On Tue, Apr 19, 2011 at 10:25 AM, Khoa Nguyen
<khoa@nmr.mgh.harvard.edu> wrote:
Got it. I'll look at it and get back to you.
On Tue, 19 Apr 2011, Allie Rosen wrote:
Hi,
http://dl.dropbox.com/u/14127241/C42.tar.gz
Here is the link to the subject. I hope this works!!
Allie
On Tue, Apr 19, 2011 at 9:38 AM, Khoa Nguyen <khoa@nmr.mgh.harvard.edu>wrote:
Another way you can try is upload it to your google doc account and send me
the link. Someone did that before.
On Tue, 19 Apr 2011, Allie Rosen wrote:
Hi,
No, I'm not from the centre. I'm working on putting the files in Dropbox
and
sending you a link to them, because apparently I don't have ftp access.
Allie
On Tue, Apr 19, 2011 at 8:37 AM, Khoa Nguyen <khoa@nmr.mgh.harvard.edu
wrote:
Are you from the center? If so you can just cd into /space/outgoing and
copy your file there. If not, you can follow the instructions in the box
at
the top using a terminal.
On Tue, 19 Apr 2011, Allie Rosen wrote:
Hi,
I'm really sorry, but I don't understand those instructions. Do I login
to
the freesurfer website? Or do I login through a terminal somehow? Do I
type
the stuff in the boxes into the terminal?
Thanks,
Allie
On Tue, Apr 19, 2011 at 8:18 AM, Khoa Nguyen <khoa@nmr.mgh.harvard.edu
wrote:
Hi Allie,
You can compress the subject dir and upload it following the
instructions
here
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Tue, 19 Apr 2011, Allie Rosen wrote:
Hi Khoa,
How do I upload subjects?
Thanks,
Allie
On Tue, Apr 19, 2011 at 8:06 AM, Khoa Nguyen <
khoa@nmr.mgh.harvard.edu
wrote:
Hi Allie,
Can you upload the subject? I'll take a look and see if I can figure
out
what's wrong.
-Khoa
On Tue, 19 Apr 2011, Allie Rosen wrote:
Hi,
This (recon-all after wm.mgz and brainmask.mgz edits) didn't work.
The
part
that wasn't included in the pial or white matter surfaces is still
not
included. The intensities in the white matter regions are no
different
than
in white matter regions that were included in the white matter. Any
other
suggestions?
Thanks,
Allie
On Mon, Apr 18, 2011 at 7:53 PM, Allie Rosen <rosen.allie@gmail.com
wrote:
Hi Bruce,
I am running recon-all tonight using wm voxels that I manually
added
(I
also edited brainmask.mgz to add missing grey matter). To me it
doesn't
really look like a case of the white matter not having a high
enough
intensity. It simply looks like the whole lobe was ignored,
regardless
of
intensity. But I'll check tomorrow to see if the intensity is low.
Thanks,
Allie
On Mon, Apr 18, 2011 at 7:38 PM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu>wrote:
What is the intensity of the white matter in the regions you drew
in?
A
couple of control points might help if it is less than 110
On Apr 18, 2011, at 12:36 PM, Allie Rosen <rosen.allie@gmail.com>
wrote:
Hi Sita,
Thanks for all the responses! I've actually had the same problem
for
multiple subjects. I'm using version 5.0.0. I'll try fixing the
cerebellum
as well. I've attached pictures of where I am adding wm voxels.
They
aren't
really in the same places as in the online tutorials. Could you
take
a
quick
look to see if they're in the right place?
Thanks,
Allie
On Mon, Apr 18, 2011 at 12:31 PM, Sita Kakunoori <<
sita@nmr.mgh.harvard.edu>
sita@nmr.mgh.harvard.edu> wrote:
Hi Allie,
pial surface which looks like this can only be corrected by
correcting
the wm.mgz. Also I would suggest to try and fix the cerebellum
and
see
if it
corrects the surfaces as well. Since part of the cerebellum is
stripped
off,
it's probably affecting the segmentation as well but I could be
wrong.
what
version of freesurfer are you using.
Sita.
On Mon, 18 Apr 2011, Allie Rosen wrote:
Hi Sita,
Can I still add voxels to wm.mgz even though the points would be
outside
even the pial boundary?
Thanks
Allie
On Mon, Apr 18, 2011 at 12:18 PM, Sita Kakunoori
< <sita@nmr.mgh.harvard.edu>sita@nmr.mgh.harvard.edu>wrote:
Hi Allie,
This probably needs white matter edits but it's hard to tell
from
one
slice. Please refer to our white matter edits wiki and
toplogical
defects
wiki and see if it helps in fixing the errors in your datasets.
Also
it
looks like part of the Cerebellum is stripped off. You might
want
to
correct
that as well.
<
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
<
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect
Sita.
On Mon, 18 Apr 2011, Allie Rosen wrote:
Hi,
Once processed, several of my subjects have had errors around
the
occipital
lobe. Attached is an example. I've already tried editing
brainmask.mgz
and
running recon-all, but as you can see, this didn't change the
pial
or
wm
borders. What can I do to fix this?
Thank you,
Allie Rosen, MSc Candidate
Graduate Student, Department of Neurosurgery
Toronto Western Hospital 14-327
399 Bathurst St.
University of Toronto
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