Re: [Freesurfer] fscalc / mris_calc problem
Hi Fred -- I'm currently traveling and have limited internet connectivity. I'll be back at the office later in the week and will take a look then. In the meantime, has this ever worked for you previously? I know that older versions of 'mris_calc' were somewhat particular about filename lengths and filename conventions, and you might be seeing the same bug here... Best -=R Sent from my iPad On Dec 28, 2012, at 7:50, Fred Lado wrote: > Hi FreeSurfer Gurus, > I am having difficulty invoking the 'upl' and 'lrl' operations in > mris_calc. The following is the message I get for 'upl': > > /usr/local/freesurfer/bin/fscalc rh.dat.mgh upl 20 --o tmp.mgh > > freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > Darwin Fred-Lados-MacBook-Pro.local 12.2.0 Darwin Kernel Version 12.2.0: Sat > Aug 25 00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64 x86_64 > mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh > mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from rh.dat.mgh... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, -0, 0) > j_ras = (-0, -1, 0) > k_ras = (-0, -0, -1) > writing to ./tmpdir.fscalc.5004/tmp.mgh... > -- > mris_calc -o ./tmpdir.fscalc.5004/tmp.mgh ./tmpdir.fscalc.5004/tmp.mgh upl 20 > Unknown operation upl failed. > > No such file or directory > > Fred Lado, MD PhD > Director, Neurology Service - Moses & North Divisions > Director, EEG Laboratory > Associate Clinical Professor of Neurology > Montefiore Medical Center > 718-920-8499 office > 718-324-3730 fax > email: ladof...@gmail.com > > > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] white/gray surface and volumetric segmentation (aseg) difference...
Hi: With some mprage images, I got differences in the volumetric segmentation (aseg) of the cortex and the white/gray surface... Why ?... I know that both methods are totally different... In the aseg I got some bad segmentation of the cortex, but it in the white/gray surface I got very better results... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] white/gray surface and volumetric segmentation (aseg) difference...
Hi Gonzalo that's one of the reasons we use the surfaces for cortical morphometry, not the aseg. cheers Bruce On Mon, 31 Dec 2012, Gonzalo Rojas Costa wrote: > Hi: > > With some mprage images, I got differences in the volumetric > segmentation (aseg) of the cortex and the white/gray surface... Why > ?... I know that both methods are totally different... In the aseg I > got some bad segmentation of the cortex, but it in the white/gray > surface I got very better results... > > Sincerely, > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
