Freesurfer September 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
200 discussions

Gaussian curvature or Mean curvature
by Hanbyul Cho 03 Oct '16

03 Oct '16

Dear FreeSurfer Team, I heard that FreeSurfer could calculate the Gaussian curvature and Mean curvature by vertex level. Do the computed curvature values be saved as the subject/surf/lh.curv or rh.curv files? When I prepared the generated mass-univariate data, I used the mris_preproc with [--meas curv] option, not [--meas thickness]. *mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh --meas curv--out lh.curv.mgh* I wonder this option is right usage to analyze the cortical curvature. And I wonder the 'curv' is what specific value is meaning. If I want to designate the specific curvature values(Gaussian or Mean curvature ) to analyze by vertex level, how can I use the [--meas] option? Thank you, Best wishes, Han.

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[Repost] question about mris_anatomical_stat
by Ali-Reza Mohammadi-Nejad 30 Sep '16

30 Sep '16

Dear Freesurfer experts Based on the FS wiki, I calculated the cortical thickness difference between the LH and RH of a subject in subject's native surface.Now, I want to use FS commands to extract the information such as "?h.aparc.stats" for this difference map (LH - RH).Now this difference map is saved in a .mgh file.I think, I can use "mris_anatomical_stats" command for this propose.But, based on the help of this command, I did not find any .mgh file as an input.Therefore, would you please help me to create such stats file?Thank you very much for your help Best regards,Alireza

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Longitudinal surface analysis of PET data
by Matthieu Vanhoutte 30 Sep '16

30 Sep '16

Dear Freesurfer’s experts, I would like to use the longitudinal mixed-effects model for surface PET analysis. Although I could find all the process to follow the longitudinal analysis of cortical thickness, I couldn’t resolve the steps/commands to apply successively to coregistered PET data on T1 MRI. Could you precise me the process and commands to use for PET longitudinal analysis ? Many thanks in advance ! Best regards, Matthieu

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get non-cortex vertices
by Dorothy Sincasto 30 Sep '16

30 Sep '16

Hi freesurfers, I am doing a connectivity analysis on cortical areas. I load the 2d fmri surface file in fsaverage5 space into matlab and I get 20484 vertices for both hemispheres. Some of which are zero because I previously specified to get only the cortex vertices. However, the number of non-cortex vertices changes across subjects. Is it possible to get from fsaverage5 any overlay mask that specifies if it is cortical or not, so when I load it into matlab i can get a logical vector of 20484 elements? Thanks Dorothy

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question about mris_anatomical_stats
by Ali-Reza Mohammadi-Nejad 30 Sep '16

30 Sep '16

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How to parcellate the whole white matter into different lobules using Freesurfer ?
by Zhiliang Long 30 Sep '16

30 Sep '16

Dear freesurfer experts: I was wondering if it would be possible to parcellate whole white matter into different lobules (e.g. white matter in frontal lobule, parietal lobule, temporal lobule, and so on) by using Freesurfer ? My goal is to compute the white matter volume, as well as FA wihtin different lobules. Best, Zhiliang

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hello experts
by A-reum Min 30 Sep '16

30 Sep '16

Hello experts. I have some question to you. I used SurfStat statistical tool to analyze the two group(control, patient) When i click the surf in fsaverage folder and then show up lh.pial and lh.pial_avg. What is the differences between lh.pial and lh.pial_avg ? lh.pial_avg means that real subjects's average pial? plz reply.

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(FSv6 dev) recon-all -base ERROR: segmentation fault
by Duygu Tosun-Turgut 30 Sep '16

30 Sep '16

Hello FreeSurfer Developers, We have been testing a dev version of Freesurfer version 6 (freesurfer-Linux-centos4_x86_64-dev-20160405) Cross-section runs were successful without any error but we have been getting a segmentation fault error while trying to generate the base image for longitudinal processing. The recon-all.log from base image generation run is attached. The command line used is: recon-all -base ABE4869G-1307-base -tp ABE4869G-1307-1 -tp ABE4869G-1307-2 -tp ABE4869G-1307-3 -tp ABE4869G-1307-4 -all Is there a change in the syntax in version 6? or is this a bug in the dev version we have been testing? Thank you

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Can I change the pial surface outline by the adding the control point?
by Seung Gul Kang 30 Sep '16

30 Sep '16

Hi Freesurfer expert, I am doing visual editing. In some subjects, the pial surface border is somewhat narrow (within the border of graymatter in my view) although there is no skull stripping error. I heard that adding the control point might extend the border of graymatter as well as that of white matter from other researcher. Is it true? Or, is there other way to edit to extend the pial surface border? Thank you. Best, Seung-Gul --- *Seung Gul Kang, M.D., Ph.D. * *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil Medical Center, Gachon University, School of Medicine, 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea *Research scholar*; Sleep Disorders Clinical Research Program, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1 Bowdoin Square, 9th floor, Boston, MA 02114, USA *Collaboration researcher*; Division of Sleep & Circadian Disorders, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston MA 02115 ᐧ

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Freesurfer compliant pediatric brain template for pediatric brain segmentation using reconall
by GAJENDRA KATUWAL (RIT Student) 30 Sep '16

30 Sep '16

Hello FreeSurfer experts, I am considering using Freesurfer recon-all for segmentation of T1 brain MRIs of young subjects (1-4 years). I am planning to use a Freesurfer compliant pediatric template to maximize the segmentation accuracy. In the publication titled *A FreeSurfer-compliant consistent manual segmentation of infant brains spanning the 0–2 year age range (* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/) by *Katyucia de Macedo Rodrigues, Emma Ben-Avi, Danielle D. Sliva, Myong-sun Choe, Marie Drottar, Ruopeng Wang, Bruce Fischl, Patricia E. Grant,and Lilla Zöllei, * it has been mentioned that "Furthermore, we are also planning on making an atlas generated from our training data sets available to the scientific community (as part of the FreeSurfer package), which can serve as a template in structural and functional studies and as a teaching tool for trainees." Has the pediatric template been released yet? Is there anyway the pediatric template can be accessed if it has been released? Is it available in the dev version or upcoming Freesurfer 6? Regards, Gajendra Jung Katuwal PhD Candidate in Imaging Science

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Freesurfer September 2016