Have you looked at the modifications for the BIDS App version:
https://github.com/BIDS-Apps/freesurfer
I believe the latest image (using FS6) is only 6.37GB and you could bypass
the run.py script with
--entrypoint bash
to run your typical recon-all commands
-Alex
-
Just out of curiosity, digging through recon-all finds this section quoted
below, however I thought -cp and -wm started at different spots?:
case "-autorecon2-cp":
case "-autorecon2-noaseg":
case "-autorecon2-wm":
set DoNormalization2 = 1;
set DoSegmentation = 1;
se
derstand. Are you really trying to generate a
> subcortical atlas? Or do you mean a subcortical segmentation? If the
> latter, then 1mm is fine. The resolution you want really depends on what
> you are trying to do
>
>
> On Tue, 24 Jan 2017, Alex Cohen wrote:
>
> generatin
017 at 12:21 PM, Bruce Fischl
wrote:
> Hi Alex
>
> cut it for what?
>
> Bruce
>
>
> On Tue, 24 Jan 2017, Alex Cohen wrote:
>
> So what resolution would make sense to use? the release notes say <1.0mm
>> but
>
So what resolution would make sense to use? the release notes say <1.0mm
but would 0.9mm isovol really cut it?
-Alex
Alexander Li Cohen, M.D., Ph.D.
E-mail: alexander.coh...@childrens.harvard.edu (Medical/Science Email)
E-mail: alex
> On Wed, 18 Jan 2017, Alex Cohen wrote:
>
> I will likely end up running each separately on several subjects to get a
>> handle on how they're behaving; however assuming I did what to average
>> them,
>> have you all found a particular method more useful th
Bruce Fischl
wrote:
> Hi Alex
>
> you get to decide whether to average your data or not. It's a totally
> empirical question which one is better - why don't you run them each and
> visually inspect the results?
>
> cheers
> Bruce
>
> On Wed, 18 Jan 20
Hi all,
What is the current best practice recommendation for using multiple T1s
and/or T2s for recon-all where the sizes of the images are slightly
different.
For instance: two T1w images of 0.9x0.9x0.9 and 1x1x1 resolution, however
the 1x1x1 image seems to have better grey-white separation, etc.
Hi all,
With Freesurfer 5.3 installed on a OS X 10.10.5 mac (MacBook Air 1.6Ghz
i5, 4GB ram), I find that scrolling through slices in Freeview is VERY slow
compared to tkmedit when surfaces are loading in addition to 1-2 volumes
(e.g., when editing pial/WM segmentations).
Any tricks/tips/help to
