Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

How to create .license file
by Kan Ding 23 May '12

23 May '12

Hi, All, As instructed by previous post, I typed " pico $FREESURFER_HOME/.license" and was able to place the three lines from my registration email into new window. What should I do after I see " File Name to Write: FREESURFER_HOME/.license" ? How do I pick up the options in this interface? I'm new to FreeSurfer and command interface. Thanks, Kan

2 1

confirm my posting
by Kushal Kapse 23 May '12

23 May '12

just want to confirm if my mail is successfully getting posted on freesurfer

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kkapse@mail.med.upenn.edu
by Kushal Kapse 23 May '12

23 May '12

kkapse(a)mail.med.upenn.edu

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Re: [Freesurfer] mri_convert and --out_orientation (once again)
by Clark Fisher 23 May '12

23 May '12

Thanks Doug, In that case, since everything seems to be working as I want it to, I'm going to leave it as-is. Do you think that this is likely to change back to it's intended (pixel data ignoring) function in future versions, or can I continue to use it like this? -Clark

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wm surface does not follow wm.mgz
by Leon 23 May '12

23 May '12

Hi, FreeSurfer experts I have seen similar posts before but did not think that I could solve the issue based on the answers from the previous posts. So I am posting it here again. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached file). It is strange that such problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. So I wonder if anyone would help on solving this issue. Thanks in advance! Leon

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A question about thickness computation for surfaces not generated by Freesurfer
by Navid Shiee 23 May '12

23 May '12

Hi, I have generated inner and pial surfaces using another method. However, I am interested in computing the cortical thickness using the method implemented in Freesurfer. My surfaces are in vtk format. I was wondering how I can do this, if this is at all possible. Thanks, -- Navid Shiee

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skullstrip eats brain and leaves skull
by Anne Uhlmann 23 May '12

23 May '12

Hi Freesurfers, I have problems with the troubleshoot of a scan that didn't run at all within autorecon (while the scan actually looks good). So I ran the skullstrip manually and came across the following phenomenon: -when using waterthreshold 25 it gives me an error message and no brainmask.mgz file gets created -when using waterthreshold 24 or lower big chunks of the brain go missing and most of the skull stays I am not sure the manual editing will be a good approach as I would have to remove the complete skull Any suggestions how I could get the skullstrip work? Thank you, Anne ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. ###

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Vermis of cerebellum segmentation
by Rafa x 23 May '12

23 May '12

Hi Freesurfers, There is avaliable a cerebelum mask in "http://surfer.nmr.mgh.harvard.edu/fswiki/CerebellumParcellation_Buckner2011" however the corregistration from MNI152 space to subject space produces a few deformation that introduce an error in the fit of the mask into the real vermis of the subject. For that reason I would like to know if it is possible to use freesurfer to segmentate the vermis of cerebellum directly in my subject. Thank you all in advance.

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Couldn't download FsFast tutorial data
by Michael Bannert 23 May '12

23 May '12

Dear freesurfer community, I seem to be unable to download the FsFast tutorial data. ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialData ) I tried each of the two links and I tried "curl -O" as well as wget but nothing worked. Any ideas? Thanks for your help! Michael -- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab CIN Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany

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insula overlabelling
by Alana Shepherd 22 May '12

22 May '12

Dear Nick and Freesurfers, I spoke to Nick at the recent course in Boston regarding this issue. I've been running a recon-all on a 1.5T MPRAGE data set using FS version 5.1, and I've been finding on a number of participants that the aparc segment is substantially over-labelling the insula (on the Desikan atlas only), extending medially to accumbens. I've attached a screen shot of one example. Am appreciative of any suggestions. Thanks, Alana

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