I have used:
recon-all -s -subcortseg
which runs through step 11 (-calabel), with the understanding re: accuracy
that Bruce pointed out.
-Julie
On 7/7/10 8:07 AM, "Bruce Fischl" wrote:
> Hi Salem,
>
> yes, you can run any individual options in recon-all. See the -help output
> and run it th
I also use FS to identify subcortical atrophy with affected HD patients;
have you checked the aseg, as well as white & pial surfaces for accuracy? I
have found in some of my older data at lower resolution (1.5 T) that the
intensities do not differ much in subcortical regions and FS has problems
dif
Yes & Yes- over 100 GB
On 2/15/10 11:25 AM, "Bruce Fischl" wrote:
> Hi Julie,
>
> do you have write access to the file
>
> aseg.auto_noCCseg.label_intensities.txt
>
> in the subject's mri dir? Is there enough disk space free?
>
> cheers
&
Bruce Fischl" wrote:
> Hi Julie,
>
> can you send us the last couple of hundred or so lines of the
> recon-all.log? You can generate this with tail -n 200 recon-all.log
>
> cheers,
> Bruce
>
>
> On Mon, 15
> Feb 2010, Julie McEntee wrote:
>
>
Hello,
The initial command to recon-all:
recon-all -i $FREESURFER_HOME/subjects/PPG1156/1156MPRage.nii.gz -autorecon1
-autorecon2 -subjid MGZ
exited with errors during SubCort Seg. At this point, I am attempting to
obtain subcortical segmentation only (aseg.mgz, wm.mgz, aseg.stats), but
would li
Assuming the results of -subcortseg should be corrected for whole brain
volume (for group comparison or use as covariate), what number should be
used: ICV, BrainSegVol, total number of voxels? Should it be obtained from
an image file (e.g., aseg.mgz) or stats (e.g., aseg.stats) file?
Thank-you,
J
Hi,
So far, I have results from autorecon1 & -subcortseg. The aseg.stats that
are obtained following these procedures contain measures of L &
R-Cerebral-White-Matter and Cerebral Cortex. If I created masks (bitmaps)
using these labels in FreeSurfer, would they be equivalent to whole-brain WM
and
Hello,
I have T1-weighted data from Philips 3 T scanner obtained at a resolution of
0.898 X 0.898 X 0.9 mm in both dicom (8 bit) and par/rec (pixel size =
int16) format. I would like to preserve the acquisition resolution of the
data in par/rec format; what is the best way to convert such data to
