Re: [Freesurfer] ERROR: aparcstats2table
The options for these 3: GausCurv FoldInd CurvInd do not exist when I use the -h Thanks, Catherine On 1/29/13, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: yes, use the -m or --meas flags. If you run it with -h, you will get help and examples doug On 01/29/2013 04:12 PM, Nucleos P wrote: Hello again! Thank you for all your help so far. Just one more question now... is there a way to specify these values to be pulled using a script: GausCurv FoldInd CurvInd ...?? Thanks, Catherine On 1/23/13, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: They must be in a single folder and the $SUBJECTS_DIR env variable must be set to that folder. If you know a little unix, you can set up folders with symbolic links to subjects' true directories. doug On 01/23/2013 02:58 PM, Nucleos P wrote: Thank you for your help Doug! I was trying to specify the path to get to the subjects. Do I have to have all the subjects in a folder called 'subjects'? I know the naming conventions are important. Thanks again, Catherine On Fri, Jan 18, 2013 at 6:31 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: actually, looking at your cmd line more I see that you have slashes (/) in the subject names. The argument to --subjects should just be a list of name. See the help (aparcstats2table -h) for examples. doug On 01/18/2013 04:58 PM, Nucleos P wrote: Hello experts: Can someone please help me understand what I am doing wrong? This is the first time I am trying this command and it will not work... COMMAND: aparcstats2table --subjects /RGS4_31p/rgs0868_raw /RGS4_31p/rgs0871_raw /RGS4_31p/rgs0883_raw/ /RGS4_31p/rgs1194_raw144/ /RGS4_31p/rgs1311a/ /RGS4_31p/rgs1370a/ /RGS4_31p/rgs1383a/ -t RGS4_31p/aparc.volume.rh -m volume --hemi=rh PATH: [/usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats]:pwd /usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats ERROR: SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files ERROR: The stats file /RGS4_31p/rgs0868_raw/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thank you, Catherine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ERROR: aparcstats2table
Hello again! Thank you for all your help so far. Just one more question now... is there a way to specify these values to be pulled using a script: GausCurv FoldInd CurvInd ...?? Thanks, Catherine On 1/23/13, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: They must be in a single folder and the $SUBJECTS_DIR env variable must be set to that folder. If you know a little unix, you can set up folders with symbolic links to subjects' true directories. doug On 01/23/2013 02:58 PM, Nucleos P wrote: Thank you for your help Doug! I was trying to specify the path to get to the subjects. Do I have to have all the subjects in a folder called 'subjects'? I know the naming conventions are important. Thanks again, Catherine On Fri, Jan 18, 2013 at 6:31 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: actually, looking at your cmd line more I see that you have slashes (/) in the subject names. The argument to --subjects should just be a list of name. See the help (aparcstats2table -h) for examples. doug On 01/18/2013 04:58 PM, Nucleos P wrote: Hello experts: Can someone please help me understand what I am doing wrong? This is the first time I am trying this command and it will not work... COMMAND: aparcstats2table --subjects /RGS4_31p/rgs0868_raw /RGS4_31p/rgs0871_raw /RGS4_31p/rgs0883_raw/ /RGS4_31p/rgs1194_raw144/ /RGS4_31p/rgs1311a/ /RGS4_31p/rgs1370a/ /RGS4_31p/rgs1383a/ -t RGS4_31p/aparc.volume.rh -m volume --hemi=rh PATH: [/usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats]:pwd /usr/local/freesurfer/subjects/RGS4_31p/rgs0868_raw/stats ERROR: SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files ERROR: The stats file /RGS4_31p/rgs0868_raw/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thank you, Catherine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Install FS on new workstation issues
Hi, Is anyone familiar with Redhat Linux workstation commands? I think the problem here was with the setenv command and I looked in root's bin and there is an env command? Just need help getting freesurfer to work. Am a total newbe. Thanks, Catherine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] freesurfer problems
I am currently using a Linux Workstation with Redhat. I recently installed
Freesurfer on this computer. It works fine on the other computers... These
are the errors I am getting: (The important points are in Bold)
proc_fs test_mgi MGI2
#start: /usr/local/freesurfer/bin/proc_fs Thu Oct 4 16:31:57
EDT 2012 #
#start: recon-all Thu Oct 4 16:31:57 EDT 2012
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/MGI2
Actual FREESURFER_HOME /usr/local/freesurfer
Linux goodman 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011
x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/subjects/MGI2/test_mgi
* mri_convert
/usr/local/freesurfer/subjects/scan_todo/test_mgi/raw/MR.1.3.12.2.1107.5.2.32.35216.2012050713483330738693562
/usr/local/freesurfer/subjects/MGI2/test_mgi/mri/orig/001.mgz
mri_convert
/usr/local/freesurfer/subjects/scan_todo/test_mgi/raw/MR.1.3.12.2.1107.5.2.32.35216.2012050713483330738693562
/usr/local/freesurfer/subjects/MGI2/test_mgi/mri/orig/001.mgz *
--
ERROR: Invalid FreeSurfer license key found in license file
/usr/local/freesurfer/.license
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
--
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from
/usr/local/freesurfer/subjects/scan_todo/test_mgi/raw/MR.1.3.12.2.1107.5.2.32.35216.2012050713483330738693562...
#
#@# MotionCor Thu Oct 4 16:32:16 EDT 2012
*ERROR: no run data found in
/usr/local/freesurfer/subjects/MGI2/test_mgi/mri. Make sure to
have a volume called 001.mgz in
/usr/local/freesurfer/subjects/MGI2/test_mgi/mri/orig.
If you have a second run of data call it 002.mgz, etc.*
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Linux goodman 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011
x86_64 x86_64 x86_64 GNU/Linux
recon-all -s test_mgi exited with ERRORS at Thu Oct 4 16:32:16 EDT 2012
For more details, see the log file
/usr/local/freesurfer/subjects/MGI2/test_mgi/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
#end: Thu Oct 4 16:32:16 EDT 2012 #
[prasad@goodman scan_todo]$
*The mri_convert is supposed to create the mri/orig/001.mgz file and works
on the other workstations...
Here is the script in detail:
*
#!/bin/tcsh
###
#Program: proc_fs #
#Author: Dhruman Goradia #
#Date: 09/19/2010 #
#Description: Runs freesurfer preprocessing#
###
set program = $0
echo #start: $program `date` #
if ( $#argv != 2 ) then
echo ${program}: Wrong no of arguments
echo Usage: ${program} dicomdir fs_subdir
exit
endif
set dirdcm = /usr/local/freesurfer/subjects/scan_todo
set fs_subid = $1
set study_id = $2
set file1 = `ls ${dirdcm}/${fs_subid}/raw | head -n 1`
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/${study_id}
echo #start: recon-all `date`
if ( -f ${SUBJECTS_DIR}/${fs_subid}/mri/orig/001.mgz) then
recon-all -s $fs_subid -all
else
*#mkdir -p ${SUBJECTS_DIR}/${fs_subid}/mri/orig
#mri_convert ${dirdcm}/${fs_subid}/raw/${file1}
${SUBJECTS_DIR}/${fs_subid}/mri/orig/001.mgz
recon-all -i ${dirdcm}/${fs_subid}/raw/${file1} -s $fs_subid -all*
endif
echo #end: `date` #
exit
*
Here is the LICENSE file:
FreeSurfer Software License Agreement (Agreement)
Version 1.0 (February 2011)
This Agreement covers contributions to and downloads from the
FreeSurfer project (FreeSurfer) maintained by The General Hospital
Corporation, Boston MA, USA (MGH). Part A of this Agreement applies to
contributions of software and/or data to FreeSurfer (including making
revisions of or additions to code and/or data already in FreeSurfer). Part
B of this Agreement applies to downloads of software and/or data from
FreeSurfer. Part C of this Agreement applies to all transactions with
FreeSurfer. If you distribute Software (as defined below) downloaded from
FreeSurfer, all of the paragraphs of Part B of this Agreement must be
included with and apply to such Software.
Your contribution of software and/or data to FreeSurfer (including prior
to the date of the first publication of this Agreement, each a
Contribution) and/or downloading, copying, modifying, displaying,
distributing or use of any
