Prompted by Rob Roach's use of betpremask on 3T data, I tried to use
betpremask on our own 3T data. I received the following output:
betpremask BT_3_2_susan BT_3_2_susan_brain
/usr/local/fsl/bin/betpremask: line 95: 24558 Segmentation fault
${FSLDIR}/bin/convert_xfm -omat ${A2}_tmp_inv.mat -ref
${FSLDIR}/etc/standard/avg152T1 -in $A1 -inverse ${A2}_tmp.mat
Could not open matrix file BT_3_2_susan_brain_tmp_inv.mat
[1]+ Terminated fsl (wd:
/mnt/supercomputer/ALS_Study/Controls)
(wd now:
/mnt/supercomputer/ALS_Study/Controls/ALS_Study_09-01-2005/T1_DEFT_LOW/BETPreTest)
Any help would be greatly appreciated.
Thanks,
Don Bigler
Rob Roach wrote:
>Hi FSL Gurus,
>
>BETpremask give much better output than BET in our 3T t1 datasets. BET
>leaves on some images large amounts of non-brain tissue.
>
>question 1: Is brain volume on the BETpremask output changed?
>
>question 2: Can I change BET input parameters (ie -f and -g and -c) in the
>BETpremask script? Newbie that I am to FSL scripts, I don't see the BET
>command line in the BetPremask script, compared say to the BETALL script.
>
>question 3: One of our ultimate goals is to use SIENA. If BETpremask is the
>beest option for our data, is there a way to pass BETpremask output to
>SIENA? Substitute BETpremask for BET in script?
>
>TIA,
>
>Rob
>
>
>
>
--
Don Bigler
The Pennsylvania State University
NMR Building
H066 Radiology
Hershey Medical Center
Hershey, PA 17033
Phone: (717)531-5858
Fax: (717)531-8486
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