What version are you running?
On Oct 11, 2011, at 4:21 PM, "James Sheehan" <jd...@nmr.mgh.harvard.edu> wrote:
> Hello,
>
> I'm having similar issues with a 1.5T data set from here that used a
> custom head coil. The talairach transforms are skewed and scaled
> incorrectly. Some are not correctable by tkmedit as the movable is too
> skewed (almost to a rhomboid shape). I'm fairly new to freesurfer so any
> suggestions would be greatly appreciated.
>
> -James
> __
> James Sheehan
> Research Laboratory Technologist
> GI Research, Massachusetts General Hospital
> Cell: (978) 505-5135
>
> you can try:
>
> -talairach -use-mritotal
>
> which will use an alternate talarairch alignment scheme (from the MNI).
> it sometimes works better.
>
> you should also probably add:
>
> -nuintensitycor-3T
>
> to the end of your recon-all command, which will run the nu_correct
> stage optimized for 3T. it wont help you with your talairach issue, but
> people have found that it produces better results for 3T data (versus
> the default nu_correct parameters, which are optimized for 1.5T).
>
> n.
>
>
> On Mon, 2011-10-03 at 15:53 +0100, _andre...@sapo.pt wrote:
>> Hi all,
>>
>> I have the same problem. I'm also working with 3T, and I need to
>> stretch the movable template with tkregister2 in almost every subject.
>> It would be nice if this wasn't necessary, is there a workaround?
>>
>> Thanks,
>> Andreia
>>
>> Citando Maria Felber <fel...@cbs.mpg.de>:
>>
>>> 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" <fel...@cbs.mpg.de>
>>> To: "Avi Snyder" <a...@npg.wustl.edu>
>>> Cc: "Sita Kakunoori\", fel...@cbs.mpg.de, \"Avi Snyder\"
>>> <a...@npg.wustl.edu, Bruce Fischl" <s...@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" <a...@npg.wustl.edu>
>>> To: "Sita Kakunoori" <s...@nmr.mgh.harvard.edu>, fel...@cbs.mpg.de,
>>> "Avi Snyder" <a...@npg.wustl.edu>
>>> Cc: "Bruce Fischl" <fis...@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" <s...@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 <fel...@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" <fis...@nmr.mgh.harvard.edu>
>>>> To: "Maria Felber" <fel...@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" <fis...@nmr.mgh.harvard.edu>
>>>>> To: "Maria Felber" <fel...@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
>>>> StephanstraÃe 1A
>>>> 04103 Leipzig, Germany
>>>> Phone: +49 341 9940-2465/2522
>>>>
>>>> --
>>>> Maria J. Felber, PhD Student
>>>> Max Planck Institute for Human Cognitive and Brain Sciences
>>>> StephanstraÃe 1A
>>>> 04103 Leipzig, Germany
>>>> Phone: +49 341 9940-2465/2522
>>>>
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>>>
>>>
>>> --
>>> Maria J. Felber, PhD Student
>>> Max Planck Institute for Human Cognitive and Brain Sciences
>>> StephanstraÃe 1A
>>> 04103 Leipzig, Germany
>>> Phone: +49 341 9940-2465/2522
>>>
>>> --
>>> Maria J. Felber, PhD Student
>>> Max Planck Institute for Human Cognitive and Brain Sciences
>>> StephanstraÃe 1A
>>> 04103 Leipzig, Germany
>>> Phone: +49 341 9940-2465/2522
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
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