Hi Esther
I don't see a volume overlay, just one on the inflated surface. Is that
what you mean? If not, can you resend and explain?
Bruce
On Thu, 2 Jun 2011, Esther Walton wrote:
>
> Thanks so much for your input.
>
> Could somebody please answer the second part of the question?
> That is, ig
Hi Bruce et al.
I have a quick question about the interpretation of surface normal
files and the various ways you can create them with Freesurfer.
As far as I know, there are two ways to get the normals information:
mris_convert -n lh.inflated lh.inflated.normals2
and
mri_surf2surf --s fsavera
Hi Michael
the ascii file is first:
vertex_nx vertex_ny vertex_nz ripflag (usually 0)
.
.
.
up to # of vertices. Then, for each face:
vertex_0 vertex_1 vertex_2 ripflag
cheers
Bruce
On Thu, 2 Jun 2011, Michael Waskom wrote:
> Hi Bruce et al.
>
> I have a quick question about the interp
Hi all,
I am running recon-all -autorecon1 -subjid subject and I have been getting
an error saying:
\n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n
talairach_avi: Command not found.
And then the program exits with errors. I looked in the transforms
directory within my subjec
Hello,
I am not able to do a regular recon-all of my data on seychelles-- I am
doing the same thing I used to do. We have started moving our data to a
different location, however, since this is all new data, I don't see how
this could be the problem.
I am using freesurfer 4, so I set this var bef
Hi Chindhuri,
we'll need to know what the error was that resulted in the non-zero exit
status.
cheers
Bruce
On Thu, 2 Jun 2011, Chindhuri Selvadurai wrote:
> Hello,
>
> I am not able to do a regular recon-all of my data on seychelles-- I am
> doing the same thing I used to do. We have started m
I'm not sure how to get that information. It does not give me an error
message in the terminal. Is there a log I could look at? Is there anything
that I need to do prior to the recon-all?
> Hi Chindhuri,
>
> we'll need to know what the error was that resulted in the non-zero exit
> status.
>
> che
http://www.nmr.mgh.harvard.edu/martinos/itgroup/seychelles.html
describes the cluster use. It will tell you how to check errors (there
are pbsjob files in your folder that contain output and error messages.
Best, Martin
On Thu, 2011-06-02 at 14:54 -0400, Chindhuri Selvadurai wrote:
> I'm not su
Hi,
I used the command:
recon-all -s subjid -label-v1
to generate the V1 label for my individual subjects and I did not face any
error. When I checked the label directory of the
corresponding subjects, I see two new labels named lh.v1.predict.label
rh.v1.predict.label but I don't see a
Hi all, we have a subject who had to end a run early, and as a result
his data is split over two sessions. The two sessions can't be
analyzed independently, since some events are missing from each, which
causes selxavg3 to fail. Instead, what I've been trying to do is take
the timecourses
Hi Finn, this is much easier to handle in 5.1. Just put all the runs in
the same bold directory and everything should work properly.
doug
Finnegan Calabro wrote:
> Hi all, we have a subject who had to end a run early, and as a result
> his data is split over two sessions. The two sessions can
Hi Jen
does the orig.mgz look right in tkmedit? That is, is axial really axial,
coronal really coronal, etc...?
Bruce
On Thu, 2 Jun 2011, Jennifer Evans wrote:
>
> Hey there,
>
> I have a very bad Talairach transform failure (from recon-all). The images
> from tmedit and tkregister2 are attach
Hello!
So, my first problem was that I wasn't able to load my new mgh files into qdec.
I tried to follow this procedure:
1. Convert a curv file from you subject into mgh:
mri_convert lh.curv lh.curv.mgh
2. Load in the mgh file to matlab
lhcurv = MRIread('lh.curv.mgh');
3. Replace the pix
Hi, FSers
We have lots of data run based on a previous version (see 5.0). Is
there any way to refine them using the FS5.1 pipeline but not to
re-run all steps of recon-all?
Many thanks!
--
Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn)
Hi Bruce,
Yes, I mean the one on the inflated surface.
I found this view easier to judge how well the label and the nii.gz match. Is
that a problem?
Thanks, Esther
> Date: Thu, 2 Jun 2011 08:36:27 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: estherkil...@hotmail.com
> CC: freesurfer@nmr.mgh.
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