Re: [caret-users] [SPAM] posting

2006-06-05 Thread Donna Dierker
Thank John Harwell for the handy dandy feature:  caret_command 
-surface-deformation-apply


The attached script calls this command on a bunch of files.

You may need to get an updated version of caret_command, if your version 
doesn't have it.  It's roughly April vintage (i.e., when we were 
regenerating a BUNCH of depth files).


On 06/05/2006 05:39 PM, Jason D Connolly wrote:


Dear Donna,

Thank you for your assistance regarding the caret command line
utilities.  The 'caret_map_fmri' utility works like a charm.

We now have many, many statistical maps (.metric files).  Therefore, a
slow down is caused by having to enter and execute the 'apply
deformation map' utility for each metric file, to warp the individual
metric file to the PALS atlas space.  Can this function also be executed
at the command line?  I didn't see anything in the list you provided. 
This would allow us to automate this step and thus would speed things up ...


Thank you,

Jason.


Jason D. Connolly, PhD  
Center for Neural Science, New York University

6 Washington Place Room 875, New York, NY 10003
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html




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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)

#!/bin/sh
set -x

ATLAS_TGT_DIR=/backup/erin/HUMAN_PALS_B12/PALS_B12.LR/BUCKNER
MAP_LIST=/tmp/map_list.$$.txt
ls $ATLAS_TGT_DIR/*map |sort > $MAP_LIST
DIR_LIST=/tmp/dir_list.$$.txt

cat > $DIR_LIST << EOF
BATCH1_FEMALE_SUMS/Human_Buckner_Case01/BUCKNER_Case01.L
BATCH1_FEMALE_SUMS/Human_Buckner_Case01/BUCKNER_Case01.R
BATCH1_FEMALE_SUMS/Human_Buckner_Case02/BUCKNER_Case02.L
BATCH1_FEMALE_SUMS/Human_Buckner_Case02/BUCKNER_Case02.R
BATCH1_FEMALE_SUMS/Human_Buckner_Case03/BUCKNER_Case03.L
BATCH1_FEMALE_SUMS/Human_Buckner_Case03/BUCKNER_Case03.R
BATCH1_FEMALE_SUMS/Human_Buckner_Case04/BUCKNER_Case04.L
BATCH1_FEMALE_SUMS/Human_Buckner_Case04/BUCKNER_Case04.R
BATCH1_FEMALE_SUMS/Human_Buckner_Case05/BUCKNER_Case05.L
BATCH1_FEMALE_SUMS/Human_Buckner_Case05/BUCKNER_Case05.R
BATCH1_FEMALE_SUMS/Human_Buckner_Case06/BUCKNER_Case06.L
BATCH1_FEMALE_SUMS/Human_Buckner_Case06/BUCKNER_Case06.R
BATCH2_MALE_SUMS/Human_Buckner_Case07/BUCKNER_Case07.L
BATCH2_MALE_SUMS/Human_Buckner_Case07/BUCKNER_Case07.R
BATCH2_MALE_SUMS/Human_Buckner_Case08/BUCKNER_Case08.L
BATCH2_MALE_SUMS/Human_Buckner_Case08/BUCKNER_Case08.R
BATCH2_MALE_SUMS/Human_Buckner_Case09/BUCKNER_Case09.L
BATCH2_MALE_SUMS/Human_Buckner_Case09/BUCKNER_Case09.R
BATCH2_MALE_SUMS/Human_Buckner_Case10/BUCKNER_Case10.L
BATCH2_MALE_SUMS/Human_Buckner_Case10/BUCKNER_Case10.R
BATCH2_MALE_SUMS/Human_Buckner_Case11/BUCKNER_Case11.L
BATCH2_MALE_SUMS/Human_Buckner_Case11/BUCKNER_Case11.R
BATCH2_MALE_SUMS/Human_Buckner_Case12/BUCKNER_Case12.L
BATCH2_MALE_SUMS/Human_Buckner_Case12/BUCKNER_Case12.R
BATCH3_FEMALE_SUMS/Human_Buckner_Case13/BUCKNER_Case13.L
BATCH3_FEMALE_SUMS/Human_Buckner_Case13/BUCKNER_Case13.R
BATCH3_FEMALE_SUMS/Human_Buckner_Case14/BUCKNER_Case14.L
BATCH3_FEMALE_SUMS/Human_Buckner_Case14/BUCKNER_Case14.R
BATCH3_FEMALE_SUMS/Human_Buckner_Case15/BUCKNER_Case15.L
BATCH3_FEMALE_SUMS/Human_Buckner_Case15/BUCKNER_Case15.R
BATCH3_FEMALE_SUMS/Human_Buckner_Case16/BUCKNER_Case16.L
BATCH3_FEMALE_SUMS/Human_Buckner_Case16/BUCKNER_Case16.R
BATCH3_FEMALE_SUMS/Human_Buckner_Case17/BUCKNER_Case17.L
BATCH3_FEMALE_SUMS/Human_Buckner_Case17/BUCKNER_Case17.R
BATCH3_FEMALE_SUMS/Human_Buckner_Case18/BUCKNER_Case18.L
BATCH3_FEMALE_SUMS/Human_Buckner_Case18/BUCKNER_Case18.R
BATCH4_MALE_SUMS/Human_Buckner_Case19/BUCKNER_Case19.L
BATCH4_MALE_SUMS/Human_Buckner_Case19/BUCKNER_Case19.R
BATCH4_MALE_SUMS/Human_Buckner_Case20/BUCKNER_Case20.L
BATCH4_MALE_SUMS/Human_Buckner_Case20/BUCKNER_Case20.R
BATCH4_MALE_SUMS/Human_Buckner_Case21/BUCKNER_Case21.L
BATCH4_MALE_SUMS/Human_Buckner_Case21/BUCKNER_Case21.R
BATCH4_MALE_SUMS/Human_Buckner_Case22/BUCKNER_Case22.L
BATCH4_MALE_SUMS/Human_Buckner_Case22/BUCKNER_Case22.R
BATCH4_MALE_SUMS/Human_Buckner_Case23/BUCKNER_Case23.L
BATCH4_MALE_SUMS/Human_Buckner_Case23/BUCKNER_Case23.R
BATCH4_MALE_SUMS/Human_Buckner_Case24/BUCKNER_Case24.L
BATCH4_MALE_SUMS/Human_Buckner_Case24/BUCKNER_Case24.R
EOF

for DIR in `cat $DIR_LIST`
do
  cd $DIR
  COMMAND="caret_command -surface-deformation-apply "
  CASE_HEM=`echo $DIR |sed 's#.*/BUCKNER_##g'| sed 's/Case0/Case/g'`
  DEFORM_MAP=`grep $CASE_HEM $MAP_LIST`
  COMMAND="$COMMAND $DEFORM_MAP SURFACE_SHAPE"
  SHAPE_IN=`ls *DEPTH_FIXED_SHN.surface_shape`
  COMMAND="$COMMAND $SHAPE_IN"
  SHAPE_OUT=$ATLAS_TGT_DIR/def_"$SHAPE_IN"
  COMMAND="$COMMAND $SHAPE_OUT"
  echo $COMMAND
  $COMMAND
  cd ../../..
done


[caret-users] [SPAM] posting

2006-06-05 Thread Jason D Connolly
Dear Donna,

Thank you for your assistance regarding the caret command line
utilities.  The 'caret_map_fmri' utility works like a charm.

We now have many, many statistical maps (.metric files).  Therefore, a
slow down is caused by having to enter and execute the 'apply
deformation map' utility for each metric file, to warp the individual
metric file to the PALS atlas space.  Can this function also be executed
at the command line?  I didn't see anything in the list you provided. 
This would allow us to automate this step and thus would speed things up ...

Thank you,

Jason.


Jason D. Connolly, PhD  
Center for Neural Science, New York University
6 Washington Place Room 875, New York, NY 10003
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html





RE: [caret-users] [SPAM] posting

2006-05-31 Thread Donald McLaren
Jason,
 
Out of curiosity, what statistics do you plan on performing on surface nodes?
 
Best Regards, Donald McLaren
=
D.G. McLaren
Washington University in St. Louis - School of Medicine
Department of Anatomy and Neurobiology
Tel: (314) 362 3555
Tel: (773) 406 2464
Fax: (314) 747 4370
=
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From: [EMAIL PROTECTED] on behalf of Jason D Connolly
Sent: Wed 5/31/2006 4:06 PM
To: Caret Users; Clayton Curtis
Subject: [caret-users] [SPAM] posting



Dear David or Donna,

We hope to import a large number of externally generated beta maps into
caret and then generate surface statistics.  Is there any way to execute
"map volume(s) to surface(s)" at the command line (Linux platform),
instead of having to open up each of the files in caret?  Moreover, is
there documentation for different caret operations processed via command
lines?

Many thanks, Jason.


Jason D. Connolly, PhD 
Center for Neural Science, New York University
6 Washington Place Room 875, New York, NY 10003
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html



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caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users


<>

Re: [caret-users] [SPAM] posting

2006-05-31 Thread Donna Dierker

Hi Jason,

Not everyone knows about these handy command line utilities:

/146Gb/caret_distribution/caret/bin/caret_copy_spec
/146Gb/caret_distribution/caret/bin/caret_map_fmri
/146Gb/caret_distribution/caret/bin/mpeg_encode
/146Gb/caret_distribution/caret/bin/mpeg_play
/146Gb/caret_distribution/caret/bin/caret_metric
/146Gb/caret_distribution/caret/bin/caret_command
/146Gb/caret_distribution/caret/bin/caret_edit
/146Gb/caret_distribution/caret/bin/caret_zip_spec
/146Gb/caret_distribution/caret/bin/caret_file_convert

Enter "caret_map_fmri -help" to get the full usage.  When you do the 
same for caret_command, redirect the output to a text file; it's 954 
lines, but it's one handy utility.


On 05/31/2006 04:06 PM, Jason D Connolly wrote:


Dear David or Donna,

We hope to import a large number of externally generated beta maps into
caret and then generate surface statistics.  Is there any way to execute
"map volume(s) to surface(s)" at the command line (Linux platform),
instead of having to open up each of the files in caret?  Moreover, is
there documentation for different caret operations processed via command
lines? 

Many thanks, Jason. 



Jason D. Connolly, PhD  
Center for Neural Science, New York University

6 Washington Place Room 875, New York, NY 10003
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html




___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users

 




--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



[caret-users] [SPAM] posting

2006-05-31 Thread Jason D Connolly
Dear David or Donna,

We hope to import a large number of externally generated beta maps into
caret and then generate surface statistics.  Is there any way to execute
"map volume(s) to surface(s)" at the command line (Linux platform),
instead of having to open up each of the files in caret?  Moreover, is
there documentation for different caret operations processed via command
lines? 

Many thanks, Jason. 


Jason D. Connolly, PhD  
Center for Neural Science, New York University
6 Washington Place Room 875, New York, NY 10003
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html