Freesurfer July 2011

freesurfer@nmr.mgh.harvard.edu

129 participants
195 discussions

talaraich ERROR
by Carolina Valencia 07 Jul '11

07 Jul '11

Hi FSexperts, I have a case of a child with *Hydrocephalus and cortical dysplasia, the patient has a subcutaneous ventriculo-peritoneal shunt that produces an artifice in all MRI sequences, I try to recon-all but it exit with ERROR* #-------------------------------------------- #@# Talairach Failure Detection Thu Jul 7 11:03:21 COT 2011 /home/cvalencia/freesurfer/subjects/volumetria/hptu_vol04/hptu_vol04/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux cvalencia-Precision-WorkStation-T3400 2.6.35-30-generic-pae #54-Ubuntu SMP Tue Jun 7 20:28:33 UTC 2011 i686 GNU/Linux recon-all -s hptu_vol04 exited with ERRORS at Thu Jul 7 11:03:21 COT 2011 is possible to process it in automated fashion? Thanks, Best regards, Carolina

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Matlab and FS
by Carolina Valencia 07 Jul '11

07 Jul '11

Hello FS'users, I'm trying to do an histogram of cortical thickness for 2 cases in matlab, but the problem is that I have Installed matlab in a computer (windows) and FS in another one (ubuntu) Can I configure something to use the FS commands in matlab in order to obtain some graphs? And also, where can I find the cortical thickness in each regions (Brodmann areas, gyrus or sulci) of the brain in order to compare a normal patient with a patiwnt who has a cortical dysplasia ? Thanks a lot for your help, Carolina

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tracula bvecs problem
by Franz Liem 07 Jul '11

07 Jul '11

Dear Freesurfers. I am trying to run trac-all on one subject and have a problem with the bvecs file at the -prep stage. After dtifit is started an error massage occurs: Error: bvecs and bvals don't have the same number of entries. I checked the dmri/bvals and dmri/bvecs. There seems to be a problem at the -corr stage (-corr alone finishes without error). My input file is one 4d .nii.gz file (with a total of 33 images, with the first being a b0 image). (I have attached the files from the dmri folder) The dmri/bvecs file only contains: 0,0000000 0,0000000 0,0000000 The original bvecs contains 3 columns and 33 lines. The dmri/bvals seems to be ok (1 column and 33 lines). eddy_correct processes 33 files (dmri/dwi_tmp0000 ... dmri/dwi_tmp0032). I am running FSL(4.6.1) and Freesurfer v5.1.0 on Mac (10.6.4) (although the recon was done with 5.0.0, but I guess this not important at this stage, is it?) ******* My Configuration File: set dtroot = $SUBJECTS_DIR/DTI set subjlist = (s02x) set dcmroot = $SUBJECTS_DIR/DTI set dcmlist = (s02x/dti4d.nii.gz) set bvalfile = /Users/.../DTI/bvals/bvals set bvecfile = /Users/.../DTI/bvals/bvecs set nb0 = 1 set doeddy = 1 set dorotbvecs = 1 set thrbet = 0.3 set doregflt = 1 set doregbbr = 0 ******* Thanks, Franz

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QDEC table
by Ignacio Letelier 07 Jul '11

07 Jul '11

Hi freesurfers Do anyone know if it's possible to automatically enter in the QDEC table the gray matter volume of every subject in the study, to avoid entering this item manually for each one ? Best regards. -- Ignacio.

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bbregister - Are 6 dof enough for MNI305?
by Joao Pereira 07 Jul '11

07 Jul '11

Dear Freesurfers, I was wondering if you could help me clarify one question I have re the recommended use of bbregister to register PET data. If I want to register my PET data to MNI305 space used in Freesurfer, is a 6 dof rigid registration enough? I notice that the tailarach function used within autorecon1 is a 12 dof affine, so I'm guessing that bbregister is unlikely to fully register the PET data to the template space in the same way that (eg) brain.mgz is registered. Thank you very much! Best, Joao Pereira

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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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Freesurfer July 2011