[Freesurfer] Freesurfer on CentOS 6.
Hi, The recommed platform for Freesurfer is CentOS 4. Can anyone advice on how stable the Freesurfer v5.1.0 will be on CentOS 6 ? We need this information to setup a new server. Thanks in advance. Shrikanth ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer on CentOS 6.
It will work fine on centos 6. N. On Nov 8, 2011, at 7:07 AM, SHRIKANTH KULASHEKHAR contactshr...@yahoo.co.in wrote: Hi, The recommed platform for Freesurfer is CentOS 4. Can anyone advice on how stable the Freesurfer v5.1.0 will be on CentOS 6 ? We need this information to setup a new server. Thanks in advance. Shrikanth ___ 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 information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Interpretation of the curvature analysis
Dear Freesurfer Users! Is it wise to interpret the increased curvature index in neurodegenerative disorders as a more expressed atrophy (which manifests as a flattening)... I am just doubting because I have never worked with curvature analysis previously and its interpretations in different articles look quite controversal... The matter is that in our work the observed increase of the curvature index was found in the majority of the thinned areas... Thank you very much beforehand. --- Regards, Alex Lebedev Stavanger University Hospital ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] surface cnr
Hi Mike, I think mris_ms_surface_CNR lets you use multiple input volumes and computes the Mahalanobis distance, while mri_cnr does the same thing but for each volume independently. I think they both have options for doing linear fitting across the boundary and looking at the slope. Sorry, they are tools we tossed together that aren't well documented. cheers Bruce On Wed, 2 Nov 2011, Michael Harms wrote: Hello, What is the difference between the mris_ms_surface_CNR and mri_cnr functions? (I couldn't find any descriptive info for either). And are either of them useful for identifying datasets with poor gray/white/csf contrast? thanks, -MH ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Resize window using Tcl command
Hi Jeff sorry, I don't know of a way to do this. Bruce On Mon, 7 Nov 2011, Jeff Sadino wrote: Hello, I was wondering if there is a Tcl command to resize the window. I saw this thread, but it would not work on my computer, and I don't see any documentation in the tkmedit tcl scripting guide. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02600.html Thank you, Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Recon-all step estimate
Is there any script that I can use to estimate which step recon-all are in? My idea is to have a progress indicator for recon-all and this script would be very useful. thanks Pedro Paulo Jr ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Recon-all step estimate
the recon-all.cmd file I think gets written to the scripts dir with every command that is run Bruce On Tue, 8 Nov 2011, Pedro Paulo de Magalhães Oliveira Junior wrote: Is there any script that I can use to estimate which step recon-all are in? My idea is to have a progress indicator for recon-all and this script would be very useful. thanks Pedro Paulo Jr ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Recon-all step estimate
Hi Pedro, Here's a script that (I think) will do what you're looking for: http://web.mit.edu/mwaskom/stuff/recon_status I hope it's useful Michael 2011/11/8 Bruce Fischl fis...@nmr.mgh.harvard.edu the recon-all.cmd file I think gets written to the scripts dir with every command that is run Bruce On Tue, 8 Nov 2011, Pedro Paulo de Magalhães Oliveira Junior wrote: Is there any script that I can use to estimate which step recon-all are in? My idea is to have a progress indicator for recon-all and this script would be very useful. thanks Pedro Paulo Jr ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Recon-all step estimate
You can look at the touch files in the touch directory. I've attached a
script that I use called rastat that does this. When I was the main
recon-all programmer, each process would create a touch file when it
completed, but I don't know if newer versions continue to do so. You can
also look at recon-all-status.log
doug
Pedro Paulo de Magalhães Oliveira Junior wrote:
Is there any script that I can use to estimate which step recon-all
are in?
My idea is to have a progress indicator for recon-all and this script
would be very useful.
thanks
Pedro Paulo Jr
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
#!/bin/tcsh -f
# rastat - get current status of recon-all processes
set VERSION = '$Id$';
set sd = ();
set subjectlist = ();
set inputargs = ($argv);
set PrintHelp = 0;
if($#argv == 0) goto usage_exit;
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 $VERSION
exit 0;
endif
goto parse_args;
parse_args_return:
goto check_params;
check_params_return:
foreach subject ($subjectlist)
if(! -e $sd/$subject) then
echo $subject CANNOT FIND
continue;
endif
set ralog = $sd/$subject/scripts/recon-all.log
if(! -e $ralog) then
echo $subject nolog
continue
endif
set d = $sd/$subject/scripts/recon-all.done
if(-e $d) then
set DoneDate = `grep DATE $d | sed 's/DATE //g'`
echo $subject done $DoneDate
continue
endif
set e = $sd/$subject/scripts/recon-all.error
if(-e $e) then
set ErrorDate = `grep DATE $e | sed 's/DATE //g'`
echo $subject error $ErrorDate
continue
endif
set isrs = (IsRunning.lh IsRunning.rh IsRunning.lh+rh)
set IsRunning = 0;
foreach isr0 ($isrs)
set isr = $sd/$subject/scripts/$isr0
if(! -e $isr) continue;
set IsRunning = 1;
set StartDate = `grep DATE $isr | sed 's/DATE //g'`
set Hemis = `grep HEMI $isr | sed 's/HEMI //g' | sed 's/lh rh/lh+rh/'`
set tmp = `ls -lt $sd/$subject/touch/*.touch | head -n 2 | tail -n 1`
#set tmp = `ls -l $subject/scripts/recon-all.env`
#set month = $tmp[6];
#set day = $tmp[7];
#set time = $tmp[8];
set dir = $tmp[9];
set cmd = `basename $dir .touch`
#echo $subject running $month $day $time $cmd
echo $subject running $Hemis $StartDate $cmd
end
if(! $IsRunning) echo $subject notsure
end
exit 0
###
--##
parse_args:
set cmdline = ($argv);
while( $#argv != 0 )
set flag = $argv[1]; shift;
switch($flag)
case -s:
if($#argv 1) goto arg1err;
set subjectlist = ($subjectlist $argv[1]); shift;
while(1 $#argv)
set a = `echo $argv[1] | cut -c 1`
if($a == -) break;
set subjectlist = ($subjectlist $argv[1]); shift;
end
breaksw
case -cwd:
case -pwd:
set sd = `pwd`;
breaksw
case -debug:
set verbose = 1;
set echo = 1;
breaksw
default:
echo ERROR: Flag $flag unrecognized.
echo $cmdline
exit 1
breaksw
endsw
end
goto parse_args_return;
--##
--##
check_params:
if($#subjectlist == 0) then
echo ERROR: need subjects
exit 1;
endif
if($#sd == 0) set sd = $SUBJECTS_DIR;
goto check_params_return;
--##
--##
arg1err:
echo ERROR: flag $flag requires one argument
exit 1
--##
--##
usage_exit:
echo
echo rastat
echo
echo
if(! $PrintHelp) exit 1;
echo $VERSION
cat $0 | awk 'BEGIN{prt=0}{if(prt) print $0; if($1 == BEGINHELP) prt = 1 }'
exit 1;
# Everything below here is printed out as part of help -#
BEGINHELP
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] Fwd: A question about recon-all
Dear Freesurfer Group I have found a problem in running my subjects. With recon-all -autorecon1 -autorecon2 -autorecon3 -subjid N? I ran several subjects after making corrections, but suddenly I received error message as following, and I can not run rest of the subjects. It is saying the subject is already running but I am running the subject elsewhere. Can you please help me to face this issue. Thanks a lot in advance. INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /Users/christine/CorrectedOnes Actual FREESURFER_HOME /Applications/freesurfer -rw-r--r-- 1 christine staff 469592 Nov 4 12:46 /Users/christine/CorrectedOnes/N3237c/scripts/recon-all.log Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 ERROR: it appears that recon-all is already running for N3237c based on the presence of /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh. It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type: rm /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh and re-run. Or you can add -no-isrunning to the recon-all command-line. The contents of this file are: -- -- SUBJECT N3237c HEMIlh rh DATE Wed Nov 2 12:03:39 EDT 2011 USER christine HOST administrators-mac-pro.local PROCESSID 40999 PROCESSOR i386 OS Darwin Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ -- Best Regards --- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * * -- Best Regards --- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * * ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] norm.mgz
Hi, I had 2 bad blocks in freesurfer/subject/mri/norm.mgz on my disk drive. I had to delete mri/norm.mgz. Is there any way that I can just creat norm.mgz? or do I need to do recon-all? thank you. YUMI ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: A question about recon-all
Hi Nooshin, you can jsut add -no-isrunning to the command line if you are sure the process has finished. This happens when it was killed in a strange way (i.e. if you hit ctrl-c during processing) cheers Bruce On Tue, 8 Nov 2011, nooshin n.zade wrote: Dear Freesurfer Group I have found a problem in running my subjects. With recon-all -autorecon1 -autorecon2 -autorecon3 -subjid N? I ran several subjects after making corrections, but suddenly I received error message as following, and I can not run rest of the subjects. It is saying the subject is already running but I am running the subject elsewhere. Can you please help me to face this issue. Thanks a lot in advance. INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /Users/christine/CorrectedOnes Actual FREESURFER_HOME /Applications/freesurfer -rw-r--r-- 1 christine staff 469592 Nov 4 12:46 /Users/christine/CorrectedOnes/N3237c/scripts/recon-all.log Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 ERROR: it appears that recon-all is already running for N3237c based on the presence of /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh. It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type: rm /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh and re-run. Or you can add -no-isrunning to the recon-all command-line. The contents of this file are: -- -- SUBJECT N3237c HEMI lh rh DATE Wed Nov 2 12:03:39 EDT 2011 USER christine HOST administrators-mac-pro.local PROCESSID 40999 PROCESSOR i386 OS Darwin Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ -- Best Regards --- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami -- Best Regards --- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] norm.mgz
Hi Yumi, just rerun recon-all with the -canorm flag on that subject Best, Martin On Tue, 2011-11-08 at 13:18 -0500, YUMI MAEDA wrote: Hi, I had 2 bad blocks in freesurfer/subject/mri/norm.mgz on my disk drive. I had to delete mri/norm.mgz. Is there any way that I can just creat norm.mgz? or do I need to do recon-all? thank you. YUMI ___ 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 information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] norm.mgz
Hi Yumi the mri_ca_normalize command creates the norm.mgz. You should be able to find it either in the scripts/recon-all.cmd or scripts/recon-all.log cheers Bruce On Tue, 8 Nov 2011, YUMI MAEDA wrote: Hi, I had 2 bad blocks in freesurfer/subject/mri/norm.mgz on my disk drive. I had to delete mri/norm.mgz. Is there any way that I can just creat norm.mgz? or do I need to do recon-all? thank you. YUMI ___ 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 information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Upgraded Freesurfer: old version no longer working + recon-all error in 5.1
Hello, I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 with no issues. I recently installed FreeSurfer 5.1 to a separate directory on the same laptop to analyze a new dataset and I am now having various issues with both FreeSurfer versions. 1. For Version 4.5, I path the freesurfer directories as follows (identical to before installing new program): setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir source $FREESURFER_HOME/SetUpFreeSurfer.csh - freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir MNI_DIR /Applications/freesurfer/mni The issue is that now various commands are no longer found in version 4.5. For example when typing tkmedit, tksurfer or qdec, I get the following type of error: tkmedit.bin: Command not found. Is it possible that, although I installed version 5.1 in a separate directory, that some files were deleted or moved in version 4.5? Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license? It is confusing since some commands appear to function, such as mri_convert and recon-all, but anything involving a GUI seems not to function. 2. For version 5.1, I believe the program is successfully installed and pathed. I have been able to use it to convert files to mgz, tkmedit and tksurfer work fine, however, I get the same error each time I run recon-all with each participant (one of which was previously successfully processed using version 4.5). The recon-all error occurs early during motion correction of the 2 structural runs: Resolution: 0 S( 512 512 352 ) T( 512 512 352 ) Iteration(f): 1 (subsample 200) mri_robust_template(3271) malloc: *** mmap(size=1048576) failed (error code=12)*** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(512, 512, 352): could not allocate 1048576 bytes for 258th slice Cannot allocate memory Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all -s SS002 exited with ERRORS at Fri Nov 4 10:04:46 EDT 2011 Any ideas on what might be causing this error? I have 4 GB memory. thanks, Jennifer Addicks University of Ottawa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: A question about recon-all
Or you can delete the IsRunning file in the scripts directory (make sure it's not actually running!). doug Bruce Fischl wrote: Hi Nooshin, you can jsut add -no-isrunning to the command line if you are sure the process has finished. This happens when it was killed in a strange way (i.e. if you hit ctrl-c during processing) cheers Bruce On Tue, 8 Nov 2011, nooshin n.zade wrote: Dear Freesurfer Group I have found a problem in running my subjects. With recon-all -autorecon1 -autorecon2 -autorecon3 -subjid N? I ran several subjects after making corrections, but suddenly I received error message as following, and I can not run rest of the subjects. It is saying the subject is already running but I am running the subject elsewhere. Can you please help me to face this issue. Thanks a lot in advance. INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /Users/christine/CorrectedOnes Actual FREESURFER_HOME /Applications/freesurfer -rw-r--r-- 1 christine staff 469592 Nov 4 12:46 /Users/christine/CorrectedOnes/N3237c/scripts/recon-all.log Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 ERROR: it appears that recon-all is already running for N3237c based on the presence of /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh. It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type: rm /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh and re-run. Or you can add -no-isrunning to the recon-all command-line. The contents of this file are: -- -- SUBJECT N3237c HEMIlh rh DATE Wed Nov 2 12:03:39 EDT 2011 USER christine HOST administrators-mac-pro.local PROCESSID 40999 PROCESSOR i386 OS Darwin Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ -- Best Regards --- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami -- Best Regards --- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Upgraded Freesurfer: old version no longer working + recon-all error in 5.1
Hi Jennifer for question 2. You run out of memory. How many within session inputs are you trying to motion correct? You can a) try downsample your hi-res images before processing b) try to only select a single input to recon-all instead of averaging inputs. Best, Martin On Tue, 2011-11-08 at 13:35 -0500, Jennifer Addicks wrote: Hello, I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 with no issues. I recently installed FreeSurfer 5.1 to a separate directory on the same laptop to analyze a new dataset and I am now having various issues with both FreeSurfer versions. 1. For Version 4.5, I path the freesurfer directories as follows (identical to before installing new program): setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir source $FREESURFER_HOME/SetUpFreeSurfer.csh - freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir MNI_DIR /Applications/freesurfer/mni The issue is that now various commands are no longer found in version 4.5. For example when typing tkmedit, tksurfer or qdec, I get the following type of error: tkmedit.bin: Command not found. Is it possible that, although I installed version 5.1 in a separate directory, that some files were deleted or moved in version 4.5? Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license? It is confusing since some commands appear to function, such as mri_convert and recon-all, but anything involving a GUI seems not to function. 2. For version 5.1, I believe the program is successfully installed and pathed. I have been able to use it to convert files to mgz, tkmedit and tksurfer work fine, however, I get the same error each time I run recon-all with each participant (one of which was previously successfully processed using version 4.5). The recon-all error occurs early during motion correction of the 2 structural runs: Resolution: 0 S( 512 512 352 ) T( 512 512 352 ) Iteration(f): 1 (subsample 200) mri_robust_template(3271) malloc: *** mmap(size=1048576) failed (error code=12)*** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(512, 512, 352): could not allocate 1048576 bytes for 258th slice Cannot allocate memory Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all -s SS002 exited with ERRORS at Fri Nov 4 10:04:46 EDT 2011 Any ideas on what might be causing this error? I have 4 GB memory. thanks, Jennifer Addicks University of Ottawa ___ 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 information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Upgraded Freesurfer: old version no longer working + recon-all error in 5.1
I see you have only two inputs. 4GB should be enough. Are you running a lot of other stuff that takes up memory? -Martin On Tue, 2011-11-08 at 13:35 -0500, Jennifer Addicks wrote: Hello, I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 with no issues. I recently installed FreeSurfer 5.1 to a separate directory on the same laptop to analyze a new dataset and I am now having various issues with both FreeSurfer versions. 1. For Version 4.5, I path the freesurfer directories as follows (identical to before installing new program): setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir source $FREESURFER_HOME/SetUpFreeSurfer.csh - freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir MNI_DIR /Applications/freesurfer/mni The issue is that now various commands are no longer found in version 4.5. For example when typing tkmedit, tksurfer or qdec, I get the following type of error: tkmedit.bin: Command not found. Is it possible that, although I installed version 5.1 in a separate directory, that some files were deleted or moved in version 4.5? Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license? It is confusing since some commands appear to function, such as mri_convert and recon-all, but anything involving a GUI seems not to function. 2. For version 5.1, I believe the program is successfully installed and pathed. I have been able to use it to convert files to mgz, tkmedit and tksurfer work fine, however, I get the same error each time I run recon-all with each participant (one of which was previously successfully processed using version 4.5). The recon-all error occurs early during motion correction of the 2 structural runs: Resolution: 0 S( 512 512 352 ) T( 512 512 352 ) Iteration(f): 1 (subsample 200) mri_robust_template(3271) malloc: *** mmap(size=1048576) failed (error code=12)*** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(512, 512, 352): could not allocate 1048576 bytes for 258th slice Cannot allocate memory Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all -s SS002 exited with ERRORS at Fri Nov 4 10:04:46 EDT 2011 Any ideas on what might be causing this error? I have 4 GB memory. thanks, Jennifer Addicks University of Ottawa ___ 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 information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Visualization of FreeSurfer-defined ROI
You can run mri_annotation2label to break the annotation up into smaller labels, then display a single label in tksurfer (you can load it from the GUI or on the cmd line with -label). doug Simmons, Andy wrote: Dear Doug, What would the equivalent process for a surface rather than a volume ? Best wishes, Andy SImmons Date: Fri, 04 Nov 2011 17:30:47 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Visulaization of FreeSurfer-defined ROI To: Jade jadein...@gmail.com mailto:jadein...@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 4eb45987.2040...@nmr.mgh.harvard.edu mailto:4eb45987.2040...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Try running mri_binarize with the --match option. The match value should be the id number for your ROI as defined in $FREESURFER_HOME/FreeSurferColorLUT.txt (eg, left hippo is 17). You can then load this as a segmentation or as an overlay in tkmedit. doug Jade wrote: Hello Freesurfer experts, I am a beginner in using Freesurfer. I want to make a figure illustrates a specific area of ROIs (e.g., lh. hippocampus). How can I visulaize the Freesurfer definded ROIs? Thanks in advance! Dr Andy Simmons Reader in Neuroimaging Consultant Clinical Scientist Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre Institute of Psychiatry, Box P089 Kings College London De Crespigny Park London, SE5 8AF, UK Email - andy.simm...@kcl.ac.uk Webpage - http://www.iop.kcl.ac.uk/staff/profile/default.aspx?go=10338 Directions - http://www.iop.kcl.ac.uk/virtual/?path=/about/how-to-find-the-institute-of-psychiatry/ ResearcherID - http://www.researcherid.com/rid/B-8848-2008 Fax +44 (0)203 228 2116 Description: Description: Untitled 1:Users:vincent:Desktop:Unknown.jpeg http://msc-neuroimaging.com/ ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Upgraded Freesurfer: old version no longer working + recon-all error in 5.1
Sorry for incremental updates: c) you can pass the -flirt-motioncor flag to recon all to revert to the old way (using flirt) If your scans are decent quality I would recommend b) as it is unclear if averaging actually helps. -Martin On Tue, 2011-11-08 at 13:45 -0500, Martin Reuter wrote: Hi Jennifer for question 2. You run out of memory. How many within session inputs are you trying to motion correct? You can a) try downsample your hi-res images before processing b) try to only select a single input to recon-all instead of averaging inputs. Best, Martin On Tue, 2011-11-08 at 13:35 -0500, Jennifer Addicks wrote: Hello, I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 with no issues. I recently installed FreeSurfer 5.1 to a separate directory on the same laptop to analyze a new dataset and I am now having various issues with both FreeSurfer versions. 1. For Version 4.5, I path the freesurfer directories as follows (identical to before installing new program): setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir source $FREESURFER_HOME/SetUpFreeSurfer.csh - freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir MNI_DIR /Applications/freesurfer/mni The issue is that now various commands are no longer found in version 4.5. For example when typing tkmedit, tksurfer or qdec, I get the following type of error: tkmedit.bin: Command not found. Is it possible that, although I installed version 5.1 in a separate directory, that some files were deleted or moved in version 4.5? Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license? It is confusing since some commands appear to function, such as mri_convert and recon-all, but anything involving a GUI seems not to function. 2. For version 5.1, I believe the program is successfully installed and pathed. I have been able to use it to convert files to mgz, tkmedit and tksurfer work fine, however, I get the same error each time I run recon-all with each participant (one of which was previously successfully processed using version 4.5). The recon-all error occurs early during motion correction of the 2 structural runs: Resolution: 0 S( 512 512 352 ) T( 512 512 352 ) Iteration(f): 1 (subsample 200) mri_robust_template(3271) malloc: *** mmap(size=1048576) failed (error code=12)*** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(512, 512, 352): could not allocate 1048576 bytes for 258th slice Cannot allocate memory Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all -s SS002 exited with ERRORS at Fri Nov 4 10:04:46 EDT 2011 Any ideas on what might be causing this error? I have 4 GB memory. thanks, Jennifer Addicks University of Ottawa ___ 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 information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Visualization of FreeSurfer-defined ROI
Dear Doug, Thanks very much for this - that worked perfectly for one region. How would I display a series of labels simultaneously, for example superiorfrontal, superiorparietal and superiortemporal ? Best wishes, Andy -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: 08 November 2011 18:52 To: Simmons, Andy Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Visualization of FreeSurfer-defined ROI You can run mri_annotation2label to break the annotation up into smaller labels, then display a single label in tksurfer (you can load it from the GUI or on the cmd line with -label). doug Simmons, Andy wrote: Dear Doug, What would the equivalent process for a surface rather than a volume ? Best wishes, Andy SImmons Date: Fri, 04 Nov 2011 17:30:47 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Visulaization of FreeSurfer-defined ROI To: Jade jadein...@gmail.com mailto:jadein...@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 4eb45987.2040...@nmr.mgh.harvard.edu mailto:4eb45987.2040...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Try running mri_binarize with the --match option. The match value should be the id number for your ROI as defined in $FREESURFER_HOME/FreeSurferColorLUT.txt (eg, left hippo is 17). You can then load this as a segmentation or as an overlay in tkmedit. doug Jade wrote: Hello Freesurfer experts, I am a beginner in using Freesurfer. I want to make a figure illustrates a specific area of ROIs (e.g., lh. hippocampus). How can I visulaize the Freesurfer definded ROIs? Thanks in advance! Dr Andy Simmons Reader in Neuroimaging Consultant Clinical Scientist Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre Institute of Psychiatry, Box P089 Kings College London De Crespigny Park London, SE5 8AF, UK Email - andy.simm...@kcl.ac.uk Webpage - http://www.iop.kcl.ac.uk/staff/profile/default.aspx?go=10338 Directions - http://www.iop.kcl.ac.uk/virtual/?path=/about/how-to-find-the-institut e-of-psychiatry/ ResearcherID - http://www.researcherid.com/rid/B-8848-2008 Fax +44 (0)203 228 2116 Description: Description: Untitled 1:Users:vincent:Desktop:Unknown.jpeg http://msc-neuroimaging.com/ -- -- ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Compilation warnings as errors
I tried your suggestion for compiling the dev release and it worked. Now, I am getting compilation errors. It seems that the vnl include directory is not found (althought it exists in my system under /usr/include/vxl/core). I tried to symlink it under /usr/include but then I encounter other problems. Any suggestions? Maybe an older or newer version of vxl library? My system has vxl-1.13 installed. Regards, Panagiotis Foteinos On Mon, Nov 7, 2011 at 4:26 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: try this: cd dev cp `which libtool` . this will overwrite the libtool created by configure with the one on the system. the newest configure.in in the dev build should do this automatically. n. On Mon, 2011-11-07 at 15:59 -0500, Panagiotis Foteinos wrote: Hello list. So, while making the build directory, I got the following output: * Making all in gpu_utils make[2]: Entering directory `/home/pfoteino/local/bin/freesurfer-bin/gpu_utils' /bin/bash ../libtool --tag=CXX --mode=link g++ -rdynamic -ldl -L/usr/lib64 -L/usr/X11R6/lib64 -o cudadetect cudadetect-cudadetect.o -lz -lm -lcrypt -ldl -lpthread -lnetcdf -lvolume_io -lminc -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib ../libtool: line 454: CDPATH: command not found ../libtool: line 1132: func_opt_split: command not found libtool: Version mismatch error. This is libtool 2.2.6b Debian-2.2.6b-2ubuntu1, but the libtool: definition of this LT_INIT comes from an older release. libtool: You should recreate aclocal.m4 with macros from libtool 2.2.6b Debian-2.2.6b-2ubuntu1 libtool: and run autoconf again. make[2]: *** [cudadetect] Error 63 make[2]: Leaving directory `/home/pfoteino/local/bin/freesurfer-bin/gpu_utils' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/pfoteino/local/bin/freesurfer-bin' make: *** [all] Error 2 * Any suggestions? I have only one version of libtool installed in my machine. Regards, Panagiotis On Mon, Nov 7, 2011 at 12:36 PM, Panagiotis Foteinos pafot...@gmail.com wrote: Thank you all for the replies. I am using Ubuntu (kernel-2.6.32-35) and gcc-4.4.3. I downloaded the stable version. So, I guess it is fine to ignore the warnings. Best Regards, Panagiotis Foteinos On Mon, Nov 7, 2011 at 12:24 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: which compiler version and OS platform are you using? and which checkout of the 'dev' trunk? dev or stable? currently the 'dev' trunk should build without warnings under gcc v4.4.5 (on Centos 6, kernel 2.6.32-131). but you can deactivate the -Werror switch to get things built on your system. n. On Mon, 2011-11-07 at 11:16 -0500, Panagiotis Foteinos wrote: Hello list. I am compiling the source code and I get some warnings as errors. Is there a good reason that the switch -Werror is activated, or I can safely deactivate it? Could I assume that the warnings I get are harmless? Best Regards, Panagiotis Foteinos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Visualization of FreeSurfer-defined ROI
You can merge different labels into one big label with mri_mergelabels. If you want an annotation with those labels, you can use mris_label2annot to recombine your favorites back into a annotation. doug Simmons, Andy wrote: Dear Doug, Thanks very much for this - that worked perfectly for one region. How would I display a series of labels simultaneously, for example superiorfrontal, superiorparietal and superiortemporal ? Best wishes, Andy -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: 08 November 2011 18:52 To: Simmons, Andy Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Visualization of FreeSurfer-defined ROI You can run mri_annotation2label to break the annotation up into smaller labels, then display a single label in tksurfer (you can load it from the GUI or on the cmd line with -label). doug Simmons, Andy wrote: Dear Doug, What would the equivalent process for a surface rather than a volume ? Best wishes, Andy SImmons Date: Fri, 04 Nov 2011 17:30:47 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Visulaization of FreeSurfer-defined ROI To: Jade jadein...@gmail.com mailto:jadein...@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 4eb45987.2040...@nmr.mgh.harvard.edu mailto:4eb45987.2040...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Try running mri_binarize with the --match option. The match value should be the id number for your ROI as defined in $FREESURFER_HOME/FreeSurferColorLUT.txt (eg, left hippo is 17). You can then load this as a segmentation or as an overlay in tkmedit. doug Jade wrote: Hello Freesurfer experts, I am a beginner in using Freesurfer. I want to make a figure illustrates a specific area of ROIs (e.g., lh. hippocampus). How can I visulaize the Freesurfer definded ROIs? Thanks in advance! Dr Andy Simmons Reader in Neuroimaging Consultant Clinical Scientist Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre Institute of Psychiatry, Box P089 Kings College London De Crespigny Park London, SE5 8AF, UK Email - andy.simm...@kcl.ac.uk Webpage - http://www.iop.kcl.ac.uk/staff/profile/default.aspx?go=10338 Directions - http://www.iop.kcl.ac.uk/virtual/?path=/about/how-to-find-the-institut e-of-psychiatry/ ResearcherID - http://www.researcherid.com/rid/B-8848-2008 Fax +44 (0)203 228 2116 Description: Description: Untitled 1:Users:vincent:Desktop:Unknown.jpeg http://msc-neuroimaging.com/ -- -- ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Compilation warnings as errors
I forgot to attach the error log in the previous email. My sincere apologies. So here it is: In file included from ../../../src/freesurfer-src/dev/utils/cpputils.cpp:42: ../../../src/freesurfer-src/dev/include/MRISOBBTree.h:54:28: error: vnl/vnl_matrix.h: No such file or directory ../../../src/freesurfer-src/dev/include/MRISOBBTree.h:55:28: error: vnl/vnl_vector.h: No such file or directory ../../../src/freesurfer-src/dev/include/MRISOBBTree.h:56:48: error: vnl/algo/vnl_symmetric_eigensystem.h: No such file or directory In file included from ../../../src/freesurfer-src/dev/include/MRISOBBTree.h:57, from ../../../src/freesurfer-src/dev/utils/cpputils.cpp:42: ../../../src/freesurfer-src/dev/include/utilsmath.h:257: error: variable or field ‘GetSortedEigenVectors’ declared void ../../../src/freesurfer-src/dev/include/utilsmath.h:257: error: ‘vnl_symmetric_eigensystem’ was not declared in this scope ../../../src/freesurfer-src/dev/include/utilsmath.h:257: error: expected primary-expression before ‘double’ ../../../src/freesurfer-src/dev/include/utilsmath.h:258: error: expected primary-expression before ‘double’ ../../../src/freesurfer-src/dev/include/utilsmath.h:259: error: expected primary-expression before ‘double’ ../../../src/freesurfer-src/dev/include/utilsmath.h:260: error: expected primary-expression before ‘double’ ../../../src/freesurfer-src/dev/include/utilsmath.h:261: error: expected primary-expression before ‘double’ ../../../src/freesurfer-src/dev/utils/cpputils.cpp:223: error: expected ‘}’ at end of input make[3]: *** [cpputils.o] Error 1 make[3]: Leaving directory `/home/pfoteino/local/bin/freesurfer-bin/utils' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/pfoteino/local/bin/freesurfer-bin/utils' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/pfoteino/local/bin/freesurfer-bin' make: *** [all] Error 2 Regards, Panagiotis Foteinos On Tue, Nov 8, 2011 at 2:06 PM, Panagiotis Foteinos pafot...@gmail.com wrote: I tried your suggestion for compiling the dev release and it worked. Now, I am getting compilation errors. It seems that the vnl include directory is not found (althought it exists in my system under /usr/include/vxl/core). I tried to symlink it under /usr/include but then I encounter other problems. Any suggestions? Maybe an older or newer version of vxl library? My system has vxl-1.13 installed. Regards, Panagiotis Foteinos On Mon, Nov 7, 2011 at 4:26 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: try this: cd dev cp `which libtool` . this will overwrite the libtool created by configure with the one on the system. the newest configure.in in the dev build should do this automatically. n. On Mon, 2011-11-07 at 15:59 -0500, Panagiotis Foteinos wrote: Hello list. So, while making the build directory, I got the following output: * Making all in gpu_utils make[2]: Entering directory `/home/pfoteino/local/bin/freesurfer-bin/gpu_utils' /bin/bash ../libtool --tag=CXX --mode=link g++ -rdynamic -ldl -L/usr/lib64 -L/usr/X11R6/lib64 -o cudadetect cudadetect-cudadetect.o -lz -lm -lcrypt -ldl -lpthread -lnetcdf -lvolume_io -lminc -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib ../libtool: line 454: CDPATH: command not found ../libtool: line 1132: func_opt_split: command not found libtool: Version mismatch error. This is libtool 2.2.6b Debian-2.2.6b-2ubuntu1, but the libtool: definition of this LT_INIT comes from an older release. libtool: You should recreate aclocal.m4 with macros from libtool 2.2.6b Debian-2.2.6b-2ubuntu1 libtool: and run autoconf again. make[2]: *** [cudadetect] Error 63 make[2]: Leaving directory `/home/pfoteino/local/bin/freesurfer-bin/gpu_utils' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/pfoteino/local/bin/freesurfer-bin' make: *** [all] Error 2 * Any suggestions? I have only one version of libtool installed in my machine. Regards, Panagiotis On Mon, Nov 7, 2011 at 12:36 PM, Panagiotis Foteinos pafot...@gmail.com wrote: Thank you all for the replies. I am using Ubuntu (kernel-2.6.32-35) and gcc-4.4.3. I downloaded the stable version. So, I guess it is fine to ignore the warnings. Best Regards, Panagiotis Foteinos On Mon, Nov 7, 2011 at 12:24 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: which compiler version and OS platform are you using? and which checkout of the 'dev' trunk? dev or stable? currently the 'dev' trunk should build without warnings under gcc v4.4.5 (on Centos 6, kernel 2.6.32-131). but you can deactivate the
Re: [Freesurfer] selxavg3 out of memory
Hi, I had the same problem with the matlab 32-bit version. Try to install the (recent) matlab 64-bit on your Mac. cheers, Erhan 2011/11/8 Douglas N Greve gr...@nmr.mgh.harvard.edu: It is only trying to allocate 1.3GB, so it might be that matlab does not have enough memory when it runs. Is there a way to give matlab more memory? If not, you can re-make your analysis with -acfbins 10. The default is 30, so this will reduce the needed memory by a factor of 3. I don't think it will affect your results much. doug Po-Jang (Brown) Hsieh wrote: Dear Doug, I saw your reply to this question a while ago. I'm using a mac pro with 16G memory but having the same problem. Do you know if this is a matlab memory issue (matlab R2009a) or an overall memory issue of the machine? I'd appreciate if you can give me some helps. (I have 12 runs, each run has 200 TRs and 20 events, TR=2s) Thanks very much! Brown ps. Here are the commands and error messages: mkanalysis-sess -analysis $ANALYSIS -TR 2 -paradigm $PARAFILE -event-related -funcstem $FUNCSTEM -nconditions 9 -mcextreg -runlistfile $RLF -fsd bold -fir 10 30 -native selxavg3-sess -s $SUBJECTID -df sessdir -analysis $ANALYSIS -no-con-ok Whitening Computing whitening matrices MATLAB(19078,0xb0987000) malloc: *** mmap(size=138240) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug ??? Out of memory. Type HELP MEMORY for your options. Error in == fast_selxavg3 at 603 Sinv = zeros(ntptot,ntptot,flac0.acfbins); pure virtual method calledOpening log file: /var/root/java.log.19078 Abort -- ERROR: fast_selxavg3() failed\n I think you might need a bigger computer. A run of that data set will require almost 1G, and there are places in the code where several data structures of the same size will need to exist simultaneously, so you can easily use 2 or 3 or 4 G to process a single run. In theory you could divide them up into smaller bits as long as you handle the stimulus schedule files properly. doug Schadwinkel, Stefan wrote: /Hi, // //as I tried to show in the posting, I tried it on 3 Machines: // //1) Linux, 1 GB memory: out of memory during OLS Residual Pass, then Java crashes //2) Linux, 2 GB memory: out of memory during Whitening //3) Mac (Mac OS X 10.5), 4 GB memory: as well: out of memory during Whitening // //Thanks a lot best regards, // //Stefan Schadwinkel / -- Po-Jang (Brown) Hsieh Neuroscience and Behavioral Disorders Program Duke-NUS Graduate Medical School 8 College Road, Singapore 169857 -- Lab website: Brain Consciousness Lab https://sites.google.com/site/brainconsciousnesslab/ ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Dipl. Psych. Erhan Genc Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt am Main -GERMANY- phone: +49 (69) 96769-471 fax: +49 (69) 96769-327 e-mail: g...@mpih-frankfurt.mpg.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Compilation warnings as errors
see ./configure --help for flags on how to point the build at your libs. also see: https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide note that typically we recommend building the 3rd party packages from scratch, as its hard to know whats really installed on your system already (see the README build notes). n. On Tue, 2011-11-08 at 14:14 -0500, Panagiotis Foteinos wrote: I forgot to attach the error log in the previous email. My sincere apologies. So here it is: In file included from ../../../src/freesurfer-src/dev/utils/cpputils.cpp:42: ../../../src/freesurfer-src/dev/include/MRISOBBTree.h:54:28: error: vnl/vnl_matrix.h: No such file or directory ../../../src/freesurfer-src/dev/include/MRISOBBTree.h:55:28: error: vnl/vnl_vector.h: No such file or directory ../../../src/freesurfer-src/dev/include/MRISOBBTree.h:56:48: error: vnl/algo/vnl_symmetric_eigensystem.h: No such file or directory In file included from ../../../src/freesurfer-src/dev/include/MRISOBBTree.h:57, from ../../../src/freesurfer-src/dev/utils/cpputils.cpp:42: ../../../src/freesurfer-src/dev/include/utilsmath.h:257: error: variable or field ‘GetSortedEigenVectors’ declared void ../../../src/freesurfer-src/dev/include/utilsmath.h:257: error: ‘vnl_symmetric_eigensystem’ was not declared in this scope ../../../src/freesurfer-src/dev/include/utilsmath.h:257: error: expected primary-expression before ‘double’ ../../../src/freesurfer-src/dev/include/utilsmath.h:258: error: expected primary-expression before ‘double’ ../../../src/freesurfer-src/dev/include/utilsmath.h:259: error: expected primary-expression before ‘double’ ../../../src/freesurfer-src/dev/include/utilsmath.h:260: error: expected primary-expression before ‘double’ ../../../src/freesurfer-src/dev/include/utilsmath.h:261: error: expected primary-expression before ‘double’ ../../../src/freesurfer-src/dev/utils/cpputils.cpp:223: error: expected ‘}’ at end of input make[3]: *** [cpputils.o] Error 1 make[3]: Leaving directory `/home/pfoteino/local/bin/freesurfer-bin/utils' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/pfoteino/local/bin/freesurfer-bin/utils' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/pfoteino/local/bin/freesurfer-bin' make: *** [all] Error 2 Regards, Panagiotis Foteinos On Tue, Nov 8, 2011 at 2:06 PM, Panagiotis Foteinos pafot...@gmail.com wrote: I tried your suggestion for compiling the dev release and it worked. Now, I am getting compilation errors. It seems that the vnl include directory is not found (althought it exists in my system under /usr/include/vxl/core). I tried to symlink it under /usr/include but then I encounter other problems. Any suggestions? Maybe an older or newer version of vxl library? My system has vxl-1.13 installed. Regards, Panagiotis Foteinos On Mon, Nov 7, 2011 at 4:26 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: try this: cd dev cp `which libtool` . this will overwrite the libtool created by configure with the one on the system. the newest configure.in in the dev build should do this automatically. n. On Mon, 2011-11-07 at 15:59 -0500, Panagiotis Foteinos wrote: Hello list. So, while making the build directory, I got the following output: * Making all in gpu_utils make[2]: Entering directory `/home/pfoteino/local/bin/freesurfer-bin/gpu_utils' /bin/bash ../libtool --tag=CXX --mode=link g++ -rdynamic -ldl -L/usr/lib64 -L/usr/X11R6/lib64 -o cudadetect cudadetect-cudadetect.o -lz -lm -lcrypt -ldl -lpthread -lnetcdf -lvolume_io -lminc -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib ../libtool: line 454: CDPATH: command not found ../libtool: line 1132: func_opt_split: command not found libtool: Version mismatch error. This is libtool 2.2.6b Debian-2.2.6b-2ubuntu1, but the libtool: definition of this LT_INIT comes from an older release. libtool: You should recreate aclocal.m4 with macros from libtool 2.2.6b Debian-2.2.6b-2ubuntu1 libtool: and run autoconf again. make[2]: *** [cudadetect] Error 63 make[2]: Leaving directory `/home/pfoteino/local/bin/freesurfer-bin/gpu_utils' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/pfoteino/local/bin/freesurfer-bin' make: *** [all] Error 2 * Any suggestions? I have only one version of libtool installed in my machine. Regards, Panagiotis On Mon, Nov 7, 2011 at 12:36 PM, Panagiotis Foteinos pafot...@gmail.com wrote: Thank you all for the replies. I am using
[Freesurfer] Loading Data Table
Dear Freesurfer experts, I created a data table with 25 subjects, 3 discrete and 6 continuous factors. Then I tried to load my data table in qdec. However, an error loading the data table occured. I received an automatic notice generated at the end of the terminal as following, This line (my last subject and his data) did not appear to end with a newline How can I fix this problem and visualize my results in qdec? . Thanks in advance! Dusan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Loading Data Table
open the table in a text editor and add a line at the end of the file. n. On Tue, 2011-11-08 at 15:11 -0800, Dusan Hirjak wrote: Dear Freesurfer experts, I created a data table with 25 subjects, 3 discrete and 6 continuous factors. Then I tried to load my data table in qdec. However, an error loading the data table occured. I received an automatic notice generated at the end of the terminal as following, This line (my last subject and his data) did not appear to end with a newline How can I fix this problem and visualize my results in qdec? . Thanks in advance! Dusan ___ 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 information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] problem with skullstrip- shoulders and neck remaining
Hi JuliaDoes the stuff left around mess anything up? You are probably fine running it that wayBruceOn Nov 8, 2011, at 9:30 PM, Julia Hill julia.h...@neura.edu.au wrote:Hi there,I am having difficulties with one of my images. On first inspection, freesurfer had performed a bad skull strip, leaving the base of the skull plus what looked to be the shoulders and neck. I decreased the watershed to 5, and the shoulders/neck still appeared, so i decreased to 2 and now sections of the brain have disappeared (see attached), do you know how i can fix this?Many thanks, Julia Hill Research AssistantSchool of PsychiatryUniversity of New South Wales Previously Prince of Wales Medical Research Institute www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 AustraliaT +61 2 9399 1268 badskullstrip1.tiffbadskullstrip2.tiff___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
