Freesurfer November 2020

freesurfer@nmr.mgh.harvard.edu

107 participants
149 discussions

Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all {Disarmed}
by Andy Worth 05 Nov '20

05 Nov '20

External Email - Use Caution Hello, We've experienced random crashes when using the -parallel flag with the official FS docker container at https://secure-web.cisco.com/1Db9ik7eIvMj7kgkeTafe0s_PlT0VyO4BIvoM6Chj4jvye…. It looks like this issue: https://secure-web.cisco.com/1RTUH2ziWrAzuafGfyVCoxnmVd6xWSC1pjYKx0ENFxB4V7…. Is there a fixed recon-all that I can use with that image (or maybe a new image coming soon)? Thanks, Andy Worth Scientific Solutions Engineer he, him, his <http://secure-web.cisco.com/1vnPdwWhDIRo0dgACPHUy8Cs0L0bRI0jZF0TyQMe6r95oCZ…>

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Question about smoothing for extracting anatomical stats {Disarmed}
by Hye Min Shin 05 Nov '20

05 Nov '20

External Email - Use Caution Hello experts, So I understand that when doing mri_glmfit you want to use smoothed surface maps to comply with random field theory while controlling for multiple comparisons (as discussed here: https://secure-web.cisco.com/1pNAU-NVIkRxQvX9B5btXENpnudT80URPA00UsXPU064w3…) But I was also wondering whether we have to smooth surface maps when using mri_anatomical_stats to extract anatomical measurements? I see that mri_anatomical_stats has the option to smooth by # of iterations but is there a way to know how many # of iterations would equal let's say 15 FWHM? Best, Julia Shin

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mri_convert error
by Georgina Angelopoulou 05 Nov '20

05 Nov '20

External Email - Use Caution Dear Freesurfer Developers, I am sorry I did not include the error message. I am attempting to convert some dicom files to mgz via mri_convert command. However, for only 5 participants from my cohort I get the following error. Could you please help me to resolve the problem? (base) Georgias-MBP:HC21 georgina$ mri_convert 1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm 001.mgz mri_convert.bin 1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm 001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm... Starting DICOMRead2() dcmfile = /Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm dcmdir = /Users/georgina/Downloads/HD/HC21 ERROR: GetDICOMInfo(): dcmGetDWIParams() 9 DICOM File: /Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm break DICOMRead.c:5228 Ref Series No = 201 Found 172 files, checking for dicoms ERROR: GetDICOMInfo(): dcmGetDWIParams() 9 ERROR: GetDICOMInfo(): dcmGetDWIParams() 9 DICOM File: /Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491025102.dcm break DICOMRead.c:5228 First Sorting Computing Slice Direction Vs: -0.99478 0.102 0.0033 Vs: -0.994779 0.102 0.0033 Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 1 nslices = 82 ndcmfiles = 82 PE Dir = (dicom read) CTABreadASCII(/Applications/freesurfer/FreeSurferColorLUT.txt): could not open file Too many open files ERROR: reading /Applications/freesurfer/FreeSurferColorLUT.txt Loading pixel data ERROR: /Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316490992042.dcm is not a dicom file 70092 Requested element (18 9089) not found in DCM_GetElementVM Thank you in advance, Georgina

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mri_glmfit_sim error
by Basavaraju, Rakshathi 05 Nov '20

05 Nov '20

External Email - Use Caution Hi all, I ran a multiple comparison correction for a surface based analysis with this command: mri_glmfit-sim --glmdir rh.project.glmdir --cache 2 abs --cwpvalthresh .05 --2spaces But I am getting the following error: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm38/abs/th13/mc-z.csd What might this error mean? I searched in the mail archives but could not get any proper answer. Kindly help me. Thanks

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Re: [Freesurfer] .mgh file unknown, GLM paired analysis {Disarmed}
by Agurne Sampedro Calvete 05 Nov '20

05 Nov '20

External Email - Use Caution Dear FS experts, I have removed the backslashes "\" and now it works, so problem solved. Thank you very much. Regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neurolab.deusto.es Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3015) El lun., 2 nov. 2020 a las 18:27, Agurne Sampedro Calvete (< a.sampedro(a)deusto.es>) escribió: > Dear Freesurfer Experts, > > I am trying to perform a paired analysis in FreeSurfer following this > tutorial https://secure-web.cisco.com/1GGOE7lAk9DEhVom372ksbhQpoUEm3yIVLX4YqDE8HfMpe… and I > have some problems when running the spatially smooth. > > I ran the following command: mri_surf2surf --s fsaverage --hemi lh --fwhm > 5\ --sval lh.paired-diff.thickness.mgh \ --tval > lh.paired-diff.thickness.sm05.mgh > > And I found this error: > ERROR: lh.paired-diff.thickness.mgh unknown freesurfer > > This file is in my subject directory, but when I see the file properties, > in the "file type" box it says: unknown. I have read that other users have > experienced the same error. > > What can I do to solve this problem? > > Thanks in advance. > > Kind regards, > > Agurne Sampedro > > > > Neuropsychology of Severe Medical Conditions Research Team > > Dpt of Methods and Experimental Psychology > Faculty of Psychology and Education > > University of Deusto > > neurolab.deusto.es > > > > Avda. de las Universidades 24, > > 48007, Bilbao (Spain) > > Phone: +34 944139000 (ext. 3015) >

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Join the Brainhack donostia
by Vicente Ferrer 05 Nov '20

05 Nov '20

External Email - Use Caution The Basque Center on Cognition, Brain and Language (BCBL) is holding a free online next week. We hope that it can be of interest to this community, and that you could forward others this information. At the BCBL, we are organizing the third edition of Brainhack Donostia (https://secure-web.cisco.com/1GC1hh4vsRCGfthBadagfSojiEis8P2rIcxlvHWMBmSe1m…) an event focused on neuroscience and the promotion of open-source resources in an accessible way across disciplines and experience levels. This year's edition is taking place from November 9 through November 13: it will be held online and will be completely free. The focus of BHD2020 will be OpenScience, covered from a variety of pertinent perspectives (e.g., MEG, fMRI and fNIRS). We are going to have the cream of the crop as invited speakers, check the schedule here: https://secure-web.cisco.com/1nN_lXzurOj1ntsI3lbjeAWTurwndamZGsnyiXQE9Xqhw7…. Even though we will be physically distant, there will be the possibility to come together and socialize on the Brainhack Donostia GatherTown platform. We will be using the platform to host exciting social activities throughout the event. Stay tuned for the social activities program! We invite all neuroscience aficionados, students of neuroscience-related subjects, professors and professionals to participate. Registrations are now open at https://secure-web.cisco.com/1d3VTvJ1ukmPmrYp15NgAyjM96L0VJDHuND2s9vyXzTZc5…. Best regards, Vicente Ferrer Predoctoral Researcher BCBL http://secure-web.cisco.com/12Abv6l6_PtwWS0hk38LzFrcDpN7GEtPA16QooQuy_XnRh0… Legal disclaimer/Aviso legal/Lege-oharra: http://secure-web.cisco.com/15zTX7kAQnbTPpg6u_ChbnA89bSxwOzqP4KMe91gP9IM05T…

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aparcstats2table
by Saman Fouladi 05 Nov '20

05 Nov '20

External Email - Use Caution hi I run in linux command: """"""""""""""""""""""""""""""""""""""""""" aparcstats2table --hemi lh --subjects /home/team33/MRI4/subj10/stats --parc aparc.a2009s --meas meancurv --tablefile /home/team33/ aparcstats .txt """"""""""""""""""""""""""""""""""""""""""" but show below error an i can not solve it nix: """"""""""""""""""""""""""""""""""""""""""" File "/usr/local/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' """"""""""""""""""""""""""""""""""""""""""" I changed the code several times, but in all cases there is this error. This error also happens to asegstats2table. please help me

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Fwd: Welcome to the "Freesurfer" mailing list {Disarmed}
by Nicholas BH NG (NUHS) 04 Nov '20

04 Nov '20

External Email - Use Caution Dear Free Surfer I followed the excellent video step by step instructions. At the last part of putting the code/ key into the terminal, I encountered the error message as below: no such file or directory. As such I think my set up was not complete. Kindly advice. Thank you Nicholas Nicholass-MacBook-Pro:~ Nic$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -bash: /Applications/freesurfer/7.1.0/SetUpFreeSurfer.sh: No such file or directory Nicholass-MacBook-Pro:~ Nic$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -bash: /Applications/freesurfer/7.1.0/SetUpFreeSurfer.sh: No such file or directory Nicholass-MacBook-Pro:~ Nic$ Begin forwarded message: From: <freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu>> Subject: Welcome to the "Freesurfer" mailing list Date: 5 November 2020 at 11:56:45 AM SGT To: <nicholas_bh_ng(a)nuhs.edu.sg<mailto:nicholas_bh_ng@nuhs.edu.sg>> Email is from external source. Do not click on links or open files if unsure of sender. Welcome to the Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> mailing list! To post to this list, send your email to: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> General information about the mailing list is at: https://secure-web.cisco.com/1K_29qNAChZ4AnViLZdS8JwRzaPLZ2r-1EzaFdh73qaScW… If you ever want to unsubscribe or change your options (eg, switch to or from digest mode, change your password, etc.), visit your subscription page at: https://secure-web.cisco.com/1YHPg5hMnhzPedgjTZmI-bNlaA-196IHzVtleFqSsyGf_Z… You can also make such adjustments via email by sending a message to: Freesurfer-request(a)nmr.mgh.harvard.edu<mailto:Freesurfer-request@nmr.mgh.harvard.edu> with the word `help' in the subject or body (don't include the quotes), and you will get back a message with instructions. You must know your password to change your options (including changing the password, itself) or to unsubscribe. It is: 3:5proverbs Normally, Mailman will remind you of your nmr.mgh.harvard.edu<http://secure-web.cisco.com/12DM9OjyeM0EhnjviHtOaarrHO9I5Ns9clnkrjpEvw9Pm_B…> mailing list passwords once every month, although you can disable this if you prefer. This reminder will also include instructions on how to unsubscribe or change your account options. There is also a button on your options page that will email your current password to you. <p></p> [cid:image94f29b.PNG@780df8a5.4f9160e3]<http://> http://secure-web.cisco.com/1hWpJjsqhqYe2T7sEck3jEb6u0xfiINDKbVq6c5EI9hMk-a…<https://secure-web.cisco.com/1E9FyN4GBZ2x_fphzzWU3DUdsQVGulA6t29D_l9RLw3aMB…> NUHS Facebook<https://secure-web.cisco.com/1BUGnmtuHJbIQx8HoAPJ8je--mJ4w9qZDDL0-2FhHHF-vu…> | LinkedIn<https://secure-web.cisco.com/1uwkRJRWBaWs7W4Quk_bvkxHvMNY-Xvr2l1O_F1xi0EKuo…> | Vimeo<https://secure-web.cisco.com/1VTRcEvWajbC0i8LV7GYL66iMky7LMy3RlL1TyM0mVpwC2…> Important: This email and its attachments are confidential and may be privileged. If you are not the intended recipient, please notify the sender and delete it immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person without prior written permission. Thank you.

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aparcstats2table
by saman fouladi 04 Nov '20

04 Nov '20

External Email - Use Caution hi I run in linux command:""""""""""""""""""""""""""""""""""""""""""" aparcstats2table --hemi lh --subjects /home/team33/MRI4/subj10/stats --parc aparc.a2009s --meas meancurv --tablefile /home/team33/ aparcstats.txt""""""""""""""""""""""""""""""""""""""""""" but show below error an i can not solve it nix: """"""""""""""""""""""""""""""""""""""""""" File "/usr/local/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' """"""""""""""""""""""""""""""""""""""""""" I changed the code several times, but in all cases there is this error. This error also happens to asegstats2table. please help me

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Re: [Freesurfer] Meta-analysing brain measure statistics across multiple cohorts using different versions of Freesurfer
by Stephanie K 04 Nov '20

04 Nov '20

External Email - Use Caution Hi, I am planning on meta-analysing the effects of regional and global cortical thickness + surface area, as well as subcortical volumes of 3 cohorts. Two of them have been processed using Freesurfer 5.3 and one one of them has been Freesurfer 6.0. Is it wrong to meta-analyse them due to differences in the pipeline? I would really appreciate your advice. Thanks

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Freesurfer November 2020