Just for the record, I accidentally e-mailed you that the slice thickness was 2
mm, I now found out that the slice thickness is just 1 mm.
Doety
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Thanks Bruce! Now it's working, and the wm.mgz looks good!
Doety
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glad to hear it
Bruce
On Thu, 17 Jul 2014, Doety Prins wrote:
Thanks Bruce! Now it's working, and the wm.mgz looks good!
Doety
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Hi Bruce,
Thanks for your answer. I was trying to use the fsl segment in freesurfer
indeed. But since I couldn't get that working, I am now trying to do the trick
with mri_segment. Sorry to ask you again, but I still have troubles with
mri_segment. So I am trying to use the -wm_low flag to
Hi Doety
for mri_segment the options have to come before the required arguments
not at the end of the command line.
cheers
Bruce
On Wed, 16 Jul 2014, Doety Prins wrote:
Hi Bruce,
Thanks for your answer. I was trying to use the fsl segment in freesurfer
indeed. But since I couldn't get that
Hi Bruce,
Thanks for your reply. Yes I realize now that this is causing me the
troubles. But since fsl is able to do a good segmentation, I think
Freesurfer should also be able to do this?
I am now using MRI_segment, in which I want to set new limits for the white
matter, but it doesn't seem to
Hi Doety
our segmentation assumes we can resolve cortex as it used an adaptive
filtering that estimates the orientation of the gray/white boundary in
spatial neighborhoods. It may be more sensitive to low resolution than FSL.
Not sure if anyone has a script for importing FSL segmentations into
Hi Doety
that is a very low contrast-to-noise image. Can you give us more details
on the acquisition? The matrix was 256x256, what is the slice thickness?
And the other parameter (sequence name? TR/TR/flip angle? acceleration?)
cheers
Bruce
On
Thu, 10 Jul 2014, Doety Prins wrote:
Hi
the 2mm slice thickness is going to be problematic and is probably why you
lose so much cortical constrast. Typically we don't recommend using
anything more than 1.5 and really no reason these days not to get closer to
1mm (for example, you can get a very nice 1.25mmx1.25x1mm mprage in a bit
slice thickness: 2 mm
Repetition time: 25 ms (I think this might have caused the low contrast)
flip angle: 30 degrees
I'm sorry, can't find any data on acceleration
Doety
On 11 jul. 2014, at 15:10, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Doety
that is a very low contrast-to-noise
Hi Bruce,
Thanks for your reply. In my previous e-mail I already tried to attach one of
my subjects, but got the response that the message was too big, and therefore
it was rejected. So how should I upload the image? The images are T1-weighted,
3D, acquired with a 3T scanner, resolution 256
Hi Doety,
Consider these options for uploading data:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
I think recon-all is expecting your wm.mgz to be conformed or 256^3.
Something like: mri_convert wm.mgz wm.conform.mgz
Hi Doety
yes, that looks pretty bad. Can you tell us about the acquisition? What
resolution/field strength/scan type was it?
If you upload the subject we will take a look
cheers
Bruce
On Wed, 9 Jul 2014, Doety
Prins
wrote:
Dear freesurfer experts,
I experienced some problems with the
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