Hi,
What exactly is the definition of
- Brain Mask Volume
- Brain Segmentation Volume
as listed in the aseg.stats file?
Moreover, and correct me if I'm wrong,
the Intracranial volume is the scaled
intracranial volume of the MNI template.
Is the latter intracranial volume just a
number or is it
Hi Ed, have you seen this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolume
doug
Ed Gronenschild wrote:
> Hi,
>
> What exactly is the definition of
>
> - Brain Mask Volume
> - Brain Segmentation Volume
>
> as listed in the aseg.stats file?
>
> Moreover, and correct me if I'm wrong,
> th
Hello All,
Does anyone know if it's possible to automatically create labels for the
clusters found
with the new feature in Qdec 1.4, *Find Clusters and Goto Max*?
I want to map the clusters onto all my subjects and then use *
mris_anatomical_stats* to get average thickness and st. deviation for
e
Hello Freesurfer Users,
I am feeling very bad when I am using mri_convert. There are two problems:
1. When I converted a file in mgz format to nii.gz format, and did some
volume calculation (mask and addition) by using fslmaths from FSL, then
converted back to mgz. If the image type is uchar, it
Well, I tried to avoid FSL, and used only Freesurfer tool to do the same
thing. I found there was the same issue when an image with 32-bit float
point data type converts to 32-bit integer. No problem for the convertion
from 32-bit float point to 8-bit unsigned integer.
Wayne
On 05/10/10 10:44 AM
Hi Wayne,
can you check to see whether it's an FSL problem or a FreeSurfer one? If
you don't use FSL do you still have the problem?
cheers
Bruce
On Tue, 5 Oct 2010, Wayne
Su wrote:
Well, I tried to avoid FSL, and used only Freesurfer tool to do the same
thing. I found there was the same is
Hi Bruce,
I used just mri_binarize, mri_mask and mri_concat and all in mgz format. I
got a 32-bit floating point image with intensity range from 0~2031. Then I
used the mri_convert to convert it to 32-bit integer also both in mgz
format. Here is the message on the screen.
mri_convert aparc+aseg.mg
FreeSurfer offers 'mris_calc' which is similar to 'fslmaths'. I'm a bit
confused with your fslmaths line, but you should be able to do a similar
operation using 'mris_calc':
(assuming you have 'right_vect_mask_inv.nii.gz' and right_vect_mask.nii.gz')
$>mris_calc -o aparc+aseg_masked.mgz aparc+a
I've never heard of DTI_TK Quick Look. Does it actually read mgz files?
What value does it give for aparc+aseg.mgz? Try loading the file into
matlab with the FreeSurfer MRIread.m function and see what it gives for
the max. Or just run
mris_calc aparc+aseg2.mgz max
doug
Wayne Su wrote:
> Hi Br
Here is the output from mris_calc:
mris_calc aparc+aseg2.mgz max
Max@(index) [ 2145516800.00 (6400402) ]
Wayne
On 05/10/10 2:05 PM, "Douglas N Greve" wrote:
> I've never heard of DTI_TK Quick Look. Does it actually read mgz files?
> What value does it give for apar
And what do you get when you run mris_calc on aparc+aseg.mgz?
Wayne Su wrote:
> Here is the output from mris_calc:
> mris_calc aparc+aseg2.mgz max
> Max@(index) [ 2145516800.00 (6400402) ]
> Wayne
>
>
> On 05/10/10 2:05 PM, "Douglas N Greve" wrote:
>
>
>> I've nev
btw, I mean the original aparc+aseg.mgz, not the one created after you
made changes using those FSL commands.
doug
Douglas N Greve wrote:
> And what do you get when you run mris_calc on aparc+aseg.mgz?
>
> Wayne Su wrote:
>
>> Here is the output from mris_calc:
>> mris_calc aparc+aseg2.mgz ma
Here is:
mris_calc aparc+aseg.mgz max
Max@(index)[ 2035.00 (7772808) ]
On 05/10/10 2:20 PM, "Douglas N Greve" wrote:
> btw, I mean the original aparc+aseg.mgz, not the one created after you
made
> changes using those FSL commands.
doug
Douglas N Gre
And when you run
mri_convert aparc+aseg.mgz aparc+aseg2.mgz -odt int
And then
mris_calc aparc+aseg2.mgz max
you get that crazy number?
I've tried this here with version 5 and cannot replicate. What version
are you using?
doug
Wayne Su wrote:
> Here is:
> mris_calc aparc+aseg.mgz max
>
Maybe my email is not clear. Try this to see what you get:
mri_convert aparc+aseg.mgz aparc+aseg1.mgz -odt float
mri_convert aparc+aseg1.mgz aparc+aseg2.mgz -odt int
mris_calc aparc+aseg2.mgz max
I tried 'mris_calc'. The output is in floating format. I have no way to
avoid converting back to int
you want noscale to be 1 (-ns 1) otherwise it will rescale the image
"intensities" in teh aparc+aseg and you'll got nonsense
On Tue, 5 Oct 2010,
Douglas N Greve wrote:
I've never heard of DTI_TK Quick Look. Does it actually read mgz files? What
value does it give for aparc+aseg.mgz? Try loadin
Ah, I see, that I can replicate. As Bruce says, use -ns 1 to keep it
from doing a funny rescaling when converting from float to int.
doug
Wayne Su wrote:
> Maybe my email is not clear. Try this to see what you get:
>
> mri_convert aparc+aseg.mgz aparc+aseg1.mgz -odt float
> mri_convert aparc+ase
Thank you, Bruce. That solved my problem.
Wayne
On 05/10/10 3:21 PM, "Bruce Fischl" wrote:
> you want noscale to be 1 (-ns 1) otherwise it will rescale the image
> "intensities" in teh aparc+aseg and you'll got nonsense
> On Tue, 5 Oct 2010,
> Douglas N Greve wrote:
>
>> I've never heard of DT
Dear All:
Just to follow up with my previous enquiry, is there any suggestion/advice over
this pial edit issue?
In addition, I would like to ask one more question if possible:
I understand that the pial surface is created by expanding the WM surface.
Hence, is there any parameter (maybe to mris
19 matches
Mail list logo
