Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

freeview error
by zhac looch 24 Oct '18

24 Oct '18

External Email - Use Caution Hello freesurfer team, How can ı fix the problem? Ubuntu-brain:~$ freeview Could not set locale No such file or directory This application failed to start because it could not find or load the Qt platform plugin "xcb" in "". Reinstalling the application may fix this problem. Aborted (core dumped) Ubuntu-brain:~$

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5th ventricle in version 6
by Keedy, Sarah [PSY] 24 Oct '18

24 Oct '18

External Email - Use Caution I’m comparing output of Freesurfer5.2 to 6 on the same set of brains. The “5th ventricle” (Cavum septum pellucidum) is not being detected by 6. I had eyeballed the output from 5.2 and convinced myself it was reasonably well detecting this developmentally abnormal finding pretty well. I am wondering what changed in version 6, if anything, that could explain this?

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Surface-based analysis of tfMRI
by Zhi Li 23 Oct '18

23 Oct '18

External Email - Use Caution Hi FreeSurfer Experts, I am trying surface-based analysis of task-fMRI with FS-FAST. However, I would like to apply ICA-based denoising and wavelet-despiking which can be not done with the 'preproc-sess'. I wonder if I can do the preprocessing with other tools before registration with FS anatomical and normalization? If it is available, how can I do it with command line? Another question is if can I use other template for parcellation during using 'recon-all', such as the template of Human Connectome Project? Looking forward to your kind reply. Thank you and best wishes, Zhi

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How to export the image and label
by Min Zhang 23 Oct '18

23 Oct '18

External Email - Use Caution Dear FreeSurfer Team : I used the freeSurfer brainstem structure to segment the brainstem from the MRI successfully. But I have several questions as followed: 1. I want to export this data in dcm file with all the ROI information, what should I do? 2. How to manually adjust the boundaries of existing brainstem segmentation results? 3. How to generate surface of brainstem based on the segmentation. Many Thanks! Best Jackie

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Physiological Noise Regression from rsMRI
by Meisler, Steven Lee 23 Oct '18

23 Oct '18

Hi all, I am currently developing a pipeline to remove physiological noise (respiratory and cardiac) from rsMRI images. I am at the point where I have created the regressors using fast_retroicor.m from the physiological data logs. When I add the columns of the regressors up and plot the result, it appears to create pulses at the times when the physiological data peaked. I was wondering if anyone knows how to incorporate the regressor files into FreeSurfer. Please let me know at your earliest convenience. Thank you, Steven -------------- Steven L. Meisler, M.S.E. Clinical Research Coordinator II Laboratory for NeuroImaging of Coma and Consciousness<https://www.massgeneral.org/neurology/research/researchlab.aspx?id=1605> 175 Cambridge Street, Suite 300 Boston, MA 02114 smeisler(a)mgh.harvard.edu<mailto:smeisler@mgh.harvard.edu> | (617)-726-1884 https://www.linkedin.com/in/steven-meisler [cid:5962d6ba-7da0-445d-a7a9-91952132a976]

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Running DICOMS versus FreeSurfer5.3 Output
by Scheffler, F, Mev [fredas＠sun.ac.za] 23 Oct '18

23 Oct '18

External Email - Use Caution Dear FreeSurfer Developers If we want to rerun FreeSurfer dev 6.1 on an old dataset, is it better to rerun with the original DICOMS or to rerun over the 5.3 output? Would that even work? Thanks very much. Kind regards, FREDA SCHEFFLER Research Assistant / PhD Candidate [email.jpg] MA Research Psychology Faculty of Medicine and Health Sciences Fakulteit Geneeskunde en Gesondheidswetenskappe Universiteit Stellenbosch University PO Box | Posbus 241, Cape Town | Kaapstad, 8000 Francie van Zijl Drive | -rylaan, Tygerberg, 7505 South Africa | Suid-Afrika Tel: +27 21 938 9771 Email | E-pos: fredas(a)sun.ac.za [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/about-us/strategic-documents> The integrity and confidentiality of this email are governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>

2 1

QDEC analysis with more that 2 fixed factors
by Azeez, Azeezat 23 Oct '18

23 Oct '18

External Email - Use Caution Hello, I would like to know how I can run statistical analysis in QDEC on a data set where there are 3 fixed factors each with 2 contrast levels. (DEVELOPMENT : old vs young, SEX: male vs female, DIAGNOSE: Control Vs disease ) Any help would be much appreciated. Thank You, -- Azeezat Azeez PhD Student Department of Biomedical Engineering || New Jersey Institute of Technology Graduate School of Biomedical Sciences || Rutgers University E: aka44(a)njit.edu

2 3

errors running mri_glmfit
by Azeez, Azeezat 23 Oct '18

23 Oct '18

External Email - Use Caution Hello I keep getting the same error and am not sure how to address the issue. I have attached the design matrix and the FSGD file and contrast file of interest Thanks for the help ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y STATS/lh.DEV_DIA_SEX.thickness.mgh --fsgd STATS/DEV_DIA_SEX.fsgd dods --C STATS/mainDEV.mat --surf fsaverage lh --cortex --glmdir STATS/lh.DEV_DIA_SEX.thickness.glmdir 2. The FSGD file (if using one) 3. And the design matrix above -- Azeezat Azeez

2 1

Myelinated cortical thickness ratio map
by Damien MARIE 22 Oct '18

22 Oct '18

External Email - Use Caution Dear experts, I am working with R1 maps that I project on the surface. The goal is to look at intra-cortical myelin. I detect interesting effects between two groups. Now I would like to compute myelinated cortical thickness ratio maps, in order to control for the effect of cortical thickness variations occurring with gyrification. Here is a paper where they describe a way to compute those myelinated cortical thickness ratio map with MIPAV and the MPI-CBS toolbox : https://www.ncbi.nlm.nih.gov/pubmed/29321232 <https://www.ncbi.nlm.nih.gov/pubmed/29321232> « The proportional thickness of the myelinated part of the cortex in relation to its overall thickness (myelinated cortical thickness) was computed with a fuzzy classification technique combining information about radial and tangential fibers. « 1- Is it possible to do the same in FreeSurfer? 2- What about dividing my individual myelin maps by the individual cortical thickness maps? Is it possible to do that in FreeSurfer? SPM ImCalc would do the job in the volume but I don’t know how I could do that in FreeSurfer. Any comments / other suggestions are welcome. Thank you and best, Damien

2 1

postdoctoral research opportunity
by Bruce Fischl 22 Oct '18

22 Oct '18

FYI ---------- Forwarded message ---------- Date: Mon, 22 Oct 2018 12:16:59 -0700 From: Rahul Desikan <rahuldesikan(a)gmail.com> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: one more favor External Email - Use Caution One more favor Bruce. If possible could you please post this on the FS/FSL lists? Many thanks! Best, Rahul UCSF, Dept. of Radiology & Biomedical Imaging is seeking a Postdoctoral Scholar for The Laboratory for Precision Neuroimaging We are seeking a postdoctoral candidate with a strong background in genetics human imaging and a desire to use a multi-disciplinary approach to pursue neurodegenerative and neurodevelopment research. The candidate should have a strong statistical/computational background with experience with data analytic tools such as Matlab, R, and PLINK and potentially, 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 immediately. Salary is commensurate with qualifications and experience. Job Requirements: 1. CV/NIH biosketch (must contain previous research experience) 2. Cover Letter - Short statement on why you are interested in this position and how this position will help you achieve your career goals 3. Three references If interested please contact Dr. Leo Sugrue at leo.sugrue(a)ucsf.edu

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Freesurfer