I start with the filling of white matter but after a while I am receiving this massage:
(...) using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_fill: could not find pons No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... INFO: Modifying dst c_(r,a,s), using the transform dst talairach cc position changed to (2.00, 29.00, -8.00) INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood...
Command Finished
could you help me with this? thanks,
wan park
Hi Wan,
you can always manually select seed points in the left and right hemisphers and in the pons and corpus callosum, then specify them in the mri_fill command line:
mri_fill -lh <lh seed> -rh <rh seed> -p <pons seed> -cc <cc seed> wm filled
from the subject's mri directory.
The better way to do this thought is to use the MNI auto talairaching and the fill will work much better.
cheers, Bruce
On Thu, 21 Oct 2004, Wan Park wrote:
I start with the filling of white matter but after a while I am receiving this massage:
(...) using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_fill: could not find pons No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... INFO: Modifying dst c_(r,a,s), using the transform dst talairach cc position changed to (2.00, 29.00, -8.00) INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood...
Command Finished
could you help me with this? thanks,
wan park
Hello, When writing par files for each functional run, do you match the timing of the stimuli to the ideal timing (starting at zero), the ideal adjusted timing for the 10 seconds of dummy scans (starting at 10 s), or the timing from the log files from Presentation? How much does this timing affect the data? Thanks, Margaret
Time 0 is the time at which the first *stored* image was acquired. So, if you have 10 sec of dummy scans that are not in the stored volume, that 10 sec would not be represented in the par file. How much effect the fine detail of the timing has depends upon the type of experiment. For blocked designs, you're generally spending more time on the plateau of the block, and timing is not as important. For event-related designs, timing is much more important.
doug
Margaret Duff wrote:
Hello, When writing par files for each functional run, do you match the timing of the stimuli to the ideal timing (starting at zero), the ideal adjusted timing for the 10 seconds of dummy scans (starting at 10 s), or the timing from the log files from Presentation? How much does this timing affect the data? Thanks, Margaret
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Bruce Fischl -
Doug Greve -
Margaret Duff -
Wan Park