Freesurfer

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30088 discussions

Re: [Freesurfer] matlab loading problem (mkcontrast, selxavg3-sess)
by Paola Binda 07 Jul '11

07 Jul '11

Hi all I'm having trouble with the interface between freesurfer and matlab too in my case, running mkcontrast does not open matlab and eventually generates an error Any help to work around this problem would be very much appreciated I'm running freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on a Mac OS X 10.6.8 (please see details of the system/command/error message in the rtf file in attach) I've just installed Freesurfer and this is the first time I try this command Paola > > > What is your platform and what version of FS are you using? > > doug > > On 12/15/10 2:42 PM, Katherine Sledge Moore wrote: > > I am having trouble with the interface between freesurfer and matlab. When I > > run mkcontrast-sess and selxavg3-sess, matlab opens, but nothing happens (the > > script does not finish.) When I force it to quit, I get the error "-display: > > Command not found." In both mkcontrast and selxavg3-sess, the command to call > > matlab is something along the lines of "matlab -display iconic". Any thoughts > > as to why the "-display iconic" part is not being interpreted? > > > > Katherine Sledge Moore > > Postdoctoral Associate > > Visual Cognitive Neuroscience Laboratory > > Yale University > > > http://camplab.psych.yale.edu/ > > > > http://pantheon.yale.edu/~khs8 > > > > > > > _______________________________________________ > > 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 > > > > 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. >

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cortical dysplasia
by Carolina Valencia 07 Jul '11

07 Jul '11

Hello FSexperts I have a MPRAGE image of cortical dysplasia, I have some regions of grey matter within the white matter, and I measured the cortical thickness in the projections of those regions and I expected to find a thinnercortex instead I found a cortical thickening. FS takes into account the embedded region of the grey matter to measure the cortical thickness? Best regards, Carolina

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freeview load fiducials from 3DSlicer
by Gabriele Arnulfo 07 Jul '11

07 Jul '11

Hi guys, I've got a list of fiducials (fcsv) from 3DSlicer, Is there a way to import them within freeview? Those points look like label,x,y,z,[flag],[flag] i.e. P,57.799,-49.1799,13.07,1,1 P,-4.05607,-47.1519,8.93645,1,1 thank in advance. g.

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generating an amygdala mask
by Michelle Umali 06 Jul '11

06 Jul '11

Dear Freesurfers, Is there a way to generate automatically generate an amygdala mask from recon-all results to fead into an FSL feat analysis? Thanks. Michelle

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glibc detected *** mris_make_surfaces: double free or corruption (!prev): 0x000000003710cc10
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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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!

2 1

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

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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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