Freesurfer June 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
107 discussions

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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neighborhood of a vertex
by R. Chen 13 Jun '06

13 Jun '06

Hi, I convert a thickness file to ascii format and the file looks like (vertex id, x, y, z, thickness) 000 -36.19709 -19.27060 66.10529 2.61633 001 -16.37191 -69.16402 59.60456 2.18290 002 -10.58665 -10.65137 50.24026 2.06269 003 -22.09574 43.85081 28.52032 1.54455 004 -57.95597 -0.45362 12.97830 2.41985 005 -48.57283 -51.02512 46.88505 2.08371 I want to do some customrized smoothing and need to know the neighborhood of a vertex. I think FreeSurfer also uses this neighborhood information in random field modelling. Could you provide some information about how to get the neighborhood? Thank you, Ron __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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resuming autorecon2
by dasoscia＠buffalo.edu 13 Jun '06

13 Jun '06

I'm running autorecon2 and i forgot to turn off the setting on my computer that automatically stalls any processes that are going at the time and asks for a log-in password when the computer sits idle for a while. I logged back in and it appears autorecon2 has stalled because of this. The command line is still there with all of the information from what has already been done in autorecon2...is there a way to resume what it was doing from this exact point and not have to start it over? thanks dave

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inflated surface not seen
by Joongnam Yang 13 Jun '06

13 Jun '06

Hi all, I've run recon-all -autorecon1 and -autorecon2, successfully. But when I opened inflated surface using tksurfer, only a tiny bit of image of the inflated surface was seen. Something was wrong in the process. Both wm, filled, brain volumes looked OK. Here is the data on the web; http://www.momoenglish.com/TEMP/TEMP.tar.gz would someone please take a look? Nam.

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error message
by Sarah J Greene 13 Jun '06

13 Jun '06

I was running the subcortical labelling script (aseg_rerun.csh) using the old version of freesurfer, and have received this error message: mri_read(): couldn't determine type of file mri_ca_register: could not open input volume -T I am not sure how to fix this error. I would appreciate any input!!

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Resuming recon-all
by Martin Ystad 13 Jun '06

13 Jun '06

Hi, some of my subjects crash due to memory-failure way into the recon-all stream. Is there any way I can resume the processing stream from where it crashed without having to write all the individual commands for the rest of the stream? For example, if my subject crashed during autorecon2 -calabel, would there be a command that re-runs -calabel and the rest of the autorecon2 stream? Thanks, Martin Ystad University of Bergen, Norway.

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Freesurfer June 2006