Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

z-value from a cluster
by stdp82＠virgilio.it 29 Oct '15

29 Oct '15

HI list, how can I extract the z-value from a cluster ?I'm referring to subject-level analysis and to resting-state fMRi data analyzed by using FS-FAST. Stefano

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no voxels in mask vcsf.config
by stdp82＠virgilio.it 29 Oct '15

29 Oct '15

Hi list, I'm using FS-FAST. For a subject I have the error reported below after fcseed-sess -s subj -cfg vcsf.config.The segmentation of the structural image is fine. $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Applications/freesurfer/subjects/fMRI cmdline mri_glmfit --y /Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz --mask /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/mask.nii.gz --qa --glmdir /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/glm --pca --no-est-fwhm sysname Darwin hostname iMac-di-Stefano.local machine x86_64 user Stefano FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz logyflag 0 usedti 0 mask /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/mask.nii.gz maskinv 0 glmdir /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/glm Loading y from /Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz Saving design matrix to /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/glm/Xg.dat Normalized matrix condition is 61.5872 Matrix condition is 1e+08 Pruning voxels by thr: 0.000000 Found 0 voxels in mask Saving mask to /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/glm/mask.mgh search space = 0.000000 DOF = 297 Starting fit and test Fit completed in 0.00075 minutes Computing temporal AR1 Writing results Computing FSNR mean maxvox sig=0 F=0 at index 0 0 0 seed=1446346479 linear maxvox sig=0 F=0 at index 0 0 0 seed=1446346479 quad maxvox sig=0 F=0 at index 0 0 0 seed=1446346479 Computing PCA (300) ERROR: no voxels in mask

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remove label from aseg
by Jacobs H (NP) 28 Oct '15

28 Oct '15

Hi, I am trying to generate a segmentation file containing the aseg+aparc but replacing the hippocampus with the hippocampal subfields. With mergeseg I was able to merge the segmentations, but unfortunately parts of the “old” hippocampus (labeled as 17 and 53) are still in there (as the area covered by the subfields is not 100% equal to the hippocampus of the aseg). How can I remove the remains of the old hippocampal labels? Many thanks! Best Heidi

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Funcroi-Table-Sess Error
by Morenikeji Adebayo 28 Oct '15

28 Oct '15

Hi there, I ran the following analysis commands: mri_cor2label --c /autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id 11106 --l /autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label funcroi-config -label labl_ACC_lh.label -analysis analysis_induc_block.lh -roi roiconfig_ACC_lh funcroi-table-sess -analysis analysis_induc_block.lh -contrast contrast_neg_V_neut -roi roiconfig_ACC_lh -sf sublist_All_SHORT_n111 -o sumtable_ACC_lh.dat After running the 'funcroi-table-sess’ command I got the following error: ERROR: There is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres of the surface has been changed since the label was created. It seems that the problem might be that the command is using my participant (in this case, nmasa_001) as the source subject BUT it’s using fsaverage as the target subject. I want the target subject to be my participant as well (not fsaverage). Is there a way that I can specify the target subjects? Or is there a more efficient way do what I’m trying to do (ie: 1. generate labels for each participant based on their aparc+aseg file and 2. calculate the mean contrast signal from each ROI for each participant). Thanks, Keji --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 keji(a)nmr.mgh.harvard.edu

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Minc-tools - cannot find required library hdf5 - Ubuntu 12.04
by Bruno LAD 28 Oct '15

28 Oct '15

Hi everybody. Could anyone help me please? I've downloaded minc-tools source code to compile and install on Ubuntu 12.04, but I've got an error when try to run the *configure* file. The log is below: root@ubuntu:~/freesurfer-source/minc-tools/minc-2.1.00# ./configure --prefix=/root/freesurfer-inst --enable-static checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking whether gcc and cc understand -c and -o together... yes checking for g77... no checking for xlf... no checking for f77... no checking for frt... no checking for pgf77... no checking for cf77... no checking for fort77... no checking for fl32... no checking for af77... no checking for xlf90... no checking for f90... no checking for pgf90... no checking for pghpf... no checking for epcf90... no checking for gfortran... gfortran checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes checking for flex... no checking for lex... no checking for bison... no checking for byacc... no checking whether time.h and sys/time.h may both be included... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for sys/stat.h... (cached) yes checking sys/wait.h usability... yes checking sys/wait.h presence... yes checking for sys/wait.h... yes checking for unistd.h... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking pwd.h usability... yes checking pwd.h presence... yes checking for pwd.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking values.h usability... yes checking values.h presence... yes checking for values.h... yes checking for int32_t... yes checking for int16_t... yes checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for dlfcn.h... yes checking whether we are using the GNU Fortran 77 compiler... (cached) yes checking whether gfortran accepts -g... (cached) yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gfortran option to produce PIC... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... yes checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for pod2man... /usr/bin/pod2man checking for library m... yes checking for library netcdf... yes checking for library z... yes checking for library hdf5... no configure: error: cannot find required library hdf5 The following libs are installed: root@ubuntu:~/freesurfer-source/minc-tools/minc-2.1.00# dpkg -l | grep hdf5 ii libhdf5-mpi-dev 1.8.4-patch1-3ubuntu2 Hierarchical Data Format 5 (HDF5) - development files - MPICH version rc libhdf5-mpich-1.8.4 1.8.4-patch1-3ubuntu2 Hierarchical Data Format 5 (HDF5) - runtime files - MPICH version ii libhdf5-openmpi-1.8.4 1.8.4-patch1-3ubuntu2 Hierarchical Data Format 5 (HDF5) - runtime files - OpenMPI version ii libhdf5-openmpi-dev 1.8.4-patch1-3ubuntu2 Hierarchical Data Format 5 (HDF5) - development files - OpenMPI version rc libhdf5-serial-1.8.4 1.8.4-patch1-3ubuntu2 Hierarchical Data Format 5 (HDF5) - runtime files - serial version I've Googled this issue, but cannot find any useful tip to solve my problem. If someone need more information, please let me know. Thank you for the help. -- Best Regards, Bruno Bragança Mendes Laboratório de Alto Desempenho LAD/PUCRS Av. Ipiranga, 6681 - Prédio 32 Térreo - Sala 120 +55 51 33538001

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error finding Matlab
by Jason Haberman 28 Oct '15

28 Oct '15

Dear Freesurfer Community, I am very new to Freesurfer and am trying to work my way through the tutorial. I am currently stuck at the mkcontrast-sess -analysis my-workmem.sm05.lh -contrast encode-v-base -a 1 section, having received the error: ERROR: cannot find matlab. Is it in your path? I have searched the forums and found one instance of this being reported, but the suggested solutions did not resolve the problem. Is there anyway further recommendations you might make? I have attached a screenshot of my .bash_profile and of my attempts to run mkcontrast. I would be most grateful for any assistance you might offer. Warm Regards, Jason [image: Inline image 1] -- Jason Haberman Assistant Professor of Psychology Rhodes College Clough Hall 119 901-843-3231 http://jasonmarchaberman.wordpress.com/

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Re: [Freesurfer] Talairach_afd error (Bruce Fischl)
by Anna I. Garcia Diaz 28 Oct '15

28 Oct '15

Hi Bruce, Thanks for the reply. The talairach.xfm file generated by the palarellizing machine is empty; it looks as follows: Talairach.xfm file: MNI Transform File % avi2talxfm Transform_Type = Linear; Linear_Transform = However, the talaraich.xfm file generated by the non-paralellizing machine is the following: MNI Transform File % avi2talxfm Transform_Type = Linear; Linear_Transform = 1.088816 -0.036409 -0.059575 1.880753 0.047590 1.030018 0.245325 -4.493217 0.029937 -0.211744 1.231518 94.663368; Anna On Thu, Oct 22, 2015 at 6:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. normalization of hippocampal volume (geschwind2013) > 2. Postdoctoral Opportunity: Multimodal MRI registration and > analysis (Frederic Andersson) > 3. Re: A mixed effect model approach in within subject dataset > {Disarmed} {Disarmed} (jorge luis) > 4. Re: Sulcal depth units (Bruce Fischl) > 5. Re: mris_expand - problem reading thickness file? (Bruce Fischl) > 6. Re: How to compute the measures on the average brain? > (Bruce Fischl) > 7. Re: Talairach_afd error (Bruce Fischl) > 8. Re: How to compute the measures on the average brain? > (Douglas N Greve) > 9. Re: normalization of hippocampal volume (Douglas N Greve) > 10. Re: per analysis with covariates (Douglas N Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 22 Oct 2015 17:18:21 +0900 > From: geschwind2013 <neurofree(a)gmail.com> > Subject: [Freesurfer] normalization of hippocampal volume > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <27AF7ECA-E1B4-4337-BB2C-4CBE4109F342(a)gmail.com> > Content-Type: text/plain; charset=euc-kr > > Hi, FS Experts, > > I?m using version 5.3 and have performed hippo-subfields analysis. > > To perform the statistics, shall I get the normalized volumes of each > hippo-subfields? > or just to do correction for ICV is enough ? > > thanks.. > > Hyon > > > ------------------------------ > > Message: 2 > Date: Thu, 22 Oct 2015 15:30:14 +0200 > From: Frederic Andersson <andersson(a)univ-tours.fr> > Subject: [Freesurfer] Postdoctoral Opportunity: Multimodal MRI > registration and analysis > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <6E3A85F5-C942-49D0-BBE0-4C51C4E8EC27(a)univ-tours.fr> > Content-Type: text/plain; charset="utf-8" > > Postdoctoral Opportunity: Multimodal MRI registration and analysis > > Context and methodology > This postdoctoral position will focus on the registration of ex-vivo onto > in-vivo MR data. Based on some recent advances extending the combined > volume and surface registration, efficient approaches can be provided for > dealing with this issue. However, these methods need to be validated and > several open theoretical questions are related to this problem and will be > investigated during this postdoctoral work. The theoretical results > obtained will be tested and used on real human data in a larger framework > aiming at tractography validation (French National Research Agency Grant > ANR 2014, collaborative study Inserm U930, Universit? de Tours, Neurospin > and Martinos Center). > > Applicant profile > Candidates should have a strong background in image registration and MR > imaging, a good publication record, and strong experience in c++ and matlab > coding. Proficiency in English is required, as well as scientific writing > skills. > Applicants should send a CV, including list of publications and a > description of previous research experience, as well as the names and > emails of two academic referees to: Clovis Tauber ( > clovis.tauber(a)univ-tours.fr <mailto:clovis.tauber@univ-tours.fr>) and > Christophe Destrieux (christophe.destrieux(a)univtours.fr <mailto: > christophe.destrieux(a)univtours.fr> ) > > Conditions > Starting date: January 2016 (adjustable) > Contract: 2 years > Location: Imaging and Brain unit, INSERM U930, Tours. > Salary: related to experience > > References > G.M. Postelnicu, L. Z?llei, B. Fischl: Combined Volumetric and Surface > Registration, IEEE Transactions on Medical Imaging 28 (4), April 2009, p. > 508--522 > Zemmoura I, Serres B, Andersson F, Barrantin L, Tauber C, Filipiak I, > Cottier JP, Venturini G and Destrieux C 2014 FIBRASCAN: a novel method for > 3D white matter tract reconstruction in MR space from cadaveric dissection > Neuroimage 103 106?118 > Serres B, Zemmoura I, Andersson F, Tauber C, Destrieux C and Venturini G > 2013 Brain Virtual Dissection and White Matter 3D Visualization Stud. > Health Technol. Inform. 184 392--396 >

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Understanding the brainstem AtlasMesh file structure format
by Jonathan Plasencia 28 Oct '15

28 Oct '15

Hello, Is the AtlasMesh under the following pathway a standard mesh structure? If so, what is it? Better yet, is there a way for those meshes in the AtlasMesh to be converted to a standard stl file or some other standard mesh file format? To be clear, I know the .gz is a compressed file; I'm referring to the data within the text. freesurfer -> average -> BrainstemSS -> atlas -> AtlasMesh.gz I ask because I would like to use this this template as a target mesh for vertex analysis with the brainstem data I processed using freesurfer. Best, Jon

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FreeSurfer pve correction tool
by m.bahri＠ulg.ac.be 27 Oct '15

27 Oct '15

Dear FreeSurfer Experts, Are there any documentation comes out for the pve correction tool implemented in the FreeSurfer V6? Many thanks in advance, Best, Mohamed

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Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study
by Don Hagler 27 Oct '15

27 Oct '15

Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study University of California, San Diego Several funded postdoctoral positions are available in image analysis method development, including automated cortical- and subcortical segmentation, advanced diffusion tractography, and fMRI mapping and time series analysis. We are looking to build a team to help build the next generation of analysis pipelines and visualization tools for a newly funded study to follow 10,000 children with longitudinal structural and functional imaging across 19 sites across the US. The study will use a cross-platform Harmonized Human Connectome Protocol, optimized for quantitative accuracy and consistency of imaging biomarkers across scanners and time. To learn more about the ABCD study, please see http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-lan… <http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-lan…>. Requirements: Applicants should have research experience in any of the above fields, with a Ph.D. or equivalent degree. They should be comfortable working in a distributed team environment, and should have a track record of quality scientific publications. Candidates are expected to be experienced in programming with Matlab, Python, and/or <> C/C++. Experience with FreeSurfer, FSL, and the Human Connectome analysis pipelines is strongly preferred. To formally apply, submit a current CV, a personal statement describing your research experience and interests, and contact information for 2-3 references to abcd(a)ucsd.edu <mailto:abcd@ucsd.edu>. Or feel free to email Dr. Donald Hagler (dhagler(a)ucsd.edu <mailto:dhagler@ucsd.edu>) or Anders M. Dale (amdale(a)ucsd.edu <mailto:amdale@ucsd.edu>) for more information. The University of California, San Diego is an Equal Opportunity/Affirmative Action Employer advancing inclusive excellence. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, protected veteran status, or other protected categories covered by the UC nondiscrimination policy.

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