Hi,
I have run a number of cases through the FS6 hippocampal longitudinal
processing steps listed at
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields
and https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing
It seems that all steps completed, but when it came
Thank you,
this is very helpful.
Octavian
On Thu, Apr 13, 2017 at 12:19 PM, Antonin Skoch wrote:
> Dear Octavian,
>
> the current philosophy with wm.mgz edits is not to directly affect voxel
> values in original T1 image.
>
> The wm.mgz serves as starting point for the white surface estimation.
Dear Ruopeng,
thank you for the feedback. Yes, the behavior is exacly like you described. I
suspected that this has something to do with resampling but I was not sure.
The stripes were result of nearest-neighbor interpolation.
Antonin
Hi Antonin,
When you load two images like that, the second
Hi
It is for computing sources correlation with symmetrical orthogonalized
correlations which is dependent on the rank of the data, so I am limited to
the number of sensors I use for estimating sources.
I would appreciate to know if there is any method to get about a 100
cortical vertices in the
Dear Octavian,
the current philosophy with wm.mgz edits is not to directly affect voxel values
in original T1 image.
The wm.mgz serves as starting point for the white surface estimation. The
?h.white surface is estimated according gradient in voxel values in
brain.finalsurfs.mgz (which is, bas
Hi Antonin,
When you load two images like that, the second image will be resampled,
using nearest neighbor method by default. And when you save, it will be
resampled back to its original space. So there will be shifted voxels
depending how oblique it is to the first image. So I think what you
Dear John, David,
To great summarization of David, I would add following:
My personal preference is to run whole -autorecon2 -autorecon3 after editing of
the brainmask.mgz.
Early stages of -autorecon2 (normalization, registration, volumetric labeling)
use brainmask.mgz, therefore I believe tha
Dear experts,
I encountered following issue with freeview:
When two images with mutually different geometry are simultaneously loaded and
one of them is saved (via save as), its pixel values get somewhat corrupted.
There are strips in image with modified pixel values. It seems to affect only
OK, thanks Amelia. That's interesting - keep me posted if you run into this
with 6.0 in any new data set.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Versace, Amelia
[versa...@upmc.edu]
Sent: Thursda
Thanks, Anastasia!!
It should be it. I had run the same command before with slightly fewer subjects
in my "set subjlist" and it did work fine. Then I rerun the -path (and added
extra 18 subjects) to update the tracts with the recent implementation that you
have done (FS 6). After, started having
Hi Shane
by far the best way to do this is if you have a T2 or FLAIR scan that is
high-enough resolution (i.e. around 1mm isotropic).
If not, you can try the graph cuts skull stripping option in recon-all.
It is more aggressive than the watershed (which is the default).
cheers
Bruce
On W
Hello FreeSurfer Developers and experts,
I am trying to run our FSPGR sequences using the -mri_watershed script, but I
am not able to set and vary the -t threshold.
The aim of my work is to calculate the BPF in order to quantify parenchymal
atrophy in patients with Multiple Sclerosis.
Instead
Hi Julie
what space is the Gordon Parcellation in? Did they use FreeSurfer? If so,
then you just need to map it to each of your subjects.
And how is a surface-based parcellation stored in a nifti file?
cheers
Bruce
On Wed, 12 Apr 2017, Julie Hall
wrote:
Hi experts,
I would like to use
Thanks . Its working now.
___T_
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: 11 April 2017 16:48
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_ca_
Hi David,
Thank you for the feedback! I followed your advice's and everything has been
resolved. Highly appreciated!
Cheers,
John
Sent with [ProtonMail](https://protonmail.com) Secure Email.
Original Message
Subject: Re: [Freesurfer] manual edits
Local Time: April 12, 2017 11:
Yes, that is why it is experimental.
However, global atrophy will affect the ventricles (they are growing) which is
an effect in the opposite direction, so maybe it cancels out to some extend.
Best, Martin
> On 12 Apr 2017, at 23:55, Arman Eshaghi wrote:
>
> Thanks Martin. Should I be worri
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