Freesurfer

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30132 discussions

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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Re: [Freesurfer] 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 I was able to circumvent the error by switching from python3 to python2. In python3 print was changed to a function making it necessary to put the arguments in brackets. Best, Falk Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> Im Auftrag von falk.luesebrink(a)med.ovgu.de Gesendet: Freitag, 25. Januar 2019 10:42 An: Freesurfer Mailinglist <freesurfer(a)nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS External Email - Use Caution Dear Juergen, Thanks for your quick reply! Actually the spelling error is in the error message. Taken from http://martinos.org/~mreuter/long/long_mris_slopes # extensive error checks # if options.fsgd is None and if options.qdec is None: # print 'ERROR: Specify --fsgd or --qedc' parser.print_help() print '\nERROR: Specify --qedc (and other required arguments)\n' sys.exit(1) # if options.fsgd is not None and options.qdec is not None: # print 'ERROR: Specify either --fsgd or --qedc, not both' # sys.exit(1) At least Martin is consistent with his typo. :D Best, Falk Von: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> Im Auftrag von Juergen Haenggi Gesendet: Freitag, 25. Januar 2019 10:35 An: Freesurfer Mailinglist <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS External Email - Use Caution Dear Falk I have no idea, but recognised that the error refers to --qedc and not to --qdec. maybe there is a spelling error somewhere that is related to your problem. HTH Cheers Jürgen ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch<mailto:j.haenggi@psychologie.uzh.ch> (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This email (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this email in error) please notify the sender immediately and destroy this email. Any unauthorised copying, disclosure or distribution of the material in this email is strictly forbidden. ----------------------------------------------------------------------------------------------------- On 25 Jan 2019, at 10:26, falk.luesebrink(a)med.ovgu.de<mailto:falk.luesebrink@med.ovgu.de> wrote: 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 ............................................... <image001.gif> 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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correction for multiple comparison: simulation vs grf vs cache
by john Anderson 24 Jan '19

24 Jan '19

External Email - Use Caution Hi Dr Greve, I would like to correct surface based analyses of PET data for multiple comparisons. I ran group comparisons in three spaces. left and right hemispheres and subcortical. I used the method --cache in mri_glmfit-sim to correct the analyses in eft and right hemispheres. I used the method --grf in mri_glmfit-sim to correct the analyses in subcortical regions. My questions are: In one of your kind responses to a collegue here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-January/035650.… you had suggested "If you want to use GRF, you should use smooth by twice the native voxel size. I would not go higher than .01 on the threshold". Would you mind clarify what it means don;t go higher than .01 is this the cwp threshold? also smoothing by twice the native voxel is this means fwhm=2mm? The methods --cache and --grf are giving me the expected results.. when I should consider using simulation --perm ? Thanks for any clarification John

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Smoothing before or after PALM (and results conversion for Surf Ice)
by Daniel Leopold 24 Jan '19

24 Jan '19

External Email - Use Caution Hello FS experts and enthusiasts, Thus far, I have used mri_concat to make 4D files of subjects' lh.thickness.fwhm15.fsaverage.mgh files to be used as input for palm. The results maps are of the .mgz format. I can convert these to .nii using mri_convert in order to use fslmaths or fslstats. My dilemma is that I'd like to use another viewing package for the palm results (i.e., Surf Ice) because of its features and some quirks I've encountered while loading results in Freeview. Surf Ice accepts a number of formats ( https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage#Supported_Fo…) including Freesurfer's .asc, .srf, .curv, .gcs, .pial, and .w (among *many* others), but I have yet to successfully convert these .mgz maps to a readable format. Surf Ice can read .nii, but loading my mri_converted .nii files results in a uniform surface with 0 at all vertices. Thus, I have two questions: 1) Can you think of a means to convert these surface "volumes" (.mgh/.mgz) to a desired format that can be read by Surf Ice? I've attempted mri_vol2surf, mri_surf2surf, and mris_convert, but cannot find an appropriate format/get things to work. In case it's helpful, readable formats are: 2) My alternative idea would be to instead use mri_concat on subjects' lh.thickness files and later apply fwhm smoothing. Would this approach be feasible? I could test whether pre-palm smoothed and post-palm smoothed results are equivalent, but I'm afraid that the variable dimensions of subjects' native thickness files would cause problems either with palm or when later trying to view the group-level results. Version information: Recon-all run with FreeSurfer 5.3.0 FSL 5.0.8 palm alpha112 Thank you in advance for any suggestions, and please let me know if any additional information would be helpful. With gratitude, Dan

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"slides" link is not working
by Peters, Douglas G 23 Jan '19

23 Jan '19

External Email - Use Caution https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples Error Message: Not Found The requested URL /pub/docs/freesurfer.groupanalysis.short.pdf was not found on this server.

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