Freesurfer July 2018

freesurfer@nmr.mgh.harvard.edu

112 participants
165 discussions

Volumetric Group Analysis
by Mr. Tass 02 Jul '18

02 Jul '18

External Email - Use Caution Good morning I hope everyone had a gr8 weekend. im new here so i hope someone can help me understand a little about the right way to use freesurfer in order to calculate the gray matter volume for different areas of the brain and compare the volume between left and right hemisphere. so far i have freesurfer installed and recon-all a couple of test subjects. and everything seems to be working fine. i have several subjects with the axial cut MRI. is the axial cut enough to output accurate results? im little concerned as the T1 representation Outputted in FREEVIEW seems a bit fuzzy im following the below link for my group analysis. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/VolumetricGroupAnalysis please if possible to sheld some light on this kind of analysis and if i am on the right track. thanks alot to you all best regards Sarah Get Outlook for Android<https://aka.ms/ghei36>

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Poor anterior temporal lobe surfaces
by Meaghan Perdue 02 Jul '18

02 Jul '18

External Email - Use Caution Hello Freesurfer experts, I have tried several times to send this out, but I haven't received a response. Please let me know if there is a way to solve this issue. I have come across a problem with several subjects in which the pial surface fails to adequately capture the anterior temporal lobes. This occurs despite accurate brainmask and wm volumes. I have included a screen shot below, in this case, the wm surface is also affected, but this is not always the case. This is pediatric data that was acquired on a 1.5T scanner and processed in Freesurfer v 5.3. The following expert options have been employed to try to improve surface rendering: mris_make_surfaces -max_gray_at_csf_border 80 -max_csf 30 -min_gray_at_csf_border 35 Please let me know how I can solve this issue. As a second question, I've heard that segmentation and surface rendering is improved with v 6.0, and I'm wondering if subjects that have been initially run through v. 5.3 and had manual edits made can then have autorecon run through v 6.0 for improvement of surfaces? Please let me know if this would be a reliable/recommended approach to improving surfaces. Thank you, Meaghan Perdue -- Meaghan Perdue PhD Student Developmental Psychology Neurobiology of Language University of Connecticut Bousfield A302

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Compute cortical thickness within VOI
by Alshikho, Mohamad J. 02 Jul '18

02 Jul '18

Dear FreeSurfer experts, I have MRS volume of interest (VOI) was placed in the motor cortex during MRS data acquisition. In order to compute the gray and white matter volume within the VOI, I synthesized this VOI using "mri_volsynth". Then I registered it to T1 Freesurfer space using "spmregister". Finally, I used "mri_segstats" to compute the gray and white matter volume for all the structures within this VOI. My question is how can I compute cortical thickness for the cortical structures within this VOI. By looking into "recon-all.log" I found that the command "mris_anatomical_stats" was used to compute cortical thickness from the surfaces. Is it a correct procedure to map this VOI onto surface using "mri_vol2surf" then feed the output into "mris_anatomical_stats" as an annotation file? Thank you for any guidance. Mohamad

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degrees of freedom
by John Absher 01 Jul '18

01 Jul '18

External Email - Use Caution In group analysis, is it better to have matched controls (1:1) or to use age, education and other characteristics as confounds in the glm? In the latter situation, we would control for these demographic variables in the glm and the control group n could be smaller, the same or larger than the test group. We are looking at TBI+ and TBI- subjects across a broad age range to look at patterns of cortical thinning. Thanks. John R. Absher, MD, FAAN GHS Neurosciences jabsher(a)ghs.org<mailto:jabsher@ghs.org> 864-350-6655 (mobile)

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Proposed addition for Freesurfer - automated control points
by Chris Adamson 30 Jun '18

30 Jun '18

External Email - Use Caution Freesurfer devs, I presented an automated control point adding tool at HBM and a few freesurfer lab people came over and had a look. I was wondering if someone would like to review it for either inclusion or to perhaps reference from the wiki as a tool for people to use if they choose? Thanks in advance, Chris. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email

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Freesurfer July 2018