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
>
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