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
