Freesurfer November 2013

freesurfer@nmr.mgh.harvard.edu

120 participants
198 discussions

error in the third stage of reconstruction using freesurfer
by Santosh Kumar 18 Nov '13

18 Nov '13

Hi experts, I came across an error in the third stage of reconstruction using freesurfer. I am rerunning freesurfer on windows 7 64 bit: freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full I have following error: #@# Sphere rh Fri Nov 15 14:28:04 EST 2013 /home/virtualuser/freesurfer/subjects/HF5015/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... *MRISreadVertexPosition(smoothwm): could not open file ../surf/rh.smoothwm* *No such file or directory* *MRISreadOriginalProperties: could not read surface file smoothwm* *No such file or directory* Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s HF5015 exited with ERRORS at Fri Nov 15 14:28:08 EST 2013. Any help! With regards, Santosh

2 1

localGI Matlabpath
by Jockwitz, Christiane 18 Nov '13

18 Nov '13

Dear Freesurfer experts, I tried to run the local GI command recon-all -s -localGI and got the following error message: >> ??? Undefined function or method 'make_outer_surface' for input arguments of type 'char'. >From earlier post I tried to fix the problem by changing the matlabpath like this: setenv MATLABPATH /directory/bin > setenv PATH ${MATLABPATH}/bin:${PATH} However, if I then check the path via "getmatlab" I still get the old path. Did I do something wrong? And is it right to set up my matlabpath to the matlab/bin folder? The scripts like make_outer_surface.m are located in the freesurfer/matlab directory. Or does the path have to point to the scripts directly? Thank you very much in advance Kind regards, Christiane ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

2 1

expand GM label into white matter
by Corinna Bauer 18 Nov '13

18 Nov '13

Hello all, Is there a way to expand a GM label into the white matter by n voxels? Corinna

3 7

.label versus .thresh.label
by krista kelly 17 Nov '13

17 Nov '13

Hi, I've just started using the newest freesurfer v 5.3 and I've noticed in the labels folder that every .label has a thresh.label. When overlaying the two, they can be quite different (for example MT.label is much larger than MT.thresh.label) or quite similar (V1.label is just a tiny bit larger than V1.thresh.label). What is the difference between the two and which is best to use? Thanks! Krista

2 6

problem feeding design matrix to mri_glmfit
by Laura M. Tully 17 Nov '13

17 Nov '13

Hello freesurfers, I'm trying to run mri_glmfit between groups analysis (patients vs. controls) with gender, age, medication (continuous), and duration of illness as covariates. Because the control group have values of zeros for medication and duration of illness (which results in an illconditioned matrix), I have created my own design matrix so that controls do not have a column for medication or duration of illness and am feeding this matrix into mri_glmfit instead of the fsgd file. However, this seems to cause a problem with the --y input; when I try to run mri_glmfit, i get an error message "error in uncompressing" - I'm not quite sure what this means, perhaps I did something wrong in creating the design matrix? See the full output below. I've also attached the design matrix, contrast file, and the original fsgd (which results in the ill conditioned matrix). Best, Laura. *Command line: * mri_glmfit --y lh_grpDiffs_thickness10.mgh --X new_mat_files/X_lh_grp_thick_med_dur.mat --C Contrast1B_grp_Diffs_HCvsSZ_Med_Dur.mtx --surf fsaverage lh --cortex --glmdir lh.grp_diffs_thickness_med_dur_112013.glmdir --illcond *Output:* Reading source surface /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /ncf/snp/04/SCORE/freesurfer_analysis/glm_analysis cmdline mri_glmfit --y lh_grpDiffs_thickness10.mgh --X new_mat_files/X_lh_grp_thick_med_dur.mat --C Contrast1B_grp_Diffs_HCvsSZ_Med_Dur.mtx --surf fsaverage lh --cortex --glmdir lh.grp_diffs_thickness_med_dur_112013.glmdir --illcond sysname Linux hostname ncfws13.rc.fas.harvard.edu machine x86_64 user ltully FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /ncf/snp/04/SCORE/freesurfer_analysis/glm_analysis/lh_grpDiffs_thickness10.mgh logyflag 0 X new_mat_files/X_lh_grp_thick_med_dur.mat usedti 0 labelmask /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.grp_diffs_thickness_med_dur_112013.glmdir IllCondOK 1 ReScaleX 1 DoFFx 0 Creating output directory lh.grp_diffs_thickness_med_dur_112013.glmdir Loading y from /ncf/snp/04/SCORE/freesurfer_analysis/glm_analysis/lh_grpDiffs_thickness10.mgh MatrixReadTxT: could not scan value [1][1] File exists ERROR: in uncompressing MATFILE5: 0 x 0, type 0, imagf 0, name '' File exists unsupported matlab format 0 (unknown) File exists Saving design matrix to lh.grp_diffs_thickness_med_dur_112013.glmdir/Xg.dat *** glibc detected *** mri_glmfit: double free or corruption (out): 0x000000003b1279c0 *** ======= Backtrace: ========= /lib64/libc.so.6[0x3229470d7f] /lib64/libc.so.6(cfree+0x4b)[0x32294711db] mri_glmfit[0x99fea2] mri_glmfit[0x5bcbe3] mri_glmfit[0x433608] mri_glmfit[0x433802] mri_glmfit[0x40f2f7] /lib64/libc.so.6(__libc_start_main+0xf4)[0x322941d994] mri_glmfit(__gxx_personality_v0+0x172)[0x40b2ba] ======= Memory map: ======== 00400000-00b86000 r-xp 00400000 00:00 0 00b86000-00c86000 ---p 00b86000 00:00 0 00c86000-26a08000 rwxp 00c86000 00:00 0 35b4b000-3d4fa000 rwxp 35b4b000 00:00 0 [heap] 3229000000-322901c000 r-xp 00000000 fd:00 557272 /lib64/ld-2.5.so 322901c000-322921c000 ---p 322901c000 00:00 0 322921c000-322921d000 r-xp 0001c000 fd:00 557272 /lib64/ld-2.5.so 322921d000-322921e000 rwxp 0001d000 fd:00 557272 /lib64/ld-2.5.so 3229400000-322954d000 r-xp 00000000 fd:00 557376 /lib64/libc-2.5.so 322954d000-322974d000 ---p 0014d000 fd:00 557376 /lib64/libc-2.5.so 322974d000-3229751000 r-xp 0014d000 fd:00 557376 /lib64/libc-2.5.so 3229751000-3229752000 rwxp 00151000 fd:00 557376 /lib64/libc-2.5.so 3229752000-3229757000 rwxp 3229752000 00:00 0 3229800000-3229882000 r-xp 00000000 fd:00 557399 /lib64/libm-2.5.so 3229882000-3229a81000 ---p 00082000 fd:00 557399 /lib64/libm-2.5.so 3229a81000-3229a82000 r-xp 00081000 fd:00 557399 /lib64/libm-2.5.so 3229a82000-3229a83000 rwxp 00082000 fd:00 557399 /lib64/libm-2.5.so 3229c00000-3229c02000 r-xp 00000000 fd:00 557398 /lib64/libdl-2.5.so 3229c02000-3229e02000 ---p 00002000 fd:00 557398 /lib64/libdl-2.5.so 3229e02000-3229e03000 r-xp 00002000 fd:00 557398 /lib64/libdl-2.5.so 3229e03000-3229e04000 rwxp 00003000 fd:00 557398 /lib64/libdl-2.5.so 322a000000-322a014000 r-xp 00000000 fd:00 557401 /lib64/libz.so.1.2.3 322a014000-322a213000 ---p 00014000 fd:00 557401 /lib64/libz.so.1.2.3 322a213000-322a214000 rwxp 00013000 fd:00 557401 /lib64/libz.so.1.2.3 322a400000-322a416000 r-xp 00000000 fd:00 557391 /lib64/libpthread-2.5.so 322a416000-322a615000 ---p 00016000 fd:00 557391 /lib64/libpthread-2.5.so 322a615000-322a616000 r-xp 00015000 fd:00 557391 /lib64/libpthread-2.5.so 322a616000-322a617000 rwxp 00016000 fd:00 557391 /lib64/libpthread-2.5.so 322a617000-322a61b000 rwxp 322a617000 00:00 0 322f000000-322f00d000 r-xp 00000000 fd:00 557370 /lib64/libgcc_s-4.1.2-20080825.so.1 322f00d000-322f20d000 ---p 0000d000 fd:00 557370 /lib64/libgcc_s-4.1.2-20080825.so.1 322f20d000-322f20e000 rwxp 0000d000 fd:00 557370 /lib64/libgcc_s-4.1.2-20080825.so.1 3237200000-32372e6000 r-xp 00000000 fd:00 3309621 /usr/lib64/libstdc++.so.6.0.8 32372e6000-32374e5000 ---p 000e6000 fd:00 3309621 /usr/lib64/libstdc++.so.6.0.8 32374e5000-32374eb000 r-xp 000e5000 fd:00 3309621 /usr/lib64/libstdc++.so.6.0.8 32374eb000-32374ee000 rwxp 000eb000 fd:00 3309621 /usr/lib64/libstdc++.so.6.0.8 32374ee000-3237500000 rwxp 32374ee000 00:00 0 3239600000-3239609000 r-xp 00000000 fd:00 557404 /lib64/libcrypt-2.5.so 3239609000-3239808000 ---p 00009000 fd:00 557404 /lib64/libcrypt-2.5.so 3239808000-3239809000 r-xp 00008000 fd:00 557404 /lib64/libcrypt-2.5.so 3239809000-323980a000 rwxp 00009000 fd:00 557404 /lib64/libcrypt-2.5.so 323980a000-3239838000 rwxp 323980a000 00:00 0 2b1225c45000-2b1225c48000 rwxp 2b1225c45000 00:00 0 2b1225c69000-2b1225c6d000 rwxp 2b1225c69000 00:00 0 2b1225c6d000-2b1225ca2000 r-xs 00000000 fd:00 3703836 /var/run/nscd/dbC3ggnz (deleted) 2b1225d6d000-2b12952bb000 rwxp 2b1225d6d000 00:00 0 7fff44349000-7fff44362000 rwxp 7ffffffe5000 00:00 0 [stack] 7fff443cb000-7fff443ce000 r-xp 7fff443cb000 00:00 0 [vdso] ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vsyscall] Aborted -- -- Laura M. Tully, PhD Post-Doctoral Fellow in Psychiatry UC Davis Imaging Research Center 4701 X Street, Sacramento, CA 95817 Phone: (916) 734-7927 Fax: (916) 734-8750 Alumnus of Social Neuroscience & Psychopathology Lab, Harvard University ltully(a)fas.harvard.edu Follow me on twitter: @tully_laura -- *Confidentiality Notice:* This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

1 0

Linux recon-all error
by krista kelly 16 Nov '13

16 Nov '13

Hello, I'm running freesurfer's recon-all using Linux and the past few subjects I've run, recon-all has exited with errors. I've ran a few subjects so far with no problems, and now all of a sudden there's an issue and I can't figure out why. I have been able to run these "problem' subjects using Linux on other computers with no issues, so it can't be a raw data issue. I have pasted the terminal window text below. If anyone has any idea why this is occurring, I'd love to know! Thanks! -------- freesurfer-Linux-centos4-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni Freesurfer Virtual Machine sudo password: freesurfer fsuser@xubuntu-VirtualBox:~$ recon-all -all -qcache -notal-check -cw256 -subjid BV33 -i ~/Desktop/nii.gzs/BV33.nii.gz WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux xubuntu-VirtualBox 3.2.0-55-generic #85-Ubuntu SMP Wed Oct 2 13:43:27 UTC 2013 i686 i686 i386 GNU/Linux -cw256 option is now persistent (remove with -clean-cw256) /usr/local/freesurfer/subjects/BV33 mri_convert /home/fsuser/Desktop/nii.gzs/BV33.nii.gz /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz mri_convert /home/fsuser/Desktop/nii.gzs/BV33.nii.gz /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/fsuser/Desktop/nii.gzs/BV33.nii.gz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999683, 0.0209404, 0.0139622) j_ras = (-0.0209424, 0.999781, 0) k_ras = (-0.0139591, -0.000292399, 0.999903) writing to /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Nov 14 10:28:28 EST 2013 Found 1 runs /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz /usr/local/freesurfer/subjects/BV33 mri_convert /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz /usr/local/freesurfer/subjects/BV33/mri/orig.mgz --conform --cw256 mri_convert /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz /usr/local/freesurfer/subjects/BV33/mri/orig.mgz --conform --cw256 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999683, 0.0209404, 0.0139622) j_ras = (-0.0209424, 0.999781, 0) k_ras = (-0.0139591, -0.000292399, 0.999903) Original Data has (1, 1, 1) mm size and (176, 230, 175) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/BV33/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/BV33/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/BV33/mri/orig.mgz /usr/local/freesurfer/subjects/BV33/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Nov 14 10:28:40 EST 2013 /usr/local/freesurfer/subjects/BV33/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux xubuntu-VirtualBox 3.2.0-55-generic #85-Ubuntu SMP Wed Oct 2 13:43:27 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s BV33 exited with ERRORS at Thu Nov 14 10:29:51 EST 2013 For more details, see the log file /usr/local/freesurfer/subjects/BV33/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting fsuser@xubuntu-VirtualBox:~$ open /usr/local/freesurfer/subjects/BV33/scripts/recon-all Couldn't get a file descriptor referring to the console fsuser@xubuntu-VirtualBox:~$

3 3

GPU considerations
by Satrajit Ghosh 16 Nov '13

16 Nov '13

Does Freesurfer's GPU bits care about single or double precision? Cheers, satra

1 0

trac-all inquiry
by David Soto 15 Nov '13

15 Nov '13

Hi - trac-all completed in all my Ps except one and I noticed that the dlabel/diff output does not contain all the files I assessed whether it could be do to poor registration, by checking the aparc+aseg file and looks allright I also checked the registration of FA maps to standard space by freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz dtifit_FA.bbr.nii.gz and seems fine also freeview -v brain_anat_orig.nii.gz lowb_brain.nii.gz which also seems fine any ideas pls? thanks! ds On Fri, Aug 16, 2013 at 5:14 PM, Anastasia Yendiki < ayendiki(a)nmr.mgh.harvard.edu> wrote: > > I suspect the current problem is caused by poor registration. Have you > checked the aparc+aseg and/or the registration from diffusion to anatomical > and from anatomical to MNI? > > > On Fri, 16 Aug 2013, David Soto wrote: > -- http://www1.imperial.ac.uk/medicine/people/d.soto/

2 1

Modifying cortical surface for large dysplasia
by Jonathan DuBois 15 Nov '13

15 Nov '13

Hi All, I have run recon-all on a subject with a large cortical dysplasia, and while the segmentation (aseg) seems to be relatively correct, there is a large region of dysplasia not included by the pail surface. The normalized intensity values for the cortex and the excluded region are very similar so it seems that there is a threshold related to the distance from the white matter surface to the pial surface, or perhaps normal gyrification that is constraining the pial surface. Is there a recon-all or expert option for surface reconstruction of abnormally thick cortex? Thanks in advance, Jonathan

2 3

Export T1 volume and a set of points in the same space
by Octavian Lie 15 Nov '13

15 Nov '13

Dear All, I need to export a T1.mgz and N points (Nx3 coordinates .mat file) of the same volume in SPM12b. N are actually intracranial electrodes. For this, I save T1.mgz as .nii prior to import into SPM. Should I use volume index, volume RAS or surface RAS coordinates for N? What other transforms I should apply to the .mat coordinate file so that when read in SPM is in the same space as T1.nii? Please advise, Thank you, Octavian.

2 1

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Freesurfer November 2013