Freesurfer

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30132 discussions

comparison of values of three MRI exams of same patient...
by Gonzalo Rojas Costa 12 Feb '10

12 Feb '10

Hi: I have three MRIs of the same patient took during different months... I need to compare the hippocampus volume fof the three exams (for example), the cortical thickness, etc... How can I do such computation ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Santiago Chile

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Problems with tksurfer display on laptop
by jentis＠nmr.mgh.harvard.edu 12 Feb '10

12 Feb '10

Hi, I have a laptop equipped with Centos and Freesurfer but I can't get tksurfer to properly display the surface files of either the fsaverage brain or individual subjects. The surfaces are either small portions of cortex or an assemblage of lines/dots. I have attached a few tiff files as examples. Is there something I can do to fix this? I have tried using freeview instead, and the surfaces do display properly, but the program does not seem to allow me to trace label files. Is there another way around this? Does a newer version of freeview include tracing ability? Thanks, Jon

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tksurfer problem and solution
by David Mischel 11 Feb '10

11 Feb '10

We have had similar problems with displays of tksurfer described in http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems. I would like to try freeview, the new solution for display. I don't know anything about freeview and no one here has ever used it. To run tksurfer I set the SUBJECTS_DIR and then use the command tksurfer <subjectCode> lh pial where subjectCode is a directory in the SUBJECTS_DIR. Could someone give me the corresponding command to use with freeview? I appreciate the help. < david David Mischel Manager of IT Center for Imaging of Neurodegenerative Diseases (CIND) <http://www.cind.research.va.gov/> http://www.cind.research.va.gov/ VA Medical Center 4150 Clement Street, 114M San Francisco, CA 94121 voice: 415-221-4810 x3864 fax: 415-668-2864

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tksurfer fill holes
by Guang Zeng 11 Feb '10

11 Feb '10

Hi, there, Is there are a command-line version of that 'Fill holes", "Dilate" and "Erode" options in tksurfer. Could I select the size of the kernel for dilation and erosion? Thanks! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/201469229/direct/01/

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subject to fsaverage
by Mishkin Derakhshan 11 Feb '10

11 Feb '10

Hi, I am looking for the transformation matrix that takes my input volume (orig.mgh) and maps it into the same space as fsaverage (or the inverse of this transformation if it already exists). I've already run recon-all -all, and -qcache, so I'm pretty sure this information exists somewhere, but after searching through the data, the wiki and the mailing list, I'm embarrassed to say that I still can't find it. If this information hasn't been stored, I imagine mri_surf2surf can calculate it for me. Would this be the best way? thanks, mishkin

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GM exclusion
by johanna feiler 11 Feb '10

11 Feb '10

Dear freesurfer experts, After running the autorecon2 process the pial surface fails to catch up pieces of gm in the medial region. I gained no improvement with setting control points. The problem lasts about twelve slices. As an illustration, I attached a screenshot with three of the problematic slices. How can I solve this problem? Any help would be appreciated! Johanna Feiler ______________________________________________________ GRATIS für alle WEB.DE-Nutzer: Die maxdome Movie-FLAT! Jetzt freischalten unter http://movieflat.web.de

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question about effect of juxta-cortical lesion
by Mehul Sampat 11 Feb '10

11 Feb '10

Hi Folks, We have a patient with a large juxta-cortical lesion (top right hand side in figure 1) Overall Freesurfer does a great job in defining the white and pial surfaces (figure 2 and 3) (It is actually amazing how well it does in this difficult case.) However, I think that due to the lesion some of the cortical gray matter is not included. Could someone advice what is the recommended procedure in such cases. Should I add control points to correct for this issue ? Also we have 3 MRI exams for this subject (each a year apart) and the lesion is present on every scan and I have the same issue on the other time-points. Thanks Mehul

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Paula Diniz wants to stay in touch on LinkedIn
by Paula Diniz 11 Feb '10

11 Feb '10

LinkedIn ------------Paula Diniz souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, I'd like to add you to my professional network on LinkedIn. - Paula Diniz Accepter l'invitation de Paula Diniz http://www.linkedin.com/e/vLfSn8bYH8_5DFBPLmfTK84Tj6M6DmxAKLgTCa4LI_82zo/bl… Voir l'invitation de Paula Diniz http://www.linkedin.com/e/vLfSn8bYH8_5DFBPLmfTK84Tj6M6DmxAKLgTCa4LI_82zo/bl… ------ (c) 2010, LinkedIn Corporation

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Re: [Freesurfer] Skull Stripping extra dura & vasculature
by Sherri Novis 10 Feb '10

10 Feb '10

Thanks Bruce. Is there anyway to address it in the intensity normalization phase? -----Original Message----- >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >Sent: Feb 9, 2010 12:29 PM >To: Sherri Novis <echotalk(a)earthlink.net> >Cc: freesurfer(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] Skull Stripping extra dura & vasculature > >Hi Sherry, > >that's pretty tough. The dura is very bright and quite close to the gm. >You may need to erase more of the dura > >Bruce > >On Tue, 9 Feb 2010, Sherri Novis >wrote: > >> Hello, >> >> I have a series of datasets with skull stripping issues - namely left over dura/vasculature in the occipital cortex, and some in frontal areas.(Attached is a jpeg of the type of issue. It's pervasive throughout the slices, across a handful of subject data.) >> >> I have rerun skull stripping changing the watershed value, however it's not making the distinction between dura and gray matter. (recon-all -skullstrip -wsthresh [tried 0..35] -clean-bm -no-wsgcaatlas -subjid [subject_id] - FS version: freesurfer-Linux-centos4-stable-pub-v4.3.0) >> >> I also attempted to edit 50% of the slices by erasing voxels to make a clear boundary between the dura and cortex and then re-ran autorecon2 to see if it would at least adjust the pial surfaces - however that did not work (pial surfaces still crossed the one pixel boundary I made into the dura). >> >> Can you recommend any other flags or things to try before I edit/erase the excess by hand? >> >> Thanks for your time - >> Sherri

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DICOM Multiframe support
by J. Gabriel Castrillón G. 10 Feb '10

10 Feb '10

Hi! Is Freesurfer compatible with the DICOM MR multiframe files? Thanks in advance, -- Gabriel Castrillón Instituto de Alta Tecnología Médica de Antioquia - IATM http://www.iatm.com.co

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