Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

-qcache error
by Krishna Patel 09 Mar '18

09 Mar '18

Hi - I would like to do group analysis on freesurfer data that is processed with verson 6. However when I try to run recon-all -s subjid -qcache I get following error after it runs for some time and generates some of the files. ERROR: cannot find surf/lh.white.K When I look at the log file - I see that this file was deleted. See following. total integrated curvature = -1.022*4pi (-12.846) --> 2 handles ICI = 169.4, FI = 1785.3, variation=28139.036 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K Does anyone have any idea of what might be the issue here? Thanks, -Krishna

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PhD position on electrophysiology and cognition in multiple sclerosis patients!
by Muthuraman Muthuraman 09 Mar '18

09 Mar '18

*Doctoral Student* *Neuroscientist with focus on electrophysiology and cognition in multiple sclerosis * The *medical faculty of the University of Mainz*, Germany, invites applications for a *PhD Student * for a functional translational neuroscience (FTN) scholarship three year position to work on electrophysiology and cognition in neuroimmunological disorders and multiple sclerosis. A project with multimodality usage of electroencephalography (EEG) and non-invasive brain stimulation technique like transcranial magnetic stimulation (TMS). The successful applicant holds a Master’s degree (or equivalent) in a relevant academic area such as *basic life sciences, neuropsychology, applied* *mathematics or biomedical engineering or similar disciplines. *German language proficiency is mandatory for communicating with the patients. The working language at the institute is English. Experience with electrophysiology and the analysis of brain signals is advantageous, but not essential. The applicant’s merits are assessed on the basis of the quality of Master’s level studies and thesis, previous experience with the brain imaging, motivation and research interests. The location for this research will mainly be the workgroups “*Section of Movement Disorders, Neurostimulation and Neuroimaging*“ of Prof. Sergiu Groppa at the Department of Neurology and “*Multimodal Signal Processing and Statistical Analyses*” of Prof. Muthuraman Muthuraman, both at the Focus Program Translational Neurosciences (http://www.ftn.uni-mainz.de/) and Neuroimaging Centre Mainz (http://www.ftn.nic.uni-mainz.de/) Expected close collaborations with national and international partners. The application should include a statement of research interests, a curriculum vitae (max. 4 pages) composed according to good scientific practice, a certificate of Master’s degree, copy of the master’s thesis and grades of Master’s level studies, the names and e-mail addresses of two referees and a proof of proficiency in English. The position will be open until filled. To apply for the position, please send the above documents as pdfs until 31.03.2018 to* Prof. Sergiu Groppa*, Department of Neurology, Section of movement disorders and neurostimulation, University of Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany, or by Email to *segroppa(at)uni-mainz.de <http://uni-mainz.de>*. For additional information please contact* Sergiu Groppa. * With regards M.Muthuraman Prof. Dr.- Ing. M.Muthuraman Biomedical statistics and multimodal signal processing unit Movement Disorders and Neurostimulation, Department of Neurology, Focus Program Translational Neuroscience (FTN) Johannes-Gutenberg-University Hospital, Langenbeckstr. 1 55131 Mainz, Germany Email: mmuthura(a)uni-mainz.de Website: http://www.dbs-info.de/mm.html

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RECON-ALL {Disarmed}
by 郑凤莲 09 Mar '18

09 Mar '18

Hi experts, I am using FS 6.0 to calculate LGI. But when l ran recon-all, there is an error: couldn't find DWI parameters. I don't know how to resolve this problem. Looking forward to your reply. Thanks very much. Sincerely, Zheng | | 13181786167 邮箱：13181786167(a)163.com | 签名由网易邮箱大师定制

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Mean Curvature
by Kasper Jessen 09 Mar '18

09 Mar '18

Hej FreeSurfer, Question regarding the meancurv extracted from the Desikan atlas using aparcstats2table. Is the meancurv the absolute mean curvature? Thus all the values are positive? Best regards Kasper Sent from [ProtonMail](https://protonmail.com), Swiss-based encrypted email. Sent with [ProtonMail](https://protonmail.com) Secure Email.

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Brainstem registration
by Chungmin Han 08 Mar '18

08 Mar '18

Dear whomever it may concern, I'm Chungmin, a graduate research assistant in University of Texas at Austin, I'm fairly new to using freesurfer, I'd appreciate to get some advice on what I'm facing, I have fMRI limited FOV collected on brainstem + little cerebellum/visual area, I've tried SPM manual registration to MNI space, falls in 1-2mm (1-2 voxels) away from accurate registering brainstem correctly, is there a way to create transformation matrix optimized to fit brainstem in MNI space? Registering cortical region slightly bit wrong is okay to me at this moment, https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures I've noticed this has been posted pretty recently, but would like to figure out how to align in standard space for comparison. I've also thought of inverse registering from MNI to each native space, however, if the transformation focuses on maximizing registration on the cortical level (T1) I don't think inverse registration solves the issue, Thank you in advance :) Best Chungmin Chungmin Han Graduate Research Assistant The University of Texas at Austin 204 E. Dean Keeton St Austin TX 78712 Mobile: 512-717-1671

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Question regarding recon-all
by Levitas, Daniel 08 Mar '18

08 Mar '18

Hello, I am running recon-all for the first time, and I am wondering when it is proper to use the -i option. My current recon-all command includes the -i option: recon-all -i T1.nii.gz -s 1020 -all, where T1.nii.gz is a nifti file of all 160 anatomical dicoms. I've seen some commands like this however: recon-all -s subjid -all?. My question is, is it safer to specify the input, and if I choose not to, do I need to create an mri/orig/001.mgz file from mri_convert? Thank you for the help, Dan

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FreeSurfer Edit Sequence Inquiry
by David S Lee 08 Mar '18

08 Mar '18

Hello FreeSurfer Group, I am writing to inquire about Editing Sequence. The "Troubleshooting your output" page (https://surfer.nmr.mgh. harvard.edu/fswiki/FsTutorial/TroubleshootingData) explains the edits sequence as brain mask --> wm volume --> white surface --> control points. Do you suggest people to absolutely stick to this particular sequence? Thanks for your time, David

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Eliminate variable which is the same for all patients from FreeSurfer's Design Matrix
by k.ohmstedt＠stud.uni-heidelberg.de 08 Mar '18

08 Mar '18

Dear all, I am trying to correlate psychometric measurements and the local Gyrification Index. To do so, I use the FreeSurfer pipeline to calculate the lGI and then PALM, following the advice in this thread (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-March/050703.ht…) All my subjects are part of the same group, so I used a FSGD with the group "main" to create the design matrix and mask for my data that are required by PALM. Having a closer look at the design matrix that was created, I found that there was a variable for the group that was the same for all my patients. As it is the same for all patients, I thought eliminating it would not be a problem. But after re-running PALM without it, there were huge differences in my results and effects were notably larger and more significant. Do any of you have any experience which option is best in this case? Is it a valid choice to eliminate the variable for the group, as it is the same for each patient anyway? Furthermore, would you recommend centering for the design matrix? I found that this can have an impact, but I am lost on in which cases it should be done and in which it shouldn't. Thank you for your help! Best regards Kai Ohmstedt

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[Freesurfer/Freeview cutting]
by Dave Yas 08 Mar '18

08 Mar '18

Hello, Can we cut the surface (for flatting later) in freeview? if yes, how? I cant find a tutorial online for that. tksurfer is not working, it crashes by it self. If i cant use freeview to cut, do you suggest another alternative? thank you

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Brain microstructure MRI postdoc (Italy)
by Jovicich, Jorge 08 Mar '18

08 Mar '18

Hello, We will soon advertise a 2-year postdoctoral fellowship at the MRI Group <http://r.unitn.it/en/cimec/mri> of the Center for Mind/Brain Sciences (CIMeC <http://www.cimec.unitn.it/en>), University of Trento <http://www.unitn.it/en/>, Italy. The focus of this position will involve the development, testing and validation of MRI techniques that allow quantification of tissue microstructure properties. The successful candidate will be part of an international multidisciplinary team developing and applying MRI techniques to study brain structure and function supporting normal higher cognitive function as well as the study of cognitive dysfunction in various neurological and neuropsychiatric conditions (including pre-surgical planning, plasticity in deaf and blind, novel markers sensitive to the progression of neurodegenerative diseases). Facilities: The CIMeC MRI neuroimaging lab will house a Siemens Prisma 3T scanner (tentatively May 2018) designed for research and clinical studies. The position will allow for training opportunities in pulse sequence development, brain anatomy, and translational clinical research. The fellow is expected to be able to work independently as well as part of a multidisciplinary team with supervisory responsibilities of graduate student research. The fellow will support research MRI users, will have opportunities to develop new ideas and advance their own research interests in an international academic environment. Requirements: Minimum qualifications are a doctoral degree in cognitive neurosciences, physics, engineering, computer sciences or related area, strong scientific publication record, and demonstrated expertise in MRI methods development and applications. The ideal candidates should be proficient in programming, such as C++, Matlab. Experience in pulse sequence design, particularly on Siemens platform, and/or image reconstruction will be a plus. Additional requirements include high self-motivation, ability of solving research problems independently, and excellent communication skills. Contact: Interested candidates please contact Jorge Jovicich, Ph.D, MSc., Assistant Professor (jorge.jovicich(a)unitn.it) -- Jorge Jovicich, Ph.D. MR Lab Head Center for Mind/Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri CIMEC: http://www.cimec.unitn.it/

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Freesurfer