Freesurfer

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30070 discussions

Reconstruction using 7.3.2 and 7.2.0 and Quality Control
by Md Mahfuzur Rahman 11 May '23

11 May '23

External Email - Use Caution Hi, I am trying to run 'recon-all' and then do some QC on the output. With 7.3.2 for skull stripping, I can fairly fix the brain mask with adjusting thresholds. But after fixing, when I run "recon-all -autorecon2 -autorecon3 -subjid <subject name>", the surface didn't change noticeably as it did with version 7.2.0. I am attaching a screenshot to make it understandable. Should there be output differences between 7.2.0 and 7.3.2? Which version is preferred? Any help will be highly appreciated. Thank you. Regards, Mahfuz Md Mahfuzur Rahman, Ph.D. Postdoctoral Research Associate (AC) Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University

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Registration, abstracts, & investigator-led abstracts open for INCF Neuroinformatics Assembly 2023!
by tibor.auer＠gmail.com 11 May '23

11 May '23

External Email - Use Caution Dear FreeSurfers, Apologies for the cross-posting! Join us for Assembly, hosted once again on the Gather platform! We are currently looking for speakers for two investigator-led sessions, poster presenters, and of course Assembly registrants. Our annual Assembly is a unique venue where neuroscience researchers, tool developers, standards developers, and infrastructure providers can meet with potential collaborators and hear about the latest advancements in neuroinformatics and FAIR neuroscience. <https://secure-web.cisco.com/1v5P1oOdLgPouWkIAGBqF_NoxTIc9jRVmC61wiHlSpSyeh… rmatics.incf.org%2Fabstract-submission&data=05%7C01%7Ct.auer%40surrey.ac.uk% 7Ceee902665e83405c46de08db521fe669%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C 0%7C638194069183698031%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV 2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=q7voF5LwBjckrNH6 G47VnClfShdjzDkdAYocDDeLFyE%3D&reserved=0> Submit an abstract (poster) <https://secure-web.cisco.com/1v5P1oOdLgPouWkIAGBqF_NoxTIc9jRVmC61wiHlSpSyeh… rmatics.incf.org%2Fip-submission&data=05%7C01%7Ct.auer%40surrey.ac.uk%7Ceee9 02665e83405c46de08db521fe669%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C63 8194069183698031%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzI iLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=JdYin6rPbirrg0iROo%2FE BZMbXdm%2FWIjNZZf20IQVjYw%3D&reserved=0> Submit an abstract (investigator-led session) Our program this year stretches from September 19 to September 21, and is centered around workshops proposed by our community. Sessions comprise presentations, investigator-led talks, round-table discussions, tutorials, and hands-on workshops. <https://secure-web.cisco.com/1v5P1oOdLgPouWkIAGBqF_NoxTIc9jRVmC61wiHlSpSyeh… rmatics.incf.org%2Fregister&data=05%7C01%7Ct.auer%40surrey.ac.uk%7Ceee902665 e83405c46de08db521fe669%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C6381940 69183698031%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJB TiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=uUNpwoQTyELiS1DAgiA5Z3cy2lU Osn7Y6hkJOHuBzxw%3D&reserved=0> Register for Assembly <https://secure-web.cisco.com/1v5P1oOdLgPouWkIAGBqF_NoxTIc9jRVmC61wiHlSpSyeh… rmatics.incf.org%2F2023%2Fprogram&data=05%7C01%7Ct.auer%40surrey.ac.uk%7Ceee 902665e83405c46de08db521fe669%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C6 38194069183698031%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMz IiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=fY3r3%2BSw7MB780OebxE sZlhM%2Bzk5HAA7Bxu82G7Kyls%3D&reserved=0> See the program <https://secure-web.cisco.com/1v5P1oOdLgPouWkIAGBqF_NoxTIc9jRVmC61wiHlSpSyeh… rmatics.incf.org%2F&data=05%7C01%7Ct.auer%40surrey.ac.uk%7Ceee902665e83405c4 6de08db521fe669%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C638194069183698 031%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1h aWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=SJIZxmdRWeRddCX12hfZ5c9Hs1uKmtHBJT6 xsSspUNI%3D&reserved=0> Learn more You don't have to be an INCF member to participate, but this is a good occasion to become one - registration for Assembly is heavily discounted for members! <https://secure-web.cisco.com/1EVc_0gkbtvaqG3q2hZ57Bxc9EMNEk1LmTccEcNb7U6jyE…. org%2Fjoin-incf%2Findividuals&data=05%7C01%7Ct.auer%40surrey.ac.uk%7Ceee9026 65e83405c46de08db521fe669%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C63819 4069183698031%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLC JBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=yONWyIRVt%2F4oYV06mFcDxDx t1oQzsr7KaAI%2Fr2V8YIM%3D&reserved=0> Become a member Important dates: May 11: Abstract submission opens May 11: Registration opens Jun 23: Deadline for abstract submission Sep 18-20: Neuroinformatics Assembly 2023 Kind regards, Tibor Auer, Tibor M.D. Ph.D. Lecturer in Biological Psychology School of Psychology, Faculty of Health and Medical Sciences University of Surrey, Guildford GU2 7XH <mailto:T.Auer@surrey.ac.uk> T.Auer(a)surrey.ac.uk <https://secure-web.cisco.com/1AtHbIx2M0ByaUPTlJMKqioZZt1L7nVxySZJKf86FaKJwV… om%2FTiborAuer&data=04%7C01%7Ct.auer%40surrey.ac.uk%7C5f32dba325f5422f5c5a08 d8becc029f%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C637469131016806177%7 CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiL CJXVCI6Mn0%3D%7C1000&sdata=wkpejqTmmo%2Fe4JA9QIaA6Z3%2BzipbFY%2FCEmRXC9UvKJs %3D&reserved=0> @TiborAuer

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Re: [Freesurfer] Question on Freesurfer v.7.4.0
by fsbuild 11 May '23

11 May '23

External Email - Use Caution 7.4.0 will show up on the rel7 downloads page and will be announced on the freesurfer mailing list once it has been released.  Until then, anything you were able to find/download should be deleted as it is incomplete. - R. On May 11, 2023, at 08:27, Codrin Mironiuc <codrinmironiuc(a)yahoo.ro> wrote:        External Email - Use Caution        Hi,I wanted to install the new freesurfer version v7.4.0, but when I entered the downloads page I realized that it's not showing up on the downloads page as of yet (https://secure-web.cisco.com/1-NQu8JvxBtTrc6iol1-ZKJSM_dzHiFWnaKChGHsrDLTr2… wanted to send a quick message to point this out, perhaps it helps.I would appreciate any response,Thank youCodrin_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Question on Freesurfer v.7.4.0
by Codrin Mironiuc 11 May '23

11 May '23

External Email - Use Caution Hi, I wanted to install the new freesurfer version v7.4.0, but when I entered the downloads page I realized that it's not showing up on the downloads page as of yet (https://secure-web.cisco.com/1Ik7kyPTfqcfyovpF4HdOSDjavPlUIQiKi3ICy0S1I64cg…) I wanted to send a quick message to point this out, perhaps it helps.I would appreciate any response, Thank youCodrin

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Question on needing forward field from registration from functional slabs to structural scans
by Codrin Mironiuc 11 May '23

11 May '23

External Email - Use Caution Hi, I am trying to use EasyReg to obtain the forward field from registering a functional slab (partial FOV) to an anatomical (T1-weighted) scan.I know that EasyReg currently does not support functional slabs. So the deformation with our slab looked very strange, even when trying --affine-only option. I was wondering - is there any possibility that EasyReg may support slabs in future releases?Or perhaps - do you think there is a workaround to this issue such that I could obtain a reliable forward field even when registering a functional slab to a T1-weighted scan? What I am interested is the forward field only, not the quality of the registration per se. But I imagine these are connected, and having poor coregistration will result in a poor forward field. Many thanks in advance!Codrin

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Question about volumetric atlas ROIs overlap
by Nadvar, Negin 10 May '23

10 May '23

External Email - Use Caution Hello, I have a general question about handing atlas ROIs after applying recon-all on a T1W image. Could you please clarify how I can minimize/prevent atlas ROIs overlap in volumetric subject-specific space when going from surface-based space to volumetric space? Please let me know if you need more information. Thanks in advance, Negin

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[FS-Fast error] SyntaxError
by 朱筱 10 May '23

10 May '23

External Email - Use Caution Hi Freesurfer Develpers, I am attempting to preprocess fMRI by running preproc-sess based on FS-Fast as command lines: preproc-sess -s sess01 -fsd rest -stc up -surface fsaverage lhrh -mni305 -fwmh 5 -per-run However, it stopped at the motion correction step (successfully and only got fmcpr.nii.gz) and prompted with error message as follows: File "/data/APP/freesurfer/bin/slicedelay", line 9 print "USAGE: slicedelay --help" SyntaxError: Missing parentheses in call to 'prit'. Did you mean print(...)? It seems to be a problem with python coding. I wonder how to solve this problem. Best, Xiao

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FSGD 3-way interaction contrast
by Fred d'Oleire Uquillas 09 May '23

09 May '23

External Email - Use Caution Dear FS experts, If I wanted to do an interaction of Handedness x ROIsInteractionTerm x Age, controlling for eTIV and Sex, would I use the following contrast? [0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5] FSGD attached. Thank you so much for your time! All the best, Fred

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Intracranial Volume after Hypothalamus Segmentation
by Asmin Alam 09 May '23

09 May '23

External Email - Use Caution Dear FreeSurfer Experts, I am running my subjects through autorecon-1 and then the mri_segment_hypothalamic_subunits function to obtain the divisions of the hypothalamus. However, I just wanted to confirm whether the results are already corrected for intracranial volume during autorecon-1 or within the hypothalamic segmentation (as I assume they would be if I were to run obtain the aseg segmentation further along the pipeline?). Or do I need to calculate eTIV separately? If so, how do you recommend going about this? Perhaps running something like mri_segstats --subject subjid --etiv-only? Any help is appreciated. Thank you, Asmin UCL Queen Square Institute of Neurology

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09 May '23

External Email - Use Caution I registered a subject to mni space using the mri_cvs_register command with the --mni flag. However, the output files do not include a new aparc.a2009s+aseg.mgz. I wanted this atlas overlayed on the mni registered subject so I could extract one of the labels. Is this possible? Thanks, Carlos

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