 0.000	intent_p3:
0.000		Date Mapped: 30.03.10 14:22	Deformed with:
deformed_Human.02Visac.R.73730.deform_map
tag-column-comment 1 CARET v5.613	Mapped to surface:
Human.02Visac.R.Fiducial.65561.coord	Mapped from volume:
cCue_EndoRight.nii	Subvolume: 0	Algorithm: Metric Enclosing Voxel	intent:
None	intent_code: 0	intent_p1: 0.000	intent_p2: 0.000	intent_p3:
0.000		Date Mapped: 30.03.10 14:22	Deformed with:
deformed_Human.02Visac.R.73730.deform_map
tag-column-comment 2 CARET v5.613	Mapped to surface:
Human.02Visac.R.Fiducial.65561.coord	Mapped from volume:
cCue_ExoLeft.nii	Subvolume: 0	Algorithm: Metric Enclosing Voxel	intent:
None	intent_code: 0	intent_p1: 0.000	intent_p2: 0.000	intent_p3:
0.000		Date Mapped: 30.03.10 14:22	Deformed with:
deformed_Human.02Visac.R.73730.deform_map
tag-column-comment 3 CARET v5.613	Mapped to surface:
Human.02Visac.R.Fiducial.65561.coord	Mapped from volume:
cCue_ExoRight.nii	Subvolume: 0	Algorithm: Metric Enclosing Voxel	intent:
None	intent_code: 0	intent_p1: 0.000	intent_p2: 0.000	intent_p3:
0.000		Date Mapped: 30.03.10 14:22	Deformed with:
deformed_Human.02Visac.R.73730.deform_map
tag-column-study-meta-data 0
tag-column-study-meta-data 1
tag-column-study-meta-data 2
tag-column-study-meta-data 3
tag-column-color-mapping 0 -1.000000 1.000000
tag-column-color-mapping 1 -1.000000 1.000000
tag-column-color-mapping 2 -1.000000 1.000000
tag-column-color-mapping 3 -1.000000 1.000000
tag-column-threshold 0 0.000000 0.000000
tag-column-threshold 1 0.000000 0.000000
tag-column-threshold 2 0.000000 0.000000
tag-column-threshold 3 0.000000 0.000000
tag-column-average-threshold 0 0.000000 0.000000
tag-column-average-threshold 1 0.000000 0.000000
tag-column-average-threshold 2 0.000000 0.000000
tag-column-average-threshold 3 0.000000 0.000000
tag-BEGIN-DATA

also I don't understand why I get the error message twice for every
condition. I'm sorry this is so persistent...

Thanks a lot,

Julia
> Julia,
>
> Okay, if I understand you correctly, deformed_RH_*.metric does NOT
contain a single column, but rather multiple columns for different
conditions for the same subject.  Thus, you can't use this:
>
>     COL_ENTRIES="$COL_ENTRIES `basename $EACHCOL` 1"
>
> ... because the " 1" means grab the first column.  I suggested this,
thinking you had only a single column in your metric file, which appears
to be not the case.
>
> So, you need to get the column name exactly right, and evidently you
haven't.
>
> Maybe instead you need:
>
> for CONDITION in `ls /mrt/Visac/*Visac/stats/*Visac_fullGLM/c*.nii` do
>   OUTFILE=my.$CONDITION.metric
>   CONDITION=`basename $CONDITION`
>   ENTRIES=""
>   for METRIC in `ls
> /mrt/Visac/group_metrics/Visac_fullGLM/deformed_RH_*Visac_beta.metric`
>   do
>     ENTRIES="$METRIC $CONDITION"
>   done
>   caret_command -metric-composite-identified-columns $OUTFILE $ENTRIES
> done
>
> Donna
>
> On 03/31/2010 09:57 AM, Julia Bender wrote:
>> 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
>>>> caret-users at brainvis.wustl.edu
>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>> _______________________________________________
>>> caret-users mailing list
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>> 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
>> caret-users at brainvis.wustl.edu
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> 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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