Hi!
I want to view only certain segmented regions on one of our subject's
brains. It seems like it should be simple but I am struggling to find the
steps. I want to display only hippocampus, amygdala, medial orbitofrontal,
lateral orbitofrontal, sulcus/gyri anterior cingulate, subcallosal gyrus,
a
Hi Doug,
Thanks again for your reply. One last question: The aseg.mgz file includes
the cortex as well. If I want to extract the cortex from the aseg.mgz
file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and
subtract them, and then use the result in the mri_segstats command, or is
If you want the volume of cortex, you should definitely not use
aseg.mgz. aparc+aseg is better, but the best is to use the surface-based
measure found in aseg.stats
doug
On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> Thanks again for your reply. One last question: Th
It looks right. Make sure that you have specified "self" when you run
mkanalysis-sess to make sure the analysis is on the subject's own
anatomy where you have MT defined
doug
On 04/20/2014 08:35 AM, Reza Rajimehr wrote:
> Hi,
>
> For my dataset, it appears to be easier to do an ROI analysis in
you have an extra blank line in your contrast matrix
On 04/19/2014 11:41 PM, Harry Hallock [hhal5...@uni.sydney.edu.au] wrote:
>
> Dear Experts,
>
>
> I am running a rmanova using FSGD file and mri_glmfit.
>
>
> I have done the mris_preproc step, and am currently trying to do the
> mri_glmfit step
Hi Doug,
I'm sorry, what I meant to ask in the previous question is whether there
is a way to come up with a segmentation volume for the mri_segstats
command that is exactly like aseg.mgz but that does not include the
cortex. The reason I'm asking is because by using the aseg.mgz volume in
the --s
Hi John, please remember to post to the list. thanks! Yes, that should
work. Use read read_surf.m to get the proper coordinates.
doug
On 04/20/2014 08:08 PM, John Pyles wrote:
> Hi Doug,
>
> Thanks so much for the reply.
>
> I had looked through the wiki on coordinates but because I'm not a big
Hi Paola, please remember to post to the list and not to us personally.
thanks! I would still use the xhemi tools for this. If you have N
subjects, you will get 2*N surfaces aligned to the fsaverage_sym atlas.
You can then just pick the ones you want to analyze further
doug
On 04/22/2014 08:34
Use mri_vol2surf with $FREESURFER_HOME/average/mni152.register.dat
On 04/21/2014 10:20 PM, charujing123 wrote:
> Hi FS experts and users,
> I created a mask volume, whose space is in MNI152 space. And I want to
> convert this volume into surface-based in fsaverage.
> How can I realize this?
> Than
Use mri_binarize with the --match option to create a mask of the
regions you want. Then use mri_mask applied to aparc+aseg to create a
new volume with only the regions you want
doug
On 04/22/2014 09:06 AM, Courtney Haswell wrote:
> Hi!
>
> I want to view only certain segmented regions on one o
Hi Andrew,
Yes you’re down for a spot. Yours wasn’t one of the two :).
Allison
On Apr 18, 2014, at 3:23 PM, Andrew Gerber wrote:
> Dear Allison,
> You have me down for a slot, right? I don't want to miss it! :-)
> Best, Andrew
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.ha
Sorry, I didn't note I was replying to you only..
Anyway, thank you for the reply! So I will apply the command I mentioned to
you in my previous e-mail to create flipped RH and LH surfaces for the
subjects with the right hemisphere affected.
Should I register to the fsaverage_sym atlas also the sub
You can just do it in matlab, somethhing like
a = MRIread('aparc+aseg.mgz');
ind = find(a.vol > 999);
a.vol(ind) = 0;
MRIwrite(a,'nocortex.mgz')
On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> I'm sorry, what I meant to ask in the previous question is whether there
>
You can register just the hemisphere you want to fsaverage_sym. But if
you have a subject whose right hemi you want, you would run the surfreg
with --rh, but later you would specify that you want the lh of subject/xhemi
doug
On 04/22/2014 12:04 PM, Paola Valsasina wrote:
> Sorry, I didn't note
Good! :-) See you soon.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Allison Stevens
Sent: Tuesday, April 22, 2014 12:02 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] 2 available spots in Boston Fre
That is great,
Thanks a lot, Doug!
>
> You can just do it in matlab, somethhing like
>
> a = MRIread('aparc+aseg.mgz');
> ind = find(a.vol > 999);
> a.vol(ind) = 0;
> MRIwrite(a,'nocortex.mgz')
>
>
>
> On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> I'm sorry, what I m
HI Courtney, please post to the list. Thanks! Get the codes from
$FREESURFER_HOME/FreeSurferColorLUT.txt. Also, you can use multiple
numbers to match all the ROIs you want at once (if that is what you
want). Eg, --match 2 26 17
doug
On 04/22/2014 03:16 PM, Courtney Haswell wrote:
> Thanks f
Hi Danielle
what does it look like withouth the FLAIR postprocessing? And what FLAIR
sequence are you using? We have only ever used the T2-space FLAIR and have
been told that it works great with that, but not as well with other FLAIR
variants.
cheers
Bruce
On Tue, 22 Apr 2014, Danielle Mil
Hi,
Trying to build a CUDA enabled PC for the lab to do processing for a variety of
neuroimaging programs including Freesurfer and FSL. Want to know input from
others about the 'recommended' PC and what the 'standard' is based on the
current PC prices and technology.
Sample build is from NCIX
Hi Sabin, I have not been able to definitively track down the source of
the negative area, but I have verified a couple of things. There is only
negative area in a couple of vertices and they are in the medial wall.
Our current development version does not result in negative area when I
run it
Hi,
I am still having some concerns using mri_convert on Skyra volumes that I'm
hoping can please be addressed.
On this occasion I have used mri_convert to convert a single dicom file to
nifti from a volume collected on a siemens Skyra scanner using Freesurfer5.3 on
CentOS5.7.
When viewing t
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