Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

ACPC alignment before processing
by Zhengchen Cai 18 Oct '21

18 Oct '21

External Email - Use Caution Hello FreeSurfer Developers, I wonder if we have a function that could automatically align T1w to ACPC before running recon-all? Or if we have an option in recon-all that could do this ACPC alignment automatically? I noticed there are such ways after running freesurfer by applying the transformation matrix, but I guess it will be less convenient than pre-alignment since we don't bother to transform all the output. Especially if we use freesurfer with other tools like fMRIPrep, all functional images will also be registered to ACPC aligned T1w. I ask this since sometimes the T1w is tilted and not desirable for visualization purposes. Thanks a lot. Best regards, Zhengchen

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Different pixel spacing for scans in the same cohort
by Castro Leal, Gonzalo 18 Oct '21

18 Oct '21

External Email - Use Caution Dear Freesurfer, I was wonderign wether processing scans and comparing their stats, e.g. cortical thickness and area, could be not recommended if the pixel spacing across all the scans was different, i.e. the range is between .9375x.9375x1.2 and 1.3542x1.3542x1.2. Many thanks, Gonzalo.

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MEMPRAGE protocol
by nicola spotorno 18 Oct '21

18 Oct '21

External Email - Use Caution Dear all, I read on the FAQ that MGH would kindly share an optimized MEMPRAGE. I was wondering how/how should I get in touch to discuss about this option. All the best, Nicola

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Job Posting - Center for Healthy Minds
by CHM Recruiting 18 Oct '21

18 Oct '21

External Email - Use Caution Hello, Would you please list the attached on the Freesurfer (listserv): Research Specialist - UW Madison, WI - Center for Healthy Minds. Thank you, Lisa Wesley Human Resources Generalist Center for Healthy Minds lawesley(a)wisc.edu

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Creating a surface parcellation from a volume atlas
by Paul Dhami 18 Oct '21

18 Oct '21

External Email - Use Caution Dear Freesurfer community, I have a .nii volume atlas (CAREN), defining 5 networks, in MNI (ICBM152) space. However, I wish to do my analysis in surface rather than volume space, and for the software I am using, that means I need to load in a .annot file. For the first step, I used: mri_vol2label --c CAREN_5networks.nii --id 1 --l 1.label and did this for values 1 to 5 (for each of the networks). However, looking at the resulting label file, the first column is nothing but -1 values. I believe this should be the vertex number, and trying to combine these labels into an .annot file is not working. Apologizes for the naive question, but can anyone share as to how I can ultimately create a surface atlas when I have the volume.nii atlas file? Was I wrong with mri_vol2label as my first step? I am using Freesurfer version 7.2.0. Thank you, Paul

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Question about 'thickness.fwhm10.fsaverage'
by Dongyue Zhou 18 Oct '21

18 Oct '21

External Email - Use Caution Dear FreeSurfer experts: I use the 'qcache' command to get the file '$SUBJECTS_DIR/subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh'. Now,I have known that cortical thickness in this file is in standard space.But I don't understand why it is an average of 40 subjects. Is it not CT measures an individual in standard space? I can get cortical thickness in each vertice by reading this file in matlab. And I know mean CT is computed by dividing sum CT of all ROI vertices by the number of ROI vertices. Is there any way I can get individual ROI in standard space if I want to compute mean CT measures of each ROI? or Can I use file '$SUBJECTS_DIR/fsaverage/label/?.annot' as atlas directly?

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Problem with intensity normalization control points
by Staci A Board 18 Oct '21

18 Oct '21

External Email - Use Caution Hello, our lab has been using freesurfer for years, dating back to version 4.3 and recently ran into a problem with a new installation of 7.2. After adding control points in the typical fashion and saving them into the subject’s tmp folder as “control.dat” and running -autorecon2-cp, mri_normalize seems to correctly identify the control points, the correct number, the mean value and the scaling. The subsequent steps complete without failure and brain.mgz is generated with 110 values in the cp spots. However, the subsequent wm.mgz and brainmask.mgz images do not seem to have been affected by the control points (e.g. the control point locations aren’t at a 110 value and the white matter is almost identical). Curious if anyone else has run into the issue? Is there a new workflow in this version of Freesurfer that I’m neglecting? So far I have tried to create a new control.dat using freeview and copied the old points into that file, and run twice with the same results.

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Postdoctoral Fellowship
by Didenur Sahin 18 Oct '21

18 Oct '21

External Email - Use Caution Dear All, Brain Development And Psychosis Lab, is pleased to announce the opening of a postdoctoral fellowship position in clinical neuroscience and cognitive neuroimaging. Please take a look at the attached advertisement. Best, Didenur Sahin *ANNOUNCEMENT OF POSTDOCTORAL FELLOWSHIP IN FMRI ANALYSIS * Brain Development And Psychosis Lab, National Magnetic Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research Centre (ASBAM) & Department of Psychology, Bilkent University, Turkey. The Brain Development And Psychosis Lab is pleased to announce a postdoctoral fellowship position in fMRI analysis. Located within the National Magnetic Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research Centre (ASBAM), the Brain Development And Psychosis Lab conducts research in adolescent brain development. The lab's primary mission is to understand the cognitive, neurobiological, and genetic mechanisms that influence an individual's susceptibility to develop serious mental illness (e.g. psychosis, schizophrenia). We seek a candidate with experience in f-MRI analysis. A Ph.D. in cognitive science, engineering, neuroscience, or related field is required. Experience in computational methods used in neuroimaging (e.g., Matlab, Python, SPM) and computer programing is also required. Advanced skill in statistical modeling, and the ability to carry out independent statistical analyses using standard software packages (e.g., SPSS, SAS, R) are desirable. The candidate will have the opportunity to analyze and interpret f-MRI data from an ongoing project on brain development, which aims to provide neurobiological insights into the genetic and environmental mechanisms of risk around the time of life when psychotic symptoms typically appear. The project is funded by The Scientific And Technological Research Council Of Turkey (TUBITAK). Postdoctoral fellows will receive mentoring in clinical/human research methodology and work in a collaborative, multi-disciplinary environment to gain experience in psychosis-centered research. The postdoctoral fellowship position is for 18 months, renewable subject to securing further funding. Please email a CV and cover letter to Prof. Dr. Timothea Toulopoulou (ttoulopoulou(a)bilkent.edu.tr) -- Didenur Şahin Ph.D. Candidate Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) Bilkent University Ankara, Turkey 06800

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FW:
by CHM Recruiting 17 Oct '21

17 Oct '21

External Email - Use Caution Hello, Can you please post the attached to the Freesurver (listserv)? Research Specialist, UW- Madison, WI, Center for Healthy Minds.<https://secure-web.cisco.com/1A_r9pG3lSDyZYMJsUtVNwH5A1tgFpm8iz07A00PeWU88F…> Thank you, Lisa A. Wesley Pronouns:<https://secure-web.cisco.com/1VbRVY9T5mcFGkLyNTqXDa7YSwOekf5hem7tT8KZzaUKj_…> She/Her/Hers Human Resources Generalist 608/262-0196 lawesley(a)wisc.edu<mailto:lawesley@wisc.edu> [cid:image001.jpg@01D7C36A.8DD846B0] P Please help conserve by considering if it is necessary to print this e-mail

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Hypothalamic segmentation
by AJ 17 Oct '21

17 Oct '21

External Email - Use Caution Hi, How does one normalize the data output from hypo_seg for the head size, with sbTIV or eTIV, which are a bit different from each other. Many thanks AJ

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