Freesurfer

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30070 discussions

recon-all -s subid exited with ERRORS
by Lee, Seonjoo 10 Jun '18

10 Jun '18

External Email - Use Caution Hi Bruce, recon-all did not run, and I could not figure out the problem. Do you have any clue what could be? The log file does not tell anything… The command was the most simplest one (using only t1). If you need more information to figure out the cause of this error, please let me know. Thank you. -Seonjoo ==== #@# MotionCor Sat Jun 9 21:04:46 EDT 2018 Found 1 runs subject/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. \n cp subject/mri/orig/001.mgz subject/mri/rawavg.mgz \n subject \n mri_convert subject/mri/rawavg.mgz subject/mri/orig.mgz --conform \n mri_convert.bin subject/mri/rawavg.mgz subject/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from subject/mri/rawavg.mgz... TR=6.81, TE=3.16, TI=0.00, flip angle=9.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to subject/mri/orig.mgz... Darwin Seonjoos-iMac.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 recon-all -s subid exited with ERRORS at Sat Jun 9 21:04:51 EDT 2018

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Prospective motion correction sequences
by Backhausen, Lea 08 Jun '18

08 Jun '18

External Email - Use Caution Dear FreeSurer experts, has anyone of you ever used prospective motion correction techniques like PROMO or BLADE/PROPELLER? We are planning a new study with children and adolescents with obsessive-compulsive disorder and thought about implementing special motion correction sequences for the structural data as we are very aware of potential motion artifacts in pediatric clinical samples like this one. Still we are not sure whether special sequences like these could potentially change the raw data in any way that may corrupt FreeSurfer reconstruction. I read a lot of positive reviews about PROMO, would you recommend it? Thank you for your input! Best Lea ------------------------------ Lea Backhausen Research Assistant Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/>

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ERROR running mkcontrast, ERROR: cannot find matlab. Is it in your path?
by 高寒 08 Jun '18

08 Jun '18

External Email - Use Caution 高寒已与你共享 OneDrive 文件。若要查看，请单击下面的链接。 <https://1drv.ms/u/s!AuDaBb5FCQKSglY7fUCYI2K7qRCu> [https://r1.res.office365.com/owa/prem/images/dc-generic_20.png]<https://1drv.ms/u/s!AuDaBb5FCQKSglY7fUCYI2K7qRCu> 终端存储的输出<https://1drv.ms/u/s!AuDaBb5FCQKSglY7fUCYI2K7qRCu> Hello FreeSurfer Developers, I am running FS-FAST on my mac. My freesurfer version is freesurfer-i386-apple-darwin11.4.2-stable6-20170119. My MAC version is macOS High Sierra 10.13.4 (17E202). I downloaded Matlbab Runtime on this site: http://www.freesurfer.net/fswiki/MatlabRuntime as constructed. When I run this command: { mkcontrast-sess -analysis my-language.sm05.lh -contrast language-v-base -a 1 }, I kept getting this error. ERROR: cannot find matlab. Is it in your path? ERROR running mkcontrast Then I downloaded Matlab runtime R2014a (8.3). I still got the same error as above. Then I downloaded Matlab runtime R2018a (9.4). Still the same error. I assume I should download a certain version of Matlab Runtime in order to run FS-FAST on freesurfer-i386-apple-darwin11.4.2-stable6-20170119 on my macOS High Sierra 10.13.4 (17E202). Could you help me? Thank you.

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-qcache in recon-all commnd
by Alexopoulos, Dimitrios 07 Jun '18

07 Jun '18

Is it recommended to use the -qcache flag in the basic recon-all -all command? What does it do and what are the advantage of using it? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Fwd: Correcting defect issue
by Julian Macoveanu 07 Jun '18

07 Jun '18

External Email - Use Caution Hi all, I have a subject that is stuck here for days (fs60): CORRECTING DEFECT 8 (vertices=18549, convex hull=3089, v0=69938) XL defect detected... The inflated.nofix surface looks like attached. What can I do to make to analysis go through? This is my first analysis so please take it easy :) Best, Julian [image: Screenshot 2018-06-07 19.27.47.png]

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Postdoctoral fellowship: fMRI in OCD at Nathan Kline Institute
by ROBERT CARY WELSH 07 Jun '18

07 Jun '18

External Email - Use Caution Post-doctoral Fellowship in Neuroimaging in Obsessive-Compulsive and Related Disorders Psychiatric NeuroCognition Lab The Nathan S. Kline Institute for Psychiatric Research The Psychiatric NeuroCognition laboratory, under the direction of Dr. Emily Stern at the Nathan S. Kline Institute for Psychiatric Research, is seeking a post-doctoral fellow to work on projects investigating brain function and structure in obsessive-compulsive disorder (OCD) using task-based fMRI, resting-state functional connectivity, and diffusion imaging approaches. Broadly speaking, the lab’s work uses a cognitive neuroscience approach to investigating brain function in psychiatric disorders, with a focus on using fMRI to tap into core constructs relevant for OCD and related disorders including interoception, rumination, decision-making, and reward processing. The person in this position will primarily work on two ongoing NIMH funded projects using fMRI to investigate neural mechanisms of sensory and other key symptoms in OCD, including a clinical trial in OCD and Tourette’s Disorder testing the effects of a novel treatment on symptoms and brain function. In addition to working on these funded studies, there will also be opportunity for the fellow to develop new studies and/or analyses relevant to the lab’s work and to obtain pilot research funding offered through the institute. NKI is a research facility of the New York State Office of Mental Health, one of only two state-funded research institutes in the U.S. dedicated entirely to investigating biological mechanisms and treatments for psychiatric disorders. NKI was founded in 1952 by Dr. Nathan Kline, whose pioneering research into psychopharmacological management of schizophrenia and major depression revolutionized treatments for serious mental illness. The Psychiatric NeuroCognition lab is part of the Clinical Research Department at NKI, which contains several investigators, trainees, and staff working on studies examining treatments and biomarkers in a variety of disorders (depression, schizophrenia, autism spectrum disorder). Research facilities at NKI include a 3T Siemens MRI scanner for human neuroimaging, an MRI-compatible EEG system, and equipment for advanced neuromodulation techniques including transcranial magnetic stimulation and transcranial direct current stimulation. NKI also has an active animal research program with a 7T small animal scanner. For the past 30 years, NKI’s academic affiliate has been the New York University School of Medicine (NYUSoM) located in midtown Manhattan, and investigators and trainees at NKI have access to many of NYUSoM’s research tools and resources. Approximately 20 miles north of Manhattan, NKI is located in suburban Rockland County, home to many beautiful hiking and cycling trails overlooking the Hudson River. Although several towns in Rockland County are accessible to Manhattan via public transportation on New Jersey Transit, a driver’s license and access to a car is highly recommended for anyone considering this position. Interested candidates should meet the follow criteria: Required: • Ph.D. in experimental psychology, clinical psychology, or cognitive neuroscience • Moderate or better proficiency with functional MRI data analysis and presentation Other desirable qualifications: • Strong interest in psychiatric disorders and applying cognitive neuroscientific techniques to OCD and related disorders • Track record of publishing and presenting fMRI data • Experience with 2 or more standard fMRI packages for data processing (SPM, FSL, AFNI, Conn, Freesurfer, DPABI/DPARSF, C-PAC) and/or experience with both task-based and resting-state functional connectivity methods • Experience with task programing software such as EPrime, Presentation, or PsychoPy • Good knowledge of basic statistical concepts and approaches • Experience with (or desire to learn) basic programming in MATLAB, bash, and/or python • Knowledge or experience in psychiatric/psychological assessment and diagnosis would be a plus but is not required Duties of the position include: • Managing and analyzing task-activation and functional connectivity data, programming fMRI and behavioral experiments, running subjects through experimental protocols • Reading the literature and publishing behavioral and neuroimaging findings in top tier journals • Presenting results at conferences and seminars • Developing new studies or analyses relevant for the ongoing work in the lab and applying for pilot and post-doctoral grants to support this work • Assisting with grant applications, NIH progress reports, and IRB applications • Assisting in the training of junior lab members including research coordinators and interns Salary is competitive and commensurate with experience. Fellows would be employed by the Research Foundation for Mental Health (RFMH), which offers a full benefits package with medical and dental benefits. The position is for 1 year initially, with the opportunity to extend based on performance. Applications should be emailed to fmripostdocnki(a)gmail.com<mailto:fmripostdocnki@gmail.com> (‘fmri’ and ‘postdoc’ and ‘nki’) and include a cover letter, CV, and the names and contact information for two referees.

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connectivity between two ROIs
by Eryilmaz, H. Hamdi 07 Jun '18

07 Jun '18

Dear all, I would like to use the fsfast functional connectivity pipeline to compute connectivity between two binarized ROIs. One of the ROIs is a surface ROI, the other is a hippocampal subfield. Based on the tutorial on http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth…, I created the time courses for the two ROIs. However, in order to regress out the signal from the ventricles, CSF, and white matter as well as the motion parameters, it seems that I need to run a whole-brain analysis (or at least one hemisphere). Is that correct? Would it be possible to compute connectivity just between two given ROIs without needing to run the analysis on the hemisphere? Thanks a lot! Best, Hamdi

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Python Developer Study
by Lussier,Desiree 07 Jun '18

07 Jun '18

External Email - Use Caution Dear Freesurfer community, We are currently interested in recruiting Python developers for a study. Information can be found below. Thank you, Désirée Lussier, MS Graduate Student Department of Psychology University of Florida [1509730522218_github]<https://github.com/dllussier> [1509730529145_linkedin-icon-14small.png] <https://www.linkedin.com/in/desiree-lussier/> [1509730538655_twitter-icon] <https://twitter.com/desiree_lussier> <http://www.psych.ufl.edu/ebnerlab/> <https://people.clas.ufl.edu/desireelussier/> [1509730546740_website] <https://people.clas.ufl.edu/desireelussier/> From: Oliveira,Daniela Sent: Thursday, June 7, 2018 12:25 PM To: Natalie Ebner; Myers,Elisha M Subject: Recruiting text (for email distribution) Subject: Recruiting Python Developers for User Study Hello All, Our lab at the University of Florida is recruiting Python developers for a research study on developer's perceptions while programming. Please help us advance Science! Compensation in US dollars (Amazon gift card): $50 for professionals working with software development and testing (employed) and $20 for senior undergrads and graduate students from Universities. Graduate students with internship experience in the industry can qualify for enrollment as professional developer. English fluency is required. Tasks: 1) Complete a multiple-choice survey about programming. 2) Complete a short questionnaire on personality and cognition. For more information and to enroll please contact: psy-ebnerlab(a)psych.ufl.edu This study has been funded by the National Science Foundation and is approved by the University of Florida Institutional Review Board (IRB). Please share our ad and/or tag someone you know will be interested! Thanks [cid:259d6abc-ad88-443e-a825-5705f49dc7db] :) _______________________________________________________________ Daniela Oliveira, PhD IoT Term Professor Associate Professor University of Florida Department of Electrical and Computer Engineering MAE 208 Gainesville, FL 32611 http://www.daniela.ece.ufl.edu/ 352.392.6618| daniela(a)ece.ufl.edu<mailto:daniela@ece.ufl.edu> Note: Under Florida Law, e-mail communications are public records. Therefore, you should have limited expectations of privacy. If you do not want your e-mail address or e-mail contents released in response to a public records request, please contact me so I can provide you with an alternate non-UF email address.

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E-TIV and Linux version: Some quick questions
by Jeff Crawford 07 Jun '18

07 Jun '18

External Email - Use Caution Dear Freesurfer Experts, I have two questions that I hope are easy to answer. 1. Would the calculation for E-TIV change if I edited the pial and reran recon-all as in this tutorial below? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview My understanding is that E-TIV should not change after minor edits to the pial segmentation, because the transform happens before these edits even happen. We start the at autorecon2-pial for the pial correction, which is after the Talairach transform computation. 2. I have two different windows computers with two VMware workstations running what I thought were the same versions of CentOS. They are both CentOS 6, but one is 6.5 and the other is 6.9. If both VMware workstations run the exact same versions of Freesurfer 6 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c), is it a problem if the CentOS versions are slightly different? I know the FS wiki says "it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS.", but would there be enough of a difference between CentOS 6.5 and 6.9 to cause major discrepancies in Freesurfer T1 processing? Thanks so much, Jeff

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poor anterior lobe surfaces
by Meaghan Perdue 07 Jun '18

07 Jun '18

External Email - Use Caution Hello Freesurfer experts, 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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