Hi Bruce and Florent,
Your comments re: isoptropic voxels raised a question for me. How is mgz
different to cor format? Does mri_convert not interpolate to 1mm3 for mgz?
The imaging parameters are:
IR prep time, 500 ms; TE minimum, 2.8 ms; TR 13.9 ms; bandwidth, 15.63 kHz; 1
NEX; 20° flip angle; 2 mm contiguous slices; FOV 24 cm; up to 128 volumes for
full brain coverage; 512 (frequency, SI) by 256 (phase) matrix, zipped to 512
in phase direction with extended dynamic range.
-----Original Message-----
From: florent segonne [mailto:[EMAIL PROTECTED]
Sent: Wed 14/09/2005 6:29 AM
To: Bruce Fischl
Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] large radius
Hi Alex,
I think that mri_watershed is 'incorrectly' assuming 1*1*1mmm isotropic
voxels. We'll update the code so that it won't stop there.
Florent
-------------------------------------
Florent Segonne
PhD Candidate
Stata Center 32-D430 CSAIL MIT
1 617 253 2986
http://people.csail.mit.edu/~fsegonne
-------------------------------------
On Tue, 13 Sep 2005, Bruce Fischl wrote:
> Hi Alex,
>
> the 2mm slice thickness could be trouble. Usually we don't recommend
trying
> to recon cortical models with any dimension greater than 1.5mm. Why do
> anisotropic? Can you describe the rest of the acquisition parameters?
>
> Bruce
>
>
> On Tue, 13 Sep 2005, Fornito, Alexander wrote:
>
>> HI,
>> I've got some 3T SPGR data (512 x 512 x 104, vox dim. 0.488 x 0.488
x 2). I
>> seem to be able to convert them to .mgz ok, but when I run
mri_watershed I
>> get an error saying "main radius too high" (output below). Any
ideas as to
>> what's happening?
>> Thanks,
>> Alex
>>
>>
>> mri_watershed 1001670.mgz 1001670_brain.mgz
>>
>>
>> ************************************************************
>> The input file is 1001670.mgz
>> The output file is 1001670_brain.mgz
>> If this is incorrect, please exit quickly the program (Ctl-C)
>>
>>
>> *************************WATERSHED**************************
>> preflooding height equal to 25 percent
>> Sorting...
>> first estimation of the COG coord: x=253 y=50 z=235 r=135
>> first estimation of the main basin volume: 10415397 voxels
>> Error
>> main radius too high
>>
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>>
>>
>>
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