Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

Integrating glmsingle with freesurfer and mri_glmfit
by Lauri Tuominen 16 May '22

16 May '22

External Email - Use Caution Dear FreeSurfer experts, I would like to use mri_glmfit to do 2nd level random effects analysis on fMRI data I fit with GLMsingle: https://secure-web.cisco.com/114IBmtjAcpPLMEdKHUFIkzufzyCZI6VANnXTx7RjQGYq5… >From GLMsingle I get standardized mean difference (SMD) for any given contrast, i.e. beta- difference map weighted by inverted square root of pooled variance. I am wondering if can I just feed those SMD maps to mri_glmfit via mri_concat or am I missing something elementary? Thank you again! Lauri Tuominen

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Perform aseg in Freeview
by R.J. Austerman 16 May '22

16 May '22

External Email - Use Caution Hello, brand new to this software and community so I apologize if this is a dumb question or if I’m asking it through the wrong channels. I understand that Freeview is just a visualizer for Freesurfer, but since I just want to use it to automatically segment brain MRIs for 3D modeling, I wondered if there was a way to do that within Freeview instead of working with it via the command line. Thank you!

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Freesurfer Passcode
by Utsav Shrestha (shrstha3) 16 May '22

16 May '22

External Email - Use Caution Hello all, I would like to request for a passcode for FS_7_2_0_Ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1Z_58ZIo4a_bMWTqfcqkaCMACuAsrRdQh6f5WruyNMb1Bx…> as being instructed in the wiki. Thank you for your time! With Regards, [UofM logo] Utsav Shrestha Biomedical Engineering Class of 2024 Research Assistant The University of Memphis https://secure-web.cisco.com/1R7Pv-5gfP8NMbNFTlLNdukObQbEhW9E7Rd8vOYudaxHuV…

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Re: [Freesurfer] Permission denied error from -localGI
by Billah, Tashrif 16 May '22

16 May '22

Just closing this thread: we have solved it in https://forum.freesurfer.net/t/permission-denied-error-from-localgi/62 Thanks, Tashrif

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Infant FreeSurfer: volumes extraction without surface
by k3ops＠free.fr 16 May '22

16 May '22

External Email - Use Caution Hi FreeSurfer team, I've been using Infant FreeSurfer for several very young subjects and it works pretty well. But after reviewing the generated surfaces, it looks like pial surface is not extended to fit the cortical grey matter as you can see here: https://secure-web.cisco.com/1bVpNYbCiS9rSsh1DZzM2NKnotXc5MALdQxso7AZkTASVm… (By the way, did you already observed such surface error for infants using Infant FreeSurfer?) I was using this command line to generate the volumes of the brain structures: mri_segstats --seg mri/aseg_CCseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab $FREESURFER_HOME/InfantASegStatsLUT.txt --subject $subjectId So now, I would like to generate the volumes of the brain structres whithout any surface information, to avoid any missleading estimates, is this command line appropriate then? mri_segstats --seg mri/aseg_CCseg.mgz --sum stats/aseg-nosurf.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --euler --ctab $FREESURFER_HOME/InfantASegStatsLUT.txt --subject $subjectId >From what I see, most of the structures volume are identical, except that cerebral grey and white is now provided by the labels and not the surface, and supratentorial/totalgray regions are now missing because only provided by surfaces. Is there another way to generate statistical values only based on labels? Do you recommend a more classic approach like counting voxels from each structure of interest and then multiplying by pixel resolution? (which is very tedious and error prone in my opinion) Thanks a lot for your feedback. Florent

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Password
by Pål Gunnar Larsson 16 May '22

16 May '22

External Email - Use Caution Hello I have run the .ova for a period, but have had some issues. Now I downloaded the new package and need the password for unpacking. It is different from the one I used to log in in prior versions. Best Pål Pål G. Larsson M.D., PhD. Senior Medical Officer Department of Neurosurgery Division of Surgery and Clinical Neuroscience Oslo University Hospital Po.box 4950 Nydalen 0424 Oslo Norway Tel: (+47) 23074407 Mobile: (+47) 93429791 E-mail: pall(a)ous-hf.no<mailto:pall@ous-hf.no> not sensitive

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Passcode for FreeSurfer VM
by Aleksandra Petrovskaia 16 May '22

16 May '22

External Email - Use Caution Dear all, I hope you are doing well. I am an intern at the University of Gothenburg, Sweden, could you please provide me with a passcode for FreeSurfer VM image? I would like to use this version: https://secure-web.cisco.com/1yZkS0R8VnbO1QWzTX29VVIIW4VCNsXbflY7tg4lYbLNqc… Best wishes, Alexandra <https://secure-web.cisco.com/1EaXcElE2e36pVP4hKX6lRltCa5zEeDsgA6QGW0ugUdxgQ…> Без вирусов. http://secure-web.cisco.com/1Qc214ZMYtI0RLObvR0XBJdDSK2mgbyIuNC7SSyx5EDNCrn… <https://secure-web.cisco.com/1EaXcElE2e36pVP4hKX6lRltCa5zEeDsgA6QGW0ugUdxgQ…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Fwd: Passcode for FreeSurfer VM
by Aleksandra Petrovskaia 15 May '22

15 May '22

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Re: [Freesurfer] VM Passcode
by fsbuild 13 May '22

13 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 13, 2022, at 12:01, Viktor Pavliska <Viktor.Pavliska(a)osu.cz> wrote:       External Email - Use Caution        hi,I would like to get a passcode for the .7z file for the VM.Thank you in advanceBest Regards._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Request VM passcode
by fsbuild 13 May '22

13 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 12, 2022, at 12:59, Santiago Fernández <santiagofdezglez(a)gmail.com> wrote:        External Email - Use Caution        Hi,I would like to use the VM with FreeSurfer. Could you send me the passcode?Thanks!Regards,Santi._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer