Hi,
I have never tested compatibility with 5.1 and would recommend against it (5.1
was released almost 9 years ago). You can try it out on one subject and check
results. There would be no support for this however.
Best, Martin
> On 17. Dec 2019, at 20:34, Greve, Douglas N.,Ph.D.
> wrote
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Hello all,
I have a series of functionally-defined ROI volumes (.nii format) that I'd
like to project into the white matter to then be used for tractography.
So far the vols have been brought from cvs_avg35 space into subject space
from using mri_vol2
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Dear Freesurfer experts,
I have a manual segmentation of a certain brain feature done in Freeview. I
want to pool these segmentations from different subjects to create some
kind of a heat map/probability map.
In order to do this, I assume I need to co
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Thank you Doug/Bruce.
We would like to project our AFNI preprocessed EPI scans (T1-registration,
motion correction, linear regression, but unsmoothed) to Freesurfer
cortical surfaces in order to obtain one file containing 250 (number of
dynamics) EPI-c
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Dear Freesurfer experts,
How can I transform an EPI-surface with LIA orientation to RAS orientation?
Thank you in advance.
Best regards,
Marina.
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ht
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Dear freesurfer experts
I am a beginner in DWI data processing and my question may be absurd, if
so, I apologize in advance.
I am using TRACULA for the analysis of my DWI data. Reviewing the outputs
of the statistics for the FA index I realized that s
Hi Benxamín - Those can occasionally arise due to noise. You're more likely to
see them if you're looking at single voxel values than average values over
multiple voxels. That sequence of values in the .9-1 range does look quite high
though. Another possibility would be miscalculation due to inc
It is right if the register.dat maps 4d_inputBOLD.nii to the conformed
subject anatomical space. You can check this with
tkregisterfv --mov 4d_inputBOLD.nii' --reg 'register.dat'
On 12/18/19 10:23 AM, Marina Fernández wrote:
>
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>
> Thank you Doug/Bruce.
>
>
I'm not sure what you mean. Surface data does not have an orientation in
the way that a volume does
On 12/18/19 10:29 AM, Marina Fernández wrote:
>
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>
> Dear Freesurfer experts,
>
> How can I transform an EPI-surface with LIA orientation to RAS
> orientation
in this case, I might try mri_vol2vol, something like
mri_vol2vol --fstal 1 --interp nearest --mov example.mgz --s subject
--regheader --o example.mni305.mgz
That is a linear transform. If you want a non-linear, I can walk you
through that too
On 12/18/19 10:13 AM, Benjamin Ineichen wrote:
>
>
Hi Corinna, if I understand correctly, you basically have cortical GM
ROIs in CVS space and you want to create an ROI of the adjacent WM. Is
that right? How far do you want to extend the ROI into WM? Do you want
to do something like a wmparc.mgz?
doug
On 12/18/19 9:55 AM, Corinna Bauer wrote:
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Hi Doug,
Yes, I have GM ROIs in CVS space and I'd like to create a corresponding WM
ROI for each of them that extends 2-3 voxels into the WM.
Would it be possible to create something akin to wmparc.mgz with these ROIs?
Corinna
On Wed, Dec 18, 2019 at
off the top of my head I can think of a couple of ways
1. replicate the wmparc.mgz stream. For this you will need to create an
annotation from your GM ROIs by combining them into a ssegmenation, then
using mri_vol2surf to create a surface-based segmentation, then using
mris_seg2annot, then use m
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Ok thanks! The first option sounds like it might provide a cleaner result,
since the second would dilate in all dimensions.
I'll let you know if I run into any trouble with it.
Thanks again,
Corinna
On Wed, Dec 18, 2019 at 2:45 PM Greve, Douglas N.,
Yes. The 2nd would dilate in all dimensions, but you would only keep
those voxels that were in WM. but the 1st is definitely cleaner
On 12/18/19 2:52 PM, Corinna Bauer wrote:
>
> External Email - Use Caution
>
> Ok thanks! The first option sounds like it might provide a cleaner
> result,
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Would it be best to do option 1 in the CVS space or in subject space?
On Wed, Dec 18, 2019 at 2:57 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Yes. The 2nd would dilate in all dimensions, but you would only keep
> those voxels that w
yes, either should work.
On 12/18/19 3:15 PM, Corinna Bauer wrote:
>
> External Email - Use Caution
>
> Would it be best to do option 1 in the CVS space or in subject space?
>
> On Wed, Dec 18, 2019 at 2:57 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Yes. T
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Hi,
I was wondering if there is any automated command/method to create a new
label that consists of the overlap of two labels? I've run two whole brain
analyses with different predictors and have regions where the clusters from
each analysis overlap. I
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