Hi FS experts and users
I have done the each subjects' surface regestration on fsaverage surface, and
merge all of them into a *.mgh. Group analysis is also completed.
Now I have two questions:
1,I want to extract the VtxMax vertex number thickness for all subjects. The
VtxMax vertex number can
Hi Virendra,
Where does this surface come from? You didn't get this one after running the
default recon-all, right?
Looking at it I noticed a lots of holes and many small unconnected components
on the medial aspect. I ran mris_euler_number and got a total of 68 defects, so
I'm afraid you'll n
Hi Virendra,
What I don't get is why you would run lGI on the white surface, and
specifically on the non topology fixed one? In principle, in mean on the
technical side, you could run lGI on the lh.smoothwm which is the corrected
surface with no hole and a single component (use mris_compute_lg
Hey Marnie, I don't think so. If Jorge is still following the FS list,
he can answer more definitely. Jorge, Marnie is asking whether a
different design matrix can be used at each voxel based upon a map
passed to it. This is used for multimodal integration in a lot of
applications (eg, does thi
Dear Freesurfers,
Is there a way to include a per voxel regressor in an LME model within the
matlab LME toolbox? Just like you can do with mri_glmfit?
Cheers,
Marnie
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asegstats2table will do it. This will give you all the segmentations as
well as global measures. If you don't want all the segmentations, you
can ask it for only only (eg, --segno 17)
doug
On 04/30/2014 05:23 PM, Shantanu Ghosh wrote:
> Dear Freesurfers,
>
> Pardon me for a very basic question
Dear Freesurfers,
Pardon me for a very basic question.
If I wanted to extract the hemisphere-wise GM and WM values for multiple
subjects using a single command, what is the best way to do it?
Thanks in advance.
Shantanu
--
Shantanu Ghosh, Ph.D.
Harvard Medical School & Massachusetts General H
Thanks a ton!
Virendra
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Wednesday, April 30, 2014 3:52 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] reading ?h.smoothwm.nofix
yup, t
yup, that's it
Bruce
On Wed, 30 Apr 2014, Virendra Mishra wrote:
Hi again,
I used mris_convert *.asc my_name and it worked!
Is this correct?
Thank you,
Virendra
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf
Hi again,
I used mris_convert *.asc my_name and it worked!
Is this correct?
Thank you,
Virendra
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Virendra Mishra
Sent: Wednesday, April 30, 2014 3:40 PM
To: Free
Hi Bruce,
Thanks for the code. I am able to read the file now. But I would rather want to
read it as a triangular one rather than a quadrangular one as the output of
this code is an input to another code that expects a triangular case. I would
be very thankful if you could help me convert the q
then you need to specify additional targets to recon-all, like -all or
-autorecon2 -autorecon3
cheers
Bruce
On Wed, 30 Apr 2014, Del Re, Elisabetta wrote:
> Bruce,
> thank you so much.
> No, I wanted to run recon-all.
> Is the input only working for autorecon1 you think?
>
> recon-all -s 01100.t
Bruce,
thank you so much.
No, I wanted to run recon-all.
Is the input only working for autorecon1 you think?
recon-all -s 01100.t1-realign-masked -i /tmp/01100.t1-realign-masked.nii.gz
-autorecon1 && cp
>> /projects/pnl/software/freesurfer5.3b/subjects/01100.t1-realign-masked/mri/T1.mgz
>> /proj
No worries, thank you for the help!
> oops, sorry, that is an option to mri_vol2vol, not vol2surf. Just
> exclude that option
>
> On 04/30/2014 02:48 PM, jaco...@nmr.mgh.harvard.edu wrote:
>> Hello Doug,
>>
>> Thank you for such a quick reply and for your insight.
>>
>> I have adjusted the cmd but
Hi Elisabetta
it looks like you only ran autorecon1, which is just the first few steps
of the processing. Was that your intent? If not, you might try -all
instead (or -autorecon2 -autorecon3 after what you have already run).
cheers
Bruce
On
Wed, 30 Apr 2014, Del Re, Elisabetta wrote:
> Hi Bru
Hi Bruce,
thank you.
No, the stats have only 2 files and aparc and aseg are missing.
Elisabetta C. del Re, Ph.D.
Instructor,
Department of Psychiatry
Harvard Medical School
phone 617 9675569
mail elisabetta_de...@hms.harvard.edu
From: freesurfer-boun...@nm
Hi Elisabetta
that is a warning that you can ignore, not an error. Did the output look
ok?
cheers
Bruce
On Wed, 30 Apr 2014, Elisabetta del Re wrote:
> I ran a few cases through freesurfer5.3 last night and
>> found that they all
>> exited with the same error. This is th
oops, sorry, that is an option to mri_vol2vol, not vol2surf. Just
exclude that option
On 04/30/2014 02:48 PM, jaco...@nmr.mgh.harvard.edu wrote:
> Hello Doug,
>
> Thank you for such a quick reply and for your insight.
>
> I have adjusted the cmd but --fstarg seems to not be recognized as an
> opt
Hello Doug,
Thank you for such a quick reply and for your insight.
I have adjusted the cmd but --fstarg seems to not be recognized as an
option ("ERROR: Option --fstarg unknown").
I also tried to include fsaverage following --fstarg, but I still received
the same error.
I am using stable53 and
The target has to be the freesurfer anatomical of the target subject (fsaverage
in this case). You can get this by specifying --fstarg. The --reg is for the
registration file; I'm surprised that the cmd actually ran. You just need to
specify an output file with extension. Try the cmd below
mri_
Hello Freesurfer Experts,
I was wondering if someone can help me understand which options I need to
include with mri_vol2surf for the following situation?
I am trying to take group stats generated within FEAT that are in
MNI152_2mm space and registrar/project those to fsaverage inflated
surface.
Hi Nick.
I can, but I'm hoping to get 5.1 working as all our data is processed in 5.1.
That being said we could at least get 5.3 working to look at data processed on
other machines.
However, I'm a little concerned that we will be forced to update our OS's at
some point which will break 5.1.
Hi Virendra
try the attached m-file. The problem was that before topology correction
the mess is a quadrangular one, which wasn't supported by read_surf. I've
fixed this, but note that the behavior of read_surf.m is a bit different
than our c code, which will internally split each quadrangle
Hi Anna
try adding -t sulc to the mris_anatomical_stats command line. That tells
it to use a "thickness" file named "sulc". Everything that it reports as
thickness would then be sulc measures
cheers
Bruce
On Wed, 30 Apr 2014, Anna Jonsson
wrote:
> hi i think what i meant to write was how to
hi i think what i meant to write was how to find exact values for sulcal
depth? using mris_anatomical_stats, so the exact command that would do this?
On Wed, Apr 30, 2014 at 1:32 PM, Bruce Fischl wrote:
> Hi Anna
>
> at the moment we take the mean out of the sulc before writing it, and use
> th
Hi Anna
at the moment we take the mean out of the sulc before writing it, and use
that as kind of the definition of the transition from gyral to sulcal. We
can add a switch to mris_inflate to inhibit this behavior if you want I
suppose.
cheers
Bruce
On Wed, 30 Apr 2014, Anna Jonsson wrote:
>
Hi I would like get a mean sulcal folding value per hemisphere and roi
data. I have two questions:
Is possible do sulcal depth analysis using qdec?
And
What is the exact command to pass to mris_anatomical_stats to get a mean
sulcal depth value /per hemisphere? I have tried some few variations wi
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