Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30062 discussions

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!!

2 1

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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smoothing
by Lars M. Rimol 13 Jun '06

13 Jun '06

Hi, In the --help output of mri_surf2surf, the following explanation is given for --fwhm-src fwhmsrc: Smooth the source or target with a gaussian with the given fwhm (mm). This is actually an approximation done using iterative nearest neighbor smoothing. The number of iterations is computed based on the white surface. This method is similar to heat kernel smoothing. This will give the same results as --nsmooth-{in,out}, but automatically computes the the number of iterations based on the desired fwhm. What is the equation used to compute the number of iterations, and is it valid for an average surface? -- yours, LMR

3 2

License
by dasoscia＠buffalo.edu 12 Jun '06

12 Jun '06

I'm confused about how to use my license key. It was sent to me, but there isn't a file names .license in my freesurfer home folder. And there isn't a license key FILE, only the three lines of text sent to me. What should I type in the command line to validate the license?

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mri_convert problem
by dasoscia＠buffalo.edu 12 Jun '06

12 Jun '06

I am trying to convert Dicom files to mgz format and I keep getting the same error even when I try some variations on what I am typing in the terminal. I have already set my subjects directory to /home/amc/freesurferstable/subjects, which is where my first data set is located, /1593-4. First I change the directory to /subjects, then I type the following with the error: [amc@amcpacs subjects]$ recon-all -i 1593-4/Image0001.dcm -s 1593-4 ######################################## program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert --version $ $Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.11 2004/02/12 05:54:22 rotor Exp $ $Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19:02:51 bert Exp $ $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49 bert Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ WM removal version $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### ERROR: Flag -i unrecognized. -i 1593-4/Image0001.dcm -s 1593-4 I dont know why it doesnt recognize the -i flag...but this is repeatedly the wall I am running into. Any ideas? Dave

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