1mm and 60 slices covers the whole brain? Usually it requires more like 160 slices.
On Mon, 6 Jan 2014, Boric, Katica A. wrote:
Its 1mm! But I found a newer study for the subject, so I will try this new one and if it still does not work, I will email back!
Thanks so much again! Katica ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, January 06, 2014 4:27 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: FW: recon-all exited w/errors
what is the slice thickness? Usually we recommend no dimension be thicker than 1.5mm or so On Mon, 6 Jan 2014, Boric, Katica A. wrote:
Hi Bruce! So it is the whole brain! Unfortunately, this is the available serie with the most number of slices!! At least we tried! Thanks Bruce!
Katica
From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, January 06, 2014 3:58 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: recon-all exited w/errors
oh, it's only 62 slices? So is it not whole brain? Or are they thick slices? Either way that is probably a show stopper On Mon, 6 Jan 2014, Boric, Katica A. wrote:
Hi Bruce! Thank you very much for your response!
The input image I used was .dcm of a Sagital MPR with 62 slices. As for the directions, it is really hard to tell! I have attached a screenshot of an horizontal image.
How do I perform the alternative or manually tailarach?
Thank you very much,
Katica ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Sunday, January 05, 2014 8:50 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited w/errors
Hi Katica
what format was the input image to recon-all? Can you verify that tkmedit has the directions correct (that is what it labels as anterior is actually anatomically anterior, etc...). If so, then the talairach just failed and you will need to either try an alternative (like the MNI or SPM talairachs) or generate it manually.
cheers Bruce
On Thu, 2 Jan 2014, Boric, Katica A. wrote:
Happy New Year freesuerfers! I run into this error while doing recon-all :
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string.
I would really appreciate if someone could give me some advice on how to fix this error.
Thank you very much!
Katica Boric,
ps: Here is the error log:
#@# Talairach Failure Detection Thu Jan 2 14:20:32 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Thu Jan 2 14:20:33 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
/home/XX/XXX/subjects/XXX_SurferOutput/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Thu Jan 2 14:21:30 EST 2014 tmpdir is transforms/tmp.talairach.34005 /home/XX/XXX/subjects/XXX_SurferOutput/mri mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 i_ras = (-1, -9.03383e-08, 0) j_ras = (-1.3411e-07, 2.66591e-08, -1) k_ras = (1.59256e-07, 1, -5.93718e-09) writing to transforms/tmp.talairach.34005/src.mnc...
mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm Legacy library shellwords.pl will be removed from the Perl core distribution in the next major release. Please install it from the CPAN distribution Perl4::CoreLibs. It is being used at /usr/local/freesurfer/mni/bin/mritotal, line 460.
Thu Jan 2 14:21:43 EST 2014 talairach done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#-------------------------------------------- #@# Talairach Failure Detection Thu Jan 2 14:21:44 EST 2014 /home/XX/XXX/subjects/XXX_SurferOutput/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s xxx_SurferOutput exited with ERRORS at Thu Jan 2 14:21:45 EST 2014
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