something wrong with mask | The R-fMRI Network

Submitted by fish on Wed, 05/20/2015 - 14:29

Dear Dr.Yan,

I am sorry to bother you again. Last time after I used your advice for TR, and starts from FunImgCore, it ran again, however it went wrong again. The report error is as follows, I think when move to nuisance covariates regression, especially for white matter and CSF, the original mask in DPARSFA is different from my data, so how can I solve the problem? Should I resmple the images in Masks to my dimension of data using Rest?

Any suggestion will be appreciated!

Best

fish

Re: [RFMRI] something wrong

You set your starting directory as T1ImgCoreg? Should set to functional images.

Best,

Chao-Gan

On Wed, May 20, 2015 at 10:29 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 SHANG JING (fish)
Dear Dr.Yan,

I am sorry to bother you again. Last time after I used your advice for TR, and starts from FunImgCore, it ran again, however it went wrong again. The report error is as follows, I think when move to nuisance covariates regression, especially for white matter and CSF, the original mask in DPARSFA is different from my data, so how can I solve the problem? Should I resmple the images in Masks to my dimension of data using Rest?

Any suggestion will be appreciated!

Best

fish

Online version of this post: http://rfmri.org/content/something-wrong-mask

Many a little makes a mickle -- your kind contributions shall make our efforts not perish from the earth. Please help The R-fMRI Network at http://rfmri.org/#overlay=HelpUs
To manage subscriptions, please visit: http://rnet.co/mailman/listinfo/rfmri.org_rnet.co
Mail comment ID: http://rfmri.org/mailcomment/redirect/%3C31.2032.0.1432132181.e205436cab70f10b74d92c719b4e38e7%40www.rfmri.org%3E

doesn't work

Dear Dr. Yan,

I don't know why it doesn't work again, because of 4D data, or dimension of my data is not the 64*64*41?Matlab have showed that normalization has finished, but why it jumps out orientation or voxel size is not the same? What's more, the report of Matlab showed that DPARSFA only analysis the rawdata in FunImgR of only the first person intead of rrawdata.I am eager to know the reasons. Any ideas will be appreciated!

Re: [RFMRI] something wrong

Please show your parameter settings.

Best,

Chao-Gan

On Thu, May 21, 2015 at 11:13 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 SHANG JING (fish)

Dear Dr. Yan,

I don't know why it doesn't work again, because of 4D data, or dimension of my data is not the 64*64*41?Matlab have showed that normalization has finished, but why it jumps out orientation or voxel size is not the same? What's more, the report of Matlab showed that DPARSFA only analysis the rawdata in FunImgR of only the first person intead of rrawdata.I am eager to know the reasons. Any ideas will be appreciated!

Online version of this post: http://rfmri.org/comment/3709#comment-3709

Many a little makes a mickle -- your kind contributions shall make our efforts not perish from the earth. Please help The R-fMRI Network at http://rfmri.org/#overlay=HelpUs
To manage subscriptions, please visit: http://rnet.co/mailman/listinfo/rfmri.org_rnet.co
Mail comment ID: http://rfmri.org/mailcomment/redirect/%3C31.2032.3709.1432221235.9acf180e9418dc3c70ed8cce097b0d43%40www.rfmri.org%3E

parameter settings

Dear Dr.Yan,

The parameter settings is as follows, we uesd 4D, nii format.

Hi,

The settings seem OK.

As you have this error: The orientations etc must be identical for this procedure. It seems there might be some problems with your data.

However, you can have a try on the latest DPARSF to see what's going on.

Best,

Chao-Gan

new problems

Dear Dr. Yan,

You are right, the first time it didn't work out because I didn't use spm to transform the nii. format, as a result of that, dparsfa cannot recognize the data. After I changed the transformation software, it did work and had some result. But I have some new problems, sorry for my so many problems.

First, there were some strange pictures in PictureForChkNormalization file , which were showed in picture1.

Second, I don't know if the regression out of six head motion, white matter and CSF was right, because the images in realignment were Ok(picture2), but I am not sure if the nomalization(picture3) and smothing(picture4) images were OK as well.

Then, the alff image(picture5) seemed similar with the imges I used spm for preprocessing and rest for processing, but I am still not sure it is right.

Furthermore I tried the latest one（v3.1), however when it moved to automask it reported error again(see picture6), I don't know why.

Last but not least, I've noticed that some recent papers about alff don't include regression out of white matter and CSF, so is the step necessary?

Sorry for so many troublesome problems. I am looking forwad to your replies.

Best

Fish