glad to hear it
Bruce
On Fri, 10 Oct 2014, Smith, Michael wrote:
We re-ran that subject and it seemed to fix the problem, thanks! We will test
it out on the other subjects with the same issue and see how that goes, but it
looks like everything is good. Thanks again!
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Varjabedian, Ani
Sent: Thursday, October 09, 2014 10:02 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] WM & Pial Segmentation Errors
Hi Michael,
I took a look at your data and it seems that you paired a T2 image with a T1
image when you submitted to recon all. Recon-all will try to average these
together, and since they have such different contrasts, you will end up with a
poor template for surfaces later on.
Try running recon-all again without the T2 and see if that helps.
-Ani
On Wed, 2014-10-08 at 17:21 +0000, Smith, Michael wrote:
Ah, sorry for some reason it just wasn’t clicking before. I was able
to upload a dataset. Thanks!
On 10/8/14, 10:59 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
Hi Michael
you need to follow the directions on this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
in particular, make sure you change directories before trying to put
cheers
Bruce
On Wed,
8 Oct 2014,
Smith,
Michael wrote:
See attached
On 10/8/14, 10:46 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
can you send us the details of your ftp command?
On Wed, 8 Oct 2014, Smith,
Michael wrote:
Hi Bruce,
Do I not have permission to transfer files to the remote machine?
I can login fine as an anonymous user but when I attempt to use
the put command it says it could not create the file.
On 10/7/14, 7:33 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Michael
sure, the T2 can help if you have it (although you'll need to
download some updated binaries), but it is impossible to tell
from these images what is going on. Looks either the intensity
normalization, mri_segment or mris_make_surfaces failed. You can
try the expert options for each one to prespecify the range of
allowable intensities for gray and white matter.
If
you upload the subject to our ftp site (the whole subject
directory tarred and gzipped) we will take a look
cheers
Bruce
On Mon, 6 Oct 2014, Smith, Michael wrote:
Hi,
I¹ve been having trouble on a few of our subjects with getting
the white matter and pial surface files to ³line up² correctly
with the volume files.
I¹ve attached a screenshot of what is happening: the pial
surface is in red and the white matter surface file is in
yellow. I have also attached an example of a ³good² subject
for comparison.
I¹ve tried looking through the tutorials online but didn¹t see
anything that was really related to my issue and I was
wondering what the best way to correct this. We have T2
weighted images for several subjects is well if that helps.
Not sure if Freesurfer can use T2 images instead of T1 in the
reconall script but I thought I would mention it. Thank you
very much in advance!
Best,
Michael S.
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