Re: [caret-users] [SPAM] posting
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 ___ 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.) #!/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
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
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 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (314) 362 3555, email, or return mail. 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 ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users <>
Re: [caret-users] [SPAM] posting
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
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
