Freesurfer October 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
170 discussions

Postdoctoral Fellowship at the Martinos Center
by Baran, Bengi 06 Oct '16

06 Oct '16

We believe this posting may be of interest for some members of the group: Postdoctoral Fellowship at the Martinos Center for Biomedical Imaging and the Psychiatric Neuroimaging. Division of the Psychiatry Department at Massachusetts General Hospital, Charlestown, MA. Project: Multimodal neuroimaging studies of sleep and memory PI: Dara S. Manoach, Ph.D. The position will involve investigating the role of sleep in memory consolidation, how these processes go awry in schizophrenia and autism, and the efficacy of pharmacological and other interventions. Our work has linked cognitive deficits to a specific heritable mechanism (sleep spindles) and we are seeking effective interventions. In collaboration with Dr. Robert Stickgold’s lab at Beth Israel Deaconess Medical Center, we are extending and expanding this basic and clinical research program using state-of-the art tools including high density EEG (polysomnography), MEG, DTI, functional connectivity MRI, fMRI, and behavioral studies. We are seeking someone to participate in these foundation and NIMH-funded investigations who is familiar with MEG/EEG methodology and data analysis, comfortable with methodological innovation, and is interested in optimizing and developing analysis streams tailored to the study aims and populations. New approaches and ideas are encouraged, as are independent projects that dovetail with current studies. The position requires working closely with the PI, as well as with Dr. Stickgold, other Martinos Center investigators, particularly Dr. Matti Hamalainen, Director of the MEG Core Lab, and lab mates to design studies, acquire data, and develop, explore, improve and apply data analytic techniques. Training in clinical research and in the acquisition, analysis, and interpretation of neuroimaging data will be provided. Requirements: PhD or MD Experience with MEG/EEG data analysis/methodology and/or other signal processing. Background in cognitive neuroscience, experimental psychology, and an interest in clinical applications are a plus. Position available immediately. Interested applicants should email: (a) CV, (b) statement of post-doctoral and career goals, (c) writing sample (e.g., a published manuscript), and (d) letters and/or contact information for three references to Dara Manoach Dara.Manoach(a)mgh.harvard.edu<mailto:Dara.Manoach@mgh.harvard.edu> Stipend levels are in line with experience and NIH. A two-year commitment is required. Best, Bengi Baran, Ph.D. Post-Doctoral Fellow Martinos Center for Biomedical Imaging Harvard Medical School Massachusetts General Hospital 149 13th Street Charlestown Navy Yard Charlestown, MA 02129 email: bbaran(a)mgh.harvard.edu<mailto:bbaran@mgh.harvard.edu> phone: 617-643-7964 fax: 617-726-4078 https://sleep.med.harvard.edu/people/trainees/1598/Bengi+Baran+MA+PhD

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ERROR: QdecGlmDesign::Create: bad factor!
by Nabin Koirala 06 Oct '16

06 Oct '16

Dear freesurfer team, I was trying to run QDEC with two discrete factors but I got this error and could not quite figure out what is wrong. Your suggestion would be highly appreciated. The table and the error is as shown below: Data table /Applications/freesurfer/subjects/qdec/qdec.table.dat loaded. Verifying subject data....................................................Subject verification complete. Input table: /Applications/freesurfer/subjects/qdec/qdec.table.dat Subj#, SubjID, Data... 1 SubBSF0_01 Pre BSF 2 SubBSF0_02 Pre BSF 3 SubBSF0_03 Pre BSF 4 SubBSF0_04 Pre BSF 5 SubBSF0_05 Pre BSF 6 SubBSF0_06 Pre BSF 7 SubBSF0_07 Pre BSF 8 SubBSF0_08 Pre BSF 9 SubBSF0_09 Pre BSF 10 SubBSF0_10 Pre BSF 11 SubBSF0_11 Pre BSF 12 SubBSF0_12 Pre BSF 13 SubBSF0_13 Pre BSF 14 SubBSF0_14 Pre HFS 15 SubBSF0_15 Pre HFS 16 SubBSF0_16 Pre HFS 17 SubBSF0_17 Pre HFS 18 SubBSF0_18 Pre HFS 19 SubBSF0_19 Pre HFS 20 SubBSF0_20 Pre HFS 21 SubBSF0_21 Pre HFS 22 SubBSF0_22 Pre HFS 23 SubBSF0_23 Pre HFS 24 SubBSF0_24 Pre HFS 25 SubBSF0_25 Pre HFS 26 SubBSF0_26 Pre HFS 27 SubBSF1_01 Post BSF 28 SubBSF1_02 Post BSF 29 SubBSF1_03 Post BSF 30 SubBSF1_04 Post BSF 31 SubBSF1_05 Post BSF 32 SubBSF1_06 Post BSF 33 SubBSF1_07 Post BSF 34 SubBSF1_08 Post BSF 35 SubBSF1_09 Post BSF 36 SubBSF1_10 Post BSF 37 SubBSF1_11 Post BSF 38 SubBSF1_12 Post BSF 39 SubBSF1_13 Post BSF 40 SubBSF1_14 Post HFS 41 SubBSF1_15 Post HFS 42 SubBSF1_16 Post HFS 43 SubBSF1_17 Post HFS 44 SubBSF1_18 Post HFS 45 SubBSF1_19 Post HFS 46 SubBSF1_20 Post HFS 47 SubBSF1_21 Post HFS 48 SubBSF1_22 Post HFS 49 SubBSF1_23 Post HFS 50 SubBSF1_24 Post HFS 51 SubBSF1_25 Post HFS 52 SubBSF1_26 Post HFS 1 Time discrete 2 1 Pre 2 Post 2 Group discrete 2 1 BSF 2 HFS Continuous Factors: Mean: StdDev: ------------------- ----- ------- Number of subjects: 52 Number of factors: 2 (2 discrete, 0 continuous) Number of classes: 4 Number of regressors: 4 ============================================================ Data table loading completed successfully. SUBJECTS_DIR is '/Applications/freesurfer/subjects' ERROR: QdecDataTable::GetFactor: '' is not in datatable! ERROR: QdecGlmDesign::Create: bad factor! Thank you. Regards, Nabin

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Postdoctoral Position at UCSF in California, USA on cognitive neuroscience of language processing
by Roeland Hancock 05 Oct '16

05 Oct '16

The Hoeft Lab (http://brainLENS.org <http://brainlens.org/> PI: Fumiko Hoeft MD PhD) at the UCSF Dept of Psychiatry and Weill Institute for Neurosciences is looking for an exceptional postdoc in the field of neurolinguistics, with advanced neuroimaging, computational, programming and organizational skills. Training in genetics is a plus. The primary project that the postdoc will be responsible for is the examination of intergenerational neuroimaging using a ‘natural’ cross-fostering design that allows dissociation of genetic, prenatal and postnatal environment on brain networks that are transmitted across generations. Related articles from our lab can be found here - Yamagata et al. J Neurosci 2016 (http://goo.gl/vMK8iy) Ho et al. Trends in Neurosci 2016 (http://goo.gl/SyXLcK) and Scientific American (http://goo.gl/YTiH6D) There are many opportunities to be involved in other projects on the neuroscience of language and literacy. The position can begin immediately. Please email info(a)brainlens.orgwith a cover letter and your CV. Please add “[Postdoc job]” and your full name in the Subject of the email. Qualified candidates will be asked to have 3 letters of reference forwarded. Roeland Hancock

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FreeView questions
by Anders Hougaard 05 Oct '16

05 Oct '16

Dear all, Please see the attached image of a surface overlay (gamma.mgh from a standard group analysis of cortical thickness with two groups and two contrasts). Any ideas why the color bar looks weird? Question 2: How do you specify rotation in 3D view like it was possible in TKsurfer, e.g. if I want to rotate the 3D brain exactly 45 degress clockwise around the z axis? Thank you :) Best, Anders

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MS lesion - white / pial surface issue
by Fire Tech 05 Oct '16

05 Oct '16

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Functional Connectivity Follow-up question
by ERIK JAHNER 05 Oct '16

05 Oct '16

Dear Free Surfer Experts, I have a follow-up question to a previous message sent by Lingqiang which you responded to on Dec 21st 2011. (I have included a copy of this message below, but here is a link https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-December/021728.… ). In a functional connectivity analysis using a subject specific SURFACE label defined priori, you suggest using mir_label2vol to convert the surface label to a volume. However, I would assume that there is some benefit to using the smoothed values found in a surface vertices after preprocessing as opposed to voxels. If we use a .mgz segmentation file this seems to sacrifice the benefits of the free surfer pipeline. Or.... is this only used for reference and using the time course stored in the vertices on the surface and not actually just the 3d volume. To clarify my question... Is the functional connectivity processing stream using the time courses associated with the surface vertices after smoothing or is it just getting the time course of the voxels nearest the targeted label vertices? Thanks Erik --------------------------------------------------- Hi Lingqiang, convert your .label file to a volume using mri_label2vol for each subject, something like cd $SUBJECTS_DIR/$subject/mri mri_label2vol --label lh.yourlabel.label --temp orig.mgz --regheader orig.mgz --subject $subject --hemi lh --proj frac 0 1 .1 --o yourlabel.mgz When you run fcseed-config specify -segmentation yourlabel.mgz -segid 1 doug konglq at nmr.mgh.harvard.edu wrote: > Hi Freesurfers, > > We are trying to do a resting-state functional connectivity analysis using > freesurfer. Instead of using the aparc+aseg segmentations as seeds, we > would like to use a subject-specific surface labels that we have defined > apriori. > > In the fcseed-config step, we then don't have a "segid" as in the > anatomical seeds case. What should we specify as the -segid and -seg > (segmentation)? > > We also looked into the ROI-based options using "-roi" but this takes > seeds from output of "funcroi-config" and requires that we specify a > contrast and an analysis. How should we just specify a surface label > without generating a new analysis and contrast? > > Any help or suggestions are appreciated. > > > Lingqiang > _______________________________________________ > Freesurfer mailing list > Freesurfer at nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve at nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html --------------------------------------------------------

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Input file in subcortical analysis using mri_glmfit
by Greenberg, Jonathan 05 Oct '16

05 Oct '16

Dear FS users I am trying to compare subcortical volumes of 3 groups (and no co-variates) pre and post an intervention using mri_glmfit in Paired-Analysis. My question pertains to which file I should specify as the input (--y) in the mri_glmfit command. The examples in the Wikis use either a preprocessed and smoothed surface file (e.g. “--y lh.paried-diff.thickness.sm05.MGH”) or “y.mgh”. The surface examples seem irrelevant since I am interested in subcortical volumes. When I try to follow the y.mgh example mri_glmfit \ --glmdir rh.paired-diff \ --y y.mgh \ --fsgd paired-diff.fsgd \ --C n-vs-w.mtx \ --C n+h-vs-w.mtx \ --C n-vs-h.mtx \ it seems it cannot locate the y.mgh file, and the following message is displayed …loading y from /autofs/space/jizo_001/Users/jonathan-bhi-SUBJECTS_DIR/qdec/y.mgh mghRead (/autofs/space/jizo_001/Users/jonathan-bhi-SUBJECTS_DIR/qdec/y.mgh -1): could not open file ERROR: loading y /autofs/space/jizo_001/Users/jonathan-bhi-SUBJECTS_DIR/qdec/y.mgh Should something be done to create y.mgh prior to running this command (given that qdec is not used)? Should a different input file be used instead? Thank you Jonathan

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FSL-compatible surfaces
by saraizad＠alumni.ubc.ca 04 Oct '16

04 Oct '16

Hi Freesurfer team, I am trying to use Freesurfer surfaces to do tractography in FSL. I extracted two ROIs, one of which is the output of the following command: label2surf –s lh.white.gii –o lh.prefrontal.gii –l lh.prefrontal.txt and the other is the output of: mri_tessellate aseg.mgz 46 rh.cerebellum.wm My question is how to convert these files to fsl-compatible surfaces usable for tractography If I have to use surf2surf, I am not clear on how to do it. Should I change both the type and the convention of the images. Thanks a lot, Sara

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QCACHE always produces zeros for some vertices in the left hemisphere
by Sam Mathias 04 Oct '16

04 Oct '16

Dear list, I'm trying to extract vertex-level measures of thickness, area, etc, for all of my subjects. I ran recon-all -all on all subjects as normal, then ran: recon-all -s {subject} -qcache where {subject} is the subject ID. This was followed by `mris_convert` to make the values human-readable: mris_convert -c {subj_dir}/surf/{hem}.{meas}.fwhm25.fsaverage.mgh {fsavg_dir}/surf/lh.sphere {subj_dir}/surf/{hem}.{meas}.fwhm25.fsaverage.asc I did this for each subject, hemisphere, and measure (thickness, area, sulc). Many of the vertices in the left hemisphere always produce values of 0, for every subject, and for every measure. The first offending vertex is #9. So if I head a randomly chosen file, I get: [sm2286@grace0 surf]$ head lh.area.fwhm25.fsaverage.asc 000 0.00000 0.00000 100.00000 0.43150 001 27.64000 -85.07000 44.72000 0.39083 002 89.44000 0.00000 44.72000 0.33804 003 27.64000 85.07000 44.72000 0.81910 004 -72.36000 52.57000 44.72000 0.41731 005 -72.36000 -52.57000 44.72000 0.37795 006 -27.64000 -85.07000 -44.72000 0.77490 007 72.36000 -52.57000 -44.72000 0.49643 008 72.36000 52.57000 -44.72000 0.00000 <--- this value This is a different subject: [sm2286@grace0 surf]$ head lh.sulc.fwhm25.fsaverage.asc 000 0.00000 0.00000 100.00000 0.00692 001 27.64000 -85.07000 44.72000 -0.45451 002 89.44000 0.00000 44.72000 0.38711 003 27.64000 85.07000 44.72000 0.17178 004 -72.36000 52.57000 44.72000 -0.54163 005 -72.36000 -52.57000 44.72000 -0.01465 006 -27.64000 -85.07000 -44.72000 -0.07269 007 72.36000 -52.57000 -44.72000 0.46408 008 72.36000 52.57000 -44.72000 0.00000 <--- this value Bizarrely this also happens when I switch the target of qcache to fsaverage5. The right hemisphere is never affected. Does anyone have any clue what's going one here? -- Samuel R. Mathias, Ph.D. Associate Research Scientist (ARS) Neurocognition, Neurocomputation and Neurogenetics (n3) Division Yale University School of Medicine 40 Temple Street, Room 694 New Haven CT 06511 http://www.srmathias.com

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From structural ROIs to functional data
by Nick Corriveau Lecavalier 04 Oct '16

04 Oct '16

Hi Freesurfer team, I used Qdec to do my group analysis (MCI vs Control). I also analyzed fMRI data with SPM. My plan is to investigate functional activity where there are group differences in thickness. Is there a way to make a ROI using Qdec and to transfer it into SPM/MarsBar format (.mat) so I can get the functional beta values in this ROI? I tried to make functional ROIs with MarsBar by taking the coordinates of the thickness clusters, but the size and shape of those ROIs are kind of arbitrary. Do you have anything to suggest? Nick Corriveau-Lecavalier, B.Sc. (Hons.) Étudiant au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur à la recherche, Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7819

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Freesurfer October 2016