Freesurfer July 2011

freesurfer@nmr.mgh.harvard.edu

129 participants
195 discussions

repost: error using recon-all function
by Ryan Hutten 06 Jul '11

06 Jul '11

Freesurfer Experts, I am reposting an error message that I receive when using the recon-all function to analyze my own data. The command which I am trying to execute is: recon-all -s 2645166 -all 2645166 is the patient ID. Running this gives an error: ERROR: avi2talxfm failed, see transforms/talairach_avi.log Linux dell3 2.6.35.6-45.fc14.x86_64 #1 SMP Mon Oct 18 23:57:44 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2645166 exited with ERRORS at Wed Jul 6 14:06:34 CDT 2011 bugr gives this: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: Fedora release 14 (Laughlin) Kernel info: Linux 2.6.35.6-45.fc14.x86_64 x86_64 --------------------------------------------------------------------- I apologize to keep asking the same questions, but until this is resolved, I am unable to process the new data obtained in my lab. I am relatively new to using this software, so any guidance would be much appreciated! Thanks!

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QDEC : Error loading the data table.
by Ignacio Letelier 06 Jul '11

06 Jul '11

Hi I have recently tried to create a new table and I received the following message after loading it in QDEC: Loading data table /home/virtualuser/apps/freesurfer/subjects/qdec.table.dat... Number of columns: 5 fsid column: 1 Number of factors: 4 Number of subjects: 10 ERROR3: QdecDataTable::Load failed to tokenize string: on line 4 of /home/virtualuser/apps/freesurfer/subjects/qdec.table.dat Error loading the data table. All the information above is right except the last one since the my number of subject is not 10. Can anyone help me solving this problem ? Best regards. -- Ignacio

2 2

Subject information
by leonardo kay 06 Jul '11

06 Jul '11

Hi all Is there someway (command line) to get direct information on each subject acquisition parameters? Best regards. -- Leo Kay.

2 1

recon-all abort with glibc error
by Knut J Bjuland 06 Jul '11

06 Jul '11

The name of the subjects is 3. The command that was used were recon-all -autorecon2-pial -s 3. I then issued the bugr and got this output. I have also included the error message. I belive that there were an double free or an corruption detected by glibc. The recon-all files is available upon request. Cheers Knut J ------------------------------------------------------------------------------ FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: Fedora release 15 (Lovelock) Kernel info: Linux 2.6.38.8-32.fc15.x86_64 x86_64 ------------------------------------------------------------------------------------ *** glibc detected *** mris_make_surfaces: double free or corruption (!prev): 0x000000003710cc10 *** ======= Backtrace: ========= /lib64/libc.so.6[0x3cdf07703a] mris_make_surfaces[0x518a39] mris_make_surfaces[0x5a7e3c] mris_make_surfaces[0x40f172] /lib64/libc.so.6(__libc_start_main+0xed)[0x3cdf02139d] mris_make_surfaces(__gxx_personality_v0+0x18a)[0x40bf5a] ======= Memory map: ======== 00400000-00cf1000 r-xp 00000000 00:00 0 00cf1000-00df0000 ---p 00000000 00:00 0 00df0000-26b79000 rwxp 00000000 00:00 0 26eb9000-383d5000 rwxp 00000000 00:00 0 [heap] 3cdec00000-3cdec1f000 r-xp 00000000 fd:01 71696709 /lib64/ld-2.14.so 3cdec1f000-3cdee1e000 ---p 00000000 00:00 0 3cdee1e000-3cdee1f000 r-xp 0001e000 fd:01 71696709 /lib64/ld-2.14.so 3cdee1f000-3cdee20000 rwxp 0001f000 fd:01 71696709 /lib64/ld-2.14.so 3cdee20000-3cdee21000 rwxp 00000000 00:00 0 3cdf000000-3cdf18f000 r-xp 00000000 fd:01 71696719 /lib64/libc-2.14.so 3cdf18f000-3cdf38e000 ---p 0018f000 fd:01 71696719 /lib64/libc-2.14.so 3cdf38e000-3cdf392000 r-xp 0018e000 fd:01 71696719 /lib64/libc-2.14.so 3cdf392000-3cdf393000 rwxp 00192000 fd:01 71696719 /lib64/libc-2.14.so 3cdf393000-3cdf399000 rwxp 00000000 00:00 0 3cdf400000-3cdf483000 r-xp 00000000 fd:01 71696792 /lib64/libm-2.14.so 3cdf483000-3cdf682000 ---p 00083000 fd:01 71696792 /lib64/libm-2.14.so 3cdf682000-3cdf683000 r-xp 00082000 fd:01 71696792 /lib64/libm-2.14.so 3cdf683000-3cdf684000 rwxp 00083000 fd:01 71696792 /lib64/libm-2.14.so 3cdf800000-3cdf816000 r-xp 00000000 fd:01 71696723 /lib64/libpthread-2.14.so 3cdf816000-3cdfa15000 ---p 00016000 fd:01 71696723 /lib64/libpthread-2.14.so 3cdfa15000-3cdfa16000 r-xp 00015000 fd:01 71696723 /lib64/libpthread-2.14.so 3cdfa16000-3cdfa17000 rwxp 00016000 fd:01 71696723 /lib64/libpthread-2.14.so 3cdfa17000-3cdfa1b000 rwxp 00000000 00:00 0 3cdfc00000-3cdfc02000 r-xp 00000000 fd:01 71696776 /lib64/libdl-2.14.so 3cdfc02000-3cdfe02000 ---p 00002000 fd:01 71696776 /lib64/libdl-2.14.so 3cdfe02000-3cdfe03000 r-xp 00002000 fd:01 71696776 /lib64/libdl-2.14.so 3cdfe03000-3cdfe04000 rwxp 00003000 fd:01 71696776 /lib64/libdl-2.14.so 3ce0000000-3ce0015000 r-xp 00000000 fd:01 71696796 /lib64/libgcc_s-4.6.0-20110603.so.1 3ce0015000-3ce0214000 ---p 00015000 fd:01 71696796 /lib64/libgcc_s-4.6.0-20110603.so.1 3ce0214000-3ce0215000 rwxp 00014000 fd:01 71696796 /lib64/libgcc_s-4.6.0-20110603.so.1 3ce0400000-3ce0416000 r-xp 00000000 fd:01 71696774 /lib64/libz.so.1.2.5 3ce0416000-3ce0616000 ---p 00016000 fd:01 71696774 /lib64/libz.so.1.2.5 3ce0616000-3ce0617000 rwxp 00016000 fd:01 71696774 /lib64/libz.so.1.2.5 3ce2000000-3ce20e8000 r-xp 00000000 fd:01 8666691 /usr/lib64/libstdc++.so.6.0.16 3ce20e8000-3ce22e8000 ---p 000e8000 fd:01 8666691 /usr/lib64/libstdc++.so.6.0.16 3ce22e8000-3ce22f0000 r-xp 000e8000 fd:01 8666691 /usr/lib64/libstdc++.so.6.0.16 3ce22f0000-3ce22f2000 rwxp 000f0000 fd:01 8666691 /usr/lib64/libstdc++.so.6.0.16 3ce22f2000-3ce2307000 rwxp 00000000 00:00 0 3cea000000-3cea05c000 r-xp 00000000 fd:01 71698673 /lib64/libfreebl3.so 3cea05c000-3cea25b000 ---p 0005c000 fd:01 71698673 /lib64/libfreebl3.so 3cea25b000-3cea25d000 rwxp 0005b000 fd:01 71698673 /lib64/libfreebl3.so 3cea25d000-3cea261000 rwxp 00000000 00:00 0 3cea400000-3cea408000 r-xp 00000000 fd:01 71698674 /lib64/libcrypt-2.14.so 3cea408000-3cea607000 ---p 00008000 fd:01 71698674 /lib64/libcrypt-2.14.so 3cea607000-3cea608000 r-xp 00007000 fd:01 71698674 /lib64/libcrypt-2.14.so 3cea608000-3cea609000 rwxp 00008000 fd:01 71698674 /lib64/libcrypt-2.14.so 3cea609000-3cea637000 rwxp 00000000 00:00 0 7f0e126d9000-7f0e189ec000 rwxp 00000000 00:00 0 7f0e189ec000-7f0e189f8000 r-xp 00000000 fd:01 71696450 /lib64/libnss_files-2.14.so 7f0e189f8000-7f0e18bf7000 ---p 0000c000 fd:01 71696450 /lib64/libnss_files-2.14.so 7f0e18bf7000-7f0e18bf8000 r-xp 0000b000 fd:01 71696450 /lib64/libnss_files-2.14.so 7f0e18bf8000-7f0e18bf9000 rwxp 0000c000 fd:01 71696450 /lib64/libnss_files-2.14.so 7f0e18bf9000-7f0e18c00000 rwxp 00000000 00:00 0 7f0e18c47000-7f0e18c49000 rwxp 00000000 00:00 0 7fff77bd7000-7fff77c08000 rwxp 00000000 00:00 0 [stack] 7fff77d9a000-7fff77d9b000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] 000: dt: 0.0000, sse=4552979.5, rms=4.03 014: dt: 0.5000, sse=5057085.5, rms=2.39 Abort (core dumped) Linux knut 2.6.38.8-32.fc15.x86_64 #1 SMP Mon Jun 13 19:49:05 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux

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measuring cortical thickness using FreeSurfer
by John Drozd 06 Jul '11

06 Jul '11

Hi, I am running freesurfer on 64 bit Fedora 10 linux. I am using version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0. Can anyone point me to a reference web page listing what steps I need to type to process a series of MRI dicom slices and use FreeSurfer to measure cortical thickness for this dicom series? Thank you, John -- John Drozd Post-Doctoral Fellow, Robarts Research Institute The University of Western Ontario London, ON, Canada http://publish.uwo.ca/~jdrozd2/index.htm

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mri_cvs_register version for CentOS4 and CentOS5
by tulu＠ms36.hinet.net 06 Jul '11

06 Jul '11

Dear FS experts I download CentOS5 x86-64 version (not CentOS4) of FS 5.1. should I need to upgrade the mri_cvs_register and applyMorph for correction ? best JLH

2 1

Problems with automatic labelling of V1 using the Hinds method in 5.1.0
by Krish Singh 06 Jul '11

06 Jul '11

Hi there, I'm using Freesurfer version 5.1.0 to automatically define labels for left and right V1 using the method outlined in Hinds et al. To do this I add the -label-v1 flag to my recon-all command line. The problem is that this always fails with the following error visible in the .out file: ------------------------------------------------------------------- mris_spherical_average -osurf v1.invivo.reg -n -o 240211-50 label lh.v1.invivo.label lh v1.invivo.reg V1_average /cubric/scratch/CCGG/Freesurf/240211-50/label/lh.v1.prob.label output surface = v1.invivo.reg painting output onto subject 240211-50. processing subject V1_average... MRISreadVertexPosition(white): could not open file /cubric/scratch/CCGG/Freesurf/V1_average/surf/lh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory ------------------------------------------------------------------- The problem seems to be with the current version of mris_spherical_average - if I modify the command line above to explicitly execute the old (4.4.0) version of mris_spherical_average then I do not get this error and the script completes without problems. I'd be grateful of any advice/help on this. Best Wishes, Krish -- Prof. Krish Singh CUBRIC School of Psychology / Ysgol Seicoleg Cardiff University / Prifysgol Caerdydd Park Place / Plas y Parc Cardiff / Caerdydd CF10 3AT, UK Tel / Ffôn: 02920 874690 / 870365 Fax / Ffacs: 02920 870339 Email / Ebost : singhkd(a)cardiff.ac.uk

2 3

calculating the surface area of each region on Desikan template
by Zhangyuanchao 06 Jul '11

06 Jul '11

hi, expert, How could I obtain the surface area of each region on the Desikan template? How can I obtain this area in both native space and the average template space? In the surf folder of each subjects, I noticed there is lh.area file, what is meaning of this file? Do I need ?h.area for calculating the area of each region? yuanchao zhang

2 1

tkmedit error message even though tksurfer runs correctly
by Sandy Goncalves 06 Jul '11

06 Jul '11

Hello! I am brand new to this software (and command for that matter) and need some help. After installing all the software, when I enter tkmedit in the xterminal, I receive an error message that looks like this: X Error of failed request: BadRequest (invalid request code or no such operation) ?? ? Major opcode of failed request: 128 (Apple-DRI) ?? ? Minor opcode of failed request: 1 () ?? ? Serial number of failed request: 16 ?? ? Current serial number in output stream: 16 Interestingly, when I type in tksurfer, this works. So I'm not sure what I should do in order to get tkmedit to work! Any help would be great! Thanks, Sandy

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Re: [Freesurfer] mri_cvs_register update
by Peter J. Molfese 06 Jul '11

06 Jul '11

Is this significant enough that we should re-run data processed using the standard recon-all stream in version 5.1? Thanks, Peter On Jun 10, 2011, at 3:28 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 2 > Date: Fri, 10 Jun 2011 12:59:34 -0400 (EDT) > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] mri_cvs_register update > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <Pine.LNX.4.62.1106101257120.4547(a)gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi, > > We found a bug in the mri_cvs_register script after the > release. Please, download the new version of applyMorph and > mri_cvs_register from one of the below links for Linux Centos4, > Linux Centos4 x86 64 and Mac Leopard respectively: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4 > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/mac-leopard-intel > > --Lilla

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Freesurfer July 2011