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Dear FreeSurfer developers,
I'm attempting to run recon-all on a set of T1-weighted images acquired in
the 1980s-1990s and am having trouble with the recon-all pipeline. I have
used the original dicom files in the recon-all using the command below.
I recently made a lot of changes to mkheadsurf. Can you download the dev
version and try it?
On 4/5/2022 4:24 PM, Megan Schendel wrote:
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Hello,
I am also trying to use mkheadsurf and getting the same errors
described in the January topic by user Yong-Jun
wow, I've never even looked at the ?h.curv files before. Looks like
there is a lot of info but only on a global (whole hemi basis). Some of
the measures are different (eg, min and max curv rather then mean or
gaussian). I don't know whether these would be helpful in your app.
On 4/5/2022
I don't know. Look at Christophe's paper.
On 4/8/2022 8:46 AM, Patricia Schwery wrote:
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Thank you Douglas for your reply.
Do you know if i can find the medial frontal gyrus in the a2009s? I
found other-regions that i need for the mPFC but this one i cantÂ
Lot's of people have adapted FS to non-human brains, just google it. For
surface analysis, you need to get the "subcortical mass" -- the
equivalent to the filled.mgz. This is the cerebral white matter +
subcort gray structures. Once you have that, you might be able to run
mris_place_surfaces.
Did you check the transform? It was the automatic failure detection that
threw the error. This can sometimes happen when the head is at a "funny"
orientation in the scanner, but at 7T there might be some bias fields
having an effect. Also, see if it works when you sample it at 1mm (just
don't
have you tried asking the ANTS people?
On 4/6/2022 10:05 AM, Nathan Kindred (PGR) wrote:
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Hi,
I have been using DenoiseImage from ANTs during pre-processing
(DenoiseImage -i T1.nii -o denoised.nii.gz -v), however for some scans
I am having an issue where
