Hi Again Everyone,
I am trying to fix a reoccurring Talairach Transform error I get when I am executing the command:
recon-all -s <SUBJECT ID> -all
Only about a third of the participants processed receive this error:
#@# Talairach Failure Detection Tue Sep 30 11:50:04 PDT 2008 /Applications/freesurfer/subjects/3012mm/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) Darwin ger341-macbk2.usc.edu 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386
I have tried following the steps indicated at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach, however my movable volume is squished and twisted (see attached). I also have no green line (the surface map?) as a guide to manually correct the volume.
I am not sure where to go from here to correct the problem. Any guidance would be greatly appreciated!
best,
-Marissa
On Mon, Sep 15, 2008 at 11:10 AM, Marissa Gorlick cosmiccarrot@gmail.comwrote:
Hello Everyone,
I have tried using both the original dicom files and the renamed brain voyager files and although it fixes the Talairach error for some subjects I keep getting the same error for others (I haven't noticed a pattern here).
Error message:
#@# Talairach Failure Detection Mon Sep 15 11:03:51 PDT 2008 /Applications/freesurfer/subjects/2824mm/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) Darwin guest-wireless-207-151-243-073.usc.edu 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386
Any idea what could be the cause?
many thanks,
Marissa
On Wed, Aug 20, 2008 at 9:08 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
yes, try the original dicoms. And post these to the list so others can answer!
On Wed, 20 Aug 2008, Marissa Gorlick wrote:
Hi Bruce,
Thank you for helping me join the mailing list.
My data is in DICOM format. I did change the names of the files using a brain voyager function before using freesurfer. Could that have eliminated the direction cosines from the files?
Thanks again,
Marissa
On Tue, Aug 19, 2008 at 7:35 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu>wrote:
Can someone help Marissa get on the FreeSurfer mailing list? Marissa:
what format is your input data in? If it was analyze, then it probably does not contain the information necessary to orient the images properly so that we are failing to know which axis is front/back etc... You are *far* better off using a format that retains the direction cosines (such as dicom or nifti).
cheers, Bruce
On Tue, 19 Aug 2008, Marissa Gorlick wrote:
Hello Freesurfer Owner,
I would like to post to your message board. I attempted to join the opensubscriber forum, however they never e-mailed me my activation code to confirm my e-mail address. I have registered freesurfer and received a licence (through my e-mail address mgorlick@usc.edu). Are there other steps I should take to become a part of the online freesurfer community?
Many thanks,
Marissa
---------- Forwarded message ---------- From: freesurfer-owner@nmr.mgh.harvard.edu Date: Tue, Aug 19, 2008 at 4:38 PM Subject: Talairach Failure Detection Help To: cosmiccarrot@gmail.com
You are not allowed to post to this mailing list, and your message has been automatically rejected. If you think that your messages are being rejected in error, contact the mailing list owner at freesurfer-owner@nmr.mgh.harvard.edu.
---------- Forwarded message ---------- From: "Marissa Gorlick" cosmiccarrot@gmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 19 Aug 2008 16:37:48 -0700 Subject: Talairach Failure Detection Help Hello Freesurfer team,
My name is Marissa Gorlick and I am new to freesurfer. I am trying to do a cortical thickness analysis but I am having trouble processing my data.
When I input the command:
recon-all -s <subjid> -all
The data processing begins for a few minutes and then spits out the error message:
Tue Aug 19 16:18:54 PDT 2008 talairach_avi done #-------------------------------------------- #@# Talairach Failure Detection Tue Aug 19 16:18:54 PDT 2008 /Applications/freesurfer/subjects/part_2/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) Darwin ger341-macbk2.usc.edu 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386
recon-all exited with ERRORS at Tue Aug 19 16:18:55 PDT 2008
I looked in the opensubscriber forum and saw a recommendation to use the "Fixing Bad Output From the Talairach Registration" tutorial to remedy the error. Following the tutorial I ran:
tkregister2 --mgz --s <subjid> --fstal
The resulting output images look strange. The TARGET image has low contrast and can only be viewed in sagittal slices (which are, oddly, displayed by clicking the coronal button). The MOVEABLE view is stranger still displaying a very small squished blurry image of the brain. (see attached images)
I would appreciate any advice you may have in how I should proceed with the analysis.
Many thanks,
Marissa Gorlick
-- Marissa Gorlick Mather Lab Manager Phone: (213) 740 - 9543 Andrus Gerontology 3715 McClintock Ave. Los Angeles, CA 90089-0191
