Yes, it is. You should use the same design matrix X and vary the Zcols
selection .
Just a note: If you find the spatiotemporal mixed effects model fitting
procedure described in the wiki too complicated (the paper explaining it is
still under revision) you have the option to use the simpler v
Thanks Doug, just to follow-up on some of these:
> - why does QDEC only provide the volume of /subcortical/
> > structures under StatsDataImport/aseg.volume, when the automatic
> > GM/WM segmentation is done for the entire brain, not just for
> > subcortical regions?
> >
> No reaso
Hi Jorge,
Thanks for correcting my misunderstanding. I will include all of the subjects
to generate the covariance estimates. Sorry to be so concrete but in comparing
models, for instance, 1 random effect versus 2 random effects, is the same
design matrix, X, used for all covariance estimates
Do you know if that version works outside of Virtualbox?
On 03/29/2013 03:13 PM, Tudor Popescu wrote:
> I'm running freesurfer-Linux-centos4-stable-pub-v5.1.0, on Windows XP
> SP3, through Virtualbox 4.2.10. QDEC version is 1.4
> THanks for your help
>
> On 29 March 2013 17:33, Douglas N Greve
Hi Luke,
if T1A is your first time point and T1B the second, you need to do the
second (create a directory for each). The first is doing something very
different, it is using both inputs for a single reconstruction, by
averaging the inputs.
Best, Martin
On 03/28/2013 12:58 PM, lukas.sch...
Dear Doug,
I am trying to analyze fMRI data where TR = 1.2 secs. For several subjects
the analysis works as expected, but for about half of the subjects when I
try to execute the command selxavg3-sess terminates with the following
error:
"OLS Beta Pass
run 1t= 0.0
ERROR: TR mismatch betwe
If you are using ASL, you do not want to use Slice timing. You must compute
the CBF maps and keep the slice timing intact.
Removing the time delay between slices will lead to the wrong CBF values as
the CBF equations have the time delay in the equation.
Best Regards, Donald McLaren
==
Hi Stephanie, in your mri_vol2surf cmd, try using --projfrac-max -.2 1.2 .1
This will search for the max along the vector normal to the surface 20%
below the white matter and 20% beyond the pial.
doug
On 03/27/2013 04:42 PM, McMains, Stephanie wrote:
> Hi all,
>
> I have been trying to take an S
If yyou just type mri_concat at the command line and nothting happens,
then something is definitely wrong. What system are you running on?
On 03/28/2013 04:17 PM, Tudor Popescu wrote:
> I tried running it by itself, to remind me of the syntax, so that I
> can do a simple concatenation to see if
If you have the T1 for colin27, then just run recon-all on it.
doug
On 03/29/2013 01:48 AM, ZhiLiangLong wrote:
> Hi FS experts:
> I am trying to map AAL template onto FS surface to create
> surface-based AAL template. Several days ago, i asked this question,
> and Garikoitz Lerma gave me s
You have specified both -surface and -native which conflict with each
other. In this case, it will use native space which forces it to use
per-session (no way to avoid this).
doug
On 03/29/2013 01:08 PM, SHAHIN NASR wrote:
> Hi,
> I used to run my mkanalysis-sess without indicating -per-r
There was a problem with bbregister running on the new CentOS 6
machines. I've attached a new version that should work.
doug
On 03/29/2013 11:41 AM, Anastasia Yendiki wrote:
Hi Sal - Would it be possible for you to run the bbregister command
that fails (you can find the command line in tra
Hi,
I used to run my mkanalysis-sess without indicating -per-run or
-per-session, assuming that when I have pre-processed my files with
-per-run flag then selxavg3-sess will do the same. But when I checked the
analysis.info I noticed "PerSession 1" which I think it means system will
use per-s
what are you using to do STC? I think by default FSL will move it to the
middle slice, but there is probably a way to make take into account the
fact that the slices are not uniform over the TR. You should contact the
list of the software you are using to get a definative answer.
doug
On 03/29
Thanks, Doug. This is very helpful!
On Fri, Mar 29, 2013 at 12:48 PM, Douglas N Greve wrote:
> The --xhemi flag causes both the left and right hemispheres of each
> subject to be stacked into the output file. So the output file will have
> number of subjects x2 frames. The order is subject1.lh,
The --xhemi flag causes both the left and right hemispheres of each
subject to be stacked into the output file. So the output file will have
number of subjects x2 frames. The order is subject1.lh, subject1.rh,
subject2.lh, subject2.rh, ...
If you add the --paired-diff, then you will get number
Hi freesurfer experts,
I'm investigating lh-to-rh asymmetry and am following instructions on this
page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi.
My question is, what does the "--xhemi" flag do in the "mris_preproc"
command? It seems to me that it calculates (lh-rh) value at each vertex for
Hi Sal - Would it be possible for you to run the bbregister command that
fails (you can find the command line in trac-all.log) using both the 5.1
and 5.2 version of bbregister and see if one of them works on your system?
a.y
On Fri, 29 Mar 2013, Salil Soman wrote:
Hi Anastasia,
Because I
Hi,
I am running a pASL sequence with a TR = 3 sec and TI2 = 1.8. I am
wondering when I do slice time correction does that move all slices to the
mid of TR that is 1.5 s prior in time or, it moves them to the timing of
the mid slice, which would be the mid of image acquisition aorund 0.6 sec
prior
Hi Sal - Had you ever tried running this in 5.1? Just trying to figure out
if it's 5.2-specific.
Thanks,
a.y
On Thu, 28 Mar 2013, Salil Soman wrote:
Thank you for your response.
I tried re-running Tracula using bbr in a subject I had successfully run using
flt.
trac-all prep and bedp work
BTW, we are using Freesurfer 5.1:
freesurfer-i686-apple-darwin9.8.0-stable5-20110525
On Fri, Mar 29, 2013 at 10:08 AM, Vy Dinh wrote:
> Dear Developers,
>
> I have a significant problem when rerunning the pial edits for the
> longitudinal data. Our dataset consists of subjects & a followup scan
Dear Developers,
I have a significant problem when rerunning the pial edits for the
longitudinal data. Our dataset consists of subjects & a followup scan (for
each sub). To be thorough, we edited brain.finalsurfs.manedit.mgz (as it
was further in the processing stream) for the cross-sectional scan
Hi Nawaf - The first error occured much earlier in the log file. Your
gradient table file could not be found. Did you set the bvecfile variable
in your configuration file?
a.y
On Fri, 29 Mar 2013, Nawaf Yassi wrote:
Hi Anastasia
Thanks for your reply
Here is the file attached (I have repla
Hi Leila
we found a problem with the mac build that we are fixing. We will put it
up again soon, hopefully today.
sorry
Bruce
On Fri, 29 Mar 2013, Leila Reddy wrote:
> Hi,
>
> I'm trying to install the latest Mac OSX 64bit FreeSurfer version but when I
> click on the download link I get an erro
Hi,
I'm trying to install the latest Mac OSX 64bit FreeSurfer version but when I
click on the download link I get an error: 550 Failed to change directory.
I can't find a file with this filename in
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ either. Is this version
not yet available (
Hi Zhiliang,
1- well, I just recon-all-ed their subject again with the newest version.
Recon-all -s Colin -all
2- maybe Doug or some other will answer this question better. I don't know
the exact differences between fs mni305 and fs mnicolin27. What I know is
that going the fsaverage path I couldn'
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