Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

tkmedit-sess result
by anisha narula 17 Dec '07

17 Dec '07

Hello, I am doing a retinotopy analysis and when I perform the sliceview-sess command, I get activation in the areas of interest. I used the tkmedit-sess command *tkmedit-sess -analysis rtopy -contrast eccen -map h -sf sessid -df sessdir -volid orig.mgz* however there is no activation. I have attached the image above. Thank You

2 1

right choroid plexus missing
by Mishkin Derakhshan 14 Dec '07

14 Dec '07

Hi, Is there any reason why aseg.stats only has a label for the left-choroid-plexus (id 31) and none for the right? I am using freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 thanks, mishkin

2 1

mri_convert options
by Mishkin Derakhshan 14 Dec '07

14 Dec '07

Hi, I am having troubles getting the right options with mri_convert. I ran: recon-all -autorecon1 -i original.mnc -s subj1 recon-all -subcortseg -s subj1 I now want to convert aseg.mgz into aseg.mnc but in the same space and with the same orientation as my original.mnc file. My original.mnc file has the following attributes: double zspace ; zspace:comments = "Z increases from patient inferior to superior" ; zspace:step = -0.9765625 ; zspace:start = 127.418768256005 ; zspace:direction_cosines = -0.0275245718714001, -0.000514697647100001, 0.999620994692302 ; double yspace ; yspace:comments = "Y increases from patient posterior to anterior" ; yspace:step = -0.9765625 ; yspace:start = 146.850463958339 ; yspace:direction_cosines = -0.0186971433325, 0.999825193136882, -2.319984599e-08 ; double xspace ; xspace:comments = "X increases from patient left to right" ; xspace:step = 1.49999999999996 ; xspace:start = -95.4780255890689 ; xspace:direction_cosines = 0.999446254069973, 0.0186900576545041, 0.0275293837630133 ; short image(zspace, yspace, xspace) ; Any help would be much appreciated. thanks, mishkin

3 4

left and right wm neighbors error
by Matt Colvin 14 Dec '07

14 Dec '07

Dear FreeSurfer folks, We recently had an error occur while processing two brains in recon2. We are using FreeSurfer version 4.0.1 for these subjects. The error message in both cases mentions that mri_fill could not find points where lh and rh wm were "nbrs" (I assume this is short for neighbors). Upon inspecting the aseg.mgz files for both brains, I found that, while there were one or two spots in each brain where lh and rh wm voxels did touch, it was much less than in other version 4.0.1 asegs that we have processed and inspected. In other words, there were plenty of places where the connection between the l and r wm was mediated by the corpus callosum label, but almost none where the wm were direct neighbors. Is there any way known for fixing this problem? Could it be related to the new corpus callosum label in the version 4 segmentation which was not present in earlier versions? Thanks in advance for any help anybody might be able to lend. Here is the end of the error message: #-------------------------------------------- #@# Fill Fri Dec 14 07:12:09 CST 2007 /disk/conte_raid1/freesurfer/Geller/02681/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.033 -0.026 0.146 -14.846; 0.010 1.114 0.190 -60.985; -0.140 -0.203 0.988 38.624; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.033 -0.026 0.146 -14.846; 0.010 1.114 0.190 -60.985; -0.140 -0.203 0.988 38.624; 0.000 0.000 0.000 1.000; reading segmented volume aseg.mgz... mri_fill: could not find any points where lh and rh wm are nbrs Linux eureka 2.6.9-22.0.2.ELsmp #1 SMP Thu Jan 5 17:13:01 EST 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Fri Dec 14 07:12:31 CST 2007

4 3

-noaparc flag
by Michael Harms 14 Dec '07

14 Dec '07

Hello, What is the role of the -noaparc flag in 'mris_make_surfaces' of FS v4? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

2 2

problems
by 顏鳳賢 14 Dec '07

14 Dec '07

Hi, I had downloaded the freesurfer to my system (Linux Fedora Core 4) and had completed all the installation procedures. Question 1: I would like to convert analyze format to .mgz. What command line do I use? Can I type "mri_convert x249.img 001.mgz "? Question 2: When I type "recon-all -s x249 -nuintensitycor", it doesn't run and has a error" nu_correct." What would I do to resolve the problem? Question 3: It doesn't find talairach.xfm. What would I do to get the file? thanks~~ FreeSurfer problem report --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v4.0.1 RedHat release: Fedora Core release 4 (Stentz) Kernel info: Linux 2.6.11-1.1369_FC4 i686 --------------------------------------------------------------------- 1) subject name x249 2) the entire command-line executed [root@cgu ~]# ksh # tcsh [root@cgu ~]# setenv FREESURFER_HOME /usr/local/freesurfer [root@cgu ~]# source $FREESURFER_HOME/SetUpFreeSurfer.csh [root@cgu ~]# cd $SUBJECTS_DIR [root@cgu subjects]# cd x249/mri/orig [root@cgu orig]# mri_convert x249.img 001.mgz [root@cgu mri]# recon-all -s x249 -nuintensitycor 3) the error message generated ERROR: nu_correct 4) optionally include the subject's /script/recon-all.log Thu Oct 4 13:38:14 CST 2007 /usr/local/freesurfer/subjects/x249 /usr/local/freesurfer/bin/recon-all -s x249 -nuintensitycor subjid x249 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v4.0.1 Linux cgu.edu.tw 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 16383 ######################################## program versions used $Id: recon-all,v 1.133.2.5 2007/09/17 16:38:00 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.7 2007/01/06 00:01:14 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:14-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.4.2 $Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $ mri_convert --version stable4 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:14-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: tkregister2.c,v 1.86.2.1 2007/08/15 15:39:42 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_normalize.c,v 1.52 2007/01/02 21:34:40 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_watershed.cpp,v 1.67 2007/06/29 13:40:47 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_segment.c,v 1.33 2007/02/14 19:59:27 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_em_register.c,v 1.57 2006/12/29 02:09:06 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_ca_normalize.c,v 1.38 2007/01/02 13:37:33 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_ca_register.c,v 1.63 2007/01/18 22:58:55 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_ca_label.c,v 1.80 2007/04/13 13:22:32 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_concatenate_lta.c,v 1.3 2007/05/17 19:56:59 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01 18:16:19 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_inflate.c,v 1.33.2.2 2007/08/16 01:40:10 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_curvature.c,v 1.25 2007/07/20 16:42:32 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_topo_fixer.cpp,v 1.26 2007/02/13 19:30:47 segonne Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_make_surfaces.c,v 1.99 2007/08/14 01:56:01 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_anatomical_stats.c,v 1.54 2007/08/02 17:37:13 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2007-08-08.gca GCASkull RB_all_withskull_2007-08-08.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs ####################################### #-------------------------------------------- #@# Nu Intensity Correction Thu Oct 4 13:38:15 CST 2007 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /usr/local/freesurfer/subjects/x249/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.7 2007/01/06 00:01:14 nicks Exp $ Linux cgu.edu.tw 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux Thu Oct 4 13:38:15 CST 2007 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 tmpdir is ./tmp.mri_nu_correct.mni.20457 /usr/local/freesurfer/subjects/x249/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20457/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20457/nu0.mnc Can't find the talairach xform '/usr/local/freesurfer/subjects/x249/mri/transforms/talairach.xfm' Transform is not loaded into mri $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.20457/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Oct 4 13:38:31 CST 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.20457/nu0.mnc ./tmp.mri_nu_correct.mni.20457/nu1.mnc [root@cgu.edu.tw:/usr/local/freesurfer/subjects/x249/mri/] [2007-10-04 13:38:31] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_20509/ ./tmp.mri_nu_correct.mni.20457/nu0.mnc ./tmp.mri_nu_correct.mni.20457/nu1.imp /usr/local/freesurfer/mni/bin/volume_stats: error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct Linux cgu.edu.tw 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Thu Oct 4 13:38:32 CST 2007

5 8

using BET prior to recon-all?
by Simon Rushton 14 Dec '07

14 Dec '07

I've been having problems with a few brains (errors during processing). I found advice on the web about running BET (the FSL brain extraction tool) prior to running recon-all http://lcni.uoregon.edu/mediawiki/index.php/SOFT:FSL_FreeSurfer I've tried this and that has helped. (Searching the mail archive I see that at least one other person on this list appears to be doing the same.) My question is, is this a sensible thing to do? I ask because looking at the output I see that at least one of the early processing stages appears to expect a non-stripped brain: mri_watershed -brain_atlas /Applications/freesurfer/average/ RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Does this suggest that I either should not try the BET trick or that if I do that I should make some modifications to the recon-all scripts? simon

4 6

Error message II
by Juergen Haenggi 14 Dec '07

14 Dec '07

Dear FS experts Here I found a warning that seem to be related to the error message I posted before. mri_convert /usr/local/freesurfer/subjects/s237/mri/rawavg.mgz /usr/local/freesurfer/subjects/s237/mri/orig.mgz --conform WARNING ==================++++++++++++++++++++++++================================== ===== The physical sizes are (299.52 mm, 299.52 mm, 176.85 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 300 slices. The freesurfer tools should be able to handle more than 256 slices. If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu) ==================================================++++++++++++++++++++++++== ============= Thanks Regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

2 1

Convert from {png,jpg} --> dicom
by Rudolph Pienaar 14 Dec '07

14 Dec '07

Hi - Does anyone have any advice/experience on converting/creating DICOMS from arbitrary image formats like png or jpg? Basically I have a set of post-processed png images that were derived from a set of DICOMS. I'd like to convert these png images back into DICOM again. Many thanks -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

1 0

Error message
by Juergen Haenggi 14 Dec '07

14 Dec '07

Dear FS experts We analysed data with FS 4.0.1. In the past, when analyzed this data with FS 3.0.5 everthing worked fine. Now with FS 4.0.1 an error occurred maybe due to a dimension mismatch. mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.971 -0.044 -0.018 10.786; 0.050 1.089 0.053 6.110; 0.023 -0.037 0.908 10.383; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 0.971 -0.044 -0.018 12.779; 0.050 1.089 0.053 1.874; 0.023 -0.037 0.908 12.727; 0.000 0.000 0.000 1.000; reading segmented volume aseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 6094 (min = 350, max = 1400), aspect = 0.84 (min = 0.10, max = 0.75) need search nearby using seed (148, 150, 159), TAL = (-20.0, 31.0, -22.0) talairach voxel to voxel transform 1.028 0.042 0.017 -11.521; -0.046 0.914 -0.055 -4.525; -0.028 0.036 1.099 -11.334; 0.000 0.000 0.000 1.000; segmentation indicates cc at (148, 150, 159) --> (-20.0, 31.0, -22.0) ERROR: mri_fill-MRIcheckVolDims: volume1 height=256 != volume2 height=300. talairach cc position changed to (-20.00, 31.00, -22.00) Erasing brainstem...Linux 130.60.235.1 2.6.9-67.ELsmp #1 SMP Wed Nov 7 13:58:04 EST 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Dec 12 03:34:18 CET 2007 How to fix that problem? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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