Dear FreeSurfer and hippocampal subfield segmentation developers,
I have noted that the FS6.0 hippocampal subfield segmentation procedure was
developed using scans of older adult brains. Has the application of this method
to kids, adolescents and/or young adults in any way been validated? Or d
Dear Kiyotaka,
It is okay to distribute the buckner_data we post on our website for tutorial
purposes.
Allison
On Jan 8, 2018, at 6:35 AM, Kiyotaka Nemoto wrote:
> Dear FreeSurfer experts,
>
> We are planning to have a one-day neuroimaging workshop in Japan. One topic
> of the workshop is "F
Dear Allison,
Thank you! It will be a big help to us.
Best regards,
Kiyotaka
2018-01-10 21:17 GMT+09:00 Allison Stevens :
> Dear Kiyotaka,
> It is okay to distribute the buckner_data we post on our website for
> tutorial purposes.
> Allison
>
> On Jan 8, 2018, at 6:35 AM, Kiyotaka Nemoto wro
Hi Getaneh,
the estimates for D and phisq for a given analysis are contained within
the data structure that is returned by the lme_fit_FS procedure.
I.e. for the tutorial data, the command was:
total_hipp_vol_stats = lme_fit_FS(X,[1 2],Y(:,1)+Y(:,2),ni);
Dhat and phisqhat are fields of the 'tot
Thank you so much for your response. I tried the 3rd solution and used
--trgsubject fsaverage and that works like a charm.
Best,
Pia
On Tue, Jan 9, 2018 at 6:04 PM, Douglas N Greve
wrote:
> You probably set up the FSFAST analysis to sample onto the fsaverage
> surface (in your mkanalysis-sess c
Dear Freesurfer experts,
I want to create mask for the midbrain and the precentral gyrus.
I used FSV6 to do the reconstruction. Then I used the flag
-brainstem-structures in recon-all to segment the brain stem.
How can I create one mask that include structures from wmpac.mgz and
brainstemSsLabels
you'll need to do it in 3 steps
mri_binarize --i wmparc.mgz --match 1024 2024 3024 4024 --o wmparc.mask.mgz
mri_binarize --i brainstemSsLabels.v10.mgz --match 173 --o bs.mask.mgz
fscalc wmparc.mask.mgz and bs.mask.mgz -o final.mask.mgz
The only problem will be if the brainstem seg is higher re
Dear Dr Greeve,
Thank you very much for the quick and detailed response.
Before your response, I tried fslmaths instead of fslcalc and I got error
message complains about misorientation between the input masks.
Now, I tried fslcalc and it failed as well to combine the masks due to a
mismatch siz
Dear Kersten,
Thank you so much.
When I run the procedure with left and right cortical thickness data I get
different phisqhat values
Phisqhat:0.2530 for the left and
Phisqhat:0.0903 for the right
The Dhat matrix is also different.
Is that Ok?
If so , shall I consider two sample sizes for
I was afraid of that. You will need to either map wmparc to the
brainstem space or the brainstem into the wmparc. Probably better to do
the first. You can use mri_label2vol with --seg wmparc.mgz --temp
brainstem.mgz --regheader wmparc.mgz --o wmparc.in-brainstem.mgz
On 01/10/2018 11:54 AM, Jo
I tried that and I got an error in the Mask function that excludes the
inter-hemispheric cut in matlab.
It doesn’t like the lh/rh.pial surfaces of the fsaverage.
This is the code:
0001 function mask = SurfStatMaskCut( surf );
0002
0003 %Mask that excludes the inter-hemisphere cut.
0004 %
Yes!! this worked. Thank you so much!
I was afraid of that. You will need to either map wmparc to the brainstem space
or the brainstem into the wmparc. Probably better to do the first. You can use
mri_label2vol with --seg wmparc.mgz --temp brainstem.mgz --regheader wmparc.mgz
--o wmparc.in-brai
I have done the changes did you suggested:
mkanalysis-sess -analysis fc.rhipposeed.mni305 -mni305 -fwhm 6 -notask -taskreg
R_Hippocampus.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4
-mcextreg -fsd rest -TR 3 -per-run -hpf 0.01 -lpf 0.1 -force
but the error persists:
GLS B
Hello,
We have some images that reflect severe atrophy in some subjects, in which gray
matter is virtually undetectable on the MRI in some regions. However, upon
checking the segmentations visually, the white/pial surfaces are reflecting a
significant cortical thickness in these areas.
Is ther
Hi Eli
it's hard to say without looking at an image. Can you upload a subject and
point us at a spot you think is incorrect? And do you really think the
thickness should be 0 - there is no gray matter left at all? That seems
unlikely
cheers
Bruce
On Wed, 10 Jan 2018, Rockers, Elijah D. w
Dear Lauri,
Would you mind sending me the log of the subfield segmentation?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 08/01/2018, 22:04, "freesurfer-boun..
Dear Christian,
They atlas is built using subfield segmentations on scans of older adult
brains, but:
1. it’s also built with whole hippocampus segmentations of scans of subjects of
a wider age range.
2. the deformation model should be able to account for large parts of the
anatomical differenc
Hi David and Noam,
I have fixed a bug in applyMorph. If you have access to the dev version of
the code base that should be available to you in a day. If not, send and
email to the list and we can provide you with it. Here are the steps:
(1) Run mri_cvs_register command. As the applyMorph cod
Hello,
In stats-table,
I did'n
t find the thickness of
basal ganglia.
Please, c
an we
get
Hi Giovanni
the basal ganglia are little balls of gray matter, so I'm not sure how
one would measure thickness there. We do supply volume for each nucleus
cheers
Bruce
On
Thu, 11 Jan 2018, Giovanni de Marco wrote:
Hello,
In stats-table,
I did'n
t find the thickness of
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