AlphaSim

Submitted by banyu on

Dear developers and users,

I'd like to use AlphaSim to correct VBM p values. The voxel size is 1.5*1.5*1.5, and smoothing used a Gaussiankernel of 8mm full width at half maximum. I wondered what the rmm and cluster size shoud be set.

Best regards,

Feng

YAN Chao-Gan

Sat, 10/26/2013 - 13:00

Permalink

Hi Feng,
If the voxel size is 1.5*1.5*1.5, then
rmm = 2 [i.e., <1.5*sqrt(2)] means face connection.
rmm = 2.5 [i.e., <1.5*sqrt(3)] means edge connection. This is SPM's default.
rmm = 3 (i.e., >1.5*sqrt(3)] means corner connection. This is FSL's default.

For smooth kernel, the effective smooth kernel may not be the same as your applied smooth kernel (8 8 8). You'd better use AFNI's 3dFWHMx or FSL's smoothest to estimate the effective smooth kernel on the residual file. -- This strategy will be automated in the next release of our software.

Best,

Chao-Gan


On Sat, Oct 26, 2013 at 4:03 AM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

By 周峰 (banyu)

Dear developers and users,

I'd like to use AlphaSim to correct VBM p values. The voxel size is 1.5*1.5*1.5, and smoothing used a Gaussiankernel of 8mm full width at half maximum. I wondered what the rmm and cluster size shoud be set.

Best regards,

Feng


Online version of this post: http://rfmri.org/content/alphasim


<

Dear Dr. Yan,
Just to follow up on this question, I wonder whether we could use rest_Smoothest.m in REST_V1.8_130303 to directly estimate the smooth kernel (e.g., using t map as input)?

Thanks,
Zhongxu


On Sat, Oct 26, 2013 at 9:00 AM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

Commented by YAN Chao-Gan (YAN Chao-Gan)
Hi Feng,
If the voxel size is 1.5*1.5*1.5, then
rmm = 2 [i.e., <1.5*sqrt(2)] means face connection.
rmm = 2.5 [i.e., <1.5*sqrt(3)] means edge connection. This is SPM's default.
rmm = 3 (i.e., >1.5*sqrt(3)] means corner connection. This is FSL's default.

For smooth kernel, the effective smooth kernel may not be the same as your applied smooth kernel (8 8 8). You'd better use AFNI's 3dFWHMx or FSL's smoothest to estimate the effective smooth kernel on the residual file. -- This strategy will be automated in the next release of our software.

Best,

Chao-Gan


On Sat, Oct 26, 2013 at 4:03 AM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

By 周峰 (banyu)

Dear developers and users,

I'd like to use AlphaSim to correct VBM p values. The voxel size is 1.5*1.5*1.5, and smoothing used a Gaussiankernel of 8mm full width at half maximum. I wondered what the rmm and cluster size shoud be set.

Best regards,

Feng


Online version of this post: http://rfmri.org/content/alphasim


<
Online version of this post: http://www.rfmri.org/comment/2922#comment-2922


YAN Chao-Gan

Sun, 10/27/2013 - 02:50

Permalink

Hi Feng,
I wrote that program to be equivalent to FSL's smoothest, and the entire (GRF correction) procedure (input T maps) to be equivalent to FSL's easythresh.

However, this procedure (easythresh as well) usually overestimates the smooth kernel than estimating the smooth kernel on the residuals. Thus, please keep in mind this procedure is pretty strict.

Best,

Chao-Gan



On Sat, Oct 26, 2013 at 9:50 PM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

Commented by zhongxu (zhongxu)
Dear Dr. Yan,
Just to follow up on this question, I wonder whether we could use rest_Smoothest.m in REST_V1.8_130303 to directly estimate the smooth kernel (e.g., using t map as input)?

Thanks,
Zhongxu


On Sat, Oct 26, 2013 at 9:00 AM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

Commented by YAN Chao-Gan (YAN Chao-Gan)
Hi Feng,
If the voxel size is 1.5*1.5*1.5, then
rmm = 2 [i.e., <1.5*sqrt(2)] means face connection.
rmm = 2.5 [i.e., <1.5*sqrt(3)] means edge connection. This is SPM's default.
rmm = 3 (i.e., >1.5*sqrt(3)] means corner connection. This is FSL's default.

For smooth kernel, the effective smooth kernel may not be the same as your applied smooth kernel (8 8 8). You'd better use AFNI's 3dFWHMx or FSL's smoothest to estimate the effective smooth kernel on the residual file. -- This strategy will be automated in the next release of our software.

Best,

Chao-Gan


On Sat, Oct 26, 2013 at 4:03 AM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

By 周峰 (banyu)

Dear developers and users,

I'd like to use AlphaSim to correct VBM p values. The voxel size is 1.5*1.5*1.5, and smoothing used a Gaussiankernel of 8mm full width at half maximum. I wondered what the rmm and cluster size shoud be set.

Best regards,

Feng


Online version of this post: http://rfmri.org/content/alphasim


<
Online version of this post: http://www.rfmri.org/comment/2922#comment-2922



Online version of this post: http://www.rfmri.org/comment/2923#comment-2923


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