Hi Carl
Did you try outputting files with names that won't be overwritten by recon-all
for the sphere.reg and annot files and see if they are correct?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Trolle, Carl
Sent: Sunday, August 28, 2022 4:32 PM
To:
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Hello Danesh,
Try putting your license.txt file into your home directory and setting the
environment variable FS_LICENSE to point to it.
$ export FS_LICENSE=$HOME/license.txt$ cd $HOME$ cat $FS_LICENSE… you should
see your email address used to
Hi!
Thank you, yes, using the Freesurfer dev-version available through the Martinos
cluster produced the desired result with the Destrieux-atlas. I’ve been using
the 711-version throughout, I hope that I specified the version in my first
email.
Is it possible to use these commands
On 8/11/2022 6:02 PM, Miriam Taza wrote:
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Hi again,
I have a few questions regarding this.
indeed it does appear that there is a bias field in all of these
scans, but this is not specific to those that fail sclimbic.
1. why do you think it is
I was under the impression that Self and Valence were ratings from the
same event (in that mail archive, they were different events and so
needed different offsets). If Self and Valence are from the same event,
then you would have something like
1. Offset
2. Self
3. Valence
4. Self*Valence
We did fix this at some point. Can you try running the 7.3 version to
see if you get the same results? Often multiple threads will yield
different results unless specifically programmed otherwise.
On 8/27/2022 4:41 AM, Giulio Siracusano wrote:
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Hi
If you have run recon-all on the case and samseg on the conformed image
(eg, orig.mgz or nu.mgz), then you can run mri_surf2volseg to insert the
cortical parcellations into the volumetic seg (look in the recon-all.log
to see the commandline used to create the aparc+aseg.mgz)
On 8/26/2022
Not sure what you are asking or saying. Is Synthseg not useful for gad
images or is it useful?
On 8/25/2022 10:54 AM, Gonzalo Rojas Costa wrote:
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>
> Hi:
>
>SynthSeg is useful for T1-GD volumetric images? Another algorithm,
> software?
>
>
Since this is longitudinal, I'm assuming that your contrast is actually
something like contrast C = (INT2-INT1)-(CON2-CON1) where 1 and 2 the
the time points. As you suggest, both (INT2-INT1) and (CON2-CON1) might
both be less than 0, but if INT is less negative than CON, then C will
be
I'm not sure what you mean by "inflate" here. Do you just mean to run
recon-all? Usually, you would run recon-all, then run segmentHA, then
register the fMRI to the anatomical (bbregister), then map the segs to
the fMRI space (mri_label2vol), then run something like mri_segstats
--seg
which version of FS are you using? There was a bug in pre 7.3.2 versions.
On 8/20/2022 11:05 AM, Fischl, Bruce wrote:
Hi Carl
Can you upload your subject including the central sulcus labels you drew?
Cheers
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Trolle, Carl
you can also
Convert a surface file to ascii (vertices are surface normals):
mris_convert -n lh.white lh.white.normals.asc
On 8/20/2022 8:41 AM, Yendiki, Anastasia wrote:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki/SurfaceNormal
The "Mean" column will be the mean lGI in the region
On 8/17/2022 4:42 AM, Steger Celine wrote:
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Dear FreeSurfer experts,
I try to explore the Gyrification Index of both hemispheres in a
population. For this I computed the LGI using the Freesurfer
Are you trying to run this from outside of recon-all? If not, can you
send the recon-all log file? Also, have you looked at the talairach
registration?
On 8/15/2022 7:50 AM, 丁晴 wrote:
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Hello FreeSurfer Developers,
I'm attempting to generate filled.mgz
Hi Giulio,
This is odd. I've run your scan on my computer two times using both a single
thread and 8 threads with the default FS 7.2 and obtained the same results
within the same number of threads.
Regarding the np.random functions, these are called only by the lesion version
-- which, by the
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