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confirm 1651acc5c3dc6a2dda865be4528eeba83c3f81df
by Zhao, Don 25 Jan '23

25 Jan '23

External Email - Use Caution Hi, May I have the password for FS_7_2_0_ubuntu_18_04_06.ova? Thank you, Don

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ROI Analysis
by Beatriz Cavendish 25 Jan '23

25 Jan '23

External Email - Use Caution Hello FreeSurfer Community! I previously asked a question about volume quantification using an external atlas (in fact, there are 20 brain masks corresponding to the regions of interest). I managed to perform the quantification with the following commands and would like to know if everything is correct: Use mri_vol2vol to upsample to 1mm: /usr/local/freesurfer/subjects# mri_vol2vol --mov '/home/pedro/Downloads/Sallet_ROIs/Cluster1_L.nii' --targ '/usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz' --regheader --o Cluster1_L_1mm.nii --interp nearest Use mri_vol2surf to create surface in XXX space: /usr/local/freesurfer/subjects# mri_vol2surf --mov Cluster1_L_1mm.nii --mni152reg --hemi lh --surf white --o lh.ROIA.mgh Visualize surface: /usr/local/freesurfer/subjects# freeview -f $FREESURFER_HOME/subjects/fsaverage/surf/lh.inflated:overlay='/usr/local/freesurfer/subjects/lh.ROIA.mgh' Convert surface to annotation file: /usr/local/freesurfer/subjects# mris_seg2annot --seg lh.ROIA.mgh --s fsaverage --h lh --ctab-auto --o lh.ROIA.annot Project the atlas to the subject's brain <https://secure-web.cisco.com/1JEN07txiABM5huyz9SEUPTihLYxW1TkkC2uDoF7TiUhSs…> : /usr/local/freesurfer/subjects# mri_surf2surf --srcsubject fsaverage --trgsubject bert --hemi lh --sval-annot fsaverage/label/lh.ROIA.annot --tval bert/label/lh.bert.ROIA.annot Calculate the atlas statistics <https://secure-web.cisco.com/1qVy6szcbmCutI-Y6GHK6daTo060hOEJXywT8OVArAV-2I…> : /usr/local/freesurfer/subjects# mris_anatomical_stats -th3 -mgz -cortex $SUBJECTS_DIR/bert/label/lh.cortex.label -f $SUBJECTS_DIR/bert/stats/lh.ROIA.stats -b -a $SUBJECTS_DIR/bert/label/lh.bert.ROIA.annot bert lh white Some questions: The projection of the mask volume in the MNI152 space onto the fsaverage space is fully matched. Are there any crucial differences between these spaces? How to get volume or surface file from annot file? Best regards, -- Beatriz Araújo Cavendish, MSc PhD student | Psychologist University of São Paulo São Paulo/SP - Brazil

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cortocal thickness / gray matter volume
by John Anderson 25 Jan '23

25 Jan '23

External Email - Use Caution Dear experts, this is the first time I have used Freesurfer. I am a clinician and I don't have previous experience. I followed wiki instructions. I have a group of T1 images. I need cortical thickness and cortical gray matter volume measurements . I ran "recon-all" and I got all the measurements. My question is about cortical thickness and cortical gray matter volume, are these two measurements have to be correlated everytime? Is it possible to find cases of cortical thinning and normal cortical gray matter volume? I don't have a solid mathematical background. I am wondering if those two numbers must always correlate with each other, otherwise I am worried that an error in the analysis may lead to cortical thinning and normal cortical gray matter volume. Thank you for your time, John

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Freesurfer 7 Temporal lobe segmentation
by Michele Valotti 25 Jan '23

25 Jan '23

External Email - Use Caution Dear Freesurfer experts, Should I expect Freesurfer 7 to significantly improve segmentation of the Temporal Lobe when compared to Freesurfer 6? I often see sub-optimal segmentation of this region in Freesurfer 6 and I am wondering if an upgrade to 7 would be worth it or not. Thank you! Best, Michele

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Problem with quantifyHAsubregions.sh
by Georgina Angelopoulou 24 Jan '23

24 Jan '23

External Email - Use Caution Hello Freesurfer experts, I have accomplished hippocampal subfields segmentation using Freesurfer 7.3.2. However, I have trouble when I try to gather all volumes of all subjects in one single txt file. I type quantifyHAsubregions.sh hippoSf T1 testhippo.txt And the output that appears is: Gathering results from subjects in: /Users/…/ALBION Using the prefix name: hippoSf Using the suffix name: T1 And writing them to: testhippo.txt However, there is no txt file in my directory. I have tried included all subjects’ names in the script and I am still facing the same problem. Do you have any ideas to resolve this? Thank you in advance, Best, Georgina

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Postdoc Position in Neuromodulation and Neuroplasticity
by Xin Niu 24 Jan '23

24 Jan '23

External Email - Use Caution The Jiang Lab at the University of Iowa Carver College of Medicine (PI: Dr. Jing Jiang, https://secure-web.cisco.com/10vUzmjBRWrQ1Vub-YnhB7SPAxb-DAoT1MPQ0v4jSvBH4J…) is seeking a highly motivated postdoctoral fellow to join our team with a two-year term (and a possibility of extension) to work on projects related to neuromodulation and neuroplasticity. Research topics may include but not limited to emotion, language, and social cognition. The lab has a variety of unique datasets ready for immediate analyses, such as concurrent transcranial magnetic stimulation (TMS)-functional magnetic resonance imaging (fMRI), concurrent TMS-intracranial electroencephalography (iEEG), as well as brain lesion data from healthy, neuropsychiatric, and neurological populations. We are an interdisciplinary team situated in the Stead Family Department of Pediatrics and Department of Psychiatry. We maintain active collaborations with faculty and teams from the Departments of Neurology, Neurosurgery, Psychological and Brain Sciences, and Biomedical Engineering at the University of Iowa, the Iowa Neuroscience Institute, and the Intellectual and Developmental Disabilities Research Center. Our lab has access to the University of Iowa’s cutting-edge imaging facility ( https://secure-web.cisco.com/192mgb7jZPH5i5Ds18c_Lq95BFqyv8OB41Xvsq_HBr9KU2…) the world-renowned Iowa Neurological Patient Registry (https://secure-web.cisco.com/1qOPlXLuKPecg09RxBLKBWQ7BSAZwgBvTlGAKVig6-uoUX…) including neuroimaging and neuropsychological testing data from over 4,400 patients with focal brain lesions, and state-of-the-art portable fNIRS, concurrent TMS-fMRI, concurrent TMS-iEEG, and concurrent es-fMRI systems. The University of Iowa is an internationally recognized leader in neuropsychology and cognitive neuroscience. The Roy J. and Lucille A. Carver College of Medicine is consistently one of the nation’s top-ranked medical schools (#39 on research by the 2022 U.S. News & World Report). The Stead Family Children’s Hospital is listed among the nation’s best in seven specialties in the 2022-23 “Best Children’s Hospitals” rankings by U.S. News & World Report (#38 in pediatrics neurology). Iowa City ranks among one of the best places to live in America (e.g., #1 Best College Town by Reviews.org) Iowa City, Johnson County, and the state of Iowa all routinely appear on national “best of” lists <https://secure-web.cisco.com/1820NySo0132mIvD01EKSA8fbYnZMtV5Q2_otNeEyStvTS…> for low cost of living, safety, access to world-class health care, and more <https://secure-web.cisco.com/1UPyZvyZ1OHLRh_2ZA_AegJ56sxGn4jhaj0ypgucw582K1…>. *Responsibilities and what you will achieve* The goal of postdoctoral training in our lab is to help you become an independent researcher. To achieve this goal, you will work with Dr. Jiang to develop a plan (e.g., independent projects, mentorship experience, grant application, job hunts, networking) that meets your career development. You will receive theoretical and methodological training and resources through ongoing projects and independent projects, mentor students and research assistants, publish impactful papers, and apply for eligible research grants. You will also be provided with networking opportunities and professional guidance for job hunts. *Requirements* - PhD and/or MD degree in Neuroscience, Computer Science, Electrical or Biomedical Engineering, Psychology, Cognitive Science, Biology, or a related field - A track record of peer-reviewed scientific journal publications in human neuroscience - Experience with programming, e.g., in MATLAB, Python, R, and/or Shell - Experience with data analyses, e.g., in fMRI, (i)EEG, brain lesion, and/or, neural network - Self-motivated, able to work independently, strong written and interpersonal communication skills To apply, please email (1) a cover letter describing your research interests and (2) your CV to Dr. Jing Jiang (jing-jiang(a)uiowa.edu) Applications will be reviewed on a rolling basis until the position is filled. Start date is flexible depending on candidate availability.

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FSL on recon-all
by Aaron Tanenbaum 24 Jan '23

24 Jan '23

External Email - Use Caution Hello FreeSurfers, I just need to know if the FSL is used in the recon-all scripts. Basically if FSL_DIR is different will the recon-all produce different values. Thank you Aaron.

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mri_glmfit
by James Brown 24 Jan '23

24 Jan '23

External Email - Use Caution Dear FS experts, I am working on a surface based analysis using FS 7.1.1 and I would like to run mri_glmfit between two groups using the flag "--label" to restrict analysis within lobes. I ran these commands on fsaverage mri_annotation2label --subject fsaverage --hemi lh --lobesStrict lobes mri_annotation2label --subject fsaverage --hemi rh --lobesStrict lobes This created annotation files within the "labels" folder of fsaverage, then I ran mri_glmfit using the flag --label lh.lobes from fsaverage I got this error message mri_glmfit: could not scan # of lines from label file I am ot sure what I am doing wrong. Thanks for guidance James

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segmentation of phantoms with own defined PVE priors
by Nederpelt, D.R. van (David) 24 Jan '23

24 Jan '23

External Email - Use Caution Hi Freesurfer developers, I am trying to segment phantoms, but I would like to base the principle of the segmentation on a "freesurfer-like" pipeline/segmentation. This is to minimize differences between the segmentation pipeline of the phantoms compared to the patient/subject segmentation. I have predefined priors of the phantoms. Would you be able to provide me with some advice regarding this or maybe a collaboration? Thank you very much in advance. Best regards, David [cid:image002.png@01D40E30.3E299A80] David R. van Nederpelt, MSc | PhD Candidate Radiology and Nuclear Medicine Amsterdam UMC, Location VUmc | PK -1 X 004 | De Boelelaan 1118, 1081 HZ Amsterdam, the Netherlands T: +31 20 444 6480 | E: d.vannederpelt(a)amsterdamumc.nl<mailto:d.vannederpelt@amsterdamumc.nl> http://secure-web.cisco.com/1at1mrWf46TOdtPx5xS0xcPHtKcjjqhnoJwny2mJmnGu4hm…<http://secure-web.cisco.com/1yt8mKzBEytW00FvP7R2l1fvv0p1Pks7wPNSutSj2uehWVn…> | http://secure-web.cisco.com/1y-o8iz8BJklocrN5kNtjdaY9roEiw9EV6YPN1Wwf9vH14d…<http://secure-web.cisco.com/1E1k3KMRyxkEmAcnW_-WFns2RvcM9ov9xv6I3gxiqAnetJC…> / http://secure-web.cisco.com/1GkQSxDF48gjZk9fcvs_RSxxTrrn8aVzrQUNoTHAGIapFGV…<http://secure-web.cisco.com/1goc8A86juC4VvHujbtKqV3uicP70Yt2xy7J6aiTJF2W-mb…> ______________________________________________________ ______________________________________________________ AmsterdamUMC disclaimer : http://secure-web.cisco.com/19CYr4N6KMaTAvugEDoUiopxGZ9zOlXs-WAapNPiU40Nisk…

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Two basic questions: brainmask file versions and qcache
by Harriott, Emily M 23 Jan '23

23 Jan '23

External Email - Use Caution Dear FreeSurfer experts, I hope this email finds you all well. I have two relatively basic questions that I am hoping to get some help with. My basic planned processing pipeline is: Run initial recon-all with gcut and ws flags Edit white matter/pial voxels and add control points (as needed) Run second recon-all with autorecon2 and autorecon3 flags Run LGI I have two questions about this: When I run the initial recon-all, I end up with three versions of the brainmask within the /mri/ folder: brainmask.auto.mgz, brainmask.gcuts.mgz, brainmask.mgz. Which brainmask version do I edit, so that my edits are incorporated into the second recon-all run and thus the second attempt at wm/gm segmentation is better? Exactly when and with what command(s) do I use the qcache flag? I apologize that these are quite basic, but sincerely appreciate any input anyone might be able to provide. Thank you so very much in advance! All the best, Emily Harriott Doctoral student at Vanderbilt University

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