Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30064 discussions

Multi-Subject Comparison in FreeSurfer
by Sherrill, John T 05 Sep '17

05 Sep '17

I am a new grad student and have been assigned a project in our Brain Imaging Research Center. I would be taking the time to push through and find these answers on my own but our program gives us 5 weeks of half days in a lab for a trial. So I am in a bit of a time crunch. I have been given a database of about 500 .nii files and been asked to find duplicates or likely duplicates. (Some subjects were duel-consented so they may have multiple scans.) What is the best way to recon-all all of the files? Individually, in small groups, or in one larger group? If I do it in groups do I need to list each file or can I just recon-all the entire directory? And if a recon-all on 1 file takes 6-20hr, will doing a recon-all on the entire data set take 500*(6-20hr)=3000-10,000hr? Any help is greatly appreciated. John Sherrill jtsherrill(a)uams.edu john_sherrill(a)me.com (870) 761-0580 ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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mris_anatomical_stats error: missing ", " in "Measure Cortex, CortexVol Total cortical gray matter volume, ..."
by Ernst Schwartz 05 Sep '17

05 Sep '17

Hi! It seems that in FreeSurfer 6, the comma between “CortexVol” and “Total cortical gray matter volume” is missing here’s the relevant part of one of my stats-files: # Table of FreeSurfer cortical parcellation anatomical statistics # # CreationTime 2017/08/23-20:19:44-GMT # generating_program /software/easybuild/software/FreeSurfer/6.0.0-centos6_x86_64/bin/mris_anatomical_stats # cvs_version $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ # mrisurf.c-cvs_version $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ # cmdline /software/easybuild/software/FreeSurfer/6.0.0-centos6_x86_64/bin/mris_anatomical_stats -mgz -cortex /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/label/lh.cortex.label -a /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/label/lh.aparc.a2009s.annot -b -f /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/stats/lh.aparc.a2009s.pial.stats sub-A00057725_ses-CLG2 lh pial # sysname Linux # hostname cn4.cir.meduniwien.ac.at <http://cn4.cir.meduniwien.ac.at/> # machine x86_64 # user ernst # # SUBJECTS_DIR /data/datasets/pediatric/CLG/ # anatomy_type surface # subjectname sub-A00057725_ses-CLG2 # hemi lh # AnnotationFile /data/datasets/pediatric/CLG//sub-A00057725_ses-CLG2/label/lh.aparc.a2009s.annot # AnnotationFileTimeStamp 2017/08/23 22:18:44 # Measure Cortex, NumVert, Number of Vertices, 121790, unitless # Measure Cortex, PialSurfArea, Pial Surface Total Area, 105158, mm^2 # Measure Cortex, MeanThickness, Mean Thickness, 2.80672, mm # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1051285.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1040194.000000, mm^3 # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1039128.584538, mm^3 # Measure Cortex, CortexVol Total cortical gray matter volume, 532907.136355, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 926570.584538, mm^3 # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 918874.584538, mm^3 # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1254280.104289, mm^3 cheers, Ernst ~ Ernst Schwartz Computational Image Research (CIR) Lab Department of Biomedical Imaging and Image-guided Therapy Medical University Vienna, Austria ----------------------------------------------------------------------

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time.dat file in Kinetic Modelling MRTM1 step - Petsurfer processing
by M Janani 05 Sep '17

05 Sep '17

Hi team, Could anyone please tell how to create the time.dat file in the Kinetic Modelling MRTM1 step mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

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Freesurfer PIB PET image processing
by M Janani 05 Sep '17

05 Sep '17

Hi Team, I apologize, I am new to Freesurfer . Currently we are processing PIB PET images. When we compare the SPM data along with FREESURFER outputs. We were able to see a large variation in the values. Could you please guide us in processing PIB PET images in Freesurfer? Since the signal of a PET image is very weak, we used MRI image as a guide to map it to Standard brain. How does Freesurfer process in this case? Your help would be grateful. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

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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

4 7

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

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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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