Hi Emil
I would need the entire subject dir plus the T2-space volume
cheers
Bruce
On Tue, 13 May
2014, Emil H.J. Nijhuis wrote:
Dear Bruce & Matt,
thank you for your help.
@Bruce: I would be happy to send you the data, just let me know by e-mail which
files you wo
uld need.
@Matt: Could you please specify the commands for the flags -nsigma_above and
-nsigma_below a
nd how you would rerun the pipeline? Also what values would be recommended?
I did not find any manual/help files regarding the flags, so it would be
helpful to document
it.
NB. I found another thread in the maillist which probably relates to the issue:
https://mail
.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033550.html . However I could not
verify this, due to expired dropbox files.
Yours,
Emil
Probably Emil¹s current example would be best because it is failing in
your recon-all setup.
Matt.
On 5/9/14, 9:31 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
>Hi Matt
>
>if you can send me an example I'll try to find time to take a look
>Bruce
>On Fri, 9
>May 2014, Matt Glasser wrote:
>
>> Hi Bruce,
>>
>> For whatever reason, sometimes the T2w surface adjustment will be way
>>off.
>> Adjusting the -nsigma_above <#> -nsigma_below <#> even a little bit up
>>and
>> down can get it out of the minimum and make it work, so there might be a
>> bug.
>>
>> Peace,
>>
>> Matt.
>>
>> From: "Emil H.J. Nijhuis" <emil.nijh...@gmail.com>
>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Date: Friday, May 9, 2014 at 4:53 AM
>> To: <freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] problem with pial surface reconstruction
>>using T1
>> (MPRAGE) and T2 (SPACE) weighted images
>>
>> Dear Bruce,
>>
>> thank you for your help.
>>
>> attached I have put an fslview, tkmedit screen-shot of the T2 image and
>>a tk
>> surfer image of lh.woT2.pial.
>>
>> It appears that without consideration of the T2 this effect does not
>>happen.
>>
>> What would be your recommendation if I would like to keep using the T2
>>weigh
>> ted image?
>>
>> Yours,
>> Emil
>>
>> Hi Emil
>>
>> how do the surfaces look before you apply the T2 deformation? And how do
>> they look visualized over the T2 instead of the T1?
>>
>> cheers
>> Bruce
>>
>> On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:
>>
>> Hi,
>>
>> I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm
>> isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T
>>Trio
>> scanner with a 32-channel head coil. Unfortunately for half of my
>>subjects I
>> receive an rather odd pial surface artefact, while the 'white' surfaces
>>do
>> not suffer from the same issue.
>>
>> The command line I have used was:
>>
>> recon-all -all -subjid <subjectid> -T2 <subjectdir>/mri/orig/T2.mgz
>>-T2pial
>> -3T
>>
>> Are you familiar with this issue and do you have some advice for me?
>>
>> Thank you very much for your help.
>>
>> Yours sincerely,
>>
>> Emil
>>
>> --
>> ----------------------------------------------
>> Emil H.J. Nijhuis, PhD
>> Researcher - Division of Diagnostic and Interventional Neuroradiology
>> University Hospital Basel
>> Petersgraben 4
>> CH 4031 Basel Switzerland
>>
>>
>>
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