command line batch DPABI_VIEW

Submitted by zhongxu on Wed, 04/20/2016 - 20:57

Dear All,

 I'd like to overlay each participant's beta estimates with his/her own anatomical image to check each individual's data. Therefore, it would be great if we could use DPABI_VIEW in command line and speicify both the underlay and overlay images. Then using a loop, we can quickly go through individual participants' data.

After looking into DPABI_VIEW.m, I have a sense that we may have to modify the code for this purporse. But I wonder whether there is an easy trick to do so, or someone has already done this and could share the code.

Thank you very much.

Best wishes,

Zhong

Forums:

YAN Chao-Gan

Thu, 04/21/2016 - 00:20

Hi Zhong,

Please try w_Call_DPABI_VIEW.m

function H = w_Call_DPABI_VIEW(BrainVolume,NMin,PMin,ClusterSize,ConnectivityCriterion,UnderlayFileName,ColorMap,NMax,PMax,H,Transparency,Position,BrainHeader)
% function H = w_Call_DPABI_VIEW(BrainVolume,NMin,PMin,ClusterSize,ConnectivityCriterion,UnderlayFileName,ColorMap,NMax,PMax,BrainHeader)
% Function to call y_spm_orthviews.
% Input:
%     BrainVolume  - 1) The 3D Brain Volume (could be thresholded), parameter 'BrainHeader' needed.
%                 or 2) the File Name of a Brain Image, e.g. '/home/T.img'
%     NMin         - The negative minimum (minimum in absolute value). Could be the negative threshold
%                  - default: calculate from BrainVolume
%     PMin         - The positive minimum. Could be the positive threshold
%                  - default: calculate from BrainVolume
%     ClusterSize  - Set a cluster (voxel number) must be no less than the specified Cluster Size.
%                  - default: 0
%     ConnectivityCriterion - Set Connectivity Criterion, could be: 1) 6 - six neighboring voxels (surface connected)? 2) 18 - eighteen neighboring voxels (edge connected, SPM use this criterion); 3) 26 - twenty-six neighboring voxels (corner connected).
%                  - default: 18
%     UnderlayFileName - The File Name of underlay
%                    default: ch2.nii in DPABI
%     ColorMap     - The color map. Should be m by 3 color array.
%                  - default: AFNI_ColorMap 12 segments
%     NMax         - The negative maximum (maximum in absolute value)
%                  - default: calculate from BrainVolume
%     PMax         - The maximum
%                  - default: calculate from BrainVolume
%     H            - The handle of the figure. Will create a new figure if this parameter is not given.
%     Transparency - The transparency of over lay. Default: 0.2
%     Position     - The position of the center cross. Default: [0 0 0]
%     BrainHeader  - If BrainVolume is given as a 3D Brain Volume, then BrainHeader should be designated.
% Output:
%     The Brain view.
%     H            - The figure handle of the Brain View.
%___________________________________________________________________________
% Written by Wang Xin-di 131204. Modified based on y_Call_spm_orthview.m
% sandywang.rest@gmail.com


Best,

Chao-Gan



On Thu, Apr 21, 2016 at 4:57 AM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
  • Log in or register to post comments