Some Useful Programs

Submitted by YAN Chao-Gan on Tue, 04/21/2009 - 23:00

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Hi, all!
     Here are some useful programs written by me. I think these codes may be helpful for you.
     1. Program for converting T/F/R statistical image to Z statistical image. y_TFRtoZ.m
     2. Program for re-orienting the un-normalized image (diagonalize the complex affine matrix): y_reorient.m
     3. Program for changing the b vector file created by MRIcroN's dcm2nii suitable for DTI Studio: y_ChangeBVector.m
     4. Program for converting the NIfTI file in talairach space into .HEAD/.BRIK format which can be displayed with AFNI in Talairach View: y_ConvertTlrcNiftiToTlrcAFNI.m
     5. Program for Shrinking or Enlarging masks: y_MaskShrink.m and y_MaskEnlarge.m
     6. Program for performing Gaussian Random Field theory multiple comparison correction like easythresh in FSL: y_GRF_Threshold.m
     7. Program for performing robust regression analysis for brain images: y_RobustFit_Image.m
     8. Program for calculating the Intraclass correlation coefficient (ICC) for brain images: y_ICC_Image.m
     9. Program for reslicing images. y_Reslice.m. Now you can find it in REST->Utilities.
     10. Program for regressing out the covaribles. rest_Y_RegressOutCovariables.m. Now you can find it in REST->Utilities.
     11. Program for extracting ROI time courses. rest_Y_ExtractROITC.m. Now you can find it in REST->Utilities.
     12. Program for converting r value to p value, you will know if your Pierson's correlation coefficients are significant: y_Corr2p.m. For an alternative way, you can use REST Slice Viewer to convert T/F/R threshold value to P value or vise visa.

     Please report here if you encounter any problem with these programs.
  
     
           Best wishes!
                                           YAN Chao-Gan

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Submitted by lvlerick on Wed, 04/14/2010 - 21:06

Hey,
for running the y_reorient, my data are in nifti. Is this ok, because it doesn't work.
Error: ??? Input argument "vx" is undefined
Kind regards,
Leslie

Submitted by YAN Chao-Gan on Thu, 04/15/2010 - 19:22

Dear Leslie,
        vx is the new voxel size.
        vx=1 means new voxel size is 1x1x1, 2 means 2x2x2.
        I am sorry just cube voxel can be used currently.
        Best wishes!
                               Chao-Gan

Submitted by YAN Chao-Gan on Thu, 10/07/2010 - 19:28

New program has been added here: Program for converting the NIfTI file in talairach space into .HEAD/.BRIK format which can be displayed with AFNI in Talairach View: y_ConvertTlrcNiftiToTlrcAFNI.m
This program is for the combination usage of AFNI and REST/DPARSF. E.g. for brain tumor patients which can not perform normalization with SPM:
1. Use DPARSF to complete the pre-normalization steps: DICOM->NIfTI, Slice Timing, Realign, sturctural T1 .hdr/img coregister to the space of realigned mean functional image.
2. Use AFNI's command '3dWarp -deoblique' and '3drefit -markers' to convert the coregistered structural T1 .hdr/img into structural .HEAD/BRIK pair.
3. Use AFNI's command '3dTcat' to convert the realigned EPI .hdr/img into functional .HEAD/BRIK pair.
4. Use AFNI to manually normalize the structural .HEAD/BRIK into talairach coordinate system. Then use 'Define Datamode'->'Warp Ulay on Demand' to save and resample the structural .HEAD/BRIK and functional .HEAD/BRIK into '+tlrc.HEAD/BRIK' files in talairach space.
5. Use AFNI's command '3dAFNItoNIFTI' to convert functional '+tlrc.HEAD/BRIK' into 4d .nii files. Then use REST->Utilities->NIfTI .nii to NIfTI pairs to convert the 4d .nii into 3d .hdr/img.
6. Use DPARSF to perform the following analysis such as 'smooth->detrend->filter->ALFF,mALFF' based on the 3d .hdr/img files.
7. Use REST or SPM to perform the Statistical analysis.
8. Use the current program 'y_ConvertTlrcNiftiToTlrcAFNI' to convert the statistical result NIfTI file (which is in talairach space) into .HEAD/.BRIK format while keeping a Talairach View.
9. Use AFNI to view the results and generate the cluster report.
  Input:
    TlrcNiftiFileName - The file name of NIfTI file in talairach space.
  Output:
    TlrcNiftiFileName +tlrc.HEAD/BRIK - The .HEAD/.BRIK file which can be
    displayed with AFNI in Talairach View.

Thanks for Dr. DU Zhuo-Ying's post about this issue.

Submitted by Cleofe on Mon, 11/22/2010 - 13:39

Hi,

Im trying to use the program nº6 and I obtain this error:

ADataDir

ADataDir =

F:\IMATGES\RESTINGS\BORJA\NORMALITZADES_MNI_BORJA_ALFF\DRET_REST1_N_detrend_filtered\FunImgNormalizedDetrendedFiltered\subject001

Regressing Out Covariables:
??? Input argument "ADataDir" is undefined.

Error in ==> rest_Y_RegressOutCovariables at 18
[AllVolume,VoxelSize,theImgFileList, Header] =rest_to4d(ADataDir);

Any suggestion will be appreciate!

Thanks!

Submitted by YAN Chao-Gan on Mon, 11/22/2010 - 14:28

It seems you did not call this functional correctly.
This function has been integrated into REST. You can find a GUI in REST->Utilities->Regress Out Covariables. You can use the GUI much easier.
Best wishes!

Submitted by Cleofe on Wed, 11/24/2010 - 06:12

Hi,

Anyway, after using the GUI I obtain this error:

     Load mask "C:\Users\Cleofé\Desktop\spm5\toolbox\REST2007V1.3_091215\REST2007V1.3_091215\mask\BrainMask_05_53x63x46.img".Warning: Values other than 0 or 1 converted to logical 1.
> In rest_loadmask at 52
  In rest_RegressOutCovariates at 27
  In rest_RegressOutCovariates_gui>Run_Callback at 238
  In gui_mainfcn at 75
  In rest_RegressOutCovariates_gui at 26

     Build mask.    Wait............................................................

     Done>>

However, it seems work.

Thanks!

Submitted by YAN Chao-Gan on Wed, 11/24/2010 - 11:18

Hi!
This warning doesn't matter.

Submitted by YAN Chao-Gan on Sat, 01/21/2012 - 01:25

Hi all!
Some new Programs Added (multiple comparison correction, robust regression, Intraclass correlation).

6. Program for performing Gaussian Random Field theory multiple comparison correction like easythresh in FSL: y_GRF_Threshold.m
7. Program for performing robust regression analysis for brain images: y_RobustFit_Image.m
8. Program for calculating the Intraclass correlation coefficient (ICC) for brain images: y_ICC_Image.m

Best,

Chao-Gan