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

Donna Dierker donna at brainvis.wustl.edu
Mon Apr 5 10:33:42 CDT 2010


Julia,

I know how frustrating it is when an old script no longer works with a new version of caret_command.  It happens to me all the time.  Usually, I rewrite the script to work with the new caret_command.  But it is also possible to have older versions of caret_command around in separate directories, called on by their full pathnames, when it's just not worth the revisions.  Generally the older versions are still available on the Caret download site.

This revision to the caret_command feature resulted from a user request the required a more general solution.  Not uncommon.

First, back up your metric files.  But then try this before your main loop:


for METRIC in deformed_RH_01Visac_beta.metric 
deformed_RH_02Visac_beta.metric
do
  caret_command -file-convert -format-convert ASCII $METRIC
  sed 's/.nii\[1\]$/.nii/g' $METRIC > $METRIC.rev
  mv $METRIC.rev $METRIC
done

It strips the "[1]" out of the column names, so make sure you edit the 
rest of your script accordingly.

Donna

On 04/02/2010 10:08 AM, Julia Bender wrote:
> 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
>>>>>>>>>>> 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
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>>
>>>>         
>> _______________________________________________
>> 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
>
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>   




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