Freesurfer July 2016

freesurfer@nmr.mgh.harvard.edu

143 participants
252 discussions

Fwd: question about volume of mask
by Dorsa Haji Ghaffari 01 Aug '16

01 Aug '16

Hi Bruce, I was able to reslice the thalamus mask correctly, but when I measure the volume of the resliced thalamus, is not the same as the original thalamus. I was wondering why that is happening and which volume is more accurate. I appreciate any suggestions. I have attached both masks. Also can you tell me how to measure the volume of the resliced thalamus in Freesurfer? Thank you Dorsa

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MNI coordinates of all the vertices of fsaverage
by Sabin Khadka 01 Aug '16

01 Aug '16

Hi Doug, I tried to pick up from the thread below to get MNI coordinates of each destrieux parcellation region. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html I created label files from mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation aparc.a2009s --outdir label_destrieux # which works fine And I tried to get the coordinates of each labels using mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel <label file> --sum <output file> --centroid --thmin 0 --hemi lh --subject fsaverage But, all left labels would produce the same coordinates and so does right labels. (I've attached few example files here with). Also, it says TalX, TalY, TalZ are these coordinates in MNI or Talairach? Thanks for help.

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postdoc position
by Bruce Fischl 31 Jul '16

31 Jul '16

FYI --- The Neuroradiology Section at the University of California, San Francisco (UCSF) is seeking an exceptional postdoctoral candidate in multimodal imaging of neuropsychiatric and neurodegenerative disorders. Combining neuroimaging, genetics, and computational methods, our group is interested in elucidating mechanisms underlying neuropsychiatric and neurodegenerative conditions ranging from obsessive compulsive disorder to dementia. Our emphasis is on using multimodal imaging (including structural and functional MRI, MR spectroscopy, EEG/MEG) and imaging genetics to develop genetic and imaging biomarkers that can be leveraged to both diagnose neuropsychiatric disease and to provide a rational framework for targeting and monitoring therapy - including emerging neuro-modulatory technologies - in individual patients. We seek a postdoctoral candidate with advanced training in neurosciences or biomedical engineering, a strong background in human imaging, and a desire to pursue translational research using a multi-disciplinary approach. The ideal candidate should have considerable experience with data analysis, simulation, and visualization using packages such as Matlab, R, or Python, as well as facility with MRI image analysis tools such as Freesurfer, FSL, and SPM. Applicants should have a Ph.D. or M.D. degree with less than five years of postdoctoral experience. Highly motivated individuals with a record of productive research are encouraged to apply. The position is available starting August 1, 2016. UC San Francisco seeks candidates whose experience, teaching, research, or community service has prepared them to contribute to our commitment to diversity and excellence. The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age or protected veteran status. Salary is commensurate with qualifications and experience. Interested applicants should send curriculum vitae/NIH biosketch, Cover Letter, and three references to: Dr. Leo Sugrue (leo.sugrue(a)ucsf.edu) and Dr. Rahul Desikan (rahuldesikan(a)gmail.com)

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Siemens SPECTRA 3T - Help with sequences
by Felipe Picon 30 Jul '16

30 Jul '16

Dear colleagues, I’m a researcher psychiatrist who is currently testing image acquisitions with different sequences on a Siemens 3T SPECTRA scanner. I would like to learn from you if any of you had experience with this scanner in the collection of high-resolution structural images (MPRAGE), DTI, and Resting State Functional Connectivity images. We only have access to a 12-channel Head Coil, though. Luckily the scanner has the possibility of acquiring 128 direction of DTI. If any of you can share with me any good quality sequences that could fit this set of characteristics it would be highly appreciated Thank you very much Best regards, Felipe Picon -- *Felipe Picon, MD, MSc* Child and Adolescent Psychiatrist ===================================================== ADHD Neuroimaging Researcher at the Adult ADHD outpatient research program PRODAH-A <http://www6.ufrgs.br/prodah/prodah/e-equipe.html> - HCPA <http://www.hcpa.ufrgs.br> - UFRGS <http://www.ufrgs.br> Porto Alegre - RS - Brazil Vice-Coordinator of the Technology Addiction Study Group - GEAT <http://dependenciadetecnologia.org/quem-somos/> Secretary of the Early Career Psychiatrists Section - World Psychiatric Association <http://www.wpanet.org/detail.php?section_id=11&content_id=1703> Corresponding Member of the American Academy of Child and Adolescent Psychiatry - AACAP ===================================================== Web based CV <http://lattes.cnpq.br/3896757276389918> Google Scholar Profile <http://scholar.google.com/citations?user=TxI0ZYYAAAAJ&hl=en> felipepicon(a)gmail.com

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Longitudinal single time point cross sectional comparison
by Emmanuel Nwosu 30 Jul '16

30 Jul '16

Dear Freesurfer users, I have longitudinal data with three time points but want to run a cross sectional comparison on the first instance between group on just one time point (using QDEC). Any Idea on how I could do that on longitudinal data. Thanks for your help. Emmanuel Nwosu

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error during longitudinal -long stream
by Jinsong Tang 30 Jul '16

30 Jul '16

Hi all, I found an error during the longitudinal -long stream: recon-all -long P1001-2 P1001 -all ...... FREESURFER_HOME /space/raid/fmri/freesurfer Actual FREESURFER_HOME /space/raid/fmri/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21 UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux ...... mris_spherical_average -erode 1 -orig white -t 0.4 -o P1001-2.long.P1001 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject P1001-2.long.P1001. processing subject lh.EC_average... MRISread(/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Not a directory mris_spherical_average: could not read surface file /space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg Not a directory Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21 UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux recon-all -s P1001-2.long.P1001 exited with ERRORS at Fri Jul 8 21:33:02 PDT 2016 Please help me fix this error! Thanks and best regards, Jinsong

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Re: [Freesurfer] significance overlay in freeview
by Caroline Beelen 30 Jul '16

30 Jul '16

Dear Ruopeng, Yes, I'm running FS 5.3. :) But then how can I see the correct significance overlay? Cause even when leaving out some commands (which may or may not work in 5.3), freeview does load, but seems to only display the DK-atlas on fs average (... and gets stuck sometimes too), as I described below. I cant find the right command ... So I guess my actual question is: Which command should i use to view a (correct) significance overlay in FS 5.3? Thank you very much for your help! Regards, Caroline Hi Caroline, Are you running FS 5.3? The command on the webpage is based on the upcoming 6.0, I believe. So some of the command line options are not available in 5.3. Best, Ruopeng > On Jul 29, 2016, at 9:11 AM, Caroline Beelen <caroline.beelen(a)kuleuven.be> wrote: > > Dear FS team, > > Apologies in advance for perhaps again a rather basic question. I attempted to load the aparc overlay in freeview by using the written command from the group analysis page, however it failed to load correctly. > > I used the following command: > freeview -f fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=roi.lh.area.dyslect_basic.glmdir/dyslect/sig.mgh:overlay_threshold=4,5 -viewport 3d > ? roi.lh.area.dyslect_basic.glmdir is the file obtained from the GLM-analysis and dyslect is the contrast folder within this file (main effect of dyslexia), containing a sig.mgh file (all seems fine) > > Unfortunately, I got an error that it does not recognize ?overlay_treshold=4,5?. I used freeview ?h and tried certain commands alike, but they didn?t work. When leaving out this part, I got another error that it failed to recognize ?annot_outline=1?. Again, leaving this out too, freeview loads itself and the DK-regions become visible. However, nothing else seems to get activated, and even not when putting ?configure overlay? (which is set to sig.mgh) to 1.3 as minimum and 3 as maximum. So basically nothing happens. > When looking at the command line it says that it implemented the colortable of DK-atlas (even twice), but it tells me nothing else. Also, after closing and reloading Freeview by using the similar command and then clicking on ?configure overlay? the screen sometimes gets stuck, giving me the impression that something must be wrong with the command. > > Could you please help me out and provide me the right command-line for loading the overlay of the significance map of ?roi.lh.area.dyslect_basic.glmdir/dyslect?? > > Thanks in advance! > > Kind regards, Caroline

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brain mask and T1 are not the same size
by Isabelle Deschamps 29 Jul '16

29 Jul '16

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Research Assistants needed for longitudinal brain development study at Boston Children's Hospital
by Gaab, Nadine 29 Jul '16

29 Jul '16

The Gaab Lab<http://www.thegaablab.com/> in collaboration with the Fetal-Neonatal Neuroimaging and Developmental Science Center<https://fnndsc.babymri.org/> at Boston Children's Hospital is looking for two Research Assistants to assist with all study phases of a new NICHD funded longitudinal project which assesses functional and structural brain development from infancy to early elementary school age. This includes subject recruitment for pediatric research studies which will include close interaction with nurseries, child care centers and elementary schools in the Boston area, scheduling of pediatric research subjects, database maintenance, implementation and maintenance of analysis software; pediatric testing (including MRI/fMRI scanning of young children and infants<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.babymri.org_&d=BQMF…>) and data analyses (psychometrics, psychophysics and structural/functional magnetic imaging), stimuli design and administrative work (e.g., preparation of internal review board proposals). These positions are ideal for anyone considering future graduate study in cognitive (developmental) neuroscience, developmental psychology, computer science, cognitive science or neuroscience. Bachelor's Degree in computer science, psychology, cognitive science, neuroscience, math, or related field required. Comfort with a heterogeneous computing environment (Linux/Unix, Mac, and Windows) as well as some programming experience preferred; knowledge of psychological experiment software (E Prime, Presentation, etc.) and/or fMRI analyses software helpful. Prior experience with infants and children would be very helpful. Demonstrable pre-existing interest in developmental psychology/ cognitive neuroscience desired; knowledge of neuroanatomy, statistics or machine learning helpful. Must be self-motivated and able to work in a fast-paced, changing environment and must like working with infants, children and families. Start date September or October 2016. Please first apply to Nadine.gaab(a)childrens.harvard.edu<mailto:Nadine.gaab@childrens.harvard.edu> with a cover letter and CV. "If we knew what it was we were doing, it would not be called research, would it?" A. Einstein (1879-1955) Nadine Gaab, PhD Associate Professor of Pediatrics Boston Children's Hospital/Harvard Medical School Department of Medicine/Division of Developmental Medicine Laboratories of Cognitive Neuroscience Mail stop code: BCH3178 1 Autumn Street (Office 643); Boston, MA 02115 nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu> phone: 857-218-3021 www.gaablab.com<http://www.gaablab.com>

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How does Optseq2 arrange order of conditions?
by 連志浩 29 Jul '16

29 Jul '16

Hello all, I'm a new user of Optseq2, and I have 2 questions about optseq2 after I got some sequences and read Dale (1999). I'll be grateful to anyone can provide help. 1. I'm curious about why optseq2 arranged the order of conditions, does anyone can provided some references to me? Dale (1999) just discussed about mean ISI and fixed/randomizes ISI design, I wonder what's the difference if I just keep the duration order of null condition (jitter) and randomly present different conditions. 2. This question is about the total duration of experiments. I'm used to execute experiments by E-Prime 2.0, and the presentation may delay in E-Prime (I know this situation can be deal with "Pre-release"). If there's a fixation period (15s) after my trials is over (but participants are still scanned), and the delay just affect the duration of the fixation period. Should I reduce the duration of delayed stimulus in terms of the delayed time? Or I don't need to care about the delay, because the key point is the order of conditions and null/jitter? Thanks for your reading. Best regards, Chih-Hao

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Freesurfer July 2016