Antonin,
This is bug in recon-all that will be fixed for the next release. You
can edit your recon-all, adding the lines with a +, to include this fix
via this diff:
set mdir=$SUBJECTS_DIR/${subjid}/mri
set sdir=$SUBJECTS_DIR/${subjid}/surf
+ set tdir=$SUBJECTS_DIR/${subjid}/touch
if (! -e $mdir/${t2flair}.mgz) then
@@ -4036,8 +4037,11 @@ if($DoT2pial || $DoFLAIRpial) then
set xopts = `fsr-getxopts mris_make_surfaces $XOptsFile`;
set nv1=(`mris_info $sdir/${hemi}.pial |& grep nvertices`)
set nv2=(`mris_info $sdir/${hemi}.wo${t2flair}.pial |& grep nvertices`)
+ set touch1=($tdir/${hemi}.pial_refine.touch)
+ set touch2=($tdir/${hemi}.pial_surface.touch)
if ( (! -e $sdir/${hemi}.wo${t2flair}.pial) || \
- ("$nv1" != "$nv2") ) then
+ ("$nv1" != "$nv2") || \
+ (`UpdateNeeded $touch1 $touch2`) ) then
set cmd = (cp -v $sdir/${hemi}.pial $sdir/${hemi}.wo${t2flair}.pial)
echo "\n $cmd \n"|& tee -a $LF |& tee -a $CF
if($RunIt) $fs_time $cmd |& tee -a $LF
N.
On Wed, 2015-05-13 at 11:31 +0200, Antonin Skoch wrote:
> Dear FreeSurfer experts,
>
> could you please look at the issue mentioned below? I did not receive
> any answer to my post, probably it got lost unattended.
>
> Antonin Skoch
>
> ______________________________________________________________
> From: Bruce Fischl [mailto:[email protected]]
> To: Antonin Skoch [mailto:[email protected]]
> Cc: Nick Schmansky [mailto:[email protected]]
> Sent: Wed, 15 Apr 2015 14:56:10 +0100
> Subject: Re: [Freesurfer] FLAIRpial refinement after manual
> editing of brainmask
>
> Hi Nick
>
> could you take a look at this and see if there is a bug in the
> logic of
> recon-all as Antonin suggests?
>
> thanks
> Bruce
> On Wed, 15 Apr 2015, Antonin Skoch wrote:
>
> > Dear Freesurfer experts,
> >
> > I am reposting this question since I did not get an answer
> to my post from
> > last week.
> >
> > We are using FLAIR images to refine pial surfaces. It
> generally performs
> > well, however in some cases there is still need for manual
> editing of
> > brainmask.
> > After manual editing of brainmask we tried to run:
> >
> > recon-all -s subj_id -autorecon-pial -FLAIRpial
> >
> > however, we faced the problem that the reconstructed pial
> surface does not
> > reflect manual changes in brainmask. We finally found that
> the files
> > ?h.woFLAIR.pial are in this case not replaced by new
> versions of pial files,
> > i.e. the commands
> > cp -v ?h.pial ?h.woFLAIR.pial
> > are not executed and "old" version of files from previous
> reconstruction
> > (created when recon-all -all -FLAIRpial is run) is used for
> FLAIRpial
> > refienement.
> >
> > After manual remove of ?h.woFLAIR.pial files the
> reconstruction of pial
> > surface works as expected (i.e. reflecting both brainmask
> edit and FLAIRpial
> > refinement).
> >
> > Is this bug or expected behavior? Or are we doing something
> wrong?
> >
> > Regards,
> >
> > Antonin Skoch
> > MR Unit
> > Institute for Clinical and Experimental Medicine
> > Czech Republic
> >
>
>
> _______________________________________________
> Freesurfer mailing list
> [email protected]
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
