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: amlungm@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: amlungm@mcmaster.ca Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html Lab Website: Cognitive Neuroscience of Addictions Laboratory (CNALab)
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: amlungm@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: amlungm@mcmaster.ca Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html Lab Website: Cognitive Neuroscience of Addictions Laboratory (CNALab)
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Bruce Fischl