Single Slice resting state analysis

Submitted by Shah on Wed, 05/11/2011 - 21:01

Hi
I am trying to do the functional connectivity analysis on a single slice (2D) of rat brain acquired with EPI, for 5 minutes, around 3000 time points.
When I loaded files ( img/hdr) in your software and tried to do detrend and low pass filtering, it is giving error, I am not sure why? May be I will make snapshot in the next reply. But it works when I do multislice 2D data. I am wondering why? Please let me know.
Thanks in advance for your help
Thanks
Shah

AttachmentSize
Image icon funcon1.jpg232.91 KB
Binary Data epi_02_cor_11_001.hdr348 bytes
Binary Data epi_02_cor_11_001.img16 KB
Image icon mask_error.jpg132.47 KB
Binary Data fun_mask.img4 KB
Binary Data fun_mask.hdr348 bytes

Submitted by YAN Chao-Gan on Thu, 05/12/2011 - 21:09

Hi!
It seems that there is something wrong with your singe slice 2D image, thus REST can not read it.
Could you upload file for one timepoint here?

Submitted by Shah on Thu, 05/12/2011 - 22:42

Hi Yan
Thanks for reply. I just uploaded a single slice file ( 2 files, img/hdr). Please let me know what is wrong.
it works with my multislice data.
Thanks
Shah

Submitted by YAN Chao-Gan on Thu, 05/12/2011 - 23:54

Hi!
REST can not read 2D Analyze file correctly in rest_ReadAnalyzeImage.
Please download the following file and replace your program: http://pub.restfmri.net/index.php?dir=&file=UnzipAndReplace.rar
Best wishes!

Submitted by Shah on Fri, 05/13/2011 - 02:19

Hi Yan
Thanks a lot, I will try to replace it. My linux and window system could not open rar file, can you make it in zip format, if not, I will have to find a program to open rar file,
Thanks in advance
Khan

Submitted by Shah on Sun, 05/15/2011 - 21:42

Thanks for your help. I am half way through in getting my data processed.
Now, It works in detrending the data and but stops during executing bandpass filtering, load mask error.
Even if I select no mask or default mask, it is giving similar error, or I choose user defined mask, it says it is not 3D mask. ( attached are both error_file and user defined mask). Could you please check these at your convenient time.
Thanks a lot
Shah

Submitted by YAN Chao-Gan on Tue, 05/17/2011 - 21:32

Hi!
Please download the following program and replace the previous version in REST: http://pub.restfmri.net/index.php?dir=&file=rest_loadmask.m
Best wishes!

Submitted by Shah on Thu, 05/19/2011 - 02:23

Hi Dr. Yan
Thanks a lot for helping this out. I am half way through it, Now, it detrends and filters,
and when I tried to select spherical roi, I randomly gave 7 2 0 4 (radius in mm) coordinates in roi file, and I could not really view ROI, it is probably looking for image tool box, it is not found in my directory,
Do I really read matlab image processing toolbox for slice viewer?
Can select a different program see the coordinates for my image file? My data is from rat brain, so I can not use other atlases ( human).
and how to give txt file, do you have sample format, I can look at it.
and after selecting some random roi coordinates, by finally clicking done, it processed and put connectivity files in the respective folder. I am wondering how to view those files. Do I have to use sliceviewer or any other program to open it. Please let me know
Thanks a lot for your time
Shah

Submitted by YAN Chao-Gan on Fri, 05/20/2011 - 22:09

Hi!
Sorry for the delay because there is something wrong with our campus network.
You can use MRIcro or MRIcroN to open your ROI file. I do not know if the coordinates are suitable for your files. You can also use MRIcro to draw an ROI definition file based on your functional image mannaully.
Best wishes!

Submitted by Shah on Sun, 06/26/2011 - 05:23

Dear Dr. Yan
I was able to run resting data successfully, without any errors, but how do I view it, rest viewer does not work in my platform, due to no matlab image processing. is there anyway I can view both F and Zfc map in a different program? and how do I see power spectrum? please let me know.
thanks
Shah

Submitted by YAN Chao-Gan on Thu, 07/07/2011 - 00:26

Hi!
You can use MRIcroN or MRIcro (www.cabiatl.com/mricro/mricron/index.html) to view your results.
For power spectrum, please see REST->Utilities->Power Spectrum to check if it works.
Best wishes!