Hi Doug,
What does the new version of mris_preproc do with area?
Don
Date: Mon, 27 Feb 2012 20:54:43 -0500
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] In Qdec, what does the 'area' mean within 'Measure'
menu in 'Design' tab
Hi,
TRACULA gives pathstats.txt which includes *weighted* averages, mentioned
on the wiki as: "weighted average over the entire support of the path
distribution".
question: weighted for what (is it the probability)?
thanks,
-joost
___
Freesurfer mailin
When mapping the area (or volume) to a target surface it assures that
the sum of the area over all vertices of the target is equal to that of
the source (conservation). The basic idea is that the area of a patch in
the target space should be the area of the patch when mapped to the
source spa
Yep, http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics.
On Tue, Feb 28, 2012 at 4:56 PM, j janssen wrote:
> Hi,
>
> TRACULA gives pathstats.txt which includes *weighted* averages, mentioned
> on the wiki as: "weighted average over the entire support of the path
> distribution"
It will do it's best, how well depends on the size of the resection. FS
it assuming that the input is an intact (though perhaps diseased) brain.
Away from the resection, it will probably do ok. Near the resection, it
will probably fail, but you can probably fix it manually.
doug
octavian lie
Mahinda Yogarajah wrote:
> Hi Doug,
>
> Thanks for the response. I have had a read about demeaning on the
> forum. I had a couple of questions:
>
> 1) If I want to include age as well as ICV as nuisance variables in a
> DODS analysis comparing thickness between patients and controls,
> should
When you add --wm, you are telling mri_binarize is give you all of white
matter (this include CC and cerebellar WM and hypointensities). When you
pass just 2 and 41, you get only cerebral WM.
doug
Palzes, Vanessa wrote:
> Could someone please explain to me the difference between mri_binarize
> a
There is something wrong with these dicoms. First, there is no Siemens
"ASCII header", so something has been done to it or it was the result of
something non-standard on the scanner. Second, the reason it cannot
figure out what the direction cosine is for the slices is that all files
have the s
Hi Tyler and others using the inter-hemispheric analysis. I have made
some modifications to this method since I last released it in Aug. I
found a slight bug in the process which I have fixed. I've also created
cached tables for multiple comparisons correction. The instructions for
installing a
Hey all,
I am running into a bit of a problem converting back from a volume into a
surface and was hoping someone would have some insight.
I have an .nii volume for a given subject, and I want to convert it into a
surface mgh file, so i can view it on tksurfer. Since its the same exact
subject, I
What is test.nii? How was it derived?
Omer Tal wrote:
> Hey all,
>
> I am running into a bit of a problem converting back from a volume into a
> surface and was hoping someone would have some insight.
>
> I have an .nii volume for a given subject, and I want to convert it into a
> surface mgh file
Hey Doug,
Test.nii is a volume nii (1x1x1mm) with values of interest per voxel,
created using the header from brain_T1.nii which was simply created by
using mri_convert from the subject's original brain.mgz. The *.nii file
loads fine and matches the subject as expected. It is when trying to go
bac
Hi Doug,
Thanks, I should have noticed this myself. These data were anonymized but I
wasn't aware that anything else was done to them. I will see if this
problem can be fixed and get back to you if I have further questions.
Thanks again.
Hemant
On Tue, Feb 28, 2012 at 1:18 PM, Douglas N Greve
wrot
Hi Doug,
Sorry to bother again and I hope I'm not becoming too annoying with my
questions. I will be very grateful if you can advise what to do for the
following:
1) I am still struggling to find a way to localize my clusters in other words
to get the nearest cortical label(annotation
I should point out that for now I am using a well known nii,
aparc+aseg.nii which I got from using mri_convert on aparc+aseg.mgz that
was made by the freesurfer reconstruction, so it really should just come
up with the same original map.
Also it tried --surf orig instead of --surf white and it see
Hi Omer,
Try removing "--srcreg identity"
doug
Omer Tal wrote:
> Hey Doug,
>
> Test.nii is a volume nii (1x1x1mm) with values of interest per voxel,
> created using the header from brain_T1.nii which was simply created by
> using mri_convert from the subject's original brain.mgz. The *.nii file
>
Hi Antonella, sorry for the delay. I have actually been working on your
first question, but I don't have a good answer for you. One way to get
this would be to load aparc+aseg.mgz when viewing fsaverage, ie,
tkmedit fsaverage orig.mgz -aparc+aseg
Then put the MNI coordinate into the GUI and see
Hey Doug,
Tried, no change unfortunately.
Here is the output, just in the case:
mri_vol2surf --src aparc+aseg.nii --surf orig --ref orig.mgz --regheader
23 --hemi lh --o test.mgh
srcvol = aparc+aseg.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = orig
hemi = lh
reshape = 0
in
Hello.
I am using FreeSurfer to generate subcortical volumes and cortical thickness
for my subjects.
Does FreeSurfer normalizes the subcortical volumes to the whole brain volume
for each subjects.
Let me know.
For among subjects comparison I am assuming that the sub cortical volumes
generat
can you post a picture?
Omer Tal wrote:
> Hey Doug,
>
> Tried, no change unfortunately.
>
>
> Here is the output, just in the case:
> mri_vol2surf --src aparc+aseg.nii --surf orig --ref orig.mgz --regheader
> 23 --hemi lh --o test.mgh
> srcvol = aparc+aseg.nii
> srcreg unspecified
> srcregold
No, it does not. All volumes are volumes in native anatomical space.
doug
Rashmi Singh wrote:
> Hello.
> I am using FreeSurfer to generate subcortical volumes and cortical
> thickness for my subjects.
> Does FreeSurfer normalizes the subcortical volumes to the whole brain
> volume for each sub
In the aseg.stats file there is a value for the whole brain volume.
doug
Rashmi Singh wrote:
> I would like know how can I get the sub-cortical volumes normalized it to
> the whole brain.
> Thanks,
> Rashmi.
>
> On 2/28/12 3:14 PM, "Douglas N Greve" wrote:
>
>
>> No, it does not. All volumes
the way you have it set up, it is sampling on the gray/white boundary
("white" surface). You can sample midway into the ribbon with --projfrac 0.5
doug
Omer Tal wrote:
> Hey Doug,
>
> Attached is a picture showing the resulting surface file. Note that the
> red regions correspond to the number 2
Hi,
I am trying to run a between group analysis in QDEC whilst controlling for
intrancranial volume. The design has one dichotomous variable (group2,
group2), one continuous (performance on behavioral task), and one nuisance
variable (intracranial volume). each time I run it qec crashes with the
f
Can you send the fsgd file that is created? Also, please send more text
output. It's hard to tell from a single line.
doug
Laura Tully wrote:
> Hi,
>
> I am trying to run a between group analysis in QDEC whilst controlling
> for intrancranial volume. The design has one dichotomous variable
> (
So, currently I am using white and using projfrac-max 0 1 .01, and it is
giving me a very clean image with maybe only .1% of the vertices
incorrect.
Seems to be the best so far.
In general, sometimes we have to use 3-D grids instead of FS grids to get
deeper sources, and then we make 3-D nii volum
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