Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

tksurfer:troubleshooting surface problems
by Chacko Cherian 20 Jun '06

20 Jun '06

Hello everyone, I have used an Analyze format data(.img) on Freesurfer and was running the Morphometry and REconstruction tutorial on the wiki.THey were running fine till i reached the automatic topology defect correction step. I used :recon-all -fix -s <subject_name> and it started fxing all the defects.There were 66 defects which took me 5 hours on my machine.After this I'm not able to view the output files at ../surf/ clearly.I can only see a small piece of the surface. Could you also please tell me how to create the final surfaces because the make_final_surfaces command is also not running through. Thanks in advance, Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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display surface tessellation
by R. Chen 20 Jun '06

20 Jun '06

Hi, I have a suface file such as lh.white. Now I try to view the surface tessellation. I use tksurfer. However, I cannot display the edge between vertices. I try Matlab and use patch function and set edge as a constant color. But it is very hard to see these edges. Could anyone recommand a tool for this task? Thank you, Ron --------------------------------- Do you Yahoo!? Next-gen email? Have it all with the all-new Yahoo! Mail Beta.

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Finding ROI and average
by Joongnam Yang 19 Jun '06

19 Jun '06

Hi All, Is there a method of isolating an area of the overlay image (functional onto anatomical) on Freesurfer as ROI and get the average of the amplitude of the ROI? Any suggestions would be appreciated. Nam.

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basic questions about cortical thickness
by Chunchun Ni 19 Jun '06

19 Jun '06

Hi, I have some basic questions about cortical thickness. 1) What's the image requirement for calculating cortical thickness? slice thickness, resolution? 2) If analyzing one brain image on basic system requirement linux machine ( 2G ram, 2G processor ). How long does it take? Thanks Chunchun

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Cortical classifier
by Satrajit Ghosh 18 Jun '06

18 Jun '06

Hi Bruce, I'm finding that sometimes the cortical autoparcellation has disjoint areas with the same label and finger like projections that don't appear anatomically accurate. 1. Is there any way I can enforce continuity of labels so that I don't get these islands? 2. Is there any way to enforce a certain level of coarse curvature control, to avoid getting the finger like projections? Thanks, Satra

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re open-source status
by Glenn Lawyer 16 Jun '06

16 Jun '06

Hi, Bruce, You mentioned on the mailing list: >If there was enough interest I guess we >could post a version that won't build, but at least will allow people to >look at the source code themselves to answer questions. YES! Please post as much as you can as soon as you can, the interest is here. And thanks for all the hard work you are putting into making an open-source release. I believe the phrase "slow and painful process" is an understatement. +glenn -- -------------------------------------- I'm only in it for the glory. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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RE: [Freesurfer] Exporting Anatomical Stats
by Goradia, Dhruman D 15 Jun '06

15 Jun '06

I have a freesurfer version that was released in Feb. (I think the version is 3.0 dev). I looked in the bin and could not find asegstat2table and aparcstat2table function files. Is it possible for anyone to send those files? Also, will those file be compatible with the version of freesurfer I am using. Thank you -Dhruman -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of dasoscia(a)buffalo.edu Sent: Thursday 15 June 2006 13:18 To: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Exporting Anatomical Stats How do I go about finding/getting these tables? Sorry, I am fairly new to the program. Quoting Jenni Pacheco <jpacheco(a)nmr.mgh.harvard.edu>: > In the latest version there is asegstats2table and aparcstats2table > which > will do what you want. > > Jenni > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of > dasoscia(a)buffalo.edu > Sent: Thursday, June 15, 2006 9:42 AM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: [Freesurfer] Exporting Anatomical Stats > > I ran all three -autorecons and also was able to get my volumetric > statistics. I was wondering if there is a way (make my life easier) > to > export all the information given in the anatomical stats directly to > a > spreadsheet format without having to copy and paste eveything. I > have > OpenOffice.org Calc on this computer, although I've never used it > before. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Exporting Anatomical Stats
by dasoscia＠buffalo.edu 15 Jun '06

15 Jun '06

I ran all three -autorecons and also was able to get my volumetric statistics. I was wondering if there is a way (make my life easier) to export all the information given in the anatomical stats directly to a spreadsheet format without having to copy and paste eveything. I have OpenOffice.org Calc on this computer, although I've never used it before.

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Bad scans/normalization
by Inge K. Amlien 14 Jun '06

14 Jun '06

Hello fellow Freesurfers! We are at the startup of a new project, and we have some concerns about the quality of our scans. There seems to be white/grey contrast problems. In the original scan (001_mgz.png) and T1 the contrasts are quite clear, but in brainmask the contrasts are almost completely gone, mainly in the superior region. We are concerned this might lead to underestimated cortical thickness, and probably a bunch of other problems as well. Can somebody tell me if there is a problem with our scans, so we can change this while still at the start of the project? Are there any freesurfer commands I should try, maybe options for normalize? Regards Inge Amlien University of Oslo ___________________ Freesurfer 3.01 Scan info from nICE: Manufacure's model name (0008,1090): Symphony Scanning sequenece (0018,0020): IR\GR Scanning variant (0018,0021): SP\MP Scan options (0018,0022): IR Acquisition type (0018,0023): 3D Scan (Sequence) Name (0018,0024): *tfl3d1 Protocol Name (0018,1030): t1_3d_mpr_sag Repetition time, TR (ms)(0018,0080): 2730.0 Echo time, TE (ms) (0018,0081): 3.2 Inversion time, TI (ms) (0018,0082): 1100.000 Flip angle (deg) (0018,1314): 15 Pixel spacing X (mm) (0028,0030): 0.5000 Pixel spacing Y (mm) (0028,0030): 0.5000 Slice thickness (mm) (0018,0050): 1.3300 Slice spacing or gap (mm) (0018,0088): 0.0000 FoV (freq*phase, mm): 256.0000 * 256.0000 Rect. FoV percentage: 100.0 No of PE steps (0018,0089): 192 Turbo Factor (ETL) (0018,0091): 1 Scan Percentage (0018,0093): 75.0 Pixel Bandwidth (Hz) (0018,0095): 190.0 Number of averages (0018,0083): 1 Recon resolution (Rows) (0028,0010): 512 Recon resolution (Columns) (0028,0011): 512 Image matrix size (X * Y pixels): 512 * 512 Scan number (0020,0012): 1 Image (instance) number (0020,0013): 128 Series number (0020,0011): 2

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mkbrainmask-sess
by Sebastian Moeller 14 Jun '06

14 Jun '06

Hi All, just a quick note to let you know that 3.0.2's (centos4 x86_64) mkbrainmask-sess does not really parse the "-run nth" parameter it specifies in its help text. Haven't found time to implement a fix yet, but it is a minor issue anyway... Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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