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.
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
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
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
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
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
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
[bschweinsburg@localhost 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 $argv | grep -e --help | wc -l` echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036 grep -e --help wc -l
** [bschweinsburg@localhost subjects]$ 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 $argv | grep -e --help | wc -l` echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036 grep -e --help wc -l
** [bschweinsburg@localhost subjects]$ 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 greve@nmr.mgh.harvard.edu Date: Tue, 27 Sep 2005 15:04:59 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu 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 greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Date: Tue, 27 Sep 2005 11:16:00 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu mailto:bschweinsburg@ucsd.edu Cc: "freesurfer@nmr.mgh.harvard.edu" mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] make_average_subject error?
Can you run make_average_surface and make_average_volume separately?
Brian Schweinsburg, Ph.D. wrote:
I ran it with make_average_subject --debug \ --subjects SC010 SC012 ...
I also tried it with --echo. It provides no output.
I checked the script and it is executable. I looked through the code and everything seems reasonable given my system except the part that says: "if person = brian; exit 0"
Brian
From: Doug Greve greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Date: Mon, 26 Sep 2005 16:40:48 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu mailto:bschweinsburg@ucsd.edu mailto:bschweinsburg@ucsd.edu Cc: "freesurfer@nmr.mgh.harvard.edu" mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] make_average_subject error?
try running it with --debug and send us the output
Brian Schweinsburg, Ph.D. wrote:
Hi Folks,
I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh without error, but does not produce anything.
make_average_subject --subjects SC010 SC011 SC012 ...
I am running the latested dev release with Fedora Core 4.
Any ideas as to the problem? Brian
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 greve@nmr.mgh.harvard.edu 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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
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 $VERSION # exit 0; #endif
This appears to be where your script is stopping, and I would like to see what it does if it gets beyond this point.
Thanks
On Fri, 2005-10-07 at 15:24 -0700, Brian Schweinsburg, Ph.D. wrote:
This sounds like a problem I am having, The same script works fine on my mac, but not on my FC4 machine. Here is the output, and a message I sent to before.
I changed the flags to ³efxv² as Doug recommended, and here is the output for make_average_subject, make_average_volume and make_average_surface. The script doesn¹t seem to be accepting my command line arguments. I am using the current dev version on a Fedora Core 4 system, if that helps.
Thanks, Brian
[bschweinsburg@localhost subjects]$ 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 $argv | grep -e --help | wc -l` echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036 grep -e --help wc -l
** [bschweinsburg@localhost subjects]$ 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 $argv | grep -e --help | wc -l` echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036 grep -e --help wc -l
** [bschweinsburg@localhost subjects]$ 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 greve@nmr.mgh.harvard.edu Date: Tue, 27 Sep 2005 15:04:59 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu 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 greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Date: Tue, 27 Sep 2005 11:16:00 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu mailto:bschweinsburg@ucsd.edu Cc: "freesurfer@nmr.mgh.harvard.edu" mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] make_average_subject error?
Can you run make_average_surface and make_average_volume separately?
Brian Schweinsburg, Ph.D. wrote:
I ran it with make_average_subject --debug \ --subjects SC010 SC012 ...
I also tried it with --echo. It provides no output.
I checked the script and it is executable. I looked through the code and everything seems reasonable given my system except the part that says: "if person = brian; exit 0"
Brian
From: Doug Greve greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Date: Mon, 26 Sep 2005 16:40:48 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu mailto:bschweinsburg@ucsd.edu mailto:bschweinsburg@ucsd.edu Cc: "freesurfer@nmr.mgh.harvard.edu" mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] make_average_subject error?
try running it with --debug and send us the output
Brian Schweinsburg, Ph.D. wrote:
Hi Folks,
I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh without error, but does not produce anything.
make_average_subject --subjects SC010 SC011 SC012 ...
I am running the latested dev release with Fedora Core 4.
Any ideas as to the problem? Brian
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 greve@nmr.mgh.harvard.edu 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
-- 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: Nick Schmansky nicks@nmr.mgh.harvard.edu Date: Fri, 07 Oct 2005 18:04:25 -0400 To: Antao Du antao@itsa.ucsf.edu Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu 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
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 -0.017 -0.677; 0.032 1.031 0.204 -17.741; 0.010 -0.214 1.079 -9.616; 0.000 0.000 0.000 1.000; Trying /apps/freesurfer/subjects/SC013/mri/orig Trying /apps/freesurfer/subjects/SC013/mri/orig.mgz -------- after --------- 1.118 -0.032 -0.017 2.509; 0.032 1.031 0.204 -17.650; 0.010 -0.214 1.079 -9.587; 0.000 0.000 0.000 1.000; ----------------- --------------------------------- INFO: Transform Matrix 1.118 -0.032 -0.017 2.509; 0.032 1.031 0.204 -17.650; 0.010 -0.214 1.079 -9.587; 0.000 0.000 0.000 1.000; --------------------------------- Reslicing using trilinear interpolation writing to /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC013.mgz... mri_average /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC012.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC013.mgz /apps/freesurfer/subjects/test/mri/orig.mgz mri_convert /apps/freesurfer/subjects/SC011/mri/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-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/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-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/T1.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/T1-SC011.mgz... mri_convert /apps/freesurfer/subjects/SC012/mri/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-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/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-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/T1.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/T1-SC012.mgz... mri_convert /apps/freesurfer/subjects/SC013/mri/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-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/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-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/T1.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 -0.017 -0.677; 0.032 1.031 0.204 -17.741; 0.010 -0.214 1.079 -9.616; 0.000 0.000 0.000 1.000; Trying /apps/freesurfer/subjects/SC013/mri/orig Trying /apps/freesurfer/subjects/SC013/mri/orig.mgz -------- after --------- 1.118 -0.032 -0.017 2.509; 0.032 1.031 0.204 -17.650; 0.010 -0.214 1.079 -9.587; 0.000 0.000 0.000 1.000; ----------------- --------------------------------- INFO: Transform Matrix 1.118 -0.032 -0.017 2.509; 0.032 1.031 0.204 -17.650; 0.010 -0.214 1.079 -9.587; 0.000 0.000 0.000 1.000; --------------------------------- Reslicing using trilinear interpolation writing to /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC013.mgz... mri_average /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC011.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC012.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC013.mgz /apps/freesurfer/subjects/test/mri/T1.mgz mri_convert /apps/freesurfer/subjects/SC011/mri/brain.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-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/brain.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-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/brain.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/brain-SC011.mgz... mri_convert /apps/freesurfer/subjects/SC012/mri/brain.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-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/brain.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-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/brain.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/brain-SC012.mgz... mri_convert /apps/freesurfer/subjects/SC013/mri/brain.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-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/brain.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-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/brain.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 -0.017 -0.677; 0.032 1.031 0.204 -17.741; 0.010 -0.214 1.079 -9.616; 0.000 0.000 0.000 1.000; Trying /apps/freesurfer/subjects/SC013/mri/orig Trying /apps/freesurfer/subjects/SC013/mri/orig.mgz -------- after --------- 1.118 -0.032 -0.017 2.509; 0.032 1.031 0.204 -17.650; 0.010 -0.214 1.079 -9.587; 0.000 0.000 0.000 1.000; ----------------- --------------------------------- INFO: Transform Matrix 1.118 -0.032 -0.017 2.509; 0.032 1.031 0.204 -17.650; 0.010 -0.214 1.079 -9.587; 0.000 0.000 0.000 1.000; --------------------------------- Reslicing using trilinear interpolation writing to /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz... mri_average /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC011.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC012.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz /apps/freesurfer/subjects/test/mri/brain.mgz Fri Oct 7 16:29:49 PDT 2005 make_average_volume done
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 --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 -0.017 -0.677; 0.032 1.031 0.204 -17.741; 0.010 -0.214 1.079 -9.616; 0.000 0.000 0.000 1.000; Trying /apps/freesurfer/subjects/SC013/mri/orig Trying /apps/freesurfer/subjects/SC013/mri/orig.mgz -------- after --------- 1.118 -0.032 -0.017 2.509; 0.032 1.031 0.204 -17.650; 0.010 -0.214 1.079 -9.587; 0.000 0.000 0.000 1.000;
INFO: Transform Matrix 1.118 -0.032 -0.017 2.509; 0.032 1.031 0.204 -17.650; 0.010 -0.214 1.079 -9.587; 0.000 0.000 0.000 1.000;
Reslicing using trilinear interpolation writing to /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC013.mgz... mri_average /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC012.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC013.mgz /apps/freesurfer/subjects/test/mri/orig.mgz mri_convert /apps/freesurfer/subjects/SC011/mri/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-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/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-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/T1.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/T1-SC011.mgz... mri_convert /apps/freesurfer/subjects/SC012/mri/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-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/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-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/T1.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/T1-SC012.mgz... mri_convert /apps/freesurfer/subjects/SC013/mri/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-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/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-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/T1.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 -0.017 -0.677; 0.032 1.031 0.204 -17.741; 0.010 -0.214 1.079 -9.616; 0.000 0.000 0.000 1.000; Trying /apps/freesurfer/subjects/SC013/mri/orig Trying /apps/freesurfer/subjects/SC013/mri/orig.mgz -------- after --------- 1.118 -0.032 -0.017 2.509; 0.032 1.031 0.204 -17.650; 0.010 -0.214 1.079 -9.587; 0.000 0.000 0.000 1.000;
INFO: Transform Matrix 1.118 -0.032 -0.017 2.509; 0.032 1.031 0.204 -17.650; 0.010 -0.214 1.079 -9.587; 0.000 0.000 0.000 1.000;
Reslicing using trilinear interpolation writing to /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC013.mgz... mri_average /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC011.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC012.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC013.mgz /apps/freesurfer/subjects/test/mri/T1.mgz mri_convert /apps/freesurfer/subjects/SC011/mri/brain.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-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/brain.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-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/brain.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/brain-SC011.mgz... mri_convert /apps/freesurfer/subjects/SC012/mri/brain.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-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/brain.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-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/brain.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/brain-SC012.mgz... mri_convert /apps/freesurfer/subjects/SC013/mri/brain.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-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/brain.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-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/brain.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 -0.017 -0.677; 0.032 1.031 0.204 -17.741; 0.010 -0.214 1.079 -9.616; 0.000 0.000 0.000 1.000; Trying /apps/freesurfer/subjects/SC013/mri/orig Trying /apps/freesurfer/subjects/SC013/mri/orig.mgz -------- after --------- 1.118 -0.032 -0.017 2.509; 0.032 1.031 0.204 -17.650; 0.010 -0.214 1.079 -9.587; 0.000 0.000 0.000 1.000;
INFO: Transform Matrix 1.118 -0.032 -0.017 2.509; 0.032 1.031 0.204 -17.650; 0.010 -0.214 1.079 -9.587; 0.000 0.000 0.000 1.000;
Reslicing using trilinear interpolation writing to /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz... mri_average /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC011.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC012.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz /apps/freesurfer/subjects/test/mri/brain.mgz Fri Oct 7 16:29:49 PDT 2005 make_average_volume done
-- 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: Nick Schmansky nicks@nmr.mgh.harvard.edu Date: Fri, 07 Oct 2005 18:52:12 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Subject: 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 $VERSION # exit 0; #endif
This appears to be where your script is stopping, and I would like to see what it does if it gets beyond this point.
Thanks
On Fri, 2005-10-07 at 15:24 -0700, Brian Schweinsburg, Ph.D. wrote:
This sounds like a problem I am having, The same script works fine on my mac, but not on my FC4 machine. Here is the output, and a message I sent to before.
I changed the flags to ³efxv² as Doug recommended, and here is the output for make_average_subject, make_average_volume and make_average_surface. The script doesn¹t seem to be accepting my command line arguments. I am using the current dev version on a Fedora Core 4 system, if that helps.
Thanks, Brian
[bschweinsburg@localhost subjects]$ 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 $argv | grep -e --help | wc -l` echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036 grep -e --help wc -l
** [bschweinsburg@localhost subjects]$ 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 $argv | grep -e --help | wc -l` echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036 grep -e --help wc -l
** [bschweinsburg@localhost subjects]$ 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 greve@nmr.mgh.harvard.edu Date: Tue, 27 Sep 2005 15:04:59 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu 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 greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Date: Tue, 27 Sep 2005 11:16:00 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu mailto:bschweinsburg@ucsd.edu Cc: "freesurfer@nmr.mgh.harvard.edu" mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] make_average_subject error?
Can you run make_average_surface and make_average_volume separately?
Brian Schweinsburg, Ph.D. wrote:
I ran it with make_average_subject --debug \ --subjects SC010 SC012 ...
I also tried it with --echo. It provides no output.
I checked the script and it is executable. I looked through the code and everything seems reasonable given my system except the part that says: "if person = brian; exit 0"
Brian
From: Doug Greve greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Date: Mon, 26 Sep 2005 16:40:48 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu mailto:bschweinsburg@ucsd.edu mailto:bschweinsburg@ucsd.edu Cc: "freesurfer@nmr.mgh.harvard.edu" mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] make_average_subject error?
try running it with --debug and send us the output
Brian Schweinsburg, Ph.D. wrote:
> > Hi Folks, > > I tried running the latest make_average_subject script (and the > make_average_surface/volume scripts) using the expected command line > syntax > and after hitting enter it immediately exits to the csh without error, > but > does not produce anything. > > make_average_subject --subjects SC010 SC011 SC012 ... > > I am running the latested dev release with Fedora Core 4. > > Any ideas as to the problem? > Brian > > > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
-- 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: Nick Schmansky nicks@nmr.mgh.harvard.edu Date: Fri, 07 Oct 2005 18:04:25 -0400 To: Antao Du antao@itsa.ucsf.edu Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu 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
There is no any output when I add --echo.
Antao
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]On 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
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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
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
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
You can use spmregister (front end for spm) or fsl_rigid_register (uses fsl). Neither spm nor fsl will accept BRIKS, but I think the wrappers will as they will convert the input to analyze using mri_convert. If not, then you'll have to convert them youself. You should also use tkregister2 to check the registrations (run with --help :).
doug
Nate Parks wrote:
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
Nate:
Is there a reason you don't want to coregister them with AFNI's coregistration?
Regardless, AFNI also has a program to covert AFNI format to ANALYZE format data.
Be aware however that AFNI supports all 48 possible data orders, while ANALYZE does not... so keep good track of the right-left aspect of your data.
Graham
At 10/7/2005 01:49 PM, you wrote:
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
Does AFNI have an automated coregistration tool? I thought you could only do manual coreg in AFNI. The problem I have with coregistering in SPM is that I have a 4D BRIK of 298 functionals. Coregistration in SPM reslices all of these functionals into anatomical space, making them enormous files. It seems that AFNI won't let me convert these huge files back into a 4D BRIK.
Quoting Graham Wideman gwlist@grahamwideman.com:
Nate:
Is there a reason you don't want to coregister them with AFNI's coregistration?
Regardless, AFNI also has a program to covert AFNI format to ANALYZE format data.
Be aware however that AFNI supports all 48 possible data orders, while ANALYZE does not... so keep good track of the right-left aspect of your data.
Graham
At 10/7/2005 01:49 PM, you wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
spmregister and fsl_rigid_register will only use one time point (1st) from your functionals to compute the register.dat. Or extract the one time point you are using for motion-correction.
doug
Nate Parks wrote:
Does AFNI have an automated coregistration tool? I thought you could only do manual coreg in AFNI. The problem I have with coregistering in SPM is that I have a 4D BRIK of 298 functionals. Coregistration in SPM reslices all of these functionals into anatomical space, making them enormous files. It seems that AFNI won't let me convert these huge files back into a 4D BRIK.
Quoting Graham Wideman gwlist@grahamwideman.com:
Nate:
Is there a reason you don't want to coregister them with AFNI's coregistration?
Regardless, AFNI also has a program to covert AFNI format to ANALYZE format data.
Be aware however that AFNI supports all 48 possible data orders, while ANALYZE does not... so keep good track of the right-left aspect of your data.
Graham
At 10/7/2005 01:49 PM, you wrote:
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
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
The AFNI program 3dvolreg does coregistration only for volumes acquired with the same kind of pulse sequence and consequently the same tissue signal values. Use it for coregistering different EPI volumes to each other or different T1-weighted structural scans to each other.
I think what Nate was asking about was coregistering EPI data to the structural scans. The AFNI program 3dAnatNudge can help with this to some extent. It uses simple iterative translational movements to find the best fit between a "skull-stripped" anatomy volume and an EPI volume. No rotation or resizing is done.
To use this program you remove the skull and other non-brain voxels from the anatomy volume. The AFNI programs 3dIntracranial and a newer program called 3dSkullStrip both do this.
Jeff
From: Graham Wideman gwlist@grahamwideman.com Date: Wed, 12 Oct 2005 11:57:15 -0700 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Coregistration?
Nate Parks wrote:
Does AFNI have an automated coregistration tool? I thought you could only do manual coreg in AFNI.
AFNI coregistration program is 3dvolreg.
See docs:
http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dvolreg.html
And if you are having trouble finding which AFNI program does what, you might like my "all afni helps on one page":
http://www.grahamwideman.com/gw/brain/afni/alldocs_afni.htm
Graham _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry all -- my mistake.
I thought our folks here were regularly registering functional to anatomical scans, and I thought it was done with 3dvolreg. Just now checking, apparently not.
And if 3dAnatNudge can't do rotation, not so helpful (though lack of resize should not be a problem).
It would be interesting to see what 3dvolreg would do if the anatomy was resampled to the same grid as that functional scans or vice versa... but starts to look like a research topic.
For Nate: It might be worth posting on the AFNI forum to see what other AFNI-sters position on this topic is... doubtless it's been thought about a lot more than by me!
Graham
Jeff Binder wrote:
The AFNI program 3dvolreg does coregistration only for volumes acquired with the same kind of pulse sequence and consequently the same tissue signal values. Use it for coregistering different EPI volumes to each other or different T1-weighted structural scans to each other.
I think what Nate was asking about was coregistering EPI data to the structural scans. The AFNI program 3dAnatNudge can help with this to some extent. It uses simple iterative translational movements to find the best fit between a "skull-stripped" anatomy volume and an EPI volume. No rotation or resizing is done.
To use this program you remove the skull and other non-brain voxels from the anatomy volume. The AFNI programs 3dIntracranial and a newer program called 3dSkullStrip both do this.
Jeff
Just in case someone hasn't mentioned it yet, try 3dWarpDrive or convert to analyze and use the AIR suite.
Graham is correct. There are past posts about this on the AFNI forum that would be helpful to you.
Good luck. Brian
Hi, When editing the wm, is it better to fill sections (eg., when thickening temporal lobe strands) using a brush with intensity at 255, or 110? I've noticed that if I fill using 110 and run autorecon2-cp with -keepwmedits the fill is basically ignored when the wm is re-segmented. Just wandering why 255 would be better than 110? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
you need to fill the wm with 255 so we know it's an edit.
Bruce On Fri, 14 Oct 2005, Fornito, Alexander wrote:
Hi, When editing the wm, is it better to fill sections (eg., when thickening temporal lobe strands) using a brush with intensity at 255, or 110? I've noticed that if I fill using 110 and run autorecon2-cp with -keepwmedits the fill is basically ignored when the wm is re-segmented. Just wandering why 255 would be better than 110? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
And would placing control points in the filled part work? Or maybe at the base of the strand, before the filled part?
Also, It seems that if I run autorecon2-cp after making pial edits to brain volume, the edits are ignored, and a new brain volume is generated, ie., my edits to the brain volume are no longer there. Does autorecon2-pial have to be run as a separate process, after autorecon2-cp? Thanks again, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
________________________________
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 14/10/2005 9:13 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface edits
you need to fill the wm with 255 so we know it's an edit.
Bruce On Fri, 14 Oct 2005, Fornito, Alexander wrote:
Hi, When editing the wm, is it better to fill sections (eg., when thickening temporal lobe strands) using a brush with intensity at 255, or 110? I've noticed that if I fill using 110 and run autorecon2-cp with -keepwmedits the fill is basically ignored when the wm is re-segmented. Just wandering why 255 would be better than 110? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
not sure about the autorecon questions, but yes, placing control points at the base of a strand can help recover the whole thing, as long as they are placed somewhere where the wm intensity is <110. On Sat, 15 Oct 2005, Fornito, Alexander wrote:
And would placing control points in the filled part work? Or maybe at the base of the strand, before the filled part?
Also, It seems that if I run autorecon2-cp after making pial edits to brain volume, the edits are ignored, and a new brain volume is generated, ie., my edits to the brain volume are no longer there. Does autorecon2-pial have to be run as a separate process, after autorecon2-cp? Thanks again, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 14/10/2005 9:13 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface edits
you need to fill the wm with 255 so we know it's an edit.
Bruce On Fri, 14 Oct 2005, Fornito, Alexander wrote:
Hi, When editing the wm, is it better to fill sections (eg., when thickening temporal lobe strands) using a brush with intensity at 255, or 110? I've noticed that if I fill using 110 and run autorecon2-cp with -keepwmedits the fill is basically ignored when the wm is re-segmented. Just wandering why 255 would be better than 110? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
that should be fine
On Fri, 7 Oct 2005, 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
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Fornito, Alexander -
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Sunaina Fotedar