Hi Michael
have you visualize the Talairach alignment to see if it indeed incorrect?
Also, can you verify that the direction cosines from your data are properly
read? That is, when you view the orig.mgz in freeview does what it thinks
is inferior/superior etc... correspond to the true (visually verified)
orientations?
cheeers
Bruce
On
Mon, 23 Nov 2015, Amlung, Michael wrote:
We are getting an error with recon-all at the stage of Talairach slignment. The
error is the one described on the known issues: Can't locate shellwords.pl in
@INC. We are running perl5.18, so I downloaded and installed perl5.12 and
changed the first line of mritotal as indicated on the ReleaseNotes. We are now
getting a different error (pasted below). It appears I need to do manual
Talairach alignment, but not entirely sure how to proceed with that (is there
documentation available)? Any other suggestions?
#@# Talairach Failure Detection Mon Nov 16 12:48:42 EST 2015
/Users/PBCAR/neuro/TNE/freesurfer_data/309/mri
\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
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
recon-all -s 309 exited with ERRORS at Mon Nov 16 12:48:42 EST 2015
********************************************
Michael Amlung, Ph.D.
Assistant Professor
Department of Psychiatry and Behavioural Neurosciences
DeGroote School of Medicine
McMaster University
Peter Boris Centre for Addictions Research
100 West 5th Street
Hamilton, Ontario L8N 3K7
Canada
Telephone: (+1) 905-522-1155, ext. 39014
Email: amlu...@mcmaster.ca
Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html
Lab Website: Cognitive Neuroscience of Addictions Laboratory (CNALab)
-----Original Message-----
From: Amlung, Michael
Sent: Monday, November 23, 2015 9:03 AM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Issue with Talaraich in recon-all
I was hoping someone could help with this issue...
********************************************
Michael Amlung, Ph.D.
Assistant Professor
Department of Psychiatry and Behavioural Neurosciences DeGroote School of
Medicine McMaster University
Peter Boris Centre for Addictions Research
100 West 5th Street
Hamilton, Ontario L8N 3K7
Canada
Telephone: (+1) 905-522-1155, ext. 39014
Email: amlu...@mcmaster.ca
Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html
Lab Website: Cognitive Neuroscience of Addictions Laboratory (CNALab)
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