Freesurfer January 2016

freesurfer@nmr.mgh.harvard.edu

130 participants
204 discussions

Re mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)
by Erik Lindberg 27 Jan '16

27 Jan '16

Dear Bruce and Freesufers, I tried to run the command and then to load it as an overlay - however I get nothing on the surface of the fsaverage brain. The program is telling me that it is including x-number of voxels into the mask but when I check I see nothing on the surface. What is going wrong here? Further the approach you proposed doing fMRI on the surface sounds interesting – but I have never used this approach. Could you give me a hint on the steps I need to take in order to do this? Thanks in advance! Eric yes, but do you want to do the fMRI analysis on the surface or in the volume? There are lots of advantages to doing it on the surface. If your sig.cluster.mgh was a surface overlay then the threholded.mgh might be exactly what you want. Load it on an inflated surface and take a look cheers Bruce

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3 years Post Doc position at the Neurofunctional Imaging Group in Bordeaux - France
by Fabrice Crivello 27 Jan '16

27 Jan '16

Dear all, Please find enclose a 3 years Post Doctoral position that may be of interest. Post Doc in data processing and databasing of large neuroimaging datasets. The Neurofunctional Imaging Group (GIN) is a CNRS-CEA joint research team of the Neurodegenerative Disease Institute, UMR 5293 at Bordeaux University. The GIN is a multidisciplinary research team gathering scientists with training in instrumentation, cognitive neurosciences, signal processing and databasing. The GIN is a partnering member of the MULTI-LATERAL (Multi-level Integrative Analysis of Brain Lateralization for Language, http://flagera.eu/?q=FLAG-ERA-call-2015-projects <http://flagera.eu/?q=FLAG-ERA-call-2015-projects>) project funded by the FLAG-ERA European consortium set up to contribute to the construction of the Human Brain Project Flagship project. This partnership aims to identify the anatomical, functional and genetic determinants of brain lateralization for language functions. Within this context, the GIN offers a 3 years Post Doc / Research Engineer position immediately available. The core work of the Post Doc will to extract accurate structural and intrinsic connectivity asymmetry phenotypes across a range of large scale imaging datasets: First, the post-doc will contribute to develop improved methods and dedicated software to reliably and automatically measure individual differences in lateralization for anatomy and resting state intrinsic connectivity. In a second phase, the Post Doc will apply the methods in brain imaging datasets (about 10 000 subjects, including the BIL&GIN, BIG, I-Share and UK-biobank neuroimaging databases) having genetic data available, for the purposes of association and rare variant analysis followed by integrated genome-level analysis with transcriptomic (lateralized gene expression) dataand genomic gene-set analysis. The applicant will benefit from the support of existing research in this topic area and preliminary works in the accurate definition of both structural and resting state asymmetry characterization together with data management of large neuroimaging cohorts. The qualified applicant should have a PhD (or equivalent) in neuro-image analysis, computer science (signal and/or image processing) or related field and a strong background / experience in neuroimaging data processing. Applicants should have experience with tools for analysis of neuroimaging data (Freesurfer, SPM,…) and a relevant programming experience (Unix, C/C++ / python, MATLAB). For further information, please contact Dr. Fabrice Crivello (fabrice.crivello(a)u-bordeaux.fr <mailto:fabrice.crivello@u-bordeaux.fr>). Salary is according to Bordeaux University salary grid depending on applicant experience. The position is limited for 3 years. Job location is in Bordeaux - France. Interested candidates should send their applications including CV with publication list and recommendation letters (names and contact information) and a written summary of research interests to fabrice.crivello(a)u-bordeaux.fr <mailto:fabrice.crivello@u-bordeaux.fr>. Dr Fabrice CRIVELLO Mob : +33 (0)6 81 06 47 53 Tel : +33 (0)5 47 30 44 03 Fax : +33 (0)5 47 30 43 94 https://www.researchgate.net/profile/Fabrice_Crivello IMN, Institut des Maladies Neurodégénératives, UMR 5293 Equipe 5 : GIN, Groupe d’Imagerie Neurofonctionnelle, CEA - CNRS - Université de Bordeaux Université de Bordeaux 146 rue Léo Saignat - CS 61292 - Case 28 33 076 Bordeaux cedex http://www.imn-bordeaux.org/

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recon-all: core dumped error
by Fengji Geng 26 Jan '16

26 Jan '16

Hello fs experts, We ran a command like ´recon-all -all -s HMN002 -hippocampal-subfields-T1T2 HMN002/T2/*.mgz T1T2´. Then, there was an error as ´Abort (core dumped)´ (which is also attached below). The error log file is also attached here. Error msg: ----------------------------------------------------------------------------------------------------- setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ reading atlas from /cell_root/software/freesurfer/dev/sys/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1592 labels changed using aseg relabeling using gibbs priors... 000: 2975 changed, 134786 examined... 001: 698 changed, 12707 examined... 002: 152 changed, 3873 examined... 003: 50 changed, 880 examined... 004: 29 changed, 284 examined... 005: 16 changed, 164 examined... 006: 7 changed, 87 examined... 007: 1 changed, 42 examined... 008: 0 changed, 4 examined... 206 labels changed using aseg 000: 105 total segments, 64 labels (264 vertices) changed 001: 43 total segments, 4 labels (14 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 1 filter iterations complete (10 requested, 0 changed) Abort (core dumped) Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s HMN002 exited with ERRORS at Tue Jan 26 00:23:40 EST 2016 Our freesurfer information: -------- freesurfer-Linux-centos6_x86_64-dev-20151215 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /cell_root/software/freesurfer/dev/sys FSFAST_HOME /cell_root/software/freesurfer/dev/sys/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /export/data/hippocampus/HMN/data MNI_DIR /cell_root/software/freesurfer/dev/sys/mni FSL_DIR /cell_root/software/fsl/new/sys Looking forward to hearing how we can resolve this error. Also, thanks in advance. Best, ----- Fengji

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How to register the workshop at Boston
by Yun Wang 26 Jan '16

26 Jan '16

Dear All, I am new to Freesurfer, so I want to take the Freesurfer Workshops at Boston this April. But It appears I have passed the deadline to register. Does anyone know how to make it happen? Thanks! Yun Wang

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DESPOT T1 map
by Worker, Amanda 26 Jan '16

26 Jan '16

Hi All, I have a T1 map which has been synthesised from a DESPOT imaging sequence and I am hoping to use this as input to recon-all. Do you know if this will be possible at all, or if there is anything I can do to prepare the T1 map to run through recon-all? Thanks in advance, Amanda

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mri_aparc2aseg BA.annot
by Qiyuan Tian 26 Jan '16

26 Jan '16

Hi, I was trying to use mri_aparc2aseg to convert the BA.annot (or BA.thresh.annot) to segmentation volume, that will be then converted to EPI space for some diffusion data. I tried both the BA.annot for the individual subject as well as the PALS_B12_Brodmann.annot in fsaverage. The command line I used was: mri_aparc2aseg --s s1 --annot BA.annot --o BAseg.mgz. It seems that this command is working, but when I view the BAseg.mgz file in freeview, the index for the BA areas seems wrong. For example, for BA1, the index says 2004 for ctx-rh-corpuscallosum. It seems that the index for BA areas in FreeSurferColorLUT are from 400 to 414. Is there a way to make the index correct? Or mri_aparc2aseg can only be used for aparc.a2009s.annot or aparc.annot? Thanks a lot. Best QT

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Qdec ROI Analysis
by Larissa McKetton 26 Jan '16

26 Jan '16

Dear Freesurfer community, I am working on an ROI analysis using qdec. I have created all aseg and aparc stats files and would like to determine if there are any differences in volume, surface area, and thickness for certain structures between two groups. I was wondering with the analysis, would it be okay to use the resulting aseg/aparc output stats from either the Desikan/Destrieux atlases and run these values through SPSS or is it better to draw ROI labels on the fsaverage brain, apply the label to each subject, and run the analyses this way. I am asking because the following tutorial states: *"Note*: If you want to use a pre-existing label and register it to fsaverage, be aware that this might involve two instances of resampling and the results might not be as accurate as they would be if you drew the label on fsaverage. Please contact the FreeSurfer team to get more details on this process if you have any concerns." http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI#Tableofth… If drawing labels on the fsaverage brain and applying them to each subject is the way to go- would I need to correct for multiple comparisons? Many thanks, Larissa

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-hippocampal-subfields-T1 fails in freesurfer-Darwin-OSX-dev-20160109
by Carl Anderson 26 Jan '16

26 Jan '16

Hi Everyone, Subfields seems to fail to run when part of the recon-all -all command line and also fails when run on its own (but gives no error). Here is the output and recon-all log attached: Thanks! Carl Fitting mesh to synthetic image from ASEG took 468.3773 seconds Transforming points Transforming points dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin//../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/local/lib/libgcc_s.1.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin//../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/local/lib/libgcc_s.1.dylib /bin/bash: line 1: 22256 Trace/BPT trap: 5 /Applications/freesurfer/bin//mri_convert tempT1.mgz T1resampled.mgz -odt float -rt cubic -vs 0.33333 0.33333 0.33333 > /dev/null /Applications/freesurfer/bin//mri_convert tempT1.mgz T1resampled.mgz -odt float -rt cubic -vs 0.33333 0.33333 0.33333 >/dev/null: Trace/breakpoint trap mghRead(/Applications/freesurfer/subjects/ParallelEveryone/CAT104/tmp/hippoSF_T1_v10_right/T1resampled.mgz, -1): could not open file error reading from volume T1resampled.mgz threshold mask volume at 0.5 mghRead(/Applications/freesurfer/subjects/ParallelEveryone/CAT104/tmp/hippoSF_T1_v10_right/T1resampled.mgz, -1): could not open file /Applications/freesurfer/bin//mri_mask: could not read source volume T1resampled.mgz /Applications/freesurfer/bin//mri_mask -T 0.5 T1resampled.mgz asegModBinDilatedResampled.mgz T1resampled.mgz >/dev/null: Signal 124 mghRead(/Applications/freesurfer/subjects/ParallelEveryone/CAT104/tmp/hippoSF_T1_v10_right/T1resampled.mgz, -1): could not open file error reading from volume T1resampled.mgz mghRead(/Applications/freesurfer/subjects/ParallelEveryone/CAT104/tmp/hippoSF_T1_v10_right/hippoMaskResampled.mgz, -1): could not open file threshold mask volume at 0.5 mghRead(/Applications/freesurfer/subjects/ParallelEveryone/CAT104/tmp/hippoSF_T1_v10_right/T1resampled.mgz, -1): could not open file /Applications/freesurfer/bin//mri_mask: could not read source volume T1resampled.mgz /Applications/freesurfer/bin//mri_mask -T 0.5 T1resampled.mgz hippoMaskResampledDilated.mgz T1resampled.mgz >/dev/null: Signal 124 Error using kvlAtlas3D_Matlab /autofs/space/panamint_005/users/iglesias/software/MAC_ATLAS_3D/Atlas3D_131025/itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x103507280): Can't find/open file: T1resampled.mgz Error in kvlReadCroppedImage (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 605) #------------------------------------------ Started at Tue Jan 26 09:17:04 EST 2016 Ended at Tue Jan 26 09:34:33 EST 2016 #@#%# recon-all-run-time-hours 0.291 recon-all -s CAT104 finished without error at Tue Jan 26 09:34:33 EST 2016 -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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Brain stem segmentation in Freesurfer 6 {Disarmed}
by Alshikho, Mohamad J. 26 Jan '16

26 Jan '16

Dear Freesurfers, After segmenting the brain stem using FS6 tools. I used Free view to visualize the final images. In Free view I opened "orig.mgz", "wmparc.mgz" and "brainstemSsLabels.v10.mgz" Then I tried to check the segmented structures by flipping the images. I noticed an overlap between Ventral DC ( left and right) and mid brain ( as an output of brain stem segmentation). I "wmparc.mgz" atlas: Ventral DC and brain stem are totally different segments. Now After segmenting the brain stem. I see that the Ventral DC belongs to the mid brain. Is this natural? Thanks in advance for any suggestion! Mohamad

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Incomplete output
by maryam koochaki 26 Jan '16

26 Jan '16

Dear experts,I am kind of new at working with freesurfer.recon-all process has completed without error, but when I look at brainmask volume on freeview, one of the issues is that lateral ventricle is completely excluded. I have tried to edit it with editing the white matter volume, but no success so far. I do not know how to correct it. Have anybody here had the same issue? Thanks,Maryam

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Freesurfer January 2016