Re: problems with register.csh
Hi Nick, This might be occuring because you have a newer version of mri_convert that does not support the -raw flag. You could use an older version with register.csh or try using mri_motion_correct2 (i think that is the name). The latter works really well, but you will need to install all of the MNI tools. check the archive for hints on mni installation. good luck. brian - Original Message - From: Nicholas Knouf [EMAIL PROTECTED] [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Wednesday, October 16, 2002 1:00 PM Subject: problems with register.csh Hi, I am trying to run register.csh (as per the FreeSurfer manual) to motion correct my anatomical scans before averaging them together. However, I get an error saying 'mri_convert: unknown flag -raw' (actual output below). Unfortunately, I can't make out from the information what options to mri_convert should actually be used. Thanks, Nick Knouf Lab Manager, Kanwisher Lab --- uninteresting data snipped -- ++ CPU time for realignment=279 s ++ Min : roll=-0.285 pitch=-0.072 yaw=-0.997 dS=+6.359 dL=+2.301 dP=+9.563 ++ Mean: roll=-0.285 pitch=-0.072 yaw=-0.997 dS=+6.359 dL=+2.301 dP=+9.563 ++ Max : roll=-0.285 pitch=-0.072 yaw=-0.997 dS=+6.359 dL=+2.301 dP=+9.563 ++ Writing dataset to disk in ./dset+orig.HEAD. ** Warning: will overwrite file regist.afni done registering rotating -0.285 -0.072 -0.997 6.359 2.301 9.563 atr_int == NULL atr_flo == NULL /pasque/nfs_data2/data/subjects/021015nk/mri/orig mri_convert -raw 256 256 256 uchar /tmp/reg.res+orig.BRIK motion_corrected_cor mri_convert: unknown flag -raw type mri_convert -u for usage pasque%
Re: Problems with csurf (tksurfer)
one workaround is to use tksurfer.static, which will be slower, but should work. Bruce On Thu, 11 Jul 2002, Nicholas Knouf wrote: I'm having problems running tksurfer on a couple Linux machines (they are running a modified version (MIT athena) of RedHat 7.1). Here is the output of the log window: env tksurferinterface=csurf patchname= /raid-5/new_fs/freesurfer_alpha/bin/Linux/tksurfer -010719ao rh inflated -tcl /tmp/TmpTclSurf.3275 Couldn't create output file .xdebug_/raid-5/new_fs/freesurfer_alpha/bin/Linux/tksurferltMNIread: could not open file /raid-5/time/reconstructions/010719ao/mri/transforms/talairach.xfm No such file or directory tksurfer.tcl: startup done Window type not found! surfer: current subjects dir: /raid-5/time/reconstructions surfer: in subjects scripts dir surfer: session root data dir ($session) set to: surfer: /mit/nklab-5/time/reconstructions/010719ao surfer: /raid-5/time/reconstructions/010719ao/mri/T1/COR-.info surfer: Talairach xform file not found (ignored) surfer: vertices=126867, faces=253728 tksurfer: interface: /raid-5/new_fs/freesurfer_alpha/lib/tcl/tksurfer.tcl tksurfer: run tcl script: /tmp/TmpTclSurf.3275 surfer: single buffered window surfer: curvature read: min=-1.54 max=1.19 The surfer tools window shows up, but no output window appears with the inflated brain. This is for a subject that we have not yet Talairached. However, when I run csurf (and tksurfer) on the same subject on machine that has an earlier version of RedHat (ie, MIT athena) installed, everything works perfectly. The only difference in the log files between the two machines (of course ignoring the tmp files) is the line (for the machine that doesn't work) Window type not found!. Now, it would be impossible for me to describe all of the differences between the two RedHat versions here (since MIT changes the default distribution radically when releasing new versions of Athena); however, the only relevant difference I can discover between the two systems is a difference in TCL-TK versions. For the system where tksurfer works, it has TCL-TK version 8.0.5 installed, while for the system where tksurfer doesn't work, it has TCL-TK version 8.3.1 installed. Do you know of any issues between these two versions of TCL-TK that might cause this problem? Or is there any clue in the log file that you might be able to use to point me in a new direction to look? Thanks, Nick Knouf
Re: Problems
Hi Felix, check the fov field in the COR-.info files in the subject's mri/orig and mri/T1 directories. It should be 0.256, but for some reason is sometimes is set incorrectly. As far as the volume/surface problem, the problem is usually the other way (okay in tkmedit, no good in tksurfer), so I'm not sure what's going on. cheers, Bruce Bruce Fischl email: [EMAIL PROTECTED] Mass. General Hosp. NMR Center.tel:(617)-726-4897 Rm. 2328, Building 149, 13th Street fax:(617)-726-7422 Charlestown, MA 02129 USA On Mon, 22 Apr 2002, Felix Blankenburg wrote: Dear Freesurfers! Does anyone know a solution for the following problem: after running freesurfer I have to zoom in the surface every time for a few hundred per cent to see it correctly in the display window (i. e. how to save the surface size)? An other problem is, when I try to overlay a statistical parametric map (SPM99) in 2D (i. e. in tkmedit) it looks misplaced whereas in 3D ( i.e. in tksurfer) it looks fine. Is there any possibility for a correct transformation in 2D or is it intended? Is there any possibility to change the colour of the surfaces? Thank you very much for your help and best greetings, Felix Blankenburg
