Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30083 discussions

FIR Analysis and task regressor
by Doll, Laura 03 Feb '21

03 Feb '21

External Email - Use Caution Hi everyone, Is it possible to do an FIR analysis using a task regressor instead of (or additional to) a paradigm file? More precisely, we want to use pupil size as task regressor. It was recorded during an auditory detection task (event related). This works when I use "-spmhrf" or other HRF options. However, for FIR I cannot get the expected time course in the single subjects data. Tksurfer ends with an error because it cannot find the file h.nii.gz: ERROR: could not determine file for [...]/S01_3/bold/PupilFIR.lh/h This file indeed does not exist, there is only one called "h-offset". The commands I used until that point are (here neglecting the original task, but using -event-related etc instead of no task results in the same error): mkanalysis-sess -fsd bold -stc up -surface fsaverage lh -fwhm 5 -notask -fir 4 20 -TR 2 -polyfit 2 -analysis PupilFIR.lh -per-run -taskreg Pupil 1 selxavg3-sess -s S01_3 -analysis PupilFIR.lh tksurfer-sess -s S01_3 -analysis PupilFIR.lh -call -tksurfer Is there any solution for this? Or any reason why it should not be done that way? Best, Laura

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define freeview colormap from command line
by Simone Cauzzo 03 Feb '21

03 Feb '21

External Email - Use Caution Dear all, Using your precious hints in a past thread, I'm now displaying several surface analyses and taking a screenshot for each of them, everything from command line using the command freeview -f ***/mni152.fnirt/surf/lh.inflated:overlay=***mni152.fnirt.lh.nii.gz:overlay_threshold=5,8 -zoom 1.6 -ss ***.tif Now, the colormap I'm using is thus by default "heat" with thresholds 5 and 8. My images are very red. Opening the "configure overlay" menu in the GUI, I noticed that the colormap is almost entirely red, and fades to yellow only in the end. If I select "custom", the colormap appears more graded, as I would like it to be. Is there any way to specify the "custom" option in the "configure overlay" menu from the command line? Thank you Simone

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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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