Freesurfer March 2018

freesurfer@nmr.mgh.harvard.edu

115 participants
161 discussions

Potential ways to overlay perfusion ROIs onto cortical thickness maps
by Arsenije Subotic 09 Mar '18

09 Mar '18

Dear experts, I am trying to figure out the best way to overlay areas of low CVR reactivity and correlate that with cortical thickness measurements in those given regions. I was able to overlay our CVR map onto an inflated cortical surface in 3D and modify the configuration to see areas of low perfusion in blue. Using QDEC, I also know that you can manually trace an ROI and generate cortical thickness measurements within that ROI for a given subject. My question is, is it possible to manually trace an ROI in freeview? I tried doing it but it doesn't allow me to use the 'new ROI' when I use the drop down menu. And additionally, is there some way to accurately generate perfusion values within that ROI and then precisely transfer this ROI outline into QDEC so that the cortical thickness ROI is as close to the ROI in the CVR map as possible? Please let me know what you think. Thanks! Arsenije

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Can't open tkmedit
by Levitas, Daniel 09 Mar '18

09 Mar '18

Hi, I tried opening tkmedit but received the following error: libGL error: No matching fbConfigs or visuals found libGL error: failed to load driver: swrast X Error of failed request: GLXBadContext Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 6 (X_GLXIsDirect) Serial number of failed request: 26 Current serial number in output stream: 25? >From what I've read online, it seems to be a graphics card issue, but I'm unsure how to resolve the problem because I'm using my university's linux cluster. Thanks for the help.

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mri_ca_normalize error: Abort (core dumped)
by Marschall, T.M. 09 Mar '18

09 Mar '18

Dear all, I’m currently running the -reconall command on 40 subjects. One of them exited the mri_ca_normalize step with an error saying: Abort (core dumped) I tried rerunning it, however the error keeps occurring. So I have search the list, but could not find a solution to my problem. Does anyone have an idea on how I can fix this problem? I attached the recon-all.log file, maybe it can help finding the error. Furthermore some information about the system I am running the analysis on: 1) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 16.04.4 LTS 3) uname -a: Linux theresa-Lenovo-IdeaPad 4.13.0-36-generic #40~16.04.1-Ubuntu SMP Fri Feb 16 23:25:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Kind regards, Theresa Marschall ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Reg Mapping automatic segmentations to functional space
by Anita S 09 Mar '18

09 Mar '18

Hello all, I have mapped a subject's fMRI Feat data onto the anatomical scan and then mapped the segmentations to the functional space using the following commands: reg-feat2anat --feat feat_folder.feat --subject sub_name aseg2feat --aparc+aseg --feat feat_folder.feat The file created does not contain Middle Frontal Gyrus which is found in 2009 or 2005 aparc versions. How do I change the aparc file used in the above step(s) -- Thanks! - Anita

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getting h/o atlas into individual surface (and then volume) space
by Dorit Kliemann 09 Mar '18

09 Mar '18

Hi, I’m trying to get an atlas (Harvard/Oxford sub&cortical) into individual space via surface registration. Motivation is to replicate a finding in volume space (functional data) in a normal population with that atlas in a lesion data set where transformation to template volume space is not feasible. I think I found a way described in principle for one region below but it seems clumsy with a lot of steps , so I’d like to check if there is a better/more accurate ways with less transforms? Any feedback appreciated! Thanks, Dorit 1) create a registration file from FSL-MNItemplate to Freesurfer space and fsaverage bbregister --s fsaverage --mov MNI152_T1_1mm_brain.nii.gz --init-fsl --init-header --reg mni2fsaverage.dat --T1 --o mni2fsaverage.nii 2) warp atlas from FSL-MNI space onto surface of fsaverage mri_vol2surf --mov HarvardOxford-cort-maxprob-thr25-1mm.nii.gz --reg mni2fsaverage.dat --projdist-max 0 1 .01 --interp nearest --hemi lh --out lh.atlas.mgh 3) writing label for id = 1 mri_cor2label --i lh.atlas.mgh --surf fsaverage lh --id 1 --l ./lh.1.atlas 4) move label from fsaverage onto individual subject space mri_label2label --srclabel lh.1.atlas --srcsubject fsaverage --trglabel lh.1.atlas --trgsubject subject --regmethod surface --hemi lh 5) create voluem form label mri_label2vol --label subject/label/lh.1.atlas --subject subject --hemi lh --identity --temp subject/mri/brain.mgz --o lh.1.atlas.volume.nii --proj frac 0 1 .01 6) fix wholes/border ribbon mri_binarize --dilate 1 --erode 1 --i lh.1.atlas.volume.nii --o lh.1.atlas.volumebin.nii --min 1 mris_calc -o lh.1.atlas.volumebinfixed.nii lh.1.atlas.volumebin.nii mul subject/mri/lh.ribbon.mgz 7) bring from subject T1-FS space (1mm) into subject's functional space bbregister --s subject --mov func.nii --init-fsl --init-header --reg anat2func_register.dat --bold 8) warp atlas image from individual subject anat space to subject bold space mri_label2vol --seg lh.1.atlas.volumebinfixed.nii --temp func.nii --reg anat2func_register.dat --fillthresh .5 --o lh.atlas.func.nii

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-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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Freesurfer March 2018