Thank you very much, Anastasia.
I have checked the related mails in the list and found not me came across this
problem.
As you said, I know how I can run my data.
But I have a question. Why would we make trac-all compatible to other scanner
or acquisitions, since we can get bvecs and bval from t
Hi Doug
This is my command line:
mris_anatomical_stats -a area_left_significant_labels.annot -t lh.area
-nsmooth 15 -f $s/stats/lh.aparc.a2005s.stats $s lh
In the past, you recommended smoothing the data with mri_surf2surf instead
of with mris_anatomical_stats.
For that purpose, I run the follo
Hi Yuko
I think you can use multiple label tags when using mri_label2vol like below:
mri_label2vol --subject $subject_name --hemi $hemi --label $label1 --label
$label2 --label $label3 --temp $template --o $output --fillthresh 0.3
--proj frac 0 1 0.1 --identity
The output volume would have non-ze
Hi Jeff
The surfaces are not based on the aseg, so I wouldn't expect them to match
Cheers
Bruce
On Jun 6, 2012, at 7:18 PM, Jeff Eriksen wrote:
> I am wondering about how the pial and white surfaces are supposed to match up
> with the aseg file. I was expecting that when I created a new surf
I am wondering about how the pial and white surfaces are supposed to match up
with the aseg file. I was expecting that when I created a new surface, usinfg
mri_surf2surf, halfway between the pial and white surfaces (which I call the
cortical ribbon), it would run right down the center of the GM.
you can use mri_cor2label, eg, for cluster #2, something like
mri_cor2label --id 2 --i cluster.mgh --o cluster2.label
doug
On 6/6/12 4:22 PM, Ilia wrote:
> Hello,
>
> How would one create a label (to be used as an input for
> "mris_anatomical_stats") based on a a statistical map generated by qde
what is your command line?
doug
On 6/6/12 5:25 AM, Jürgen Hänggi wrote:
> Dear FS experts
>
> I have done group comparisons wrt thickness and surface area. The
> found clusters were written out as annotations, transformed into each
> individual space, and then the corresponding values were extract
What is your command-line and what is the terminal output? Also, please
post to the list instead of to me directly.
thanks
doug
On 6/6/12 5:24 AM, lordowen wrote:
> Dear Prof. Greve:
>
> Sorry to reply this very old post, but we encountered the same
> problem. We processed our data following the i
Hi Marie, you have to pass it as a command-line option with --fsgd
doug
On 6/6/12 4:19 AM, Marie Schneider wrote:
Dear FreeSurfer experts,
I am trying to start mris_preproc, but unfortunately it doesn't find
my created fsgd file. I saved it in the foulder where you can find all
subjects data.
It depends on how graceful you want to be with resolving the overlap.
One simple way would be the following:
1. Change the binary values in B.mgz to 2 and C.mgz to 3 (A.mgz is
already 1). This can be done with mri_binarize
2. mri_concat A.mgz B.mgz C.mgz --max-index --o D.mgz
D.mgz will have a v
The argument to --sval-area is the surface that you want to get the area
from. If you want the area of the white surface, then just put "white"
there. Or you can use "--sval lh.area" instead of "--sval-area white".
doug
On 6/6/12 9:28 AM, Jürgen Hänggi wrote:
> Dear FS expert
>
> I try to smooth
Hi Corinna,
looks like a mem problem. try running only the mri_robust_template
command (should be in the log file, before this error occurred) on a
machine with nothing else running.
Best, Martin
On Wed, 2012-06-06 at 16:16 -0400, Corinna Bauer wrote:
> Hi all,
> I was creating the longitudina
Hello,
How would one create a label (to be used as an input for
"mris_anatomical_stats") based on a a statistical map generated by qdec
(for example, the result of a Monte Carlo simulation such as
"mc-z.abs.th23.sig.cluster.mgh").
The goal is to obtain average cortical thickness for regions where
Hi all,
I was creating the longitudinal template for a subject when I got this
error while on the third time point. Is this a memory problem or is it
something else?
Thanks,
Corinna
Resolution: 0
Iteration(single-prec): 1 -- diff. to prev. transform: 0.0425184
Iteration(single-prec): 2mri_
I think the linesearch message is a red herring. We've seen it lots of
times when the process runs fine. Are you sure some that there isn't
something else?
On Wed, 6 Jun 2012, Jeff Thompson wrote:
> Hi -
>
> Was there ever a solution found for this? I am currently having the same
> problem.
>
or use mri_mask. Or binarize to 2,4,8 etc.. them and add them, then replace
the unique overlap values with something else
On Wed, 6
Jun 2012, Joshua Lee wrote:
> Well you could mri_binarize the three volumes, then subtract regions
> using fslmaths from the FSL suite. Of course this would crea
Hi -
Was there ever a solution found for this? I am currently having the same
problem.
Thanks,
Jeff Thompson
Can you send us e recon-all.log file?
On Aug 8, 2011, at 4:30 AM, "Irwin, William" wrote:
> Hi-
>
>
>
> I’m at a bit of a loss as to how to address and/or fix these errors.
>
Well you could mri_binarize the three volumes, then subtract regions
using fslmaths from the FSL suite. Of course this would create gaps
between your formerly adjacent regions.
Joshua
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, D
hi doug and fellow FS users,
i am going thru the recon_checker.log file to look into anat SNR, mWM, stdWM
and voxWM.the ones with lowest SNR are seemed to be marked with
arrowmay i know the reason why some of them have lowest SNR and they are
marked with arrow in front of em?..the data
Dear Freesurfer experts,
How can I transform from MNI coordinates to RAS surface coordinates?
Regards,
Yolanda
2012/6/5 Yolanda Vives
> Dear Freesurfer experts,
>
> I have performed a VBM analysis with SPM, using some VOIs. Now I would
> like to compare the volumetric results obtained with SP
Dear FS expert
I try to smooth surface area files with the following command:
mri_surf2surf --hemi lh --s MOREA_KG002 --sval-area area --fwhm 15 --tval
lh.area.15.mgh --cortex
But there is an error:
srcsubject = MOREA_KG002
srcval = (null)
srctype=
trgsubject = MOREA_KG002
trgval =
Dear FS experts
I have done group comparisons wrt thickness and surface area. The
found clusters were written out as annotations, transformed into each
individual space, and then the corresponding values were extracted.
When using mris_anatomical_stats, values are different for thickness maps
dep
Dear FreeSurfer experts,
I am trying to start mris_preproc, but unfortunately it doesn't find my
created fsgd file. I saved it in the foulder where you can find all
subjects data. Shall I save it somewhere else?
Thanks for your help,
best Marie
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