Hi Bruce,
It looks like I was using wrong command to view output in tkmedit. I
changed it following:
tkmedit bert
/home/raghav/Desktop/MRI_DATASETS/SATA/freesurfer/testing-images/8/8/mri/normgz
-segmentation
/home/raghav/Desktop/MRI_DATASETS/SATA/freesurfer/testing-images/8/8/mri/aseg.mgz
And no
Hi Bruce,
I used following command:
recon-all -subject 8 -i /home/raghav/Desktop/MRI_DATASETS/SATA/freesurfer
/testing-images/8/8.nii.gz -sd /home/raghav/Desktop/MRI_DATASETS/SATA/
freesurfer/testing-images/8 -all -cw256
I had to use -cw256 option due to the fact that in third dimension my
volume
Hello Freesurfer experts,
I'm really struggling with my study.
I have a 27 scans that I analyze in QDEC. Scans are from Siemens machine,
mprage protocol, TR1620, TE 4.3, FOV 240*256, acq. matrix 232*256, slice
thickness 0,9mm.
After I enter model and have some initial significant clusters (thresho
Hi Raghav
We don't resample into MNI (or any other space). Was your input already
resampled? In general you should send us your full command line and screen
output
Cheers
Bruce
> On Oct 9, 2016, at 1:39 PM, Raghav Mehta wrote:
>
> Raghav
___
Fre
Hi Bruce,
I ran recon-all -all pipeline, but I am getting output in MNI space and not
in native space, so question is, is there in way in which I can get output
directly in native space or I have to transform them back into native space
using inverse transform??
Thanks for your help.
Raghav Meht
Hi Raghav
there are individual steps that can be run, but part of the strength of
FreeSurfer is that the comprehensive nature of our modeling gives us
greater accuracy. For example, the cortical surface models are used to
automatically correct the subcortical segmentation and such. In general
Hi,
I am new to freesurfer. I would like to know the command for subcortical
segmentation of brain MRI volume. I read on freesurfer wiki page the
recon-all -autorecon2 stage is useful for this. *My question is what exact
command should I use for this purpose.* I am familiar with FSL. In FSL
'FIRST
Hi Katherine,
You need to run the data through all three steps of the longitudinal pipeline. The *.long.* directories are created in the last step (recon_all -long ... ). See also the wiki ( Google longitudinal processing freesurfer )
Best Martin
On Oct 8, 2016 21:19, Katherine Damme wrote:Hello e
