Gray matter volume AAL regions

Submitted by joana on

YAN Chao-Gan

Sun, 07/06/2014 - 04:09

Permalink

Hi Joana,

I think the most convinient way will be this:

1. Use DPARSFA to do VBM and DARTEL  (either usual resting-state processing, or VBM processing, see DPARSFA template parameters).

2. Organize the mwc1* files into one directory e.g., /Work/GM.

3. Then you can use DPARSFA to extract AAL volumes or Dosenbach volumes. Click "blank" template -> Extract ROI time courses -> Working Dir: /Work -> Starting Dir: GM. Or you can sse REST->Utilities->Extract ROI Signals to extract the AAL volumes. 

Best,

Chao-Gan

Thanks Chao-Gan, it worked!

2014-07-06 6:09 GMT+02:00 The R-fMRI Network <rfmri.org@gmail.com>:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi Joana,

I think the most convinient way will be this:

1. Use DPARSFA to do VBM and DARTEL  (either usual resting-state processing, or VBM processing, see DPARSFA template parameters).

2. Organize the mwc1* files into one directory e.g., /Work/GM.

3. Then you can use DPARSFA to extract AAL volumes or Dosenbach volumes. Click "blank" template -> Extract ROI time courses -> Working Dir: /Work -> Starting Dir: GM. Or you can sse REST->Utilities->Extract ROI Signals to extract the AAL volumes. 

Best,

Chao-Gan


Online version of this post: http://www.rfmri.org/comment/3113#comment-3113


<

hello,
i am planning to do VBM analysis of T1 images.  i want GM WM and CSF for each individual AAL volumes.
i have put all files into a single folder T1Raw/ T1img (nifti files)
please tell me if i can use DPARSF to only segment T1 images. i dont have functional dataset for these subjects.
further DPARSF A does not seem to have AAL
DPARSF although has it but it is not recognising the subjects in the folder T1raw (for raw images) or T1img(for nifti images with extn coxxx)
please help in this regard
 
Thanks & Regards

Dr. Mohit Saxena 
(Ph.D Neurology)
Department of Neurology,
Room No. 702, 7th Floor, CN Center,
All India Institute of Medical Sciences,
Ansari Nagar, New Delhi-110029
+919968569874


On Monday, 7 July 2014 11:30 PM, The R-fMRI Network <rfmri.org@gmail.com> wrote:


Hi,

1. Yes, DPARSF to only segment T1 images. Please use the parameter template of VBM processing.

2.  "Then you can use DPARSFA to extract AAL volumes or Dosenbach volumes. Click "blank" template -> Extract ROI time courses -> Working Dir: /Work -> Starting Dir: GM. Or you can sse REST->Utilities->Extract ROI Signals to extract the AAL volumes."

-- AAL is not a checkbox now, but you can select AAL template from the ROI definition.

Best,

Chao-Gan

Dear all, I would like to extract the gray matter volumes from the labels of the AAL and Dosenback atlases included in DPARSF. I read on the webpage that this is only possible by command line. Can anyone advise me how to do this? Many thanks, joana