Hi experts,
A quick question: I installed FS 5.1 a month ago, should I replace with this recon-all file and run it with flag -clean-tal in the future? why the steps have to be switched?
Thanks!
2012-04-19
Chunhui Chen _________________
State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875
发件人： Nick Schmansky 发送时间： 2012-04-17 22:53:40 收件人： Ed Gronenschild 抄送： freesurfer 主题： Re: [Freesurfer] How to switch order of Talairach and nu-correctionstages in recon-all
Ed, email probably trounced it. recon-all is a text file. attached is a gzipped version. use gunzip to unpack it. N. On Tue, 2012-04-17 at 16:45 +0200, Ed Gronenschild wrote:
Hi Nick,
It does not work properly, it only produces an error message, even with no option at all:
'nknown option: '- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ...].
Ed
On 17 Apr 2012, at 16:28, Nick Schmansky wrote:
a modified recon-all is attached. it will run nu_correct prior to the talairach stage, as will be the case with v5.2. so you can just run:
recon-all -s subjid -all -clean-tal
n.
On Tue, 2012-04-17 at 08:58 +0200, Ed Gronenschild wrote:
Hi Nick,
The option -talairach-nu is not recognized in version v5.1.0.
How can I proceed now?
Ed
On 16 Apr 2012, at 17:32, Nick Schmansky wrote:
Ed,
Hi, no there is not an option to switch them. The nu correct stage in 5.1 needs the talairach to run.
However, if your intent is to get a better talairach result by using the nu corrected input (as it did prior to v5.1), then you can do the following:
recon-all -s subjid -motioncor -talairach -nuintensitycor
then run:
recon-all -s subjid -all -talairach-nu -clean-tal
on the second run, it will use the nu.mgz in the talairach stage.
Note that in the next version, v5.2, one iteration of nu_correct will be run prior to the talairach stage to use as input to the talairach stage, in order to get the better talairach results that people were seeing prior to v5.1. it will still run the current nu_correct stage to create nu.mgz (the nu used in talairach gets discarded).
Nick
On Mon, 2012-04-16 at 09:10 +0200, Ed Gronenschild wrote:
Hi,
As of version 5.1 the Talairach stage precedes the nu-correction stage. Is there an option or possibility to switch this order?
Cheers, Ed _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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<recon-all>
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