[Freesurfer] sequence]
Hello all, Im a new user of FreeSurfer. We would like to start processing a large number of the scans. We have acquired three different sequences using a 1.5T GE scanner (a three dimensional T1-weighted SPGR sequence, and two dimensional PD and T2 sequences). We have already processed those sequences using BRAINS2, and we have obtained a segmented image. I was wondering which sequence would fit best with FreeSurfer: 1) The T1-weighted SPGR sequence. 2) The T1-weighted SPGR sequence and the PD sequence together. 3) The segmented image obtained using BRAINS2. Thanks a lot Roberto Roiz __ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ubuntu recon-all
Dear all, I have just installed freesurfer-Linux-rh9-stable-pub-v4.0.2-full.tar.gz on Ubuntu 7.10. I have tried to test the installation and after sorting out some problems with the video card drivers, I obtain the following message when trying to run "recon-all -s bert -autorecon1": *roberto-desktop:/usr/local/freesurfer> sudo recon-all -s bert -autorecon1 *sudo: recon-all: command not found *roberto-desktop:/usr/local/freesurfer> However, when I run "recon-all --help | less" everything looks ok. Anyone having the same problem? Thanks in advance Roberto Roiz Santiañez ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ERROR: talairach_afd: Talairach Transform:
Dear all. I have tried to run recon-all -s subject -autorecon1 with a sequence acquired in a 3T Philips scanner. I have transformed the image into Analise using MRIcro and then run recon-all. I got the following error: talairach_avi done # [EMAIL PROTECTED] Talairach Failure Detection Fri Dec 21 16:24:50 CET 2007 /usr/local/freesurfer/subjects/roberto/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050) Linux roberto-desktop 2.6.22-14-generic #1 SMP Sun Oct 14 23:05:12 GMT 2007 i686 GNU/Linux recon-all exited with ERRORS at Fri Dec 21 16:24:50 CET 2007 However when I do the same wit ha different sequence acquired in a 1.5 GE scanner everything runs nice. Any idea where the problem could be? Best wishes and Happy Christmas Roberto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Phillips 3T
Hi When I bring the images up with tkmedit everything is messed up. When I open the coronal view it brings up the axial view, when I open the axial view it brings up the sagital view and when I open the sagital view it brings up the coronal view. As I mentioned before this happens when I acquired the sequence in the sagital plane. When the sequence is acquired in the axial plane everything runs ok Regards Roberto Roiz > if you bring them up in tkmedit does it show them properly? That is, when > it says "coronal" etc... is it really? > > And please post these to the list so other people can answer :) > > Bruce > On Sat, 19 > Jan 2008, Roberto Roiz > Ssantiáñez wrote: > >> Hi Bruce, >> I'm using >> freesurfer-Linux-rh9-stable-pub-v4.0.2-full.tar.gz run on Ubuntu. >> The error I get when runnig a sequence acquired on the sagital plane is >> is: >> >> Sat Jan 19 11:38:02 CET 2008 >> talairach_avi done >> # >> [EMAIL PROTECTED] Talairach Failure Detection Sat Jan 19 11:38:02 CET 2008 >> /usr/local/freesurfer/subjects/pilot2_sag/mri >> >> talairach_afd -T 0.005 -xfm transforms/talairach.xfm >> >> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >> ***FAILED*** (p=0., pval=0. < threshold=0.0050) >> Linux roberto-desktop 2.6.22-14-generic #1 SMP Tue Dec 18 08:02:57 UTC >> 2007 i686 GNU/Linux >> >> recon-all exited with ERRORS at Sat Jan 19 11:38:02 CET 2008 >> >> >> >> However when the same sequence is acquired on the axial plane the >> recon-all runs perfectly. >> I have converted both sequences using MRICRO. I attached an image of >> both >> the sagital and the axial sequences. >> >> Regards >> Roberto Roiz >> >> >> >>> Hi Roberto, >>> >>> what version of FS are you using? Usually this isn't a problem for us. >>> You can drop an example on our filedrop if you want and we'll take a >>> look. >>> >>> cheers, >>> Bruce >>> On Wed, 2 Jan 2008, Ron KILLIANY wrote: >>> >>>> Dear Roberto, >>>> >>>> I'm glad to hear that the sequence ran well. I'm going to include >>>> Bruce >>>> Fischl on this e-mail to see if he can help you with the orientation >>>> problem you seem to be having. To my knowledge we haven't experienced >>>> that problem. >>>> >>>> I hope you had a happy new year celebration! >>>> >>>> --ron >>>> >>> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
