Dear Ms. Kakunoori,
sorry to bother you again, but as I did not get a reply to my last message to everyone so far troubled with my question, I am trying here for a second time. It is indeed the case, that all my data were scanned with a 3T. And if that is indeed the problem Dr. Snyder figured out, then what can I do about it? Or is anyone already working on this problem? I can hardly imagine I am the only one recording with a 3T instead of a 1.5T. Yours sincerely, Maria Felber
----- Forwarded Message ----- From: "Maria Felber" felber@cbs.mpg.de To: "Avi Snyder" avi@npg.wustl.edu Cc: "Sita Kakunoori", felber@cbs.mpg.de, "Avi Snyder" <avi@npg.wustl.edu, Bruce Fischl" sita@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 15, 2011 10:46:55 AM Subject: Re: [Freesurfer] Talairach transformation
Dear all,
indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria
----- Original Message ----- From: "Avi Snyder" avi@npg.wustl.edu To: "Sita Kakunoori" sita@nmr.mgh.harvard.edu, felber@cbs.mpg.de, "Avi Snyder" avi@npg.wustl.edu Cc: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Sita,
Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from those of the target. This condition can easily occur if the target is based on 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images tend to be relatively bright in the center of the head.) Gd++ contrasted MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible.
Avi ----------------------------------------------- On 9/13/11 2:26 PM, "Sita Kakunoori" sita@nmr.mgh.harvard.edu wrote:
I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this e-mail. Hi Dr.Snyder, Not sure if you remember but we saw something similar in a dataset here at the center where the talairach was much smaller than the orig.mgz volume and you created a new talairach template to be used with that dataset. I just wondered if this issue is similar to that.
Thanks much, Sita. ---------- Forwarded message ---------- Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) From: Maria Felber felber@cbs.mpg.de To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach transformation
Hi Bruce,
so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I always see that my talairach volume (the transform) is always smaller, which can be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of course I can make the adjustments as descriped in the short instructions. But this also means I ran the recon-all precess anew for another 30 h per subject. And that is the reason, why I asked if this is normal that the tailarach transform is a) always smaller than the original brain, and b) if I can make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it possible to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
you can use tkregister2 to check the accuracy of the talairach.xfm transform ("xform" for short), and correct it if you want.
cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote:
Hi Bruce,
thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and
DCM-Modeling with my data, I guess the correct talairach coords are kind of important for later comparisons.
Thanks again, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
as long as the tal xform is reasonable I wouldn't worry about it, unless for some reason you care a lot about the accuracy of the talairach coords.
cheers Bruce
p.s. not sure why it would be smaller
On Fri, 9 Sep 2011, Maria Felber wrote:
Dear all,
sorry, if that question came up before in the mailing list and I simple have been unable to find the thread.
Following the wiki reconstruction workflow, I ran yesterday the recon-all -all process. The process finished without errors. So the next step was to check the talairach transform. Now, according to the FsTutorial/Talairach I have to make some adjustments and then run the whole process again. That is all nice and good.
However, why is it, that the talairach volume is always, no matter which subject I look at, is always significantly smaller than the target volume? Is that normal? Has it to be fixed? Or is that just normal? Attached find one example. As I am using freesurfer for the first time, I am really unsure about that.
Thanks for the help, Maria
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-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
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