Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

Re: [Freesurfer] Aseg2feat: Missing segmentations
by Douglas N Greve 19 Nov '13

19 Nov '13

Those are some big segs. Have you checked the registration? On 11/19/2013 02:41 PM, Sudhin A. Shah wrote: > yes :) For example in this 1 subject segs ( > 2005 2008 2010 2011 2013 2021 2023 2025 2029 1005 1008 1011 1013 1021) are all missing.. > > The missing segs are not consistent across subjs(i.e. other subjs have different segs missing). I chose a list of 86 segs to 'cover' the brain and not sure if I was over-reaching..Also some segs are reading with value 100 (i.e. all voxels have a value of 100)? > > > > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Tuesday, November 19, 2013 2:34 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Aseg2feat: Missing segmentations > > there were probably some small segmentations that were lost. Is this > causing a problem? > On 11/19/2013 02:22 PM, Sudhin A. Shah wrote: >> Hello, >> >> This is regarding the registration of functional data to freesurfer >> parcellations >> (http://freesurfer.net/fswiki/FsTutorial/MapSegmentationsToFunctionalSpace) >> >> The rsfMRI is sampled at 2x2x2. >> >> After running reg-feat2anat and aseg2feat >> >>>> a = MRIread('aparc+aseg'); %Original aparc+aseg output from >> freesurfer recon-all >>>> size(unique(a.vol(:))) % 114 segs >>>> a = MRIread('aparc+aseg'); % this is the output file after aseg2feat >>>> size(unique(a.vol(:))) % 98 segs >> Any advice? >> >> Thanks >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Aseg2feat: Missing segmentations
by Sudhin A. Shah 19 Nov '13

19 Nov '13

Hello, This is regarding the registration of functional data to freesurfer parcellations (http://freesurfer.net/fswiki/FsTutorial/MapSegmentationsToFunctionalSpace) The rsfMRI is sampled at 2x2x2. After running reg-feat2anat and aseg2feat >> a = MRIread('aparc+aseg'); %Original aparc+aseg output from freesurfer recon-all >> size(unique(a.vol(:))) % 114 segs >> a = MRIread('aparc+aseg'); % this is the output file after aseg2feat >> size(unique(a.vol(:))) % 98 segs Any advice? Thanks

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Re: [Freesurfer] localGI Matlabpath
by Marie Schaer 19 Nov '13

19 Nov '13

Christiane, The log you sent me doesn't correspond to the error you first wrote in your email. The error reads as follow in your log: --------------- >> reading filled volume... closing volume... {??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); } >> ERROR: make_outer_surface did not create output file '/data/Projekte/Freesurfer/Prob1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux beo-08 2.6.32.59-ql-beowulf-37 #1 SMP Sat Mar 31 14:31:51 CEST 2012 x86_64 GNU/Linux recon-all -s Prob1 exited with ERRORS at Tue Nov 19 08:02:22 CET 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting --------------- It doesn't find the fspecial.m function, probably because you don't have the licence for the image processing toolbox in your installation. Is there a way you can add the toolbox to your matlab installation? Marie NB: no need to change the matlab path, it's already correctly set up On Nov 18, 2013, at 11:26 PM, "Jockwitz, Christiane" <c.jockwitz(a)fz-juelich.de<mailto:c.jockwitz@fz-juelich.de>> wrote: Hi Marie, with the old path I ment that the path just did not change. Here is my entire log. Thank you very much for your help. Kind regards Christiane Von: Marie Schaer [mailto:Marie.Schaer@unige.ch<http://unige.ch>] Gesendet: Montag, 18. November 2013 21:03 An: Jockwitz, Christiane Cc: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] localGI Matlabpath Hi Christiane, What do you mean when you say that you get the old path with getmatlab? In any case, the error seems not related to a matlab path issue. Can you please attach the entire log? Marie On Nov 18, 2013, at 12:03 AM, "Jockwitz, Christiane" <c.jockwitz(a)fz-juelich.de<mailto:c.jockwitz@fz-juelich.de>> wrote: 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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. <recon-all.log>

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Neuroimaging Research Technician II Position at VA Boston
by Benjamin Trotter 19 Nov '13

19 Nov '13

*Neuroimaging Research Technician--II* A Neuroimaging Research Technician position is available in the VA Boston Healthcare System (VABHS) Neuroimaging Research for Veterans (NeRVe) Center (Director: Dr. David Salat). Applicants must be a U.S. citizen. The Neuroimaging Research Technician will provide technical support for image preprocessing and analysis (using programs such as FSL and FreeSurfer), maintenance and development of in-house custom processing codes (script writing in unix/linux, matlab, etc), and assist staff members in the conduct of neuroimaging research as well as administrative tasks related to the Center. This includes developing expertise and training other investigators with the operation of current MRI hardware (scanner console, goggles, headphones, BioPac system, etc) and software for data processing and analysis. Additional responsibilities will include management of online documentation and center resources. Technical skills and familiarity with Linix/Unix, Matlab, and imaging software packages such as FSL and FreeSurfer is beneficial. Applicants should have a minimum of a Bachelor’s degree, with a background in Neuroscience, Computer Science, Engineering, Math or Physics. A two year commitment is required. Interested candidates should email a cover letter, resume, and contact information for two professional references to Dr. Meghan Robinson at meghan.robinson(a)va.gov.

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longitudinal 5.3 used with baseline fs 5.1 recon-all
by Knut J Bjuland 19 Nov '13

19 Nov '13

Hi,we have finished cross sectional scanworkups in Freesurfer 5.1 and gone through qa. Can we use these scanworkups for further processing in the longitudinal stream in Freesurfer 5.3? Knut J

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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

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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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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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

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.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

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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.

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