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30090 discussions

aparc.DKTatlas+aseg.mgz
by John Anderson 05 Sep '17

05 Sep '17

Dear experts, looking into the output of Freesurfer in this page https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles I see that there should be a file named "aparc.DKTatlas+aseg.mgz". Do I need FLAIR images to get this file. I ran the command recon-all --s subj --all and I can';t find this file thank you for any clarification John

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Contrast matrix for PVR
by Sahil Bajaj 05 Sep '17

05 Sep '17

Hi everyone, >From FreeSurfer manual and discussion forum, I found that volume and LGI can be correlated using mri_glmfit command with -pvr flag. For that, my fsgd file has age, gender as covariates and the file is as following: GroupDescriptorFile 1 Class Male Class Female Variables Age Input zerek1 Male 21 Input zerek2 Male 25 etc. My concern is: To run mri_glmfit command, I am not sure how to define my contrast matrix if I am interested in removing the effect of age and sex. 1st option I tried is: 0 0.5 0.5 0 1 Here, I think first 0 regresses out age, 0.5 0.5 should be averaging over males and females and last 0 1 correlates between volume and LGI. But this looks like it is not giving me correct correlations maps, although there is no error. 2nd option I tried is: 0 0 0 0 1 This looks like its working and maps look correct to me but I want to make sure this is the correct contrast matrix and I am not sure how this matrix is regressing out age and gender or 1st option is correct contrast matrix? Thank you so much ! Best, Sahil

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Fwd: Postdoctoral Position Available at Cincinnati Children’s Hospital Medical Center
by Lili He 05 Sep '17

05 Sep '17

Postdoctoral Position Available at Cincinnati Children’s Hospital Medical Center, Perinatal Institute The multidisciplinary team in the laboratory of Nehal Parikh, DO, MS is seeking a creative and highly motivated individual with solid training in image processing, computer science, and/or neuroscience to conduct research to develop advanced MRI (diffusion, functional) biomarkers in high-risk neonates and infants. The lab’s research goals are to: 1) develop prognostic biomarkers of neurodevelopmental impairments (e.g., intellectual impairments, learning disabilities, autism) using advanced statistical approaches (e.g. machine learning); and 2) develop neuroprotective therapies in high-risk newborns. Programming expertise in Matlab, C/C++ and in UNIX environment preferred. The work promises to be challenging and presents a highly exciting opportunity to work on two NIH R01 projects. *Website: **https://www.cincinnatichildrens.org/bio/p/nehal-parikh* <https://www.cincinnatichildrens.org/bio/p/nehal-parikh> *Qualifications: *Qualified applicants will have a PhD with high-quality peer-reviewed research publications, a developing expertise and strong interest in image processing, biomedical engineering, machine learning, and/or neuroscience, and highly motivated to develop an independent research program in the areas of neuroimaging, or computational sciences as it relates to newborns and infants. Please submit your application to Dr. Sivaprasad with the following information: A cover letter, a statement of interest, and a CV with contact details for 3 referees. Contact: Uma Sivaprasad, PhD; Scientist Recruiter, HR Email: siv9ni(a)cchmc.org Cincinnati Children’s Research Foundation Cincinnati Children’s Hospital Medical Center (CCHMC) is a premier pediatric research institution with over 900 diverse and productive faculty members. Here, researchers work collaboratively across specialties and divisions to address some of the biggest challenges we face today in improving child health. A strong network of research support services and facilities, along with institutional commitment to research, push our team of faculty, postdocs and support staff to explore the boundaries of what is possible, leading to significant breakthroughs. We are driven by our mission to improve child health and transform the delivery of care through fully integrated, globally recognized research, education and innovation. Post-doctoral research fellows at Cincinnati Children’s are valued for their unique interests and strengths, and are supported by our institution’s strong programming for post-docs through the Office of Postdoctoral Affairs and the Office of Academic Affairs and Career Development. Mentoring, support for international students and an emphasis on crafting high-quality grant proposals are only a few of the features that set our program apart. Cincinnati Children’s is a respected part of the broader, and very vibrant, Cincinnati community. With a thriving arts scene, numerous festivals celebrating music and food, a passionate fan following for our college and professional sports teams, and a variety of opportunities for outdoor activities, our region is truly a great place to work and live. Please visit our website for more information about Postdoctoral Research at CCHMC: http://www.cincinnatichildrens.org/education/research/postdo ctoral/default/ *To apply online go to: **http://www.cincinnatichildrens.org/careers/apply/default.htm * <http://www.cincinnatichildrens.org/careers/apply/default.htm>*and search for job (requisition) number 93065.*

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Fwd: Research Associate Position Available at Cincinnati Children’s Hospital
by Lili He 05 Sep '17

05 Sep '17

Research Associate Position Available at Cincinnati Children’s Hospital Medical Center, Perinatal Institute The multidisciplinary team in the laboratory of Nehal Parikh, DO, MS is seeking a creative and highly motivated individual with solid training in image processing, computer science, and/or neuroscience to conduct research to develop advanced MRI (diffusion, functional) biomarkers in high-risk neonates and infants. The lab’s research goals are to: 1) develop prognostic biomarkers of neurodevelopmental impairments (e.g., intellectual impairments, learning disabilities, autism) using advanced statistical approaches (e.g. machine learning); and 2) develop neuroprotective therapies in high-risk newborns. Programming expertise in Matlab, C/C++ and in UNIX environment preferred. The work promises to be challenging and presents a highly exciting opportunity to work on two NIH R01 projects. *Website: **https://www.cincinnatichildrens.org/bio/p/nehal-parikh* <https://www.cincinnatichildrens.org/bio/p/nehal-parikh> *Qualifications: *Qualified applicants will have a PhD and post-doctoral experience with peer-reviewed research publications and expertise in image processing, biomedical engineering, machine learning, and/or neuroscience, and highly motivated to work in the areas of neuroimaging, brain development, and/or computational sciences as it relates to newborns and infants. Please submit your application to Dr. Sivaprasad with the following information: A cover letter, a statement of interest, and a CV with contact details for 3 referees. Contact: Uma Sivaprasad, PhD; Scientist Recruiter, HR Email: siv9ni(a)cchmc.org Cincinnati Children’s Research Foundation Cincinnati Children’s Hospital Medical Center (CCHMC) is a premier pediatric research institution with over 900 diverse and productive faculty members. Here, researchers work collaboratively across specialties and divisions to address some of the biggest challenges we face today in improving child health. A strong network of research support services and facilities, along with institutional commitment to research, push our team of faculty, postdocs and support staff to explore the boundaries of what is possible, leading to significant breakthroughs. We are driven by our mission to improve child health and transform the delivery of care through fully integrated, globally recognized research, education and innovation. Post-doctoral research fellows at Cincinnati Children’s are valued for their unique interests and strengths, and are supported by our institution’s strong programming for post-docs through the Office of Postdoctoral Affairs and the Office of Academic Affairs and Career Development. Mentoring, support for international students and an emphasis on crafting high-quality grant proposals are only a few of the features that set our program apart. Cincinnati Children’s is a respected part of the broader, and very vibrant, Cincinnati community. With a thriving arts scene, numerous festivals celebrating music and food, a passionate fan following for our college and professional sports teams, and a variety of opportunities for outdoor activities, our region is truly a great place to work and live. Please visit our website for more information about Postdoctoral Research at CCHMC: http://www.cincinnatichildrens.org/education/research/ postdoctoral/default/ To apply online go to: http://www.cincinnatichildrens.org/ careers/apply/default.htm and search for job (requisition) number 93066.

1 0

Question on surface-based analysis
by Mehta, Chintan 05 Sep '17

05 Sep '17

Dear FreeSurfer users, I am new to surface based analysis in FreeSurfer (version 6.0). My data consists of T1-weighted scan from normally developing youth of 8 to 21 years of age. I have two questions on assumptions of this analysis for pediatric data: (a) Is "fsaverage" an appropriate common template for all subjects of ages 8 to 21? Online tutorials suggest that fsaverage is the most commonly used template in FreeSurfer analyses and, furthermore, imply that FreeSurfer can be used on scans of normally developing children as young as five years old. I am running analyses separately over different age groups (like ages 8 to 12, 13 to 16, 17 to 21) to ensure robustness. However, would combining results be inaccurate? (b) Previous posts in this forum and FreeSurfer documentation strongly recommend somehow normalizing for head size or total brain volume in models of ROI area/volume. Would the eTIV covariate also be appropriate for surface-based analysis of scans registered to fsaverage when using mri_glmfit? To me, it appears that scans registered to fsaverage have been warped to Talairach space, so the whole brain adjustment has been implicitly made. Thank you in advance for your great insights! Best, Chintan

3 2

Functional Connectivity Motion Regression
by Leathem, Logan Daniel 04 Sep '17

04 Sep '17

Hi Freesurfer list, My group is switching to the fsfast functional connectivity pipeline. We would like to continue regressing out the six-parameter rigid body head motion as a nuisance variable. In order to do this, which file should we flag: is it fmcpr.mcdat or mcprextreg? Thank you! Best, Logan Logan D. Leathem Clinical Research Coordinator Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Rm 2602A Charlestown, MA 02129 Phone: 617-643-4441

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Version 6.0 - ?h.white.preaparc vs. ?h.white for determining the need to edit brainmask.mgz, wm.mgz, add control points, etc.
by Mira Michelle Raman 04 Sep '17

04 Sep '17

Hi, My main question to the 6.0 experts is: Is the lh.white.preaparc close enough to the lh.white to determine whether editing is needed (brainmask.mgz, wm.mgz,control points) or do we need to run the full pipeline and get ?h.white? Here's the reasoning behind this question. In previous versions of Freesurfer we have run -autorecon1 -autorecon2, then checked surfaces, made edits if needed, and then only after we were satisfied with the surfaces we ran -autorecon3. Primarily we have done this for 2 reason, first is to save processing time, on both the initial pass and running -autorecon2-cp or -autorecon2-wm. We also use this as a quality control method, in which ONLY subjects whose surfaces have been verified, have been through -autorecon3, those that haven't, don't have stats files, and thus can't get inadvertently included with finished data. If ?h.white.preaparc doesn't topologically differ from the ?h.white could we use it for determining what edits to do? if it does differ obviously we will have to run the whole pipeline. Thank you in advance for your guidance. Sincerely, Mira _______________________________________________ Mira Michelle Raman Lead Scientific Programmer The Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd, Ste. 1356

2 1

Using Total Cortical White Matter Volume as a "whole brain" covariate
by Mehta, Chintan 04 Sep '17

04 Sep '17

Dear FreeSurfer Developers, I am using FreeSurfer 5.3 to analyze whether a risk factor explains variation in brain structures related to surface area, mean thickness, and subcortical volumes. Documentation suggests using estimated Total Intracranial Volume (eTIV) as a covariate to adjust for brain size in analyses of surface area and volumes: (https://surfer.nmr.mgh.harvard.edu/fswiki/eTIV) Previous posts have also suggested using BrainSegNotVent or Total Gray Matter Volume as covariates as a "whole brain" covariate, with the choice of covariates representing different hypotheses regarding local vs. global atrophy. However, it seems to me that using BrainSegNotVent or Total Gray Matter Volume as covariates could lead to a significant loss in power in detecting effects on area/thickness measures from a risk factor associated with atrophy across many regions. On the other hand, eTIV may suffer from not accounting accounting for local atrophy (in addition to heightened measurement error, as frequently alluded into previous posts). But still, a normalization covariate is needed to account for differences in brain size need to be accounted In the analysis of cortical surface area or mean cortical thickness among normal populations, could it make sense to use cortical white matter volume as the "whole brain" covariate? In normal populations, cortical white matter volume is significantly correlated with surface area, mean thickness, and gray matter volumes but its value is not derived from the gray matter structures. My understanding is that FreeSurfer sets cortical surface area as the area at the boundary of white and gray matter. As a covariate in models of cortical surface area or mean thickness, white matter volume could side-step the loss in power in detecting effects lead to both global atrophy in gray matter volume while also partly adjusting for total brain differences. Cortical white matter volume is not a standard "whole brain" covariate in the literature (in the way eTIV or Total Gray Matter Volume are). However, am I misunderstanding how FreeSurfer computes these Cortical White Matter that makes it unsuitable as a "whole brain" covariate? Thank you. Best, Chintan

2 1

Cerebellum Segmentation
by José Gómez-Feria Ferreiro 04 Sep '17

04 Sep '17

Dear Freesurfer, I have been doing some MRI segmentations using the "mri2mesh" command (which does "recon all"). However, I noticed the cerebellum segmentation is not correctly done. It considers the cerebellum as white matter but it also has grey matter. Is there a way to make a more precise segmentation of the cerebellum? Best regards, José Gómez-Feria Ferreiro MD/PhD candidate Grupo de Trastornos del Movimiento. Lab 104 Programa de Investigación de Neurociencias Instituto de Biomedicina de Sevilla (IBiS) Hosp.Univ. Virgen del Rocío/CSIC/Univ. de Sevilla Avda. Manuel Siurot s/n. 41013 - Sevilla (España)

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volume registration; volume connections;
by Daniel van de Velden 04 Sep '17

04 Sep '17

Dear Freesurfer-Team, I am trying to study volume based neuronal activities via a Spatio Temporal Clustering Test. Therefore I need to morph my subjects to an average subject. I couldn't find a non-linear morphing command to perform this. Is there any function and can I extract to resulting morphing map that was used to morph the subjects ? Something like the /'hemisphere'.sphere.reg/ files, which are automatically created by the 'recon-all' function. Additionally is it possible to extract the volume neighboring connection from a /'hemisphere'.volume/ file ? For further information: I am going to use mne-python to perform the Spatio-Temporal-Clustering. They are extracting the vertice connections via a function ( /_get_subject_sphere_tris(subject_from, subjects_dir)/ ) from the /'hemisphere'.sphere.reg/ files. Can I also do this for volume data files created by FreeSurfer. Looking forward to your reply. I am glad to any kind of corporation, I really want this study to work, since the results will be very interesting. Yours sincerely, Daniel van de Velden

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