need more info, like command lines for mri_glmfit, mri_glmfit-sim, and
freeview
On 8/31/15 9:27 PM, Erik Lindberg wrote:
Hi,
I am running mri_glmfit followed by mri_glmfit-sim
running the left hemisphere everything works perfect all the way to
the visualization in freeview - then I just chif
Try running
mri_aparc2aseg --s subject --volmask
On 8/31/15 10:51 PM, fmri wrote:
after several attempts with multiple subjects
command -autorecon2-noaseg -subjid mysubject
followed by command recon-all -aparc2aseg
aseg.mgz edits, are Not reflected onto the aparc+aseg.mgz
On Aug 25, 2015
Hello,
I'd like to study measurements of Brodmann Areas 9 and 46 but they don't seem
to be included in the FS package.
Do you know if there are any regions that FS generates that can be used instead?
Thank you very much!
AS
This email
Hi all experts,
I have the error message when trying to use mri_compute_layer_fractions.
mri_compute_layer_fractions $SUBJECTS_DIR/fMRI/register.lta
$SUBJECTS_DIR/white_lh.mgz test
reading registration file
/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/fMRI/register
Hi Andre
sorry, we haven't gotten to 9 and 46 yet
Bruce
On Tue, 1 Sep 2015, Son, Andre
wrote:
Hello,
I’d like to study measurements of Brodmann Areas 9 and 46 but they don’t
seem to be included in the FS package.
Do you know if there are any regions that FS generates that can be used
i
you need to use mris_expand to generate the family of intermediate
surfaces
cheers
Bruce
On Tue, 1 Sep 2015, Yun Wang wrote:
Hi all experts,
I have the error message when trying to use mri_compute_layer_fractions.
mri_compute_layer_fractions $SUBJECTS_DIR/fMRI/register.lta
$SUBJECTS_DIR/wh
I do have 5 intermediate surfaces, should I combine them together?
> On Sep 1, 2015, at 10:43, Bruce Fischl wrote:
>
> you need to use mris_expand to generate the family of intermediate surfaces
>
>
> cheers
> Bruce
> On Tue, 1 Sep 2015, Yun Wang wrote:
>
>> Hi all experts,
>> I have the erro
Thank you!
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Tuesday, September 01, 2015 11:42 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Brodmann areas
Hi Andre
sorry, we haven'
I use the mris_expand like this:
mris_expand -thickness lh.white 0.2lh.white_outer0.2GM
mris_expand -thickness lh.white 0.4 lh.white_outer_0.4GM
mris_expand -thickness lh.white 0.6lh.white_outer0.6GM
mris_expand -thickness lh.white 0.8 lh.white_outer_0.8GM
anything wrong?
> On S
no, you just need to name them in the way that
mri_compute_layer_fractions is expecting (e.g. lh.gwdist000 for white,
etc...)
On Tue, 1 Sep 2015, Yun Wang wrote:
> I do have 5 intermediate surfaces, should I combine them together?
>
>> On Sep 1, 2015, at 10:43, Bruce Fischl wrote:
>>
>> you nee
Thanks! But it looks this script keeps looking for the lh.gwdist00N forever,
here is the error message:
mri_compute_layer_fractions: could not load lh surface 5 from
/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/output/surf/lh.gwdist005
I do not have lh.gwdist005. How
you can use -n to change the name of the surfaces, and -nlayers
to specify the number of layers it computes (# of surfaces = 1+number
of layers I think)
On Tue, 1 Sep 2015, Yun Wang wrote:
Thanks! But it looks this script keeps looking for the lh.gwdist00N forever,
here is the error message:
Dear Experts,
I have 3 groups: A, PC, HC
I did a VBM analysis in SPM and found group differences in grey matter volume
in 2 clusters:
1) Bilateral pre-/SMA, left middle/superior frontal gryi
2) left inferior/middle temporal/fusiform/inferior/middle occipital
gyri/superior/inferior posterior ce
Hello Ali,
As you have observed, when there is an alignment failure using the
talairach method, freesurfer reverts to the mni tool "mritotal". The mni
tools will error out with mritotal because mritotal references
"shellwords.pl" which no longer ships with new version of perl (starting
around
Thank You Much Buddy
That did it :) , Manual edits to aseg.mgz reflected onto aparc+aseg.mgz.
Just to clarify;
Is this the correct order?
1. manual edit aseg.mgz
2. -autorecon2-noaseg -subjid mysubject*
3. recon-all -aparc2aseg
4. mri_aparc2aseg --s subject --volmask
On Sep 1, 2015, at 2:4
Thanks Douglas for your help! If I understand correctly, I will simply use
the aforementioned mri_label2vol script in my previous post but simply add
the option --regheader brainmask.mgz at the end?
On Mon, Aug 31, 2015 at 11:36 AM, Douglas Greve
wrote:
>
> I'm not sure what is going wrong, but
Dear Noah,
It is hard to say just by looking at these images. It seems that you may need
to edit the wm.mgz to push out the white surface, which will push out the pial
surface to include more gray matter. This could be done by directly editing
the wm volume, and/or adding control points. Yo
After I try the code:
mri_compute_layer_fractions -nlayers 4
$SUBJECTS_DIR/fMRI/register.lta
$SUBJECTS_DIR/fMRI/HIP001_rest_preproc_norm.nii test.mgz
open test.mgz using freeview like this! Not binarize according different
layers! Also the frontal part of the brain is missing!
> On Sep 1
Dear Z K,
I have put them in transfer/incoming folder. The file name is example.tar.gz
Thanks in advance,
Ali
On Tue, Sep 1, 2015 at 1:33 PM, Z K wrote:
> Hello Ali,
>
> As you have observed, when there is an alignment failure using the
> talairach method, freesurfer reverts to the mni tool "m
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