Issue with Nuisance Covariates Regression

Submitted by phil1022 on


On Wed, Apr 1, 2015 at 11:20 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 Xiaosong He (phil1022)

Dear Chao-Gan,

I am a new user of DPARSF (newest edition embedded in DPABI). Before
doing anything I followed the regular setting suggested by a friend
studying in Beijing Normal University, therefore I believe my settings
should be fine.

The program worked perfectly until the 'Nuisance Covariates Regression'
step. During this step, the 'Polynomial trend' was set as 1 as default;
'Friston 24' was chosen as default, and I left everything in the 'Nuisance
regressors (WM, CSF, Global)' as default. I assume the Friston 24
corresponded to head motion, and by default the WM signal and CSF signal
was chosen and the Global (GM) was not. I think for the masks of WM and
CSF, the program took some pre-determined masks although I have run the New
Segment + DARTEL.

On the left is the functional image after slice timing and realign. It
looks normal. On the right, is the one after Nuisance Covariates
Regression. It looks definitely not normal.

[image: Inline image 4][image: Inline image 3]

There were not other steps (on functional image) between realign and
regression. The normalization and smoothing are done after the regression
by the default setting. There must be something wrong except that I don't
know what is going on. I really appreciate your help with this issue!

In addition, during the process, I did not notice any particular
warning or error message.

Thank you very much in advance!

With kind regards.

Sincerely,
Xiao-Song He

I also got another issue with automask which will be addressed in
another topic.


Online version of this post: http://www.rfmri.org/content/issue-nuisance-covariates-regression


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Dear Chao-Gan, I am a new user of DPARSF (newest edition embedded in DPABI). Before doing anything I followed the regular setting suggested by a friend studying in Beijing Normal University, therefore I believe my settings should be fine. The program worked perfectly until the 'Nuisance Covariates Regression' step. During this step, the 'Polynomial trend' was set as 1 as default; 'Friston 24' was chosen as default, and I left everything in the 'Nuisance regressors (WM, CSF, Global)' as default. I assume the Friston 24 corresponded to head motion, and by default the WM signal and CSF signal was chosen and the Global (GM) was not. I think for the masks of WM and CSF, the program took some pre-determined masks although I have run the New Segment + DARTEL. On the left is the functional image after slice timing and realign. It looks normal. On the right, is the one after Nuisance Covariates Regression. It looks definitely not normal. [image: Inline image 4][image: Inline image 3] There were not other steps (on functional image) between realign and regression. The normalization and smoothing are done after the regression by the default setting. There must be something wrong except that I don't know what is going on. I really appreciate your help with this issue! In addition, during the process, I did not notice any particular warning or error message. Thank you very much in advance! With kind regards. Sincerely, Xiao-Song He I also got another issue with automask which will be addressed in another topic.