Freesurfer June 2008

freesurfer@nmr.mgh.harvard.edu

58 participants
77 discussions

Slow Processing
by Marlisa Isom 11 Jun '08

11 Jun '08

Hi All, We have 3 Mac Pros with Leopard which we use to process data (version 4). Two of them process a brain in 30-36 hours, but one takes a week to process ONE brain if not more. While the processors are slightly different (3GHz vs 2.6), not amazingly so. This is seemingly the only difference. Does anyone have any ideas? All the machines are updated etc. Marlisa

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Fixing Bad Output From the Talairach Registration
by skgtgac＠ucl.ac.uk 11 Jun '08

11 Jun '08

Hi, my name is giovanni, hope you can help me... i started the command recon-all -s patient_lyp -all on a folder containing the data of one of my patients... after few minutes I got this error message: ########################################################################### Thu Jun 5 08:13:09 BST 2008 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Jun 5 08:13:10 BST 2008 /home/gacocco/freesurfer/subjects/patient_lyp/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5852, pval=0.2817 >= threshold=0.0050) awk -f /home/gacocco/freesurfer/bin/extract_talairach_avi_QA.awk /home/gacocco/freesurfer/subjects/patient_lyp/mri/transforms/talairach_avi.log TalAviQA: 0.95959 z-score: -4 ERROR: Talairach QA check failed! z-score = -4 <= -4 = threshold Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux pc244-174 2.6.24-17-generic #1 SMP Thu May 1 14:31:33 UTC 2008 i686 GNU/Linux recon-all exited with ERRORS at Thu Jun 5 08:13:11 BST 2008 ############################################################################ I went to the page indicated by the message http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach and followed the instructions... so I typed in the terminal: gacocco@pc244-174:~/freesurfer/subjects$ tkmedit control_dr orig.mgz and i got this message: ############################################################################ Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl % gacocco@pc244-174:~/freesurfer/subjects$ tksurfer control_dr rh pial surfer: current subjects dir: /home/gacocco/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/gacocco/freesurfer/subjects surfer: Reading header info from /home/gacocco/freesurfer/subjects/control_dr/mri/T1.mgz surfer: vertices=108452, faces=216900 Loading /home/gacocco/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(control_dr) surfer: using interface /home/gacocco/freesurfer/lib/tcl/tksurfer.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % gacocco@pc244-174:~/freesurfer/subjects$ tksurfer control_dr rh pial surfer: current subjects dir: /home/gacocco/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/gacocco/freesurfer/subjects surfer: Reading header info from /home/gacocco/freesurfer/subjects/control_dr/mri/T1.mgz surfer: vertices=108452, faces=216900 Loading /home/gacocco/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(control_dr) surfer: using interface /home/gacocco/freesurfer/lib/tcl/tksurfer.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) Found embedded color table in annotation. surfer: dmin=12.2021, vno=73320, x=45.2575, y=-2.4731, z=41.6030 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 73320 marked (curv=0.000000, stat=0.000000) x = (45.3, -2.5, 41.6), n = (-0.3, 0.9, 0.4). surfer: dmin=0.3104, vno=76989, x=36.2031, y=1.3400, z=30.5769 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 76989 marked (curv=0.000000, stat=0.000000) x = (36.2, 1.3, 30.6), n = (0.7, 0.5, 0.5). surfer: dmin=0.4661, vno=76851, x=33.4849, y=1.2373, z=45.7916 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 76851 marked (curv=0.000000, stat=0.000000) x = (33.5, 1.2, 45.8), n = (0.3, 0.9, -0.4). surfer: dmin=0.2625, vno=71233, x=20.1145, y=-4.2706, z=67.2250 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 71233 marked (curv=0.000000, stat=0.000000) x = (20.1, -4.3, 67.2), n = (0.4, 0.9, -0.0). surfer: dmin=0.6131, vno=66208, x=37.6014, y=-9.3269, z=62.7725 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 66208 marked (curv=0.000000, stat=0.000000) x = (37.6, -9.3, 62.8), n = (0.9, 0.3, -0.3). surfer: dmin=0.6404, vno=70561, x=57.4662, y=-4.9873, z=31.2062 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 70561 marked (curv=0.000000, stat=0.000000) x = (57.5, -5.0, 31.2), n = (0.8, 0.4, 0.4). surfer: dmin=0.6560, vno=73265, x=44.8697, y=-2.3008, z=44.3611 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 73265 marked (curv=0.000000, stat=0.000000) x = (44.9, -2.3, 44.4), n = (0.1, 0.9, -0.4). gacocco@pc244-174:~/freesurfer/subjects$ tkmedit patient_lyp brainmask.mgz Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl gacocco@pc244-174:~/freesurfer/subjects$ tkregister2 --mgz --s patient_lyp --fstal --surf origsurfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 ZeroCRAS 1 $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $ Diagnostic Level -1 % tkregister2 talairach.xfm --------------------- 1.263 -0.018 -0.037 1.562; 0.062 1.083 0.453 4.335; 0.041 -0.467 1.180 20.571; 0.000 0.000 0.000 1.000; INFO: loading target /home/gacocco/freesurfer/subjects/patient_lyp/mri/orig.mgz Zeroing CRAS of target new xfm ----------------- 1.263 -0.018 -0.037 4.634; 0.062 1.083 0.453 5.415; 0.041 -0.467 1.180 -14.586; 0.000 0.000 0.000 1.000; --------------------- INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /home/gacocco/freesurfer/average/mni305.cor.mgz INFO: changing move type to float Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.263 -0.018 -0.037 4.634; 0.062 1.083 0.453 5.415; 0.041 -0.467 1.180 -14.586; 0.000 0.000 0.000 1.000; subject = patient_lyp Reading lh surface orig MRISread(/home/gacocco/freesurfer/subjects/patient_lyp/surf/lh.orig): could not open file No such file or directory tkregister2.bin: could not read surface orig No such file or directory gacocco@pc244-174:~/freesurfer/subjects$ ############################################################################ So I typed: tkregister2 --mgz --s patient_lyp --fstal This time the utility starts, according to waht it says in the tutorial, but i do not see the green lines that should help me to stretch, translate, and rotate my MOVEABLE volume. Where am i wrong? best regards giovanni antonio cocco

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Re: [Freesurfer] wiki problem
by Liat Levita 11 Jun '08

11 Jun '08

Hi Krish, I am afraid we had no joy with either option. No one in lab can get access, we have used both Mozilla Firefox, and Internet Explorer, neither can establish a connection. We never had a problem before. I have tried making changes to my computer firewall, again no joy. Liat ----- Original Message ----- From: Krish Subramaniam <krish(a)nmr.mgh.harvard.edu> Date: Tuesday, June 10, 2008 8:01 pm Subject: Re: [Freesurfer] wiki problem > Liat, > > Could you tell us the browser you are using? Because we have been > using the fswiki without problems. ( and I can access fswiki from > my > home, hence we can rule out the case that fswiki is not available > external to our center ) > > https://surfer.nmr.mgh.harvard.edu/fswiki > > and > > http://surfer.nmr.mgh.harvard.edu/fswiki > > both should work with the first one asking you to accept a > certificate. ( secure http connection ) > > -Krish > > On Jun 10, 2008, at 6:52 PM, Liat Levita wrote: > > I am sure you are aware of this problem, but since last week we > have > > been unable to access the FreeSurfer wiki > (http://surfer.nmr.mgh.harvard.edu/docs/index.html > > ). Is it down for maintenance? and if so when will it be up again? > > > > I have just started using FreeSurfer, hence having major > problems > > without the freesurfer wiki to guide me along. > > > > Thank you so much for you help. > > > > L > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Re: [Freesurfer] wiki problem
by Liat Levita 11 Jun '08

11 Jun '08

No, it is really strange, I don't get it. I am not sure if it is a problem with our own network at Cornell. Safari could not open the page http://surfer.nmr.mgh.harvard.edu/fswiki because the server is not responding. Safari could not open the page https://surfer.nmr.mgh.harvard.edu/fswiki because the server is not responding. ----- Original Message ----- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date: Wednesday, June 11, 2008 8:33 am Subject: Re: [Freesurfer] wiki problem > so you can't get to: > > https://surfer.nmr.mgh.harvard.edu/fswiki > > or > > http://surfer.nmr.mgh.harvard.edu/fswiki > > I have no problem with either site... > Bruce > > > On Wed, 11 Jun 2008, Liat Levita > wrote: > > > Hi Krish, > > > > I am afraid we had no joy with either option. > > > > No one in lab can get access, we have used both Mozilla Firefox, > and Internet Explorer, neither can establish a connection. > > > > We never had a problem before. I have tried making changes to my > computer firewall, again no joy. > > > > Liat > > > > > > ----- Original Message ----- > > From: Krish Subramaniam <krish(a)nmr.mgh.harvard.edu> > > Date: Tuesday, June 10, 2008 8:01 pm > > Subject: Re: [Freesurfer] wiki problem > > > >> Liat, > >> > >> Could you tell us the browser you are using? Because we have been > >> using the fswiki without problems. ( and I can access fswiki from > >> my > >> home, hence we can rule out the case that fswiki is not available > >> external to our center ) > >> > >> https://surfer.nmr.mgh.harvard.edu/fswiki > >> > >> and > >> > >> http://surfer.nmr.mgh.harvard.edu/fswiki > >> > >> both should work with the first one asking you to accept a > >> certificate. ( secure http connection ) > >> > >> -Krish > >> > >> On Jun 10, 2008, at 6:52 PM, Liat Levita wrote: > >>> I am sure you are aware of this problem, but since last week we > >> have > >>> been unable to access the FreeSurfer wiki > >> (http://surfer.nmr.mgh.harvard.edu/docs/index.html > >>> ). Is it down for maintenance? and if so when will it be up again? > >>> > >>> I have just started using FreeSurfer, hence having major > >> problems > >>> without the freesurfer wiki to guide me along. > >>> > >>> Thank you so much for you help. > >>> > >>> L > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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wiki problem
by Liat Levita 10 Jun '08

10 Jun '08

I am sure you are aware of this problem, but since last week we have been unable to access the FreeSurfer wiki (http://surfer.nmr.mgh.harvard.edu/docs/index.html) Is it down for maintenance? and if so when will it be up again? I have just started using FreeSurfer, hence having major problems without the freesurfer wiki to guide me along. Thank you so much for you help. L

3 2

White Matter Regional Volumes
by hranilovich＠ucla.edu 10 Jun '08

10 Jun '08

My name is Jennifer as well, and I work in the same lab as Jennifer Bramen, who originally wrote to you, below. I am writing while she's out of town to follow up on your reply below. Mainly, I am a little confused by your suggestion to use asegstats2table command, because the resultant text file when this command is run on the wmparc.mgz file is not openable in excel - it has too many columns/is too large. Unfortunately, the --maxsegno flag is not helpful because the white matter volumes are the second half of the segmentations listed in the wmparc.mgz file. Thus, the --maxsegno command will only yield an output file that has none or some of the white matter volumes, rather than only the white matter volumes. Any suggestions? Thanks- Jennifer Hranilovich Quoting Jenni Pacheco <jpacheco(a)mail.utexas.edu>: Hi Jen, In Doug's absence, let me try and give you the best answer I can! The wmparc.mgz uses the cortical parcellation and grows each label down through the white matter - giving a label of the white matter underneath each cortical unit. Because of this there will be both cortical (ctx) and white matter (wm) measures in the wmparc.stats - the ctx regions being taken directly from the cortical parcellation, and the wm regions resulting from growing those inward. Depending on what version you are using, you can use asegstats2table to tabulate these results, as you would the subcortical segmentation. Check the help on this file, there may be an option to do it directly, or you may have to use a flag to specify a new stats table (i.e., wmparc.stats instead of aseg.stats). Hope this is helpful, Jenni On Wed, Apr 30, 2008 at 8:17 AM, Jenni Pacheco <jenni.pacheco(a)gmail.com> wrote: Hi Jen, In Doug's absence, let me try and give you the best answer I can! The wmparc.mgz uses the cortical parcellation and grows each label down through the white matter - giving a label of the white matter underneath each cortical unit. Because of this there will be both cortical (ctx) and white matter (wm) measures in the wmparc.stats - the ctx regions being taken directly from the cortical parcellation, and the wm regions resulting from growing those inward. Depending on what version you are using, you can use asegstats2table to tabulate these results, as you would the subcortical segmentation. Check the help on this file, there may be an option to do it directly, or you may have to use a flag to specify a new stats table (i.e., wmparc.stats instead of aseg.stats). Hope this is helpful, Jenni On Wed, Apr 30, 2008 at 7:04 AM, Bruce Fischl < fischl(a)nmr.mgh.harvard.edu> wrote: Hi Jen, Doug is out of town at the fBIRN meeting, and he's the one that will answer this so you might have to wait a bit. cheers, Bruce On Tue, 29 Apr 2008, Jennifer Bramen wrote: I posted the below question regarding white matter volumes to the list last Friday. I think it fell through the cracks because I sent it out in the late afternoon, and was hoping someone could help me understand 1) the outputs of indicvidual wmparc.stats files and 2) how to tabulate these data like we can with gray matter volumes. Thanks again. Jen Hi Freesurfer Users, This may be a newbie question. I am trying to evaluate regional volumes. I have been able to tabulate the gray matter volumes, but cannot figure out how to tabulate all the white matter volumes. I see that in individual folders, there is a file called wmparc.stats. Do any of the tools query this file, or will I need to pull the data manually? Inside this file, I see some of the regions listed as wm-?h-<regionname>. Next to these are sometimes a lot of zeros and sometimes a bunch of values. I am wondering why so many of these do not have values associated with them. I am also wondering why only some of the regions listed in this file are labeled wm, when the file suggests it contains white matter stats... If there is somewhere on the site that explains white matter volumetric analyses, could someone please send me the link? Thank you Jennifer Bramen

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Topological defects in LGI
by Martin Kavec 10 Jun '08

10 Jun '08

Hi, I get the following warning followed by error in LGI calculation: ________________________________________________________ ... remeasuring lGI value for vertex iV = 6301. It may take a few minutes. WARNING -- Problem for vertex iV = 6301, lGI value is aberrantly high (lGI=48.6447)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file 'tmp-mris_compute_lgi/rh.pial_lgi.asc'! Linux antarctica 2.6.24-gentoo-r8 #1 SMP Sat May 17 14:07:35 CEST 2008 x86_64 Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz GenuineIntel GNU/Linux recon-all exited with ERRORS at Sun May 25 09:22:16 CEST 2008 ________________________________________________________ The suggested mris_euler_number gives: ________________________________________________________ mris_euler_number rh.pial euler # = v-e+f = 2g-2: 155756 - 467454 + 311636 = -62 --> 32 holes F =2V-4: 311636 != 311512-4 (-128) 2E=3F: 934908 = 934908 (0) total defect index = 64 ________________________________________________________ If I just rerun the LGI calculation, as suggested on the LGI web page, the calculation stops at exactly the same place. I am not sure, if I understand the execution correctly in this case, but while observing the commands, one of the first ones is removing the tmp-.... in the surf directory. Can anybody suggest me please, how to correct the defect in that particular vertex. The topological defect repair described on the web deals with dura matter pixels removal. Thanks in advance, Martin

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ERROR in autorecon1
by p.s.bjerkan＠studmed.uio.no 10 Jun '08

10 Jun '08

Dear experts! Have a little problem that hopefully is easy to answer. When running autorecon1 with the 4.0.4 version I have the following ERROR (at the end of this excerpt): ________________________________________________________________ mri_convert ./tmp.mri_nu_correct.mni.11745/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.11745/nu2.mnc nu.mgz --like orig.mgz WARNING: --like does not work on multi-frame data $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from ./tmp.mri_nu_correct.mni.11745/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 8.05145e-09, -3.11374e-08) j_ras = (-7.66902e-08, -2.80897e-09, -1) k_ras = (3.66e-08, 1, -5.54119e-10) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... Tue Jun 10 11:51:25 CEST 2008 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Tue Jun 10 11:51:25 CEST 2008 /home/batch/subjects/1030/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm /home/batch/subjects/1030/mri /home/freesurfer/freesurfer_4.0.4/bin/talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $ Linux millais.comp.neuro 2.6.23.8-63.fc8 #1 SMP Wed Nov 21 18:51:08 EST 2007 i686 i686 i386 GNU/Linux Tue Jun 10 11:51:25 CEST 2008 -------------------------------------------- mri_convert nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from nu.mgz... TR=2730.00, TE=3.93, TI=1000.00, flip angle=7.00 i_ras = (-1, 8.05145e-09, -3.11374e-08) j_ras = (-7.66902e-08, -2.80897e-09, -1) k_ras = (3.66e-08, 1, -5.54119e-10) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 125.111; 0.000 -0.000 1.000 -71.398; -0.000 -1.000 -0.000 116.126; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 -------------------------------------------- mpr2mni305 talsrcimg Tue Jun 10 11:51:28 CEST 2008 /home/freesurfer/freesurfer_4.0.4/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.3 2007/08/04 02:23:35 nicks Exp $ target=711-2C_as_mni_average_305 --------------------------------------------------------------------- analyzeto4dfp talsrcimg -O0 -y --------------------------------------------------------------------- $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Tue Jun 10 11:51:30 2008 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- gauss_4dfp: error while loading shared libraries: libg2c.so.0: cannot open shared object file: No such file or directory ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=127 ERROR: mpr2mni305 execution aborted ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux millais.comp.neuro 2.6.23.8-63.fc8 #1 SMP Wed Nov 21 18:51:08 EST 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue Jun 10 11:51:30 CEST 2008 ________________________________________________________________ Seems that it´s a problem with the shared libraries. Think I remember that we had to deal with this kind of problem previously, but now exactly how... We have been running several other versions recently without changing things too much (I think). Anything apart from this that I have to be aware of? Thanks in advance! Petr S. Bjerkan Dept. of psychiatry University of Oslo

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scuba bus error on MacBook
by akram＠nmr.mgh.harvard.edu 09 Jun '08

09 Jun '08

Hello all, We installed freesurfer on a brand new MacBook and downloaded some high resolution MRI data on the hard drive. we can open the volumes in tkmedit but not in scuba, it returns a Bus error. Any ideas? Thanks! Akram.

2 2

sub-voxel projections
by Ben Kennedy 09 Jun '08

09 Jun '08

Dear Freesurfer, I've been playing around with Freesurfer and monkey MR volumes, and I'm trying to find some sort of foothold to use Freesurfer more effectively. I have the surfaces and inflated volumes of the brain, and I also have a bunch of sub-voxel coordinates (in the T1 volume) of recorded sites that I want to project onto these surfaces and inflations. Is there any straightforward (but I'll take convoluted also) way to do this? Thanks, Ben K

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Freesurfer June 2008