Freesurfer September 2014

freesurfer@nmr.mgh.harvard.edu

120 participants
164 discussions

Post Doc Position
by Fabrice Crivello 12 Sep '14

12 Sep '14

The Neurofunctional Imaging Group (GIN) is a CNRS-CEA joint research unit of the Bordeaux University (UMR 5296, dir. Bernard Mazoyer) and a core member of the TRAIL Laboratory of Excellence. The GIN is a multidisciplinary research unit gathering scientists with initial training in mathematics and instrumentation, cognitive neurosciences, signal processing and databasing. One objective of the current GIN research project is to develop new tools to characterize and describe the gray matter anatomical connectivity networks. Within this area we have a position for a 2 years Post Doc. Description of the position Recent work on brain connectivity modeling revealed that the topographic organization of this connectivity is not limited to large-scale anatomical pathways generally observable in diffusion MRI, thus reinforcing the interest of studies focusing on the characterization of cortical structural connectivity and its variability. Therefore, the estimation of relevant grey matter connectomes strongly relies on the choice of an ad'hoc cerebral parcellisation. We propose a post doc project to first implement a probabilistic cortical atlas derived from cortical parcellisations defined individually to optimally extract cortical thickness and volume of each individual. The second aim of the post doc project is to compute cortical structural connectivity to quantify the inter-individual variability of brain organization together with the effects of specific factors such as gender, manual preference, functional lateralization or cognitive skills. The strength of the present project is that it will benefits from the already acquired BIL&GIN database composed of 453 healthy volunteers balanced for gender and handedness. Hence, the first probabilistic cortical atlas will be operated over a large sample, the 453 participants having been previously pre-processed. Qualification and experience The qualified applicant should have a PhD in neuro-image analysis, cognitive neuroscience, computer science or related field and a background in neuroimage processing. Applicants should have experience with existing tools for analysis of neuroimaging data (SPM, FSL, Freesurfer.) and a relevant programming experience (MATLAB). For further information, please contact Dr. Fabrice Crivello (fabrice.crivello(a)u-bordeaux2.fr) Employment and payment are determined by Bordeaux University (2 400 € per month, net salary). Job location is in Bordeaux, France. Interested candidates should send their applications including CV with full publication list, the names and contact information and a summary of research interests to fabrice.crivello(a)u-bordeaux2.fr. Dr. Fabrice CRIVELLO Groupe d'Imagerie Neurofonctionnelle UMR 5296 - CNRS CEA Université Bordeaux Université de Bordeaux 146, rue Léo Saignat CS 61292 33076 Bordeaux Cedex Mob : +33 618 064 753 Tel : +33 547 304 402 Fax : +33 547 304 394 www.gin.cnrs.fr See my publications : https://www.researchgate.net/profile/Fabrice_Crivello

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from freesufer label to diffusion mask
by Xiang-zhen Kong 11 Sep '14

11 Sep '14

Hi, all. I want to convert a freesufer label to diffusion mask with the following approach. # tkregister2 --mov S0001_FA.nii.gz --noedit --s S0001 --regheader --reg register.dat # mri_annotation2label --subject S0001 --hemi rh --outdir ./labels --annotation aparc.a2009s tkregister2 --mov S0001_FA.nii.gz --noedit --s S0001 --regheader --reg register.dat # mri_label2vol --label ./labels/rh.entorhinal.label --temp S0001_FA.nii.gz --subject S0001 --hemi rh --o rh.entorhinal.nii.gz --proj frac 0 1 .1 --fillthresh 0.3 --reg register.dat I wonder whether this is correct? In particular, what I am not sure about is the generation about the register.mat in the first line cmd. Best, Xiang-zhen 【小孔成像】http://www.conxz.net

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Compiling Freesurfer from source ends with error regarding libtool version mismatch
by Arman Eshaghi 11 Sep '14

11 Sep '14

Hi, I'm trying to compile Freesurfer current dev version from read only cvs repo according to developers guide on my machine with Ubuntu 14.04, gcc 4.8.2, I proceed as follows in dev/ directory: 1- ./setup_configure: which finishes without error 2- ./configure with vxl and mni library directory flags, also finishes without errors 3- make: it finishes with errors, specifically it seems to be a problem regarding the libtools mismatch of version, here is an example error I get from mri_segment source: /bin/bash ../libtool --tag=CC --mode=link g++ -I../include -L/usr/lib64 -L/usr/X11R6/lib64 -L/opt/mni_library/lib -L/opt/vxl/build/lib -o mri_segment_ms mri_segment_ms.o ../utils/libutils.a ../fsgdf/libfsgdf.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lz -lm -lcrypt -ldl -lpthread -lnetcdf -lvolume_io -lminc -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib ../libtool: line 469: *CDPATH: command not found libtool: Version mismatch error. This is libtool 2.4.2 Debian-2.4.2-1.7ubuntu1, but the libtool: definition of this LT_INIT comes from an older release. libtool: You should recreate aclocal.m4 with macros from libtool 2.4.2 Debian-2.4.2-1.7ubuntu1 libtool: and run autoconf again. make: *** [mri_segment] Error 63* Error message seems to be pretty obvious and what I have done so far (in vain) are: 1- autoreconf -ivf 2- deleting alocal.m4 from dev, reconfiguring 3- issuing the command `make maintainer-clean` and reconfiguring and recompiling with make 4- libtoolize --force 5- deleting config.status, configure, Makefile.in, autom4te.cache I would be much grateful if anyone could help me here. All the best, Arman

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mri_glmfit-sim montecarlo analysis with mask
by Jon Alan Wieser 11 Sep '14

11 Sep '14

HI freesurfer experts We were wondering if it is possible to restrict the Monte Carlo analysis run by mri_glmfit-sim to a specific region fo the surface , instead of the whole surface, by using a mask or label to specify the ROI? I didn't see a --mask or --label option in mri_glmfit-sim Thank Jon

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aparc+aseg.mgz to nifti conversion
by Gabor Perlaki 11 Sep '14

11 Sep '14

Dear all, I'd like to convert the aparc+aseg.mgz to nifti and use it in the space of the original MR image. The basic conversion from mgz to nifti works fine "mri_convert aparc+aseg.mgz aparc+aseg.nii". However if I reslice it in the space of the original MRI than something fails and even negative intensities are presented in the converted aparc+aseg2raw.nii file " mri_convert -rl rawavg.mgz -rt nearest aparc+aseg.mgz aseg+aparc2raw.nii". Any idea how to convert it? Best Regards, Gabor

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Re: [Freesurfer] about issues with "recon-all"
by Lei, Chia-Ming 11 Sep '14

11 Sep '14

Thank you again for the reply, Bruce! After I typed: which mri_convert It came up with: Desktop/freesurfer/bin/mri_convert Let me know if any other info you need please. Thank you! PS. I changed the subject of this email from the Digest to my original question-related one. Really sorry, but I'm still trying to figure out how to manage/operate with this mailing list. -Abel (Chia-Ming) ________________________________________ ------------------------------ Message: 6 Date: Sat, 6 Sep 2014 16:02:05 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] about issues with "recon-all" To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.03.1409061601220.23927(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" after you run the source command can you type: which mri_convert and let us know what it says? This is not a FreeSurfer issue - it's a problem with your path Bruce On Sat, 6 Sep 2014, Lei, Chia-Ming wrote: > Thank you for the reply, Bruce. (Really sorry but I just changed my email address, so I decided to reply again with the currently subscribed email...) > > I'm running on Linux 3.13.0-35-generic with Ubuntu 14.04. I couldn't set up the permanent shell switched to .tcsh, i.e. when I opened a new terminal, nothing happened. So I deleted the .tcsh file I created and manually input the following steps when I opened a terminal: > > 1. setenv FREESURFER_HOME Desktop/freesurfer 2. source $FREESURFER_HOME/SetupFreeSurfer.csh > *note: the following message shows up withe the source command, > "-------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME Desktop/freesurfer > FSFAST_HOME Desktop/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR Desktop/freesurfer/subjects > MNI_DIR Desktop/freesurfer/mni" > > 3. setenv SUBJECTS_DIR $FREESURFER_HOME/subjects > *note: I also tried to set SUBJECTS_DIR to the specific folder where the .dcm files are. > 3.1 setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/Dickey-Pilot/003 > > 4. recon-all -i $SUBJECTS_DIR/Dickey-Pilot/003/003-0001-00003-0.dcm -s mike-dickey -all > *OR > 4.1 recon-all -i $SUBJECTS_DIR/003-0001-00003-0.dcm -s mike-dickey -all > > Then the long error message pasted in the first email (below attached) showed up. Please let me know if any other info you need to figure out the issue is. > Again, thank you so much for your help! > > -Abel > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Saturday, September 6, 2014 9:56 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] about issues with "recon-all" > > Hi Abel > > what OS are you running on? Did you source the file > > $FREESURFER_HOME/FreeSurferEnv.csh > > ? > > cheers > Bruce > > > On Sat, 6 Sep 2014, Abel Lei > wrote: > >> >> Hi FreeSurfers, >> >> ? >> >> I'm a very beginner to both the Linux OS and the FreeSurfer program. >> After finally setting up the FreeSurfer, I was trying to do recon-all >> for my trial subject. But when I ran the "recon-all" command, it >> returned with a long error message indicating many commands not found. >> The message is copied and pasted below. I also attached the >> recon-all.log and recon-all.error in this email, which (probably) contains two failed attempts of the same command. >> Please let me know if you need any other info from me. I appreciate >> your help and time greatly! Thank you so much! >> >> >> Chia-Ming (Abel) Lei >> >> PhD Student/Graduate Student Researcher >> >> Language and Brain Lab (LABlab) & Adult Language Lab >> >> Department of Communication Sciences and Disorders >> >> School of Health and Rehabilitation Science >> >> University of Pittsburgh >> >> >> -----below is the long~ error message------ chiaming-PORTEGE-R835:~> >> recon-all -all -s mike_dickeySubject Stamp: >> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> INFO: SUBJECTS_DIR is >> /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot >> Actual FREESURFER_HOME /home/chia-ming/Desktop/freesurfer >> -rw-rw-r-- 1 chia-ming chia-ming 2119 Sep? 6 >> 01:34/home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dic >> key/script >> s/recon-all.log >> Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug >> 15 >> 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux >> mri_motion_correct.fsl: Command not found. >> talairach_avi: Command not found. >> tkregister2_cmdl: Command not found. >> nu_correct: Command not found. >> mri_make_uchar: Command not found. >> mri_normalize: Command not found. >> mri_watershed: Command not found. >> mri_gcut: Command not found. >> mri_segment: Command not found. >> mri_label2label: Command not found. >> mri_em_register: Command not found. >> mri_ca_normalize: Command not found. >> mri_ca_register: Command not found. >> mri_ca_label: Command not found. >> mri_pretess: Command not found. >> mri_fill: Command not found. >> mri_tessellate: Command not found. >> mri_concatenate_lta: Command not found. >> mri_normalize_tp2: Command not found. >> mris_smooth: Command not found. >> mris_inflate: Command not found. >> mris_curvature: Command not found. >> mris_sphere: Command not found. >> mris_fix_topology: Command not found. >> mris_topo_fixer: Command not found. >> mris_ca_label: Command not found. >> mris_euler_number: Command not found. >> mris_make_surfaces: Command not found. >> mris_register: Command not found. >> mris_volmask: Command not found. >> mris_anatomical_stats: Command not found. >> mrisp_paint: Command not found. >> mris_curvature_stats: Command not found. >> mris_calc: Command not found. >> mri_robust_register: Command not found. >> mri_robust_template: Command not found. >> mri_and: Command not found. >> mri_or: Command not found. >> mri_fuse_segmentations: Command not found. >> mri_segstats: Command not found. >> cp: cannot stat 'Desktop/freesurfer/bin/recon-all': No such file or >> directory >> #-------------------------------------------- >> #@# MotionCor Sat Sep? 6 01:40:13 EDT 2014 >> ERROR: no run data found in >> /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/mri. >> Make sure to >> have a volume called 001.mgz in? >> /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/m >> ri/or >> ig. >> If you have a second run of data call it 002.mgz, etc. >> See also: >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion >> Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug >> 15 >> 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s mike_dickey exited with ERRORS at Sat Sep? 6 01:40:13 EDT >> 2014 >> >> For more details, see the log >> file/home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dick >> ey/script >> s/recon-all.log >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> ? >> >> ? >> >> >> > > _______________________________________________ > 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 End of Freesurfer Digest, Vol 127, Issue 8 ******************************************

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mri_label_volume
by Flavia Niccolini 11 Sep '14

11 Sep '14

Dear Freesurfer expert, I am trying to normalized for ICV subcortical volume (Buckner et al. 2004) using the following:' mri_label_volume [options] <volume> <label 1> <label 2> ...' where options are either '-atlas_icv <fname> <scalefactor> ' or '-eTIV <fname> <scalefactor> '. My version of freesurfer is 5.3.0. But I get this problem: $ mri_label_volume -atlas_icv '/home/fniccoli/freesurfer/subjects/HD/Control_1/mri/transforms/talairach.xfm' 1948 '/home/fniccoli/freesurfer/subjects/HD/Control_1/mri/aseg.mgz' 11 50 ltMNIreadEx:/home/fniccoli/freesurfer/subjects/HD/Control_1/mri/transforms/talairach.xfm does not start as 'MNI Transform File' mri_label_volume: could not open atlas transform file /home/fniccoli/freesurfer/subjects/HD/Control_1/mri/transforms/talairach.xfm $ mri_label_volume -eTIV '/home/fniccoli/freesurfer/subjects/HD/Control_1/mri/transforms/talairach.xfm' 1948 '/home/fniccoli/freesurfer/subjects/HD/Control_1/mri/aseg.mgz' 11 50 ltMNIreadEx:/home/fniccoli/freesurfer/subjects/HD/Control_1/mri/transforms/talairach.xfm does not start as 'MNI Transform File' mri_label_volume: could not open atlas transform file /home/fniccoli/freesurfer/subjects/HD/Control_1/mri/transforms/talairach.xfm Could you please help me?

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lh.BA.annot vs lh.BA.thresh.annot ... generalization question
by Krieger, Donald N. 11 Sep '14

11 Sep '14

Hi Anastasia or anyone, Are there any other groups of labels which are, by default, produced in comparable less vs more restrictive ways? For instance, is there a way to produce lh.aparc.thresh.annot with comparably constrained labels? And does it make sense to do so? Regards, Don <snip> > > > On 14-09-08 12:39 PM, Anastasia Yendiki wrote: > > Hi David - On the difference between .thresh and "not .thresh" labels: > > The BA labels come from averaging histologically derived labels from > > a set of post mortem brains. The non-thresholded version is just the > > sum of the corresponding labels from the different brains in > > fsaverage space. So vertices are included even if only one of the > > brains had their BA in that vertex, which means that these labels > > are going to be rather large. In the thresholded version, a > > threshold has been applied to the average BA label, to make it have > > an area as close as possible to the average area of the individual BA labels. I hope this makes sense. > > > > a.y <snip>

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HCP Pipelines v3.4.0 Released
by Jennifer Elam 10 Sep '14

10 Sep '14

*News from the Human Connectome Project (HCP)* *September 10, 2014* *HCP Processing Pipelines Released * The WU-Minn HCP Consortium is pleased to announce the open source release of HCP data processing pipelines at https://github.com/Washington-University/Pipelines. To download, click *releases* (near the top of the page), then under v3.4.0, click the “Source code (zip)” or “Source code (tar.gz)” button. These v3 pipelines were used to process HCP image data from the HCP 500 Subjects Release (June 2014). The HCP Pipelines are set of tools (primarily, but not exclusively, shell scripts) for processing MRI images for the Human Connectome Project <http://www.humanconnectome.org>. Among other things, these tools implement the Minimal Preprocessing Pipeline (MPP) described in Glasser et al. 2013 <http://www.ncbi.nlm.nih.gov/pubmed/23668970>. We are releasing the HCP Pipelines now for use to the community, but we are still in the process of making the scripts more robust, well-documented, and usable in other environments (other versions of operating systems, other queueing systems, other versions of prerequisite tools, etc.). We cannot guarantee that you will not have to make modifications to the scripts for them to be used successfully in your environment. The HCP Pipelines require installation of FSL 5.0.6, FreeSurfer v5.3.0-HCP, and Connectome Workbench v1.0. See the README.md <https://github.com/Washington-University/Pipelines/blob/master/README.md> in the GitHub repository for detailed information on prerequisite software versions, installation and processing instructions, example data, and processing resource requirements. Answers to frequently asked questions can also be found on our Github Repository: HCP Pipeline FAQ <https://github.com/Washington-University/Pipelines/blob/master/FAQ.md>. We encourage user feedback and improvement suggestions on the HCP Pipeline tools and the documentation. Discussion of HCP Pipeline usage and improvements can be posted to the hcp-users discussion list. Sign up for hcp-users at http://humanconnectome.org/contact/#subscribe Best, The WU-Minn HCP Consortium Jennifer Elam, Ph.D. Outreach Coordinator, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elamj(a)pcg.wustl.edu www.humanconnectome.org

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Re: [Freesurfer] mri_cvs_register
by Lilla Zollei 10 Sep '14

10 Sep '14

Could you also send the log file along? Thanks, Lilla On Wed, 10 Sep 2014, BigBen2293(a)web.de wrote: > I'm using the version stable v5.3.0. > Ben > >

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Freesurfer September 2014