Yes, I'm multiplying the image intensities by a scaling factor. Sorry if
that wasn't clear.
-Brent
On Aug 4, 2015 12:09, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
> Hi Brent
>
> a quick look and it seems that your answer is "yes"? You are multiplying
> the image intensities by some scale factor?
> Bruce
>
>
> On Tue, 4 Aug 2015, Brent Womble wrote:
>
> Yes. Here is the MATLAB script:
>>
>> for i = [1:20]
>>
>> %Load the original image and gray matter mask
>>
>> raw=load_nii([pwd,'/', num2str(i), '/pre.nii'])
>>
>> a=single(squeeze(raw.img));
>>
>>
>> c1_raw=load_nii([pwd,'/', num2str(i), '/c1pre.nii']);
>>
>> c1=squeeze(c1_raw.img);
>>
>> %Mask is gray around edges. Threshold to make it binary
>>
>> c1(c1>0.1)=1;
>>
>> %Convert mask to logical
>>
>> c1=logical(c1);
>>
>>
>> %%Generate a 3D gaussian kernel
>>
>> %Specify the origin, size, and intensity of the kernel
>>
>> k_origin=origins(i,:); %origins is an i by 3 vector to store
>> all coordinates
>>
>> k_size=20;
>>
>> k_intensity=100;
>>
>>
>> k=1-fspecial3('gaussian',k_size).*k_intensity;
>>
>> k(k<0)=0;
>>
>>
>> %Expand the kernel to the size of the original image
>>
>> padsize_pre=k_origin - (k_size/2);
>>
>> padsize_post=size(a) - k_origin - (k_size/2);
>>
>>
>> k=padarray(k,padsize_post,1,'post');
>>
>> k=padarray(k,padsize_pre,1,'pre');
>>
>>
>> %Restrict the kernel to the gray mask
>>
>> b=k.*c1;
>>
>> b(~c1)=1;
>>
>>
>> %%Apply the kernel to the original image
>>
>> c=b.*a;
>>
>>
>> %Write to .nii
>>
>> raw.img=c;
>>
>> save_nii(raw,[pwd,'/', num2str(i), '/dense-synth.nii']);
>>
>> end
>>
>> On Tue, Aug 4, 2015 at 11:52 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu
>> >
>> wrote:
>> Hi Brent
>>
>> are you saying you just multiplied the gray matter intensities
>> by some scale factor (>1)?
>> Bruce
>>
>> On Tue, 4 Aug 2015, Brent Womble wrote:
>>
>> Hi everyone,
>> I've been making synthetic brains to test how
>> Freesurfer handles various
>> structural changes.
>>
>> One of the changes I'm testing is increased density
>> (like in VBM). To
>> simulate increased density, I used a spherical
>> Gaussian multiplication
>> kernel, with a radius of 20 voxels. I centered this
>> kernel at a point in
>> the right superior frontal gyrus and masked the
>> changes to grey matter using
>> the segmentation output from SPM12.
>>
>> Here is an example, a difference image (synth.nii -
>> pre.nii):
>> [IMAGE]
>>
>> Around that area, Freesurfer didn't detect a change
>> (as I expected):
>> Inline image 2
>>
>> Original in red and blue, synthetic in pink and
>> light blue.
>>
>> The problem is that the longitudinal streams in
>> Freesurfer found a bunch of
>> changes in random parts of the brain.
>>
>> We looked at the recons for each subject
>> individually, and saw some noise
>> around the clusters that were significant in the
>> two-stage model. This
>> doesn't make sense, because the actual voxels were
>> exactly the same in that
>> region. For example:
>>
>> [IMAGE]
>>
>> I redid the recon-all with the -nonormalization
>> flag. It didn't fix the
>> problem. For example (same subject as above):
>>
>> [IMAGE]
>>
>> I thought it might have been an issue caused by my
>> increased density method,
>> so I ran it again, this time with the kernel
>> centered in the cerebellum
>> (still masked to grey matter). I still got weird
>> changes in unrelated parts
>> of the cortex. For example (same subject as above):
>>
>> [IMAGE]
>> Note: light blue/red and blue/red are reversed in
>> this one, just because of
>> the order I loaded it in Freeview.
>>
>> In summary, Freesurfer found a bunch of weird
>> changes that were nowhere near
>> the changes I actually made.
>>
>> Where should I go from here?
>>
>> -Brent
>>
>>
>>
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