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Re: [Freesurfer] SUBJECTS_DIR not defined in environment
by Matthew Goldfinger 30 Jul '12

30 Jul '12

Ok the main email is CC'd. Below is what I did and the output I received. The goal is to get a brain volume, Subdural space and/or a CSF volume to estimate how much room for displacement/deformation the brain has. Thanks in advance for your help. Matthews-MacBook-Pro-2:~] matthew% printenv SUBJECTS_DIR /Applications/freesurfer/subjects [Matthews-MacBook-Pro-2:~] matthew% sudo mri_segstats --seg /Applications/freesurfer/subjects/bert/mri/aseg.mgz --sum /Applications/freesurfer/subjects/bert/stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --subject bert --brainmask mri/brainmask.mgz --brain-vol-from-seg $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg /Applications/freesurfer/subjects/bert/mri/aseg.mgz --sum /Applications/freesurfer/subjects/bert/stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --subject bert --brainmask mri/brainmask.mgz --brain-vol-from-seg sysname Darwin hostname Matthews-MacBook-Pro-2.local machine x86_64 user root ERROR: SUBJECTS_DIR not defined in environment On Mon, Jul 30, 2012 at 10:38 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Matthew > Could you cc the list so others can answer? Can you also send us the > screen output showing exactly what you did? > Thanks > Bruce > > > > On Jul 30, 2012, at 8:19 PM, Matthew Goldfinger <mattgoldfinger(a)gmail.com> > wrote: > > Bruce, > When I execute printenv it gives me the correct path name > (/Applications/freesurfer/subjects). Upon original set up I automatically > sourced to freesurfersetup.csh as was described in the setup instructions. > How should I source to have Freesurfer commands available without running > into this problem? > > Matthew S. Goldfinger > > > > On Mon, Jul 30, 2012 at 8:02 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> Hi Matthew >> >> >> what shell are you using? If you type >> >> printenv SUBJECTS_DIR >> >> right before calling mri_segstats, what does it return? And when do you >> get that output? Are you sourcing the FreeSurferEnv.csh file? Don't execute >> it as otherwise it pushes a new shell, sets all that stuff, then pops out >> of it erasing all the stuff it set >> >> cheers >> Bruce >> >> >> >> On Mon, 30 Jul 2012, Matthew Goldfinger wrote: >> >> Dear Freesurfers, >>> Forgive me for asking about what appears to be a very simple issue >>> but I am stumped. I have defined my SUBJECTS_DIR as evidenced by this >>> output. >>> ----- freesurfer-Darwin-leopard-**i686-stable-pub-v5.1.0 -------- >>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>> FREESURFER_HOME /Applications/freesurfer >>> FSFAST_HOME /Applications/freesurfer/**fsfast >>> FSF_OUTPUT_FORMAT nii.gz >>> SUBJECTS_DIR /Applications/freesurfer/**subjects >>> MNI_DIR /Applications/freesurfer/mni >>> >>> But upon trying to execute the following: >>> mri_segstats --seg /Applications/freesurfer/**subjects/bert/mri/aseg.mgz >>> --sum >>> /Applications/freesurfer/**subjects/bert/stats/aseg.stats --pv >>> mri/norm.mgz >>> --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in >>> mri/norm.mgz --in-intensity-name norm --etiv --surf-wm-vol --surf-ctx-vol >>> --totalgray --ctab $FREESURFER_HOME/**FreeSurferColorLUT.txt --subject >>> bert >>> --brainmask mri/brainmask.mgz --brain-vol-from-seg >>> >>> I get the error that "SUBJECTS_DIR not defined in environment." My code >>> has >>> been edited to not even use this variable and yet the issue stills >>> stands. >>> Please advise on how to circumvent this error. >>> >>> Ever thankful, >>> Matthew Goldfinger >>> >>> >>> >> >> 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<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. >> > >

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SUBJECTS_DIR not defined in environment
by Matthew Goldfinger 30 Jul '12

30 Jul '12

Dear Freesurfers, Forgive me for asking about what appears to be a very simple issue but I am stumped. I have defined my SUBJECTS_DIR as evidenced by this output. ----- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni But upon trying to execute the following: mri_segstats --seg /Applications/freesurfer/subjects/bert/mri/aseg.mgz --sum /Applications/freesurfer/subjects/bert/stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --subject bert --brainmask mri/brainmask.mgz --brain-vol-from-seg I get the error that "SUBJECTS_DIR not defined in environment." My code has been edited to not even use this variable and yet the issue stills stands. Please advise on how to circumvent this error. Ever thankful, Matthew Goldfinger

2 1

Error with recon-all import step. ERROR: the pixel data cannot be loaded as it is JPEG compressed.
by Nathan Hutcheson 30 Jul '12

30 Jul '12

I am trying to import an MPRAGE structural sequence of 160 images acquired from a Siemens Allegro. Only one of my subjects displays the following error message when I try to import him using the "recon-all -s Subject -i" function. Below is the brief error message and full log. Thanks in advance for any assistance. *ERROR: the pixel data cannot be loaded as it is JPEG compressed.* Full Log Below: [Jill:freesurfer/subjects/RawDicoms] lab% recon-all -s SZ0069TS -i SZ0069TS/IM-0001-441581576-0001.dcm Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin Jill.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 /Applications/freesurfer/subjects/SZ0069TS \n mri_convert /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm /Applications/freesurfer/subjects/SZ0069TS/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm /Applications/freesurfer/subjects/SZ0069TS/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm... Getting Series No INFO: Found 163 files in /Applications/freesurfer/subjects/RawDicoms/SZ0069TS INFO: Scanning for Series Number 20 Scanning Directory INFO: found 160 files in series INFO: loading series header info. RunNo = 19 INFO: sorting. INFO: (256 256 160), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; *ERROR: the pixel data cannot be loaded as it is JPEG compressed.* (Transfer Syntax UID: 1.2.840.10008.1.2.4.70) Darwin Jill.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 recon-all -s SZ0069TS exited with ERRORS at Mon Jul 30 11:38:40 CDT 2012 For more details, see the log file /Applications/freesurfer/subjects/SZ0069TS/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Take care, Nathan Hutcheson Graduate Research Assistant 501 Sparks Center 1748 7th Ave South Birmingham, AL 35233

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Label to ROI volume
by mmoayedi＠uhnres.utoronto.ca 30 Jul '12

30 Jul '12

Dear FS Experts, I have run recon-all on my subjects. I'm looking to convert the V1 and various BA labels to ROIs in 3D anatomical space (orig.mgz). How would I convert my freesufer label files to ROIs. Thank you! Massieh Moayedi

2 1

Non rigid registration
by SHAHIN NASR 30 Jul '12

30 Jul '12

Hi, In our functional MRI studies, we co-registration the functional images to anatomical scans (a part of preproc-sess routine in version 5) before measuring the contrasts. But for one of our studies, a reviewer has asked if a “non-rigid image registration” would change results when we are assessing activity within artifact-prone brain areas (e.g. anterior temporal areas). As far as I know, freesurfer registration works fine and even in this study, we have found very strong activity/contrast within anterior tempotal lobe. But I was wondering whether you have tested this possibility or not. If yes, then I appreciate if you can introduce me a reference (published article) to support our answer. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

2 1

problem when convert dcm to mgz
by Liu Yawu 30 Jul '12

30 Jul '12

Hi, I recently install Freesurfer under ubuntu. I tested two own data. It works in one our own case, but did not work for other cases. The problem is the Freesurfer "not found or unknown file type for file /home/d4201z/Desktop/im_4/20001108150735000005086.dcm" when convert convert dcm to mgz. Any helps are appreciated! Here are detailed inf: FREESURFER_HOME: /usr/local/src/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-27-generic x86_64 1. the entire command-line executed recon-all -s APauli \ -i /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.20000829111709000005084.dcm 2. the error message generated file not found or unknown file type for file /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.20000829111709000005084.dcm 3. the subject's /script/recon-all.log Fri Jul 27 12:20:31 EEST 2012 /usr/local/src/freesurfer/subjects/APauli /usr/local/src/freesurfer/bin/recon-all -s APauli -i /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.20000829111709000005084.dcm subjid APauli setenv SUBJECTS_DIR /usr/local/src/freesurfer/subjects FREESURFER_HOME /usr/local/src/freesurfer Actual FREESURFER_HOME /usr/local/src/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux d4201z-CELSIUS-M470-2 3.2.0-27-generic #43-Ubuntu SMP Fri Jul 6 14:25:57 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 95900 maxlocks unlimited maxsignal 95900 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 12298252 2880484 9417768 0 127152 973356 -/+ buffers/cache: 1779976 10518276 Swap: 19529724 0 19529724 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /usr/local/src/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/src/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /usr/local/src/freesurfer/subjects/APauli mri_convert /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.20000829111709000005084.dcm /usr/local/src/freesurfer/subjects/APauli/mri/orig/001.mgz mri_convert /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.20000829111709000005084.dcm /usr/local/src/freesurfer/subjects/APauli/mri/orig/001.mgz file not found or unknown file type for file /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.20000829111709000005084.dcm #------------------------------------------ recon-all -s APauli finished without error at Fri Jul 27 12:20:34 EEST 2012 Regards, Yawu

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recon-all
by Susan Alice McLaughlin 30 Jul '12

30 Jul '12

Hi Freesurfer experts, We’ve been collecting structural (1mm isotropic) and functional (2.75x2.75x3mm) data on a Philips 3T scanner using an 8-channel head coil. We are reconstructing each subject’s surface and mapping functional data processed in FSL’s FEAT to the surface. For some subjects, we have only 1 MPRAGE, but for others, we have multiple (2 or 3) MPRAGEs, acquired in separate scanning sessions. Looking back at the list serve and FSLwiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FsQuizAnswers) it appears that our SNR should be good enough that we do not need -- and perhaps SHOULD NOT use --multiple MPRAGEs when using recon-all. Is there general agreement on this? How does one go about quantitatively comparing one surface reconstruction derived from 1 MPRAGE to another derived from 2 MPRAGEs? Thank you, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington

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Thickness and variable plot in glmfit
by Jeni Chen 30 Jul '12

30 Jul '12

Hello again, In Qdec we get a plot of the data for a particular vertex showing the variable and the thickness in the x, y axis respectively. Is there a way to get the same plot when using glmfit? Where do I find the data for the plot? Thank you! Jeni Chen

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Re: [Freesurfer] Smoothing in -qcache and the -fwhm option in mri_glmfit
by Douglas N Greve 30 Jul '12

30 Jul '12

Hi Jeni, you should not smooth with both. If you want to smooth within a given label with surf2surf, pass that label to surf2surf then don't smooth with glmfit. doug On 07/30/2012 12:46 AM, Jeni Chen wrote: > Hi Doug, > > When you say "If you smooth using surf2surf, then do not smooth using > glmfit..." are you referring to smoothing the whole hemisphere, or > with a label? In other words, if I had asked surf2surf to smooth only > inside a label, then no need to smooth again in glmfit. But if I did a > smoothing of 10mm in surf2surf on the entire hemisphere instead (i.e. > without "--label" option in surf2surf), then I will need to do > smoothing in glmfit. Did I get it right? > > By the way, thank you for replying- on midnight Sunday! (unless you > are in a different time zone...) > > Jeni > > > On 2012-07-30, at 12:04 AM, Douglas Greve wrote: > >> Hi Jeni, usually you smooth with surf2surf and include a mask or >> label to indicate that it should only be smoothed inside the >> mask/label. mri_glmfit will create a mask from non-zero voxels; if >> you ask glmfit to smooth, then it will only smooth inside of the >> mask. If you smooth using surf2surf, then do not smooth using glmfit. >> doug >> >> >> >> >> >> On 7/29/12 11:49 PM, Jeni Chen wrote: >>> Now I'm confused... So if I included a mask in my GLM analysis >>> (which I did), then I should add the -fwhm option in mri_glmfit? If >>> that's the case, does that mean my -y input file should be >>> unsmoothed to avoid double-smoothing? >>> >>> Jeni >>> >>> >>> On 2012-07-29, at 11:31 PM, Douglas Greve wrote: >>> >>>> Mostly yes. The one in mri_glmfit will also do smoothing within a >>>> given mask by default, but basically they do the same thing. >>>> doug >>>> >>>> On 7/29/12 11:15 PM, Jeni Chen wrote: >>>>> So essentially the -fwhm option in mri_glmfit does the same thing >>>>> as mri_surf2surf --fwhm ? Just want to make sure... Thanks again! >>>>> >>>>> Jeni >>>>> >>>>> >>>>> >>>> >>>> >>>> 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 greve(a)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

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Re: [Freesurfer] tcsh: tailarach_avi: Command not found
by Fidel Vila 30 Jul '12

30 Jul '12

Hi Doug. The missing files are NOT in $FREESURFER_HOME/bin; So, I guess that's why they are not found even though the path is set up in the system PATH variable. Suggestions? Fidel Are the missing files in $FREESURFER_HOME/bin and is that path in your system PATH variable? On 07/26/2012 01:29 PM, Fidel Vila wrote: > Thanks for your prompt reply, Doug. > > I've been checking and following the wiki instructions with regards to > setting up proper paths, and I could not find an obvious (to me) > problem there. > > I attach a file with things I have tried and issues I have found. > > Further advice will be greatly appreciate it. > > Many thanks, > > Fidel > > > > > > On 25-Jul-12, at 8:22 PM, Douglas Greve wrote: > >> did you set up your environment so that your path environment >> variable has all the proper paths in it? Look at the wiki for >> instructions. >> doug >> >> On 7/25/12 7:57 PM, Fidel Vila wrote: >>> Hi Freesurfer experts, >>> >>> I recently installed FS (PowerPC architecture version available on >>> FS website) on a Mac OS X 10.4.11 and I get the attached output >>> error when running recon-all. >>> >>> Advice on how to troubleshoot this would be appreciate. >>> >>> Thanks, >>> >>> Fidel >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Fidel Vila-Rodriguez, MD, FRCPC Clinical Assistant Professor, Faculty of Medicine, Dpt. of Psychiatry, University of British Columbia UBC Clinician Investigator Fellow UBC Graduate Program in Neuroscience Ph.D Candidate BC Mental Health and Addiction Research Institute A3-128-4, 938 West 28th Ave Vancouver, BC V5Z 4H4 Tel: 604-875-2000 Ext. 4732 Fax: 604-875-3871

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