Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30076 discussions

Extracting thickness values using labels
by Anders Hougaard 07 Oct '16

07 Oct '16

Dear Freesurfers, This is probably a very basic question, but I was unable to find an answer in the mailing list: I did a paired cortical thickness group analysis: mris_preproc --fsgd /home/paired.fsgd --target fsaverage --hemi lh --meas thickness --out lh.paired.00.mgh --paired-diff (smoothing) mri_glmfit --y lh.paired.05.mgh --fsgd diff.fsgd --osgm --surf fsaverage lh --cortex --glmdir lh.05_diff.glmdir I found an area of difference in cortical thickness and I would like to know the thickness values of this area for all of the input in paired.fsgd, not just the differences I get from the y.ocn.dat file. How do I extract thickness values from the lh.paired.00.mgh file using the label file of the significant cluster? All the best, Anders

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mris_make_face_parcellation
by Mamashli, Fahimeh 07 Oct '16

07 Oct '16

Dear Freesurfers, I have used mris_make_face_parcellation to divide the brain into smaller parcellations and then used mri_annotation2label to generate the labels. However, the problem is that the labels are ordered based on numbers and it is not clear which label belongs to which parcellation. For example, I would like to use lh.aparc.annot as parcellations. Can you please help me what should I do? Or is there anyway to figure out how to assign a parcellation (e.g. superior temporal) to the small labels generated based on mris_make_face_parcellation? Thank you very much, Fahimeh

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Research Position in Genetics and Neuroimaging
by Juan Domingo Gispert López 07 Oct '16

07 Oct '16

The Barcelonaβeta Brain Research Centre (BBRC), research institution of the Pasqual Maragall Foundation (PMF) and the Centre for Genomic Regulation (CRG) invites applications for a full-time research position to study the genetic modulation of cerebral phenotypes based on genome-wide associations with neuroimaging data, as part of its clinical research program. The primary responsibility of this position includes the analysis and interpretation of genome-wide association studies (GWAS) data in association with quantitative phenotypes extracted from neuroimaging modalities. The candidate will be working under the guidance of the Principal Investigators Roderic Guigó and Stephan Ossowski of the CRG and the Neuroimaging Group Principal Investigator of the BBRC, Juan-Domingo Gispert. The aim of this project is to improve our understanding of genetic modulation of cerebral phenotypes in healthy subjects and to identify spatially varying patterns of genetic control that may not be evident from summary variables. For additional details please visit: https://fpmaragall.org/wp-content/uploads/2014/07/ Postdoc_CRG_BBRC_Oct2016.pdf Deadline: Please submit your application by November 18th, 2016. -- *Juan D Gispert* Head Neuroimaging Research *Barcelona**β**eta **Brain Research Center - Fundació Pasqual Maragall* T. (+34) 93 326 31 90 C/ Wellington, 30 08005 Barcelona *www.fpmaragall.org <http://www.fpmaragall.org/>*

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Processing 7T data
by Damien MARIE 07 Oct '16

07 Oct '16

Dear experts, I plan to process some MRI 7T data, 0.6 mm^3 isotropic voxel size. The aim is to look a R1 maps. I was wondering what was your opinion concerning the downsampling to 1 mm^3 (performed by the current FreeSurfer version if I am correct). What do you think would be the best: FreeSurfer 5.3 , FreeSurfer 5.3-HCP or FreeSurfer beta 6.0? Thank You and Best, Damien

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Question about Cortical Thickness
by Funk, Quentin 06 Oct '16

06 Oct '16

I have a few questions regarding the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness The instructions assume that there is an ROI in the same space as the T1.mgz map. Then they do the following: 1) Register the T1 to fsaverage 2) resample the ROI to the cortical surface of fsaverage 3) map the thickness data of the subject to fsaverage 4) measure the thickness data Why is the registering to fsaverage helpful? It seems as if this computation could be done in the native space. Why couldn't one make the following changes: 1) in mri_vol2surf, the reg option could be replaced with regheader MYSUB. 2) Then the surf2surf command becomes unnecessary. -- Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003 Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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mris_divide_parcellation
by Mamashli, Fahimeh 06 Oct '16

06 Oct '16

Dear Freesurfer group, I am going to divide a brain parcellation into divisions using mris_divide_parcellation. As far as I know from the help comment, this function "divides one or more parcellations into divisions perpendicular to the long axis of the label". Is there any other program that does not make the divisions perpendicular to the long axis? Thank you, Fahimeh

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[Dev Build] Processing very high resolution dataset
by Falk Lüsebrink 06 Oct '16

06 Oct '16

Dear all, I am currently trying to process a MPRAGE with an isotropic resolution of 250 µm acquired in vivo. Downsampling the data to .5 and 1 mm resulted in no errors and surfaces look good. However, while processing the data at native resolution I receive a segmentation fault during topology fixation. May this be related to the number of vertices / faces? Surfaces look okay and not totally corrupted. Memory and disk space are available plentiful. INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781 2016/06/13 21:20:50 fischl Exp $ before topology correction, eno=-2042 (nv=2743306, nf=5490696, ne=8236044, g=1022) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 1461809 ambiguous faces found in tessellation segmenting defects... Segmentation fault Uploading of the dataset is currently not possible. Best, Falk

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Job opening: AFNI group (NIMH, NIH, USA)
by P Taylor 06 Oct '16

06 Oct '16

There is a job opening in the AFNI group at NIHM, NIH, USA. Please see this link if you or someone you know is a scientific programmer: https://kelly.secure.force.com/CandidateExperience/CandExpJobDetails?id=a7V… Applications are made directly through the Kelly Services company (not through the AFNI group itself). If you have questions, please feel free to email: Robert W Cox, PhD Director, Scientific and Statistical Computing Core (AKA the AFNI group) NIMH & NIH email: robertcox(a)mail.nih.gov http://afni.nimh.nih.gov

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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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