Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Ref FAST and results visualization issue
by stdp82＠virgilio.it 27 Jan '16

27 Jan '16

Hi list, I have two requests please. A- I need to have a reference for FS-FAST (seed based analysis on rs data) B- I have difficulties for results visualization. How can I do to visualize the the cortical areas which are functionally connected with the controlateral seed? For example, my seed are right and left amygdala.To visualize RIGHT amygdala - RIGHT cortex connectivity I'm doing: cd my-group/fc.ramgseed.surf.lh/R_Amygdala tksurfer fsaverage rh inflated -aparc -overlay my-glm.wls/intercept/sig.nii.gz and all is fine. To visualize RIGHT amygdala - LEFT cortex connectivity I'm doing: tksurfer fsaverage lh inflated -aparc -overlay my-glm.wls/intercept/sig.nii.gz but the image is so confused. It seem to be the translated image which I have projected in the right semi. Thanks Stefano

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Re: [Freesurfer] FreeSurfer Lateral Ventricles Error
by Allison Leigh Rainford 27 Jan '16

27 Jan '16

Attached are screenshots of the initial issue and the issue after my attempt to correct it. [cid:CB5F258E-AFA1-430D-B7E6-167D5A5FE966][cid:8F112E13-A56B-4C1B-9310-15436F1F4FF4]

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Postdoctoral Fellow at Emory University
by Junjie Wu 27 Jan '16

27 Jan '16

The Departments of Medicine and of Radiology and Imaging Sciences at Emory University is seeking a postdoctoral fellow to work with a team of physicians and neuroscientists focused on neuroimaging (MRI: Arterial Spin Labeling and cerebrovascular reactivity). The position provides excellent opportunity to work in an interdisciplinary environment and have close interactions with MR physicists, radiologists, neurologist, internists and neuroscientists. Accesses are available to two dedicated research MR 3T Siemens Tim-Trio scanners, one 9.4T animal scanner, and a powerful computer-cluster. Close collaboration with the Emory University Hospital, which houses a clinical 3T Siemens Tim-Trio and five 1.5T MR scanners, allows easy translation of technical developments to clinical settings. The qualifications of a successful candidate should include · A PhD degree in Electrical Engineering, Biomedical Engineering, Physics, or other related fields · Strong background in signal processing, image processing and quantitative analysis. Excellent proficiency with Matlab and/or C/C++ programming language. · Demonstrated independent research capabilities and good organizational and inter-personal skills. Previous experiences with medical image processing including freesrufer, FSL and SPM are desirable; The candidate is expected to work on projects involving performing image processing using existing tools and development of new methodologies. Potential research projects depend on the mutual interests of the candidate and the PI. These may include but are not limited to: (1) analyzing CO2-vasoreactivity images; (2) reconstruction and analysis methods for quantitative susceptibility mapping (QSM), (3) quantification and analysis methods for arterial spin labeling, dynamic susceptibility contrast imaging and diffusion imaging. Plans to obtain independent funding is highly desirable. Emory University provides competitive salaries commensurate with experience. This position is funded by NIH grants for at least 5 years. To apply, please send your CV to Ihab Hajjar, MD (ihajjar(a)emory.edu) and Deqiang Qiu, PhD (dqiu3(a)emory.edu)

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tracula quality assessment dwi_motion.txt units
by Ruth Carper 27 Jan '16

27 Jan '16

What are the units of measure for translation and rotation as output in the dwi_motion.txt file from Tracula? It's not stated in the output file or on the page http://freesurfer.net/fswiki/FsTutorial/TraculaOutputsI would have assumed mm and degrees, but the rotation values are consistently less than 0.01, which doesn't seem likely. --Ruth

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FreeSurfer Lateral Ventricles Error
by Allison Leigh Rainford 27 Jan '16

27 Jan '16

?Good morning, I am editing a brain using FreeSurfer version 5.1 and I have a pial and white matter boundary issue that persists in the lateral ventricles, specifically where the software would draw a boundary between the right and left hemispheres of the brain. Upon running it through the recon-all pipeline, it reconstructed those ventricle boundaries in a way that the boundaries did not even touch the walls of the ventricles and had the boundary lines cutting through the middle of the left and right lateral ventricles. After fully filling the ventricles with 255's on the wm.mgz file (to match the general reconstruction of other brains we have worked on), the issue still largely persists. The pial and white matter boundaries now more accurately follow the outer edges of the ventricles but the boundaries that separate the left and right hemisphere are still very messy. This issue can be found in over 60 slices throughout the brain. Any and all help is appreciated. Best, Allison

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Statistical analyses with QDEC
by Francesco Cardinale 27 Jan '16

27 Jan '16

Dear Freesurfer experts, I have some questions about statistical analyses. How to adjust for sex and age? I use the precompiled Freesurfer 5.3.0 MacOSX version, and its tool QDEC to compare cortical thickness between two groups. I would like to use age and sex as nuisance factors. No problem with the age, but I don’t see the sex in the list of usable variables if I code it as a categorical variable (male / female). On the opposite, If I code it as numbers (male = 1, female = 2) I can use it, but how can I declare that it is a factor and not a continuous numerical variable? I don’t want that “female” affects the fitting of the GLM with a value that means “male” * 2. What about the use of other morphometric properties as nuisance factors? For example, how could I use sulcality or LGI as nuisance factors? Is it possible to use more than one scalar simultaneously? Similarly to question 2, is it possible to use home-made *.mgh scalars as a nuisance factors? How? Do the command-line tools allow such analyses better than QDEC? Related to my questions, which features do they add? In this field of interest, are there any major advantages coming with Freesurfer 6.0? Thanks a lot and best regards Cico Francesco Cardinale, MD Neurosurgeon "Claudio Munari" Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda "Ca' Granda" Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia <x-apple-data-detectors://0/0> phone 0039 02 64442917 <tel:0039%2002%2064442917> fax 0039 02 64442868 <tel:0039%2002%2064442868> e-mail francesco.cardinale(a)ospedaleniguarda.it <mailto:francesco.cardinale@ospedaleniguarda.it>

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Re: [Freesurfer] Reg: CORRECTING DEFECT 126 (vertices=61161, convex hull=14255)
by Bruce Fischl 27 Jan '16

27 Jan '16

Hi Jesu can you please post this type of question to the FS list so others can reply and/or learn from the answer? This defect is too big - the defect correction grows quadratically in time with the number of vertices in the defect. vertices=61161 means that you have a defect that is about half the size of the total surface. You need to look at the ?h.orig.nofix and/or the ?h.inflated.nofix and figure out what the defect is and correct it by either editing the wm.mgz or adding control points. If you can't figure this out you can upload the entire subject dir to our ftp site and one of us will take a look. cheers Bruce On Wed, 27 Jan 2016, Jesu Kiran Spurgen wrote: > Dear Prof. Fischl, > Good Afternoon! I have been running freesurfer for a patient data, and have > to find this retesselalation of defect. I have successful with some data but > for some others it looks frozen even after 4 days. Could you please kindly > suggest what I could do here? How could I get some results overriding this > particular step? > > I would extremely grateful for your kind reply and help. > > Warm regards, > > > Jesu Kiran Spurgen > Postgraduate Student, Advanced Medical Imaging > KU Leuven, Belgium > >

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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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