I was finally able to run linear mixed models with my data - thank you
very much Martin for your precious help!
No I would need some help/advice for visualization and description of
my results
The command fs_write_Y(sided_pval,mri,'spval.mgh') is not working on
my matlab. This is the message erro
thanks, Doug! sorry, I had misinterpreted the --surf argument when I had
originally checked --help. Got the proper label created AND got the
overlay.mgz to work as well. All my labels are there in the overlay.mgz
created using mri_vol2surf once I change the thresholds of the overlay - I
can then is
You can just average the runs together, then concatenate the averaged
runs, ie,
mri_concat sess01/bold1/analysis1/contrast/ces.nii.gz \
sess01/bold2/analysis2/contrast/ces.nii.gz \
sess01/bold3/analysis3/contrast/ces.nii.gz
--mean --o sess01/contrast.ces.nii.gz
then concatenate/staack the ses
Does the hippocampal subfields create a segmentation in the conformed
space? Ie, the 256^3, 1mm^3 volume, eg orig.mgz, aseg.mgz, etc. If so,
then you can specify that volume with the -seg option to fcseed-config
On 04/20/2016 06:12 AM, Julio Alberto González Torre wrote:
> Hi Freesurfers.
>
> As
nope, you need to give it just the name of the subject and the
hemisphere. Run it with --help for more info
On 04/20/2016 11:35 AM, Trisanna Sprung-Much wrote:
> Hi Doug
>
> I had run mri_cor2label using the --surf option. Is what I did below
> correct?
>
>
> trisanna@kaplan:~$ mri_cor2label --i
Hi Patrizia,
Usually you would allow the intercept to be a random effect (1st
column). Basically random effect means, you allow each subject to have
their own intercept, which usually makes sense. That could be sufficient
for your model, you can also test if having two random effects is better
Hi Doug
I had run mri_cor2label using the --surf option. Is what I did below
correct?
trisanna@kaplan:~$ mri_cor2label --i
/data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l
/data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial
$Id: mri_cor2label.c,v 1.12 2011/03/
You can use mkheadsurf to create a surface of the outside of the head
On 04/20/2016 10:59 AM, dgw wrote:
> Hi Chiara,
>
> look at the -surf option and the -useSRAS option
>
>
> We often use multi-echo FLASH/ PD images for generating these
> surfaces, because standard MPRAGE type sequences lack co
I think the problem is that this is being interpreted as a volume label.
The first column is the surface vertex number which you can see is all
-1s indicating no vertex. To create a surface label, run mri_cor2label
with the --surf subject hemi option. Ruopeng, can you add something to
freeview
can you send me the label file?
On 04/20/2016 10:49 AM, DeCross, Stephanie N. wrote:
> I /think/ it’s really a label file? I took my binarized nii.gz and ran
>
> mri_cor2label -- c NAME.nii.gz -- id 1 -- l ./newname.label
>
> and I was under the impression that this turned it into a label file
Hi Chiara,
look at the -surf option and the -useSRAS option
We often use multi-echo FLASH/ PD images for generating these
surfaces, because standard MPRAGE type sequences lack contrast for
bone, see figure 17 here:
http://www.nmr.mgh.harvard.edu/~fischl/reprints/Neuroimage_Segonne_watershed.pdf
I think it’s really a label file? I took my binarized nii.gz and ran
mri_cor2label -- c NAME.nii.gz -- id 1 -- l ./newname.label
and I was under the impression that this turned it into a label file.
Yes, I get exactly the same errors when I try to open the label in both
programs from the c
Many thanks Dr. Fischl for your support.
My goal is to create a mesh completed of skull and scalp to be able to perform
the Monte Carlo simulation on it.
To do it, I need to start from a well segmented brain, so I decided to go for
FreeSurfer.
I have read something about the mri_watershed, but
Hi Doug and Bruce
*This what I get when I run the head command on the label:*
trisanna@kaplan:~$ head
/data-01/trisanna/freesurfer/icbm-102/label/labeltest.label
#!ascii label , from subject lh.pial vox2ras=TkReg
1651
-1 -29437.500 -0.500 0.500 0.00
-1 -30660.500 -0.500 0.500 0.000
Thanks, Bruce! Unfortunately, we don't have additional sequences for this
data set but it's good to know that we have the best segmentation possible.
:)
Best,
Mihaela
On Tue, Apr 19, 2016 at 12:34 PM, Bruce Fischl
wrote:
> Hi Mihaela
>
> adolescent girls probably have thicker cortex than older
Hi Chiara
you can look at the mri_watershed help to see how to generate other tissue
classes or boundary models, but typically you need some other image
contrast(s) like T2/PD. What are you trying to accomplish?
As for your second question, you should be able to use mri_surf2surf with
the ta
Dear FS-Group
I am attempting to use the lme matlab tools
for my longitudinal analysis.
My dataset consists of 2 time-points and 2
groups (patients and controls). I will not use covariates since the groups are
well matched for age, gender and education.
I am trying to a
Dear all,
I've been reading the manuscript on version 6 freesurfer hippocampal
subfield segmentation "A computational atlas of the hippocampal
formation using ex vivo, ultra-high resolution MRI: application to
adaptive segmentation of in vivo MRI"
Can you please tell me if the type of sequence
Dear FreeSurfer users,
I am a PhD student from Birkbeck University and I am trying to segment some
structural images of infants data.
After the classical segmentation done with the ‘-recon all’ function, I am
stuck with two issues:
1. How can I add the CSF, the skull and the scalp in my model?
Hi Freesurfers.
As I'm currently performing the Funcional Conectivity workflow with FSFAST,
the 4th step requires me to choose the areas to use as seeds. I would like
to use the hippocampal subfields as seeds, but I can't select them because
the aparc+aseg.mgz doesn't contains those labels. The on
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