[Freesurfer] Group analysis
Dear all, Would it be feasible to do a group analysis with the present developmental release of freesurfer on the subjects which were individually analyzed on the previous(old) version of freesurfer? In other words, is the Group analysis module of present version sensitive to the version in which the data was preprocessed/ reconstructed ? Thanks Sunaina Fotedar Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Group analysis
I don't think it will matter. Sunaina Fotedar wrote: Dear all, Would it be feasible to do a group analysis with the present developmental release of freesurfer on the subjects which were individually analyzed on the previous(old) version of freesurfer? In other words, is the Group analysis module of present version sensitive to the version in which the data was preprocessed/ reconstructed ? Thanks Sunaina Fotedar Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Group analysis
Hello. I used paint-sess-new and surf-sess-new, and they opened a nice overlay without trouble. When I selected the configure overlay command from the menu, I get an error - 'error! expression didn't have a numeric value' The details are below. What can I do? expression didn't have numeric value expression didn't have numeric value (processing -coords option) invoked from within $iWidget marker create line -coords [list $gaLinkedVars(fthresh) -Inf $gaLinkedVars(fthresh) Inf] -name thresh -outline red (procedure SetMin line 7) invoked from within SetMin $gbwHisto $gaLinkedVars(fthresh) (procedure DoConfigOverlayDisplayDlog line 222) invoked from within DoConfigOverlayDisplayDlog invoked from within .w.fwMenuBar.mbwView.mw.cmw5 invoke active (uplevel body line 1) invoked from within uplevel #0 [list $w invoke active] (procedure tk::MenuInvoke line 47) invoked from within tk::MenuInvoke .w.fwMenuBar.mbwView.mw.cmw5 1 (command bound to event) Doug Greve wrote: I don't think it will matter. Sunaina Fotedar wrote: Dear all, Would it be feasible to do a group analysis with the present developmental release of freesurfer on the subjects which were individually analyzed on the previous(old) version of freesurfer? In other words, is the Group analysis module of present version sensitive to the version in which the data was preprocessed/ reconstructed ? Thanks Sunaina Fotedar Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Daniel Goldenholz - Cell: 617-935-9421 http://people.bu.edu/danielg/ Mavet v'chaim b'yad halashon Life and death are in the hands of language - Proverbs 18:21 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] invalid command name PNG
Xander, I haven't encountered this error message, and can't seem to track down its origin. Is it possible to upgrade your 2003 version of freesurfer to a newer version? If not, if you can email me the csurf file found in the $FREESURFER/bin directory, I might be able to figure out the problem. Nick On Thu, 2005-10-06 at 22:50 +0700, [EMAIL PROTECTED] wrote: Hi, I've got a Mac box running OS X 10.3.9 and Freesurfer ,v 1.3 2003/08/05 19: 19:16, and just recently when I start up freesurfer I get an error. To reproduce the error I do: source /Applications/Freesurfer/SetUpFreeSurfer.csh Setting up enviroment for FreeSurfer/FS-FAST $Id: FreeSurferEnv.csh,v 1.3 2003/08/05 19:19:16 kteich Exp $ FREESURFER_HOME /Applications/Freesurfer FSFAST_HOME /Applications/Freesurfer/fsfast AFNI_DIR/Applications/Freesurfer/afni FSL_DIR /Applications/Freesurfer/fsl SUBJECTS_DIR/Users/xmeadow/subjects csurf Application initialization failed: invalid command name PNG Then Freesurfer opens up normally. I was just wondering what this error message means. I've looked online and seen that PNG stands for 'Portable Network Graphics' (I think), but I don't know if I have it installed or if I need it installed. Is there something I can do to get Freesurfer to load without errors? Thanks very much. Xander ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Coregistration?
Hello, I was wondering if anybody has any insight into the best way to coregister functionals with anatomicals in Freesurfer. I am looking for an automated method of coregistration. I noticed the spm_coregister command, but I am working with AFNI BRIK files, and I assume this requires Analyze format. Any suggestions? Thanks. Nate Parks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] difference between dev version and the final stable version?
I have a question about the current dev release - how different is the new 'stable' release going to be different from it? Probably not very different, but we are still working on a few critical bug fixes, and adding some final touches to the GUI programs. Can I start processing some brains using dev release and then continue processing using new 'stable' release? The nature of the bug fixes might make this a problem. In general we don't recommend mixing versions within the same study or series of result comparisons. We are working on improving our ability to detect changes in results from version to version, but we're not there yet. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Group analysis
hi Daniel- i've encountered this before. see whta the value of fthresh is currently: puts $fthresh if it is an integer. add a decimal place to it: set fthresh 1.0 you may have to check each of the following: fthresh fmid fslope thanks, brian On Fri, 7 Oct 2005, Daniel Goldenholz wrote: Hello. I used paint-sess-new and surf-sess-new, and they opened a nice overlay without trouble. When I selected the configure overlay command from the menu, I get an error - 'error! expression didn't have a numeric value' The details are below. What can I do? expression didn't have numeric value expression didn't have numeric value (processing -coords option) invoked from within $iWidget marker create line -coords [list $gaLinkedVars(fthresh) -Inf $gaLinkedVars(fthresh) Inf] -name thresh -outline red (procedure SetMin line 7) invoked from within SetMin $gbwHisto $gaLinkedVars(fthresh) (procedure DoConfigOverlayDisplayDlog line 222) invoked from within DoConfigOverlayDisplayDlog invoked from within .w.fwMenuBar.mbwView.mw.cmw5 invoke active (uplevel body line 1) invoked from within uplevel #0 [list $w invoke active] (procedure tk::MenuInvoke line 47) invoked from within tk::MenuInvoke .w.fwMenuBar.mbwView.mw.cmw5 1 (command bound to event) Doug Greve wrote: I don't think it will matter. Sunaina Fotedar wrote: Dear all, Would it be feasible to do a group analysis with the present developmental release of freesurfer on the subjects which were individually analyzed on the previous(old) version of freesurfer? In other words, is the Group analysis module of present version sensitive to the version in which the data was preprocessed/ reconstructed ? Thanks Sunaina Fotedar Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] RE: make_average_surface
Hi, When I run make_average_surface --subjects AD1293 AD1297 AD1299 --out average_cn, it finished within 1 second without any output and any error message. I don't know what is wrong. Any helps there? I have not updated my freesurface so I downloaded make_average_surface from a post by Nick in July, 2005. Thanks, Antao ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] RE: make_average_surface
Add --echo to the command to print its activity, and then send me the output. On Fri, 2005-10-07 at 15:00 -0700, Antao Du wrote: Hi, When I run make_average_surface --subjects AD1293 AD1297 AD1299 --out average_cn, it finished within 1 second without any output and any error message. I don't know what is wrong. Any helps there? I have not updated my freesurface so I downloaded make_average_surface from a post by Nick in July, 2005. Thanks, Antao ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] RE: make_average_surface
This sounds like a problem I am having, The same script works fine on my
mac, but not on my FC4 machine. Here is the output, and a message I sent to
before.
I changed the flags to ³efxv² as Doug recommended, and here is the output
for make_average_subject, make_average_volume and make_average_surface. The
script doesn¹t seem to be accepting my command line arguments. I am using
the current dev version on a Fedora Core 4 system, if that helps.
Thanks,
Brian
[EMAIL PROTECTED] subjects]$ make_average_subject --out average_bcs
--subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021
SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
SC036
set VERSION = '$Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp
$'
set VERSION = $Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp
$
set PrintHelp = 0 ;
set PrintHelp = 0
if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif
set average_subject=average
set average_subject=average
set ddir = ${SUBJECTS_DIR}/${average_subject}
set ddir = /apps/freesurfer/subjects/average
set transform_fname=
set transform_fname=
set XFORM_FLAG=
set XFORM_FLAG=
if ( $#argv == 0 ) then
if ( 27 == 0 ) then
set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l
**
[EMAIL PROTECTED] subjects]$ make_average_volume --out average_bcs
--subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021
SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
SC036
set VERSION = '$Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp
$' ;
set VERSION = $Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp $
set PrintHelp = 0 ;
set PrintHelp = 0
set cleanup = 0 ;
set cleanup = 0
set transform_fname = talairach.xfm
set transform_fname = talairach.xfm
if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif
set average_subject = average
set average_subject = average
set cmdargs = ( $argv ) ;
set cmdargs = ( --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015
SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027
SC030 SC031 SC032 SC033 SC034 SC035 SC036 )
if ( $#argv == 0 ) then
if ( 27 == 0 ) then
set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l
**
[EMAIL PROTECTED] subjects]$ make_average_surface --out average_bcs
--subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021
SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
SC036
set VERSION = '$Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve
Exp $' ;
set VERSION = $Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve Exp
$
set PrintHelp = 0 ;
set PrintHelp = 0
if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif
set average_subject=average
set average_subject=average
set ddir = ${SUBJECTS_DIR}/${average_subject}
set ddir = /apps/freesurfer/subjects/average
set transform_fname=
set transform_fname=
set XFORM_FLAG=
set XFORM_FLAG=
if ( $#argv == 0 ) then
if ( 27 == 0 ) then
set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l
From: Doug Greve [EMAIL PROTECTED]
Date: Tue, 27 Sep 2005 15:04:59 -0400
To: Brian Schweinsburg, Ph.D. [EMAIL PROTECTED]
Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] make_average_subject error?
Try editing those scripts so that the first line is:
#!/bin/tcsh -efxv
ie, adding xv
This turns on all kinds of debugging
Brian Schweinsburg, Ph.D. wrote:
Re: [Freesurfer] make_average_subject error? Hi Doug,
The same thing happens when I try to run them separately. It exits to the
prompt with no messages.
Brian
--
Brian C. Schweinsburg, Ph.D.
Assistant Adjunct Professor of Psychiatry
University of California, San Diego
Office: 858-552-8585 x6109
Cell: 858-354-3756
From: Doug Greve [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
Date: Tue, 27 Sep 2005 11:16:00 -0400
To: Brian Schweinsburg, Ph.D. [EMAIL
Re: [Freesurfer] RE: make_average_surface
This is a puzzling problem. Unfortunately I don't have access to a FC4
system to try to recreate what you are seeing.
However, can you edit your make_average_subject/surface/volume scripts
to comment-out these lines (shown here with comment-out chars added):
#set n = `echo $argv | grep -e --help | wc -l`
#if($n != 0) then
# set PrintHelp = 1;
# goto usage_exit;
#endif
#set n = `echo $argv | grep -e --version | wc -l`
#if($n != 0) then
# echo $VERSION
# exit 0;
#endif
This appears to be where your script is stopping, and I would like to
see what it does if it gets beyond this point.
Thanks
On Fri, 2005-10-07 at 15:24 -0700, Brian Schweinsburg, Ph.D. wrote:
This sounds like a problem I am having, The same script works fine on my
mac, but not on my FC4 machine. Here is the output, and a message I sent to
before.
I changed the flags to ³efxv² as Doug recommended, and here is the output
for make_average_subject, make_average_volume and make_average_surface. The
script doesn¹t seem to be accepting my command line arguments. I am using
the current dev version on a Fedora Core 4 system, if that helps.
Thanks,
Brian
[EMAIL PROTECTED] subjects]$ make_average_subject --out average_bcs
--subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021
SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
SC036
set VERSION = '$Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp
$'
set VERSION = $Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp
$
set PrintHelp = 0 ;
set PrintHelp = 0
if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif
set average_subject=average
set average_subject=average
set ddir = ${SUBJECTS_DIR}/${average_subject}
set ddir = /apps/freesurfer/subjects/average
set transform_fname=
set transform_fname=
set XFORM_FLAG=
set XFORM_FLAG=
if ( $#argv == 0 ) then
if ( 27 == 0 ) then
set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l
**
[EMAIL PROTECTED] subjects]$ make_average_volume --out average_bcs
--subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021
SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
SC036
set VERSION = '$Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp
$' ;
set VERSION = $Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp $
set PrintHelp = 0 ;
set PrintHelp = 0
set cleanup = 0 ;
set cleanup = 0
set transform_fname = talairach.xfm
set transform_fname = talairach.xfm
if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif
set average_subject = average
set average_subject = average
set cmdargs = ( $argv ) ;
set cmdargs = ( --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015
SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027
SC030 SC031 SC032 SC033 SC034 SC035 SC036 )
if ( $#argv == 0 ) then
if ( 27 == 0 ) then
set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l
**
[EMAIL PROTECTED] subjects]$ make_average_surface --out average_bcs
--subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021
SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
SC036
set VERSION = '$Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve
Exp $' ;
set VERSION = $Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve Exp
$
set PrintHelp = 0 ;
set PrintHelp = 0
if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif
set average_subject=average
set average_subject=average
set ddir = ${SUBJECTS_DIR}/${average_subject}
set ddir = /apps/freesurfer/subjects/average
set transform_fname=
set transform_fname=
set XFORM_FLAG=
set XFORM_FLAG=
if ( $#argv == 0 ) then
if ( 27 == 0 ) then
set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l
From: Doug Greve [EMAIL PROTECTED]
Date: Tue, 27 Sep 2005 15:04:59
Re: [Freesurfer] RE: make_average_surface
Can you tell me which OS you are running? Type: cat /etc/redhat-release and uname -a On Fri, 2005-10-07 at 15:00 -0700, Antao Du wrote: Hi, When I run make_average_surface --subjects AD1293 AD1297 AD1299 --out average_cn, it finished within 1 second without any output and any error message. I don't know what is wrong. Any helps there? I have not updated my freesurface so I downloaded make_average_surface from a post by Nick in July, 2005. Thanks, Antao ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] RE: make_average_surface
Nick, This appears to have done the trick. Make_average_subject ran and created the surfaces. It echos the following error message many times, but I assume this does not matter as it occurs with recon-all as well: INFO: Volume /tmp/mritotal_9750/nu_8_dxyz.mnc cannot be found. It also specifies the following and created an error log (that later disappeared) saying: INFO: Volume unknown cannot be found. INFO: Volume unknown cannot be found. corRead(): can't open file ./../mri/orig/COR-.info I assume that this is because I am using mgz files rather than COR? The appropriate volumes were written out in mgz format. The volumes and surfaces look okay to me. I included the make_average log file below in case there was something specific that you wanted to see. Thanks for your help. Brian ***make_average log file* Fri Oct 7 16:23:33 PDT 2005 /apps/freesurfer/subjects /apps/freesurfer/bin//make_average_volume --out test --subjects SC011 SC012 SC013 setenv SUBJECTS_DIR /apps/freesurfer/subjects SC011 SC012 SC013 mri_convert /apps/freesurfer/subjects/SC011/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz --apply_transform /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC011 mri_convert /apps/freesurfer/subjects/SC011/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz --apply_transform /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC011 reading from /apps/freesurfer/subjects/SC011/mri/orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Applying transformation from file /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm... Reading transform INFO: devolving XFM (SC011) before - 1.078 -0.019 -0.014 0.327; 0.020 1.035 0.187 -11.399; 0.010 -0.185 1.025 -15.094; 0.000 0.000 0.000 1.000; Trying /apps/freesurfer/subjects/SC011/mri/orig Trying /apps/freesurfer/subjects/SC011/mri/orig.mgz after - 1.078 -0.019 -0.014 0.812; 0.020 1.035 0.187 -11.390; 0.010 -0.185 1.025 -15.089; 0.000 0.000 0.000 1.000; - - INFO: Transform Matrix 1.078 -0.019 -0.014 0.812; 0.020 1.035 0.187 -11.390; 0.010 -0.185 1.025 -15.089; 0.000 0.000 0.000 1.000; - Reslicing using trilinear interpolation writing to /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz... mri_convert /apps/freesurfer/subjects/SC012/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC012.mgz --apply_transform /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC012 mri_convert /apps/freesurfer/subjects/SC012/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC012.mgz --apply_transform /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC012 reading from /apps/freesurfer/subjects/SC012/mri/orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Applying transformation from file /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm... Reading transform INFO: devolving XFM (SC012) before - 1.073 0.022 0.034 0.454; -0.028 1.071 0.189 -11.925; -0.034 -0.211 1.188 -18.689; 0.000 0.000 0.000 1.000; Trying /apps/freesurfer/subjects/SC012/mri/orig Trying /apps/freesurfer/subjects/SC012/mri/orig.mgz after - 1.073 0.022 0.034 0.401; -0.028 1.071 0.189 -11.924; -0.034 -0.211 1.188 -18.687; 0.000 0.000 0.000 1.000; - - INFO: Transform Matrix 1.073 0.022 0.034 0.401; -0.028 1.071 0.189 -11.924; -0.034 -0.211 1.188 -18.687; 0.000 0.000 0.000 1.000; - Reslicing using trilinear interpolation writing to /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC012.mgz... mri_convert /apps/freesurfer/subjects/SC013/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC013.mgz --apply_transform /apps/freesurfer/subjects/SC013/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC013 mri_convert /apps/freesurfer/subjects/SC013/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC013.mgz --apply_transform /apps/freesurfer/subjects/SC013/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC013 reading from /apps/freesurfer/subjects/SC013/mri/orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Applying transformation from file /apps/freesurfer/subjects/SC013/mri/transforms/talairach.xfm... Reading transform INFO: devolving XFM (SC013) before - 1.118 -0.032
Re: [Freesurfer] RE: make_average_surface
Brian, Glad it worked. Clearly that portion of the script needs to be updated for better compatibility. The messages you are seeing (about nu_8_dxyz.mnc and COR-.info) can be ignored, as they are not errors. In the newest dev release, these messages have been suppressed, because they do not indicate any useful information and give the impression of errors. You do not need to get this new dev release though, as your current release produces valid average surface and volume files. Nick On Fri, 2005-10-07 at 16:36 -0700, Brian Schweinsburg, Ph.D. wrote: Nick, This appears to have done the trick. Make_average_subject ran and created the surfaces. It echos the following error message many times, but I assume this does not matter as it occurs with recon-all as well: INFO: Volume /tmp/mritotal_9750/nu_8_dxyz.mnc cannot be found. It also specifies the following and created an error log (that later disappeared) saying: INFO: Volume unknown cannot be found. INFO: Volume unknown cannot be found. corRead(): can't open file ./../mri/orig/COR-.info I assume that this is because I am using mgz files rather than COR? The appropriate volumes were written out in mgz format. The volumes and surfaces look okay to me. I included the make_average log file below in case there was something specific that you wanted to see. Thanks for your help. Brian ***make_average log file* Fri Oct 7 16:23:33 PDT 2005 /apps/freesurfer/subjects /apps/freesurfer/bin//make_average_volume --out test --subjects SC011 SC012 SC013 setenv SUBJECTS_DIR /apps/freesurfer/subjects SC011 SC012 SC013 mri_convert /apps/freesurfer/subjects/SC011/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz --apply_transform /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC011 mri_convert /apps/freesurfer/subjects/SC011/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz --apply_transform /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC011 reading from /apps/freesurfer/subjects/SC011/mri/orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Applying transformation from file /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm... Reading transform INFO: devolving XFM (SC011) before - 1.078 -0.019 -0.014 0.327; 0.020 1.035 0.187 -11.399; 0.010 -0.185 1.025 -15.094; 0.000 0.000 0.000 1.000; Trying /apps/freesurfer/subjects/SC011/mri/orig Trying /apps/freesurfer/subjects/SC011/mri/orig.mgz after - 1.078 -0.019 -0.014 0.812; 0.020 1.035 0.187 -11.390; 0.010 -0.185 1.025 -15.089; 0.000 0.000 0.000 1.000; - - INFO: Transform Matrix 1.078 -0.019 -0.014 0.812; 0.020 1.035 0.187 -11.390; 0.010 -0.185 1.025 -15.089; 0.000 0.000 0.000 1.000; - Reslicing using trilinear interpolation writing to /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz... mri_convert /apps/freesurfer/subjects/SC012/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC012.mgz --apply_transform /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC012 mri_convert /apps/freesurfer/subjects/SC012/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC012.mgz --apply_transform /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC012 reading from /apps/freesurfer/subjects/SC012/mri/orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Applying transformation from file /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm... Reading transform INFO: devolving XFM (SC012) before - 1.073 0.022 0.034 0.454; -0.028 1.071 0.189 -11.925; -0.034 -0.211 1.188 -18.689; 0.000 0.000 0.000 1.000; Trying /apps/freesurfer/subjects/SC012/mri/orig Trying /apps/freesurfer/subjects/SC012/mri/orig.mgz after - 1.073 0.022 0.034 0.401; -0.028 1.071 0.189 -11.924; -0.034 -0.211 1.188 -18.687; 0.000 0.000 0.000 1.000; - - INFO: Transform Matrix 1.073 0.022 0.034 0.401; -0.028 1.071 0.189 -11.924; -0.034 -0.211 1.188 -18.687; 0.000 0.000 0.000 1.000; - Reslicing using trilinear interpolation writing to /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC012.mgz... mri_convert /apps/freesurfer/subjects/SC013/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC013.mgz
RE: [Freesurfer] RE: make_average_surface
There is no any output when I add --echo. Antao -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Nick Schmansky Sent: Friday, October 07, 2005 3:04 PM To: Antao Du Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] RE: make_average_surface Add --echo to the command to print its activity, and then send me the output. On Fri, 2005-10-07 at 15:00 -0700, Antao Du wrote: Hi, When I run make_average_surface --subjects AD1293 AD1297 AD1299 --out average_cn, it finished within 1 second without any output and any error message. I don't know what is wrong. Any helps there? I have not updated my freesurface so I downloaded make_average_surface from a post by Nick in July, 2005. Thanks, Antao ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] RE: make_average_surface
Dear Antao, Check the recent archives with the subject make_average_subject error? and the recent exchange with Nick. On Doug's advice, I added 'xv' to the beginning of each make_average* script So, #!/bin/tcsh -efxv Instead of #!/bin/tcsh -ef This produced the output that allowed the freesurfer developers to pinpoint the error. Also on Doug's suggestion, try adding --debug to the make_average_subject command. Nick's recommendation a few posts ago fixed the problem that I was having on a fedora core 4 machine. Based on your initial post, we seem to have similar problems, so give the above suggestions a try. If needed, comment out the offending information in make_average_subject, make_average_volume, and make_average_surface as Nick suggested (if you receive the same error message that I received). Good luck. Brian -- Brian C. Schweinsburg, Ph.D. Assistant Adjunct Professor of Psychiatry University of California, San Diego Office: 858-552-8585 x6109 Cell: 858-354-3756 From: Antao Du [EMAIL PROTECTED] Date: Fri, 7 Oct 2005 17:27:41 -0700 To: Nick Schmansky [EMAIL PROTECTED] Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] RE: make_average_surface There is no any output when I add --echo. Antao -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Nick Schmansky Sent: Friday, October 07, 2005 3:04 PM To: Antao Du Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] RE: make_average_surface Add --echo to the command to print its activity, and then send me the output. On Fri, 2005-10-07 at 15:00 -0700, Antao Du wrote: Hi, When I run make_average_surface --subjects AD1293 AD1297 AD1299 --out average_cn, it finished within 1 second without any output and any error message. I don't know what is wrong. Any helps there? I have not updated my freesurface so I downloaded make_average_surface from a post by Nick in July, 2005. Thanks, Antao ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
