Hi Donna,

yes that works. The problem is that in the end I'll have 13 subjects with
12 conditions total, so calling each composition manually would be very
complicated.  The lab I have the script from, is using caret 5.51. I hoped
that there would be a way to loop through things like this:

for EACHCOL in `ls /data/Visac/*Visac/stats/*Visac_fullGLM/c*.hdr`
do
/usr/local/caret-5.51/bin/caret_command
-metric-or-shape-composite-named-column `basename $EACHCOL .hdr`
$CURRDIR/RH_$METRIC_BASENAME_`basename $EACHCOL .hdr`.metric
deformed_RH_*.metric
done

I understand that this is not working anymore with the new caret release.
But isn't there a way to "update" this code for the new release?

Julia

> This seems to work on my end:
>
> caret_command -metric-composite-identified-columns test.metric
> deformed_RH_01Visac_beta.metric 'cCue_EndoLeft.nii[1]'
> deformed_RH_02Visac_beta.metric 'cCue_EndoLeft.nii[1]'
>
> I end up with this:
>
> Column      Minimum      Maximum           Mean     Sample Dev     %
> Positive     % Negative   Column Name
>      1       -0.071        0.052          0.001          0.011
> 49.951         50.049   cCue_EndoLeft.nii[1]
>      2       -0.066        0.089          0.001          0.011
> 44.949         55.051   cCue_EndoLeft.nii[1]
>
> The first is subject 1's cCue_EndoLeft.nii[1] column; the second is
> subject 2's cCue_EndoLeft.nii[1].
>
>
> On 04/02/2010 07:42 AM, Julia Bender wrote:
>> Hi Donna,
>>
>> I tried your 2nd suggestion and it ALMOST worked:
>> for CONDITION in `ls /mrt/Visac/*Visac/stats/*Visac_fullGLM/c*.nii`
>> do
>>     OUTFILE=RH_`basename $CONDITION .nii`.metric
>>     CONDITION=`basename $CONDITION`[1]
>>
>>     ENTRIES=""
>>     for METRIC in `ls
>> /mrt/Visac/group_metrics/Visac_fullGLM/deformed_RH_*Visac_beta.metric`
>>     do
>>        ENTRIES="$METRIC $CONDITION"
>>     done
>>     caret_command -metric-composite-identified-columns $OUTFILE $ENTRIES
>> done
>>
>> The code is running through and is creating four metric files with
>> correct
>> names. But the output metric files only contain the information of
>> sub02.
>> So somehow the code seems to overwrite the information of sub01 and does
>> not combine the information of the two subjects:
>>
>> Filename: RH_cCue_EndoLeft.metric (output file)
>> Number of Nodes: 73730
>> Number of Columns: 1
>> Column      Minimum      Maximum           Mean     Sample Dev     %
>> Positive     % Negative   Column Name
>>      1       -0.066        0.089          0.001          0.011
>> 44.949         55.051   cCue_EndoLeft.nii[1]
>>
>>
>> Filename: deformed_RH_02Visac_beta.metric (input sub02)
>> Number of Nodes: 73730
>> Number of Columns: 4
>> Column      Minimum      Maximum           Mean     Sample Dev     %
>> Positive     % Negative   Column Name
>>      1       -0.066        0.089          0.001          0.011
>> 44.949         55.051   cCue_EndoLeft.nii[1]
>>      2       -0.039        0.102          0.005          0.011
>> 60.243         39.757   cCue_EndoRight.nii[1]
>>      3       -0.025        0.103          0.005          0.011
>> 60.221         39.779   cCue_ExoLeft.nii[1]
>>      4       -0.025        0.116          0.007          0.011
>> 64.321         35.679   cCue_ExoRight.nii[1]
>>
>> So somehow caret_command doesn't get the arguments the way it needs to.
>> I've tried to feed in the input files without the *for loop* but then
>> the
>> 2nd input file is taken as condition name. I wondered how the structure
>> of
>>  ENTRIES looks like: [METRIC_1 METRIC_2 CONDITION_1 CONDITION_2
>> CONDITION_3 CONDITION_4]? It seems like ENTRIES is the key here.
>>
>> I couldn't figure out how to do your first approach (my computational
>> skills are very basic), but as far as I understand,the above problem
>> would
>> occur as well so, right?
>>
>> thanks a lot!
>>
>> Julia
>>
>>
>>
>>
>>> Julia,
>>>
>>> The problem is a trailing bucket index '[1]' in the column name, e.g.:
>>>
>>> caret_command -metric-information
>>> /upload/deformed_RH_01Visac_beta.metric
>>>
>>>      1       -0.071        0.052          0.001          0.011
>>> 49.951         50.049   cCue_EndoLeft.nii[1]
>>>      2       -0.050        0.076          0.005          0.010
>>> 65.433         34.567   cCue_EndoRight.nii[1]
>>>      3       -0.044        0.060          0.005          0.009
>>> 70.949         29.051   cCue_ExoLeft.nii[1]
>>>      4       -0.078        0.072          0.001          0.011
>>> 52.947         47.053   cCue_ExoRight.nii[1]
>>>
>>> I haven't had a chance to figure out exactly how to get around this,
>>> but
>>> there are two approaches:
>>>
>>> * strip the '[1]' from the column-name -- probably using a combination
>>> of caret_command -metric-information (to get the current name), sed (to
>>> strip the trailing '[1]'), and caret_command -metric-set-column-name
>>> (to
>>> set the column-name to the stripped version).
>>>
>>> * massage CONDITION in the script to add the '[1]'; this is easy
>>> enough,
>>> but I think to make the shell happy, you'll need for the whole
>>> column-name to be in single quotes, which is a bit tricky to pull off.
>>> Getting those quotes to survive this part is the tricky bit:
>>>
>>>         ENTRIES="$METRIC $CONDITION"
>>>
>>>
>>> Try your hand at one or both of these approaches.  Let me know if you
>>> get stuck.
>>>
>>> Note:  I'm taking tomorrow afternoon off.
>>>
>>> Donna
>>>
>>> On 04/01/2010 02:52 PM, Julia Bender wrote:
>>>
>>>> Donna,
>>>>
>>>> I've uploaded both deformed*.metric files, so you can have a look.
>>>> Thanks so much for your help.
>>>>
>>>> Julia
>>>>
>>>>
>>>>
>>>>> Julia,
>>>>>
>>>>> Please upload deformed_RH_02Visac_beta.metric here:
>>>>>
>>>>> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>>>>
>>>>> Also, where your script reads like so:
>>>>>
>>>>>     OUTFILE=RH_$CONDITION.metric
>>>>>     CONDITION=`basename $CONDITION`
>>>>>
>>>>> ... change it to read:
>>>>>
>>>>>     CONDITION=`basename $CONDITION`
>>>>>     OUTFILE=RH_"$CONDITION".metric
>>>>>
>>>>> I didn't realize the basename step should have preceded the OUTFILE
>>>>> definition until I had already hit send.
>>>>>
>>>>> The quotes around $CONDITION are needed due to the RH_ preceding the
>>>>> variable name.
>>>>>
>>>>> But that error suggests your actual column names do not match the
>>>>> volume
>>>>> names exactly.  For example, might they be preceded by "AFM " or "MFM
>>>>> "
>>>>> or
>>>>> something like that?  Looking at your actual metric file will help me
>>>>> pinpoint the problem.
>>>>>
>>>>> Donna
>>>>>
>>>>>
>>>>> On 04/01/2010 06:20 AM, Julia Bender wrote:
>>>>>
>>>>>
>>>>>> Hi Donna,
>>>>>>
>>>>>> yes, you're right, that's exactly what I want. Unfortunately the
>>>>>> script
>>>>>> you've sent me doesnt' go through and I don't know why. I did:
>>>>>>
>>>>>> for CONDITION in `ls /mrt/Visac/*Visac/stats/*Visac_fullGLM/c*.nii`
>>>>>> do
>>>>>>     OUTFILE=RH_$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
>>>>>>>>>> [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
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>>
>
> _______________________________________________
> 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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