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Hello FreeSurfer Developers,
I'm attempting to compute gray matter volume average thickness.Can I use them
from stats file to compare two groups (HC and diesease) through t test?1)
FreeSurfer version:
but when you click on the vertex, is the value in the freeview the same
value in the summary file? Note, you must load the sig.mgh file, not the
corrected map.
On 5/5/2020 4:58 PM, Xiaojiang Yang wrote:
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Hi Douglas,
Not only vertex 10738. For all
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Thank you both.
I've made edits and these are the current commands:
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
--trgsurfval {output_dir}/registered_lh.white
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Hi Douglas,
Not only vertex 10738. For all vertexes listed in the summary file, they
all have a very big Max value (absolute) that is out of the visual range.
Please see the video I grabbed from my screen: https://imgur.com/a/kkSO7sT
*Thank you for
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It would appear not, as I'm getting an error on my pial output files but
not my white ones. Here are my commands:
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white
--trgsubject fs_target --trgsurfval ./registered_lh.white --trg_type w
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Thanks Bruce, extremely helpful.
Can I just check that the "w" format is what is used by both the
lh/rh.pial and the lh/rh.white files? I only ask because my surf2surf
command outputs the exact output filename if the end is ".white", but if
it's
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Bruce, I've read the docs on mri_surf2surf - I wish to get surface files
out (again, lh.pial, rh.pial, lh.white, and rh.white) rather than values
for something such as thickness - is there an option for mri_surf2surf
to allow this?
On 05/05/2020
You should load the surfaces in FV. If it load in FV ok but nibable is
crashing, you should contact them.
On 5/5/2020 1:05 PM, Ian Hardingham wrote:
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Thank you both.
I've made edits and these are the current commands:
mri_surf2surf --hemi lh --srcsubject
You should load that volume along with the orig.nofix hemisphere that is
giving you problems and look for a large area that should not be within
the surface
On 5/5/2020 1:23 PM, Zeng, Qi wrote:
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Hi Douglas,
The cerebrum is removed and with no skull
Don't specify a --trg_type. But add --tval-xyz
mris_apply_reg will do the same thing, but the interface might be a
little easier
On 5/5/2020 12:49 PM, Bruce Fischl wrote:
no definitely not "w" format, which we don't use for anything anymore.
YOu should use tval-xyz also I think
On Tue, 5 May
no definitely not "w" format, which we don't use for anything anymore.
YOu should use tval-xyz also I think
On Tue, 5 May 2020, Ian Hardingham
wrote:
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It would appear not, as I'm getting an error on my pial output files but not
my white ones.
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Dear Dough,
No worries, this was helpful too. Probably, I will test it on a subset of
subjects and compare the two for possible discrepancies.
Thank you,
Sneha
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent:
sorry, did not see this before I responded. Ignore what I said
On 5/5/2020 11:13 AM, Iglesias Gonzalez, Juan E. wrote:
Dear Sneha,
We use cortical and white matter parcels in the hippocampal subfields,
which is more reliable than using the whole white / gray matter to
compute parameters.
In theory it is possible, though I don't know if it is better or worse.
You can run samseg, then run samseg2recon (this creates a folder that
looks like it was created by recon-all), then run subfields on that folder
On 5/5/2020 10:45 AM, Sneha Pandya wrote:
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You should look at the wm.mgz to see where the defect is. Probably
cerebellum is still attached or maybe a big piece of skull.
On 5/4/2020 11:19 PM, Zeng, Qi wrote:
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Hi,
I've conducted longitudinal T1 recon-all. One subject's last-scan ran
into error in
Not sure. Are you visiting vertex 10738 ?
On 5/4/2020 10:01 PM, Xiaojiang Yang wrote:
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Hi FS developers,
I have used mri_glmfit-sim to do multiple comparison like below:
mri_glmfit-sim --glmdir lh.thickness.0.glmdir --cache 3 abs --cwp
0.05
yes, check out options like:
--sval-xyz
if you need further help though I'll have to defer to Doug :)
Bruce
On Tue, 5 May 2020, Ian Hardingham wrote:
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Bruce, I've read the docs on mri_surf2surf - I wish to get surface files out
(again, lh.pial,
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Dear Eugenio,
Thank you for quick response. That will be great if we could achieve it with
whole-head segmentation too, considering its shorter run time, but can
understand that it could be less reliable. If implemented, is it something that
will
Dear Sneha,
We use cortical and white matter parcels in the hippocampal subfields, which is
more reliable than using the whole white / gray matter to compute parameters.
But it could be hacked, albeit it would be a bit less reliable. I’ll add this
to the wishlist / to-do list (unfortunately it
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Dear experts,
I want to revisit if anyone has ran subfield analysis just by running samseg?
If it is possible is it as reliable as from running regular routine with "-all"
recon-all flag?
Thank you,
Sneha
From: Sneha Pandya
Sent: Thursday, April
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Hi Freesurfers.
I have a subject S with recon-all having been run on it.
I have the subject-specific surface files /surf/lh.pial, rh.pial,
lh.white, and rh.white.
I would like an Atlas's lh.pial, rh.pial, lh.white, and rh.white in
subject space.
Hi Ian
you can use mri_surf2surf to map surfaces between subjects, but our atlas
isn't really a surface. You can use the surfaces in the fsaverage dir, but
they are meant for visualization and are much smoother than individuals
cheers
Bruce
On Tue, 5 May
2020, Ian wrote:
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