Dear FS experts,
I'm trying to use T2 weighted image to refine the pail surface. I have this
error message :
ERROR: you must have the FSLDIR environment variable defined and pointing to
the FSL installation
In release notes, I saw that in "known issues" : fslregister (and so
bbregister with --in
here you go
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslregister
On 10/9/13 5:22 AM, Sophie Maingault wrote:
Dear FS experts,
I'm trying to use T2 weighted image to refine the pail surface. I have
this error message :
ERROR: you must have the FSLDIR environment variable d
Just wondering if anyone has attempted to process T1-mpr data for a 1yr-old
subject or if this is possible with FS.
Our data is of reasonable spatial resolution (1mm isotropic), however the flip
in gm/wm intensities is still occurring at this age.
I presume these data would also be problematic d
Hi Doug, did you already have a chance to look into this? Thanks, Caspar
2013/10/4 Caspar M. Schwiedrzik
> Done. Thank you very much for looking into this.
> Caspar
>
>
> 2013/10/4 Douglas N Greve
>
>> Can you tar up you glmfit dir and drop it to me on our file drop?
>>
>>
>> On 10/04/2013 05:
Hi Freesurfers,
I am interested in creating new atlas for Freesurfer reconstruction, and I
am having some trouble figuring out where to start and where to edit my
labels though I have been researching it for some time. I have emailed Mark
Plantz, who has been asking you similar questions with UNC'
Oh, yes, sorry. The reason that mri_glmfit_pcc is failing is because
this is a one-sample group mean (design matrix a column of all 1s). What
are you trying to compute the correlation between? Or do you just want
to convert the p-values to a correlation coefficient?
On 10/09/2013 01:26 PM, Ca
Hi Doug,
this is coming from a seed-based resting state analysis. I would like to
show effect size instead of p-values.
I thought you calculate them from the slopes or the t-values?
Caspar
2013/10/9 Douglas N Greve
>
> Oh, yes, sorry. The reason that mri_glmfit_pcc is failing is because this
>
If it is just an effect size you can compute gamma.mgh/rstd.mgh
doug
On 10/09/2013 01:39 PM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> this is coming from a seed-based resting state analysis. I would like
> to show effect size instead of p-values.
> I thought you calculate them from the slopes or
Hi Doug,
I would ideally like something that is as close as possible to the pcc map
that comes out of selxavg3 (the single subject analysis). How is that
computed?
Thanks, Caspar
On Wednesday, October 9, 2013, Douglas N Greve wrote:
> If it is just an effect size you can compute gamma.mgh/rstd.mg
so you want the mean ppc over subjects? That would be gamma.mgh
On 10/09/2013 03:10 PM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> I would ideally like something that is as close as possible to the pcc
> map that comes out of selxavg3 (the single subject analysis). How is
> that computed?
> Than
Hi,
Using FS 5.3, I ran a group analysis with mri_glmfit-sim to identify clusters
where my two groups differed (along with many other analyses, e.g. age slope
for each group). For each cluster, I would like to see what the mean group
difference is, in mm. So, I used this command:
mri_segstats
That is not possible, but there is an easy work-around which is to use
mri_segstats --i gamma.mgh --sum group_effectsize_clusters.txt --seg
mc-z.th1.3.pos.sig.ocn.mgh --excludeid 0
On 10/09/2013 03:24 PM, Kayle Sawyer wrote:
> Hi,
>
> Using FS 5.3, I ran a group analysis with mri_glmfit-
Dear Freesurfer friends,
I am wondering if there is a confidence value or correction index for the
volumetric data in aseg.stats. Thanks for your help!
Daniel Moadel
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Hi Daniel
no, I don't think so. What would a correction index be?
cheers
Bruce
On Wed, 9 Oct 2013,
Daniel Moadel wrote:
> Dear Freesurfer friends,
>
> I am wondering if there is a confidence value or correction index for the
> volumetric data in aseg.stats. Thanks for your help!
>
> Daniel Mo
Hi Bruce,
Thanks for your prompt reply. I guess I'm asking if there is any measure of
how confident I can be in the specific volumes. Correction index is a vague
term, you're right, but is there anything in the output that speaks to the
uncertainty of the volumes based on the quality of the scans?
Hi Daniel
not really. You can look at our segmentation papers in which we give
error bars on the volumes. In general it's pretty stereotyped that
amygdala and pallidum for example are difficult (small and low contrast)
cheers
Bruce
On
Wed, 9 Oct 2013, Daniel Moadel wrote:
> Hi Bruce,
> Thanks
Hi all,
I've written a function that can write mgh files from R (
http://www.r-project.org/). Hopefully some of you will find it useful. It's
more or less a translation of save_mgh.m.
If you're looking for a function that can read mgh files into R, load.mgh.R
is included in a package I wrote whic
Thanks Allison,
So to be clear, I just need to rename talairach.auto.xfm as talairach.xfm and
then rerun recon-all from the normalization step? However, I'm not sure how
to run recon starting from the normalization stage. Would you be able to
help with that?
Also, I've been doing manual edits to
Also, just to add to this, if I rerun recon in 5.1 starting from the
normalization stage when I initially ran all subjects in 5.0, will this be
a problem?
On Wed, Oct 9, 2013 at 8:05 PM, krista kelly wrote:
> Thanks Allison,
>
> So to be clear, I just need to rename talairach.auto.xfm as talai
Sorry, just one last thing. If the pial matter and white matter borders
came out fine initially, is it necessary to rerun the whole recon-all
automatic pipeline? I'm just asking because I have about 40 people that i
will need to rerun because of this problem.
Thanks again!
Krista
On Wed, Oct 9,
It would be really helpful if your Wiki had a page that collected all of the
available commands (e.g. contents of /bin) and listed them with brief
descriptions of their functions. Something like part 4 of the page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommands
(Might reduce the n
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