Freesurfer

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30132 discussions

Fwd: NeuroCon 2020 - save the date
by ezgi arikan 15 Jan '20

15 Jan '20

External Email - Use Caution Dear all, We are happy to announce the first meeting of the young German Neuroscience Society (jNWG), NeuroCon 2020 (see the attached flyer). The meeting will take place in September 25-27, 2020 in Ulm, Germany, and is designed specifically for early career scientists who would like to present their projects, build academic skills and connect with other colleagues in the field. The meeting is open to any neuroscience field, so a wide array of topics will be on display. Detailed information regarding the program and registration will be soon on our website: jnwg.org Best Regards, B. Ezgi Arikan

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Email info for free surfer mailing list
by ezgi arikan 15 Jan '20

15 Jan '20

External Email - Use Caution Best Regards Ezgi Arikan

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Max threshold marked as '-inf' in cluster summary file
by Bronwyn Overs 14 Jan '20

14 Jan '20

External Email - Use Caution Dear Freesurfer Mailing List, I have completed an LME analysis in matlab and have generated a number of different cluster summary files for my various contrasts. In many of resulting cluster summary files the 'Max' value for the largest cluster which encompasses most of the brain surface is reported as infinity ('-inf'). Please find an example file attached. As I was hoping to use these values to generate effect size estimates, can you please tell me what alternate value I could substitute here for 'Max'? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

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Thalamus segmentation
by sara ponticorvo 14 Jan '20

14 Jan '20

External Email - Use Caution Hi Freesurfer expert, I have a question regarding the segmentation of the thalamus. After the “standard” segmentation from the recon-all (aseg), in label thalamus-Proper is included the medial geniculate body? Thanks, Sara

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Re: [Freesurfer] how to include Schaefer atlas into freesurfer and compute surface statistics
by Kate Marvel 14 Jan '20

14 Jan '20

External Email - Use Caution Thank you very much! Much appreciated Prof Leo. On Tue, Jan 14, 2020, 6:46 PM Thomas Yeo <yeoyeo02(a)gmail.com> wrote: > Hi Kate, > > You can see the instructions here: > https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parc… > > The gcs files will be incorporated into freesurfer at some point. > Aihuiping (cc-ed) will attach the gcs files in the next email. > > Thanks, > Thomas > > On Wed, Jan 15, 2020 at 7:40 AM Kate Marvel <kmarvel54(a)gmail.com> wrote: > >> Dear Freesurfer team, >> >> I would like to include Schaefer atlas into freesurfer. The Schaefer >> atlas can be found in the link below: >> >> >> https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parc… >> >> My question is how can I integrate the atlas in the freesurfer so that I >> can run recon-all and calculate the statistics using Schaefer >> parcellations, just like aparc_DK40 or aparc_a2009s atlases already >> pre-installed in freesurfer >> >> >> Thank you, >> >> -- >> kate >> >

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how to include Schaefer atlas into freesurfer and compute surface statistics
by Kate Marvel 14 Jan '20

14 Jan '20

External Email - Use Caution Dear Freesurfer team, I would like to include Schaefer atlas into freesurfer. The Schaefer atlas can be found in the link below: https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parc… My question is how can I integrate the atlas in the freesurfer so that I can run recon-all and calculate the statistics using Schaefer parcellations, just like aparc_DK40 or aparc_a2009s atlases already pre-installed in freesurfer Thank you, -- kate

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Re: [Freesurfer] Right Lateral Ventricle Omitted from white and pial surfaces
by Rachel Hoel 14 Jan '20

14 Jan '20

External Email - Use Caution Thank you, I am still checking in with my supervisors about sending the subject. For now, if we are only interested in looking at grey matter data, do we need to be concerned if the subcortical segmentation isn’t accurate? Best, Rachel

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Skipping bias field correction
by Patrick 13 Jan '20

13 Jan '20

External Email - Use Caution Dear Freesurfer experts, I am trying to run recon-all but I want to skip bias field estimation and correction step. I have tried the following: 1) Run recon-all by specifiying -nonuintensitycor2) Running recon-all by specifying "motioncor" followed by "talairach" (additionally copying "orig" file and renaming it as "nu" However, in both the cases, it looks like Freesurfer is still running bias correction. How can I go about skipping bias field correction? Thanks and RegardsPatrick

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Re: [Freesurfer] average subject with 5th order icosahedron tesselation
by Marina Fernández 13 Jan '20

13 Jan '20

External Email - Use Caution That's it! Thank you Doug! Best wishes, Marina.

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hippocampal subfield segmentation question
by Gabor Perlaki 12 Jan '20

12 Jan '20

External Email - Use Caution We have a sagittal 1 mm isotropic whole-brain 3D T1 mprage (morphometry protocol suggested on Freesurfer's page) and a coronal anisotropic (0.4mm inplane, 2mm thickness, similar to ADNI protocol) T2 measurement acquired perpendicular to the hippocampus. We'd like to use both measurements simultaneously in the segmentation. However, on the fswiki it is suggested that T2 should be coarsely aligned to the main T1 scan, but I'm not sure about how to understand it, especially since our 3D T1 is acquired in sagittal plane, while T2 is in coronal. (a) Should T1 and T2 acquired in the same (e.g. coronal plane) with the same or little angulation? or (b) Is it enough if they are just aligned based on the physical/anatomical coordinate system (which is automatically ensured if both images were acquired in the same session with no repositioning and little or no head movement of the subject between the two measurements)? Best, Gabor

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