Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

White matter parcellation
by Graterol Pérez, José Alberto 03 Feb '21

03 Feb '21

External Email - Use Caution Dear FreeSurfer experts, I need help trying to understand how the white matter gets parcellated. I have a clinical dataset, which means that the resolution is not as research images, but it ran without a problem. I would like to measure the volume of the basal ganglia and looking at wmparc.mgz I am not sure how Freesurfer decides where a structure ends and the other one begins. I am attaching two images to show what I mean. I would really appreciate some clarification. I am using FreeSurfer 7.1.1 Thanks in advance. José -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | http://secure-web.cisco.com/1UyleYcIW9IpIEav-uaSJpfZckYD_6rdaRbxs9DgAhomEce… Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

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Hypothalamus segmentation - Freesurfer 7.1
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 02 Feb '21

02 Feb '21

External Email - Use Caution Dear Freesurfer experts, I am having some trouble getting the hypothalamus segmentation recognized on the command line for FreeSurfer 7.1.0. Is it even available for this version? If not, will it work on the 6.0 or the 7.1.1 version? Thanks and stay safe! All the best, Alex

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label to surface
by Sam W 02 Feb '21

02 Feb '21

External Email - Use Caution Hi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam

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cortical thickness ROI
by Sara Lyn 02 Feb '21

02 Feb '21

External Email - Use Caution Hi Freesurfer developers, I wanted to know if I could use an ROI obtained from cortical thickness group analysis to obtain FA values from that same ROI for each of the subjects. Appreciate any guidance, thank you. Sincerely, Sara

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White matter Parcellation
by Graterol Pérez, José Alberto 01 Feb '21

01 Feb '21

External Email - Use Caution Dear FreeSurfer experts, I need help trying to understand how the white matter gets parcellated. I have a clinical dataset, which means that the resolution is not as research images, but it ran without a problem. I would like to measure the volume of the basal ganglia and looking at wmparc.mgz I am not sure how Freesurfer decides where a structure ends and the other one begins, because the structures are not really visible. I could upload two screenshots to show what I mean. I would really appreciate some clarification. I am using FreeSurfer 7.1.1 Thanks in advance. José -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | http://secure-web.cisco.com/1fL7_mV1HnVXx_pK-xzWgX0hp1IPRmxfnHHvyPV6axEvIN9… Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

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Postdoctoral fellowship opportunity in diffusion MRI and functional vision
by Corinna Bauer 01 Feb '21

01 Feb '21

External Email - Use Caution *Thalamocortical connectivity and multicomponent T2 relaxometry in youths with neonatal periventricular white matter injury* NIH-funded Postdoctoral fellowship at the Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School in Boston, MA We are seeking a full-time postdoctoral fellow to work with Dr. Corinna Bauer on an NIH-funded project investigating the impact of neonatal thalamic injury on the development of vision-processing networks in the brain and corresponding visuo-perceptual dysfunctions. The project employs structural, diffusion, and relaxometry based MRI methods to target thalamo-cortical changes in morphometry, neural networks, and MRI-based markers of myelin. The position is available beginning Spring/Summer 2021. The initial time frame will be for 18 months with the possibility of extension. *Required Qualifications:* • Doctoral degree required with 0-1 years of related work experience • Strong coding skills in python, MATLAB, bash, etc. • Advanced skills in the processing and analysis of diffusion (including connectivity, DKI, and NODDI approaches) data, particularly focusing on network-based approaches • Strong publication record in neuroimaging, with a preference for a focus on multimodal techniques in neurodevelopmental disorders • Good command of the oral and written English language • Strong organizational and data management skills • Prior experience reviewing, analyzing, and summarizing scientific literature • Excellent attention to detail and interpersonal, organizational, writing, and project management skills *Preferred Qualifications:* • Experience with multicomponent T2 relaxometry • Experience working with clinical pediatric populations • Experience with psychophysical assessments of functional vision • Experience with fMRI design and analysis Interested candidates should send a cover letter including, a brief summary of their research interests and career goals, their C.V., and the names and phone numbers of three references to Corinna Bauer ( Corinna_Bauer(a)meei.harvard.edu) Review of applications will begin immediately and continue until the position is filled. Additional details can be found at: https://secure-web.cisco.com/1aWE_5wlqXvxDWmzy4gy3dtCobaxYZF4YKpgZiy1P01DGE… *Massachusetts Eye and Ear is proud to be an equal-opportunity employer and is committed to providing a workplace free from harassment or discrimination. All employment decisions are made without regard to race, color, age, gender, gender identification, sexual orientation, religion, marital status, sex, pregnancy or conditions related to pregnancy, national origin/ancestry, citizenship, disability, military status, genetic information, or any other basis prohibited by law. These protections extend to all management practices and decisions, including recruitment and hiring practices, appraisal systems, promotions, training, and career development programs*

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White matter Parcellation
by Jose Graterol 01 Feb '21

01 Feb '21

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(no subject)
by Rahul Sharma 01 Feb '21

01 Feb '21

External Email - Use Caution Hi, Hope all are safe and well. Can anyone help me in finding any biomarker for Alzheimer's Disease or any guidance related to that? Waiting for response. Regards: Rahul Sharma Research Scholar 9827834360 *"Manners Maketh Man"*

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recon all
by 郑凤莲 01 Feb '21

01 Feb '21

External Email - Use Caution Hi experts, We have segmented hippocampus using Freesurfer 6.0. I have a question that is there "head motion correct" in this step? If yes, how does it examined? I am looking forward to your reply. Thanks very much. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0105(a)163.com | 签名由网易邮箱大师定制

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the T2.mgz in subject/mri should be skull stripped or not?
by shan chen 01 Feb '21

01 Feb '21

External Email - Use Caution Hi all, I encountered a problem about the T2.mgz in subject/mri. I ran my data using recon-all -all -i T1path -s name -T2 T2path -T2pial(7.1.1 or 7.1.0), but the results were inconsistent, sometimes the mri/T2.mgz had skull sometimes it didn't. That is weird. I read the recon-all.log T2.mgz with skull, the code is: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% writing normalized volume to /xx/subject/mri/T2.norm.mgz #VMPC# mri_normalize VmPeak 978796 mri_normalize done @#@FSTIME 2021:01:31:21:55:47 mri_normalize N 18 e 42.55 S 2.36 U 40.16 P 99% M 723884 F 0 R 925502 W 0 c 78 w 4 I 0 O 78480 L 62.01 61.65 61.48 @#@FSLOADPOST 2021:01:31:21:56:29 mri_normalize N 18 61.84 61.65 61.49 mri_mask -transfer 255 -keep_mask_deletion_edits /xx/subject/mri/T2.norm.mgz /xx/subject/mri/brain.finalsurfs.mgz /xx/subject/mri/T2.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Writing masked volume to /xx/subject/mri/T2.mgz...done. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% when it comes to no skull, the code is: writing normalized volume to /xx/subject/mri/T2.norm.mgz mri_mask /xx/subject/mri/T2.norm.mgz /xx/subject/mri/brainmask.mgz /xx/subject/mri/T2.mgz DoAbs = 0 Writing masked volume to /xx/subject/mri/T2.mgz...done. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% it seems that the pial is not refined by the T2 image if the T2.mgz is with-skull. anybody know what's going on here? Thanks, Yijun.

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