what are MNI surface coords?
On 5/14/19 5:30 PM, Song, Da-Yea wrote:
>
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>
> Hello,
>
> We have an anatomical atlas that we have incorporated in the
> FreeSurfer pipeline. Is it possible to convert this voxel based atlas
> into MNI152 surface coordinates? Any
I can't replicate the error (even when using the same subject name), so
I'm not sure what to say. The only think I can think of is that it is
something in your environment that is causing the strangeness. Can
someone you work with run the command to see if the same error happens?
On 5/14/19 5:0
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Hello,
We have an anatomical atlas that we have incorporated in the FreeSurfer
pipeline. Is it possible to convert this voxel based atlas into MNI152 surface
coordinates? Any suggestions or comments would be greatly appreciated.
Thank you,
Da-Yea
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-cubic only affects the very first part of the stream, so it should not
affect processing when you re-run after edits
-custom-tal-atlas also only affect the first part of the stream
-qcache should only be run after you have done all of your processing.
If you do not re-run it, then qdec will us
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Hi Doug:
I used the following command:
[airhunger:Structural_for_7T] (nmr-stable6-env) aparcstats2table --subjects
100610 --hemi rh --meas thickness --tablefile aparc_stats.txt
However, I got an error message:
File "/usr/local/freesurfer/stable6/b
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Hello freesurfers,
Our lab has been using freesurfer 5.3 for a while. We use the following
flag when we run the initial recon-all
-mprage -hippo-subfields -qcache -cortparc3 -parcstats3 -cubic -pctsurfcon
-custom-tal-atlas TRIO_PIB_NDC_as_mni_average_3
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Yes. Smoothing in the volume may smooth across sulci and other tissue
types. I would like to use ICA-AROMA to denoise the data, especially remove
the head motion component. However, this toolbox do not support
surface-based data, and according to the su
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Thanks a lot Bruce.
On Tue, May 14, 2019 at 10:21 AM Bruce Fischl
wrote:
> it's not the morphometric measures that are smooth, it is the gradient
> nonlinearities. So they warp the gray and white surface by pretty much the
> same amount and preserve
Why do you want to smooth in the volume before sampling onto the
surface? That would defeat one of the main reasons to sample on the
surface (ie, surface-based smoothing instead of volume-based).
Volume-based smoothing in the subcortical regions is automatically done
when you specify a FWHM in
it's not the morphometric measures that are smooth, it is the gradient
nonlinearities. So they warp the gray and white surface by pretty much the
same amount and preserve the thickness (unless you are using a head-only
system, which you are not)
On Tue, 14 May 2019, Martin Juneja wrote:
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Thank you so much Martin, Matthew and Bruce for all the detailed
information.
Just to answer your question regarding MRI data: T1-weighted data were
collected using a 3.0 Tesla Siemens Tim Trio scanner (Siemens, Erlangen,
Germany). T1-weighted magnet
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Sorry for the confusing expression. I mean smooth on the volume before
resampling volume to the three standard spaces (left and right surface and
subcortical space). Anyway, I think I have figured it out. In the last two
steps of 'preproc-sess', the vol
There is not a "direct" mask, but you can use
mri_binarize --i aparc+aseg.mgz --csf --o csf.mgz
On 5/14/19 12:05 PM, Yaoshen Yuan wrote:
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> Dear Freesurfer team,
>
> I am planning to get the CSF binary mask using Freesurfer. I saw
> previous discussion
I created a matlab file called annotval2surfoverlay.m. Does this do what
you want?
surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile)
Example:
I have three annotations
annotnames = strvcat('superiortemporal','insula','postcentral');
with matchine values
anno
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Dear Freesurfer team,
I am planning to get the CSF binary mask using Freesurfer. I saw previous
discussion about combining several labels in aparc+aseg.nii to create the
CSF mask. I am now using Freesurfer v6.0.0. I am wondering does FS now
offer a d
sorry, I'm not sure what you are trying to do. When you say you would like to
smooth the data then resample, do you mean smooth on the surface? and do you
mean resample to the standard surface or volume space?
On 5/13/2019 11:26 AM, Zhi Li wrote:
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Dear Frees
what version of FSL are you running? That program (mni152reg) is just a front
end for running flirt, so you can always run flirt by itself.
On 5/13/2019 8:49 AM, vin rasa wrote:
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Dear Freesurfer Experts!
The idea is to transform freesurfer output in to the M
did you check the output? I think it should have the appropriate number of
frames. You can use mri_info to check the dimensions
On 5/13/2019 7:35 AM, Robert Austin Bruce Benn wrote:
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Hi There,
I’m currently trying to run mri_vol2surf on some animal data and
You can use something like mri_surf2surf --s subject --src-area midsurf --hemi
--trgval lh.area.midsurf
run with --help to get examples
On 5/14/2019 10:42 AM, Bruce Fischl wrote:
Hi Tim
not sure about area (Doug might have something), but for curvature you can do:
mris_curvature -w lh.area.midg
probably easier to do the other way around, eg,
tkmeditfv subjectname orig.mgz -surfs -ov example_func.nii.gz -reg reg.dat
This is a frontend that will run freeview
On 5/14/2019 5:57 AM, Sam W. wrote:
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Thank you Douglas for your response. That's what I thought
Hi Tim
not sure about area (Doug might have something), but for curvature you
can do:
mris_curvature -w lh.area.midgray
this will create mean (*.H) and Gaussian (*.K) curvature files. You might
add a bit of smoothing with e.g. -a 5, which is what we do by default when
we create the [lr]h.cu
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I hava a data set of 240 patients, 60 Healthy Control, 60 MCI, 60 cMCI
and 60 AD, with 429 cortical
and subcortical features.
68 of this features are cortical thickness standard desviation features
(ie,
lh_bankssts_thicknessstd, lh_caudalanteriorci
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Dear list,
I have created a custom surface at 50% thickness between the white and pial for
my subjects (`mris_expand -thickness lh.white 0.5 lh.graymid`).
Is there a way to compute measures like curv and area for this surface using
FreeSurfer tools?
the gradient nonlinearities have almost no effect on thickness. Since they
are spatially smooth they warp both the white and pial surfaces similarly,
so the distance between them doesn't change much.
B0 effects can be large locally depending on your field strength and
bandwidth. These are prett
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For most scanners, gradient nonlinearity correction is a relatively small
effect that is most prominent in the periphery of the FOV (it is a bit larger
in the HCP custom scanner because of design constraints). For 3D structural
images (e.g. T1w, T2w
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Thank you Douglas for your response. That's what I thought but wasn't sure.
I have another question if you don't mind. I would like to load the wm
surfaces as well, and overlay them on top of the mean functional scan.
However they are in conformed space
Hi Martin,
probably the reviewer does not mean anything related to FS. Rather,
there is distortion during image acquisition (e.g. gradient non-
linearities). The reviewer probably wants to know if gradient
unwarparing was done prior to running FS. That is why Matthew asked
what MRI data was colle
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