glad to hear it worked out
Bruce
On Thu, 27 Jun 2019, Loïc Daumail wrote:
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Hi Tim,
Thanks a lot for the effort!
Indeed, I self-created an mgh file from a matrix of 10242x1x1 elements.
After a few adjustments, it perfectly works in order to view the
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Hi Tim,
Thanks a lot for the effort!
Indeed, I self-created an mgh file from a matrix of 10242x1x1 elements.
After a few adjustments, it perfectly works in order to view the data on
Freeview.
I overlayed the individuals' data on lh.pial of fsaverage5 (
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Just a short note regarding these errors:
> > Le lun. 24 juin 2019 à 16:50, Loïc Daumail a
> > écrit :
> >
> >> However, using mri_convert, I still get the same message with tclsh.
> >> "
> >> mri_convert lh.thickness template.mgh
> >> /usr/share/modu
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I found it hard to read the quoted mails and to follow along, but if I'm not
mistaken you are trying to overlay a self-created mgh file with dimension
10242x1x1 onto the pial surface of sub-002 at sub-002/surf/lh.pial.
How many vertices does sub-002/
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Hi Freesurfer,
Getting back the former request,
I am still trying to load an overlay of my data onto a surface.. but it
still doesn't work well.
Here is the info of my overlay:
" mri_info lh_emb_comp_sub-002.mgz
Volume information for lh_emb_comp_sub-00
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I also tried saving the last file in 10242 x 1 x 1.. but nothing is coming
neither.
Thanks,
Sincerely,
Loïc
Le lun. 24 juin 2019 à 16:50, Loïc Daumail a
écrit :
> Hi Doug,
>
> Thanks for your help!
>
> However, using mri_convert, I still get the s
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Hi Doug,
Thanks for your help!
However, using mri_convert, I still get the same message with tclsh.
"
mri_convert lh.thickness template.mgh
/usr/share/modules/init/bash: line 36: /usr/bin/tclsh: No such file or
directory
/usr/share/modules/init/bash:
It is probably using a tcsh shell to do the compression.
Try using MRIwrite instead. You will have to create an mri structure. The
easiest way to do that is to
mri_convert lh.thickness template.mgh
then read the template in to matlab
template = MRIread('template.mgh');
template.vol = yourdata
MRIw
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Hi Bruce and Doug,
To respond to your questions:
I projected the BOLD data on the surface using mri_vol2surf function. Then
obtained a .mgz file of size 10242 x 1 x 1 x 200.
Then I performed diffusion embedding (unsupervised dimensionality reduction
t
I don't think it matters but I would use eye instead of nan for M. But the
critical issue is where you get your data and what dimensions it has
cheers
Bruce
On Fri, 21 Jun 2019, Loïc Daumail wrote:
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Me again,
Also, here is how I save the matrix on
why do you have 18715 elements? How did you create it? You can run mri_info
on the .mgz volume to see if it has the correct dimensions.
BTW: you might repost your original question early next week if you haven't
resolve things. Doug is back and probably has an easy way to do what you
want
ch
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Me again,
Also, here is how I save the matrix on matlab:
M = nan(4,4);
save_mgh('freeview_overlay',
['/home/loic/Documents/emb_output/mgh_format/lh_emb_' char(subjectsList(1))
'_' char(statesList(1)) '.mgz'], M);
Thanks,
Sincerely,
Loïc
Le ven. 21
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Hi Bruce,
Thanks for your tip. Unfortunately, I am still running through an error...
I have a matrix of 18715 elements regarding both hemispheres.
The size of fsaverage5 is 20484 I believe, so I filled the remaining
elements with zeros, and also tried
Hi Loïc
the .mgz file should having dimensions nvertices x 1 x 1 for freeview to
know it is a surface overlay I believe
cheers
Bruce
On Thu, 20 Jun 2019, Loïc Daumail wrote:
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Hi Bruce,
I am reaching out to you, as I am trying to load the surf
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Hi Bruce,
I am reaching out to you, as I am trying to load the surface scalar values
of diffusion embedding for overlay on a pial surface in Freeview.
I used save_mgh to save a scalar matrix containing surface embedding values
in an .mgz format.
Howev
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Hi Tim,
Your link works perfectly, it's awesome!
Thanks a lot,
Best,
Loïc
Le lun. 27 mai 2019 à 11:43, Loïc Daumail a écrit :
> Hi Tim,
>
> 'mean_rest' is a diffusion embedding map, which contains scores for every
> vertex on fsaverage5 surface re
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Hi Tim,
'mean_rest' is a diffusion embedding map, which contains scores for every
vertex on fsaverage5 surface resolution.
'surf.b' is the pial surface of both hemispheres of fsaverage5... I also
tried forjust lh hemisphere, but it gives me the same re
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Hi Loïc,
that does not look correct, the data is definitely off. I'm not sure where the
variables `mean_rest` and `surf.b` come from in your code, and I suspect that
something is wrong with them.
In the meantime, I got interested in this myself and
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Afaik SurfStat is not maintained anymore and I think it's been this way for
quite a while now. Maybe someone else knows better?
The website is at http://www.math.mcgill.ca/keith/surfstat/ and it says
'Updated 26 September 2008'. I'm not sure whether
Hi Loic
sorry, can you ask whoever maintains surfstat? Or maybe someone else on the
list knows? I don't. You can label surfaces manually with the dev version
of freeview if you want.
cheers
Bruce
On Thu, 23 May 2019, Loïc
Daumail wrote:
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Hi
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Hi Loïc,
you can load the atlases using `read_annotation` in Matlab, then of course use
them for whatever purpose you like (including in surfstat). This code should
get you started:
subjects_dir = '/data/mystudy';
subject_id = 'subject1';
hemi = 'l
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Hi Bruce,
I am coming back to this request as I was wondering:
would it be possible to load freesurfer surface atlases in surfstat in
order to label my surfaces?
Is their format compatible? I saw surfstat only accepts a limited array of
formats...
Tha
sure. All the fsaverages are in the same space (they are subsets of
fsaverage)
On Mon, 20 May 2019, Loïc Daumail wrote:
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Hi Bruce,
Thanks for your response. Is it also fine for fsaverage5 surface or I need to
switch my data to
fsaverage?
Thanks,
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Hi Bruce,
Thanks for your response. Is it also fine for fsaverage5 surface or I need
to switch my data to fsaverage?
Thanks,
Sincerely,
Loïc
Le lun. 20 mai 2019 à 15:52, Bruce Fischl a
écrit :
> Hi Loic
>
> if you are on the fsaverage surface you
Hi Loic
if you are on the fsaverage surface you can save the -log10(p) values
using save_mgh.m, then load them in freeview and threshold them or
whatever
cheers
Bruce
On Mon, 20 May 2019, Loïc Daumail wrote:
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Also, one more thing:
My data is on
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Also, one more thing:
My data is on fsaverage5 resolution.
Thanks in advance,
Sincerely,
Loïc
Le lun. 20 mai 2019 à 09:49, Loïc Daumail a écrit :
> Dear Freesurfer community,
>
> I obtained score matrices of surfaces after performing diffusion em
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Dear Freesurfer community,
I obtained score matrices of surfaces after performing diffusion embedding
map on fMRI data.
I am now using the SurfStat toolbox(Matlab) in order to obtain p-value maps
to compare between two groups.
After obtaining the p-v
Hi Andre
they look right, but check the FreeSurferColorLUT.txt file - that is the
definitive location
cheers
Bruce
On Fri, 24 Apr 2015, André Schmidt wrote:
Dear freesurfer experts,
I intend to create ROIs from the aparc+seg.mgz file and would like to ask
whether the following assignments ar
Dear freesurfer experts,
I intend to create ROIs from the aparc+seg.mgz file and would like to ask
whether the following assignments are correct (sorry for the long list):
10: left_thalamus
11: left_caudate
12: left_putamen
13: left_pallidum
17: left_hippocampus
18: left_amygdala
26: left_accumb
Hi Koushik, it just uses the label of the maximum.
doug
On 04/19/2012 05:30 PM, Govindarajan, Koushik Athreya wrote:
> Hi,
>
>I have a question regarding how the clusters are labeled after the results
> of a Monte-Carlo Simulation. Similar regions from 2 different patient
> populations seem
Hi,
I have a question regarding how the clusters are labeled after the results of
a Monte-Carlo Simulation. Similar regions from 2 different patient populations
seem to be labeled differently. On one of my results, the cluster has been
labeled as in the precentral region and a similar region
Hi Christine,
what subject are you overlaying the results on? If it's fsaverage (our
average subject) then it should have ?h.aparc.annot files in the label
subdirectory that you can load file->label->import annotation.
cheers,
Bruce
On Fri, 25 Jan
2008 [EMAIL PROTECTED] wrote:
Hi I am us
Hi I am using Freesurfer version 3.0.5 via Linux and I am trying to label
my results on tksurfer. I have already loaded the group descriptor file
and the overlay. I can visualize my results but when I click on these
specific reasons, it does not tell me where these areas lie. How do I go
about labe
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