Freesurfer January 2019

freesurfer@nmr.mgh.harvard.edu

119 participants
167 discussions

Italian Summer School: Interdisciplinary Research on Brain Network Dynamics
by Jovicich, Jorge 28 Jan '19

28 Jan '19

External Email - Use Caution Dear all, we are organizing an international summer school on interdisciplinary research oriented to the study of brain network dynamics (June 24-28, 2019). More information: https://event.unitn.it/brandyschool2019/ Feel free to disseminate to relevant groups. Regards, Jorge -- 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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Orientation by direction cosines
by Ritesh Mahajan 26 Jan '19

26 Jan '19

External Email - Use Caution Hello Team, Can any one please explain how we come to know whether it is RAI or RAS or any other orientation through direction cosines: Below is the direction cosine: I saw some non zero and negative values in non diagonal values of matrix. What does this signify ? 0.999377 0 -0.0352819 -0.00916448 0.965676 -0.259588 0.0340709 0.25975 0.965075 Suppose it is Head First Supine. Any help will be really appreciated. Thanks, Ritesh Mahajan

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dispaly retinotopy result
by starxifd 25 Jan '19

25 Jan '19

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FSFAST poor registration
by Keri Woods 25 Jan '19

25 Jan '19

External Email - Use Caution Hi I have a problem very similar to this one: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23206.html I've tried the suggestions given there, but it didn't fix my problem. I'm running the FSFAST preproc-sess stream and the quality of the registration is very poor for most of the subjects. I've tried initializing the registration differently, using bbregister with --init-fsl, --init-spm and init-header, which didn't improve the results at all. I've also tried register-sess with --init-fsl, --init-spm and init-header, as well as spmregister-sess and fslregister-sess. Is there anything else I could try? Using the SPM GUI, the registration was fine, so I thought that spmregister-sess would have been an improvement, but it wasn't. Is there anyway I can import the registration obtained using the SPM GUI? Thanks for your help. Thanks, Keri

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Surface to volume conversion
by Bunting, Emma 25 Jan '19

25 Jan '19

External Email - Use Caution Hi! I’m trying to convert my sig.mgh output from GLM into a .nii file using mri_convert, and when I load the resulting volume in freeview this is what I see. The command I’m using is: mri_convert —in-type mgh —out_type nii.gz —out_orientation RAS /(root to sig.mgh file)/sig.mgh /(root to output file)/sig.nii.gz, Is there something I should be doing differently? Many thanks, Emma

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Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS
by falk.luesebrink＠med.ovgu.de 25 Jan '19

25 Jan '19

External Email - Use Caution Dear all, Has anyone run the longitudinal pipeline successfully using the WSL? I'm running it with Ubuntu 18.04.1 LTS and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. I'm trying to process my first longitudinal data set following the instructions of the tutorial as close as possible. The data has been processed without issues and now I want to do the statistical analysis. When I run: long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR I get the following error: File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448 print '\nERROR: Specify --qedc (and other required arguments)\n' ^ SyntaxError: invalid syntax I get comparable errors for any other long_* command I try to run, e.g. long_qdec_table with or without any arguments gives: File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119 print '\nERROR: Specify --qedc' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('\nERROR: Specify --qedc')? Does anyone have a clue where this error originates from using either WSL or Ubuntu 18.04? Best, Falk ............................................... [klinikum_logo_schmal_e-mail_blau] Universitätsklinik für Neurologie Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg Telefon: +49-391-6117-512 falk.luesebrink(a)med.ovgu.de<mailto:falk.luesebrink@med.ovgu.de> http://www.kneu.ovgu.de/kneu.html

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Error in running make_average_subject
by Emanuel Alvaredo 25 Jan '19

25 Jan '19

External Email - Use Caution Hello!, I am getting the following error using the command make_average_subject mri/norm.mgz: could not load norm volume from (null) I have found this page with a path for de issue https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008… But I dont know how to apply the path. Can you give some information about this? Thanks! Emanuel

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move statistical map onto the cerebellum surface
by john Anderson 25 Jan '19

25 Jan '19

External Email - Use Caution Dear FS experts, I ran surface based PET analysis on subcortical regions. Then corrected the results for multiple comparisons using the method --grf in the command mri_glmfit-sim. I can visualize the output of multiple comparisons (i.e. the file grf.th1.3.pos.sig.cluster.mgh) on volume using tkmedit, this statistical map shows difference between the groups in the cerebellum.... Instead of visualizing the results on volume, I want to move this file to the cerebellum surface. I already created the cerebellum surfaces from aseg.mgz file in fsaverage using the command mris_tesselate. How can I move the the file grf.th1.3.pos.sig.cluster.mgh from volume space and map it on the cerebellum surface? I tried mri_vol2surf but this command requires the flag --hemi as a result it will map the file "grf.th1.3.pos.sig.cluster.mgh" on cerebral hemispheres (lh or rh) but not the cerebellum.. How can I map the file "grf.th1.3.pos.sig.cluster.mgh" on the cerebellum surface? Thanks for any suggestions, John

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mri_convert
by N Saf 25 Jan '19

25 Jan '19

External Email - Use Caution Dear Bruce, I had a problem with bringing aseg.mgz into my subject space and you recommend this command before: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.resliced.mgz which perfectly worked for me but now when I want to try it in new version6 it does not work and the aseg.resliced file contains just corpus callosum!, I don't know which I do wrong because it worked before and still work with the analysis which I done with last version. would you please help me to figure it out?thank you very much for your help. best regards, Nazain PS:the link of previous mail:https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50794.h…

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Neuroscientist with focus on electrophysiology and imaging in Parkinson disease patients!
by Muthuraman Muthuraman 25 Jan '19

25 Jan '19

External Email - Use Caution *Doctoral Student* *Neuroscientist with focus on electrophysiology and imaging in Parkinson disease patients * The *clinic of neurology, imaging and neurostimulation group (http://imaging-neurostim.com <http://imaging-neurostim.com>) 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 imaging in Parkinson disease (PD) patients. A project with multimodality usage of modalities like electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) to analyze network fingerprints in PD patients. 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 “*Biomedical Statistics and Multimodal Signal Processing Unit*” 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 15.02.2019 to* Prof. Sergiu Groppa*, and *Prof. Muthuraman Muthuraman*, 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>; mmuthura(at)uni-mainz.de <http://uni-mainz.de>*. For additional information please contact* Muthuraman Muthuraman. *

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Freesurfer January 2019