something wrong with mask

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

Forums:

YAN Chao-Gan

Wed, 05/20/2015 - 15:20

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

Chao-Gan


fish

Thu, 05/21/2015 - 15:13

 


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!



YAN Chao-Gan

Thu, 05/21/2015 - 15:40

Please show your parameter settings.
Best,

Chao-Gan


fish

Fri, 05/22/2015 - 15:03

Dear Dr.Yan,


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


 

YAN Chao-Gan

Fri, 05/22/2015 - 23:41

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

fish

Wed, 05/27/2015 - 12:37

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


YAN Chao-Gan

Thu, 05/28/2015 - 19:30

Hi,

1. Seems DPARSF can not find the normalized images. Does this happen with DPARSF V3.1?

2. Please refer to http://rfmri.org/faq #4.

3. DPARSF needs Image Processing toolbox.

4. I will suggest you to include nuisance regression.

Best,

Chao-Gan

fish

Wed, 06/24/2015 - 14:01

Dear Dr. Yan,


Thanks for your answer. The strange picture, I mean strange normalized images are dependent on version 2.3, and I have rest1.8, xjview as well.


Best


Jing