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
Attachment | Size |
---|---|
funcon1.jpg | 232.91 KB |
epi_02_cor_11_001.hdr | 348 bytes |
epi_02_cor_11_001.img | 16 KB |
mask_error.jpg | 132.47 KB |
fun_mask.img | 4 KB |
fun_mask.hdr | 348 bytes |
Submitted by YAN Chao-Gan on Thu, 05/12/2011 - 21:09 Permalink
Re
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 Permalink
Hi Yan Thanks for reply. I
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 Permalink
Re
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 Permalink
Hi Yan Thanks a lot, I will
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 Fri, 05/13/2011 - 23:40 Permalink
I unzipped it and let me try
I unzipped it and let me try it
Thanks
shah
Submitted by Shah on Sun, 05/15/2011 - 21:42 Permalink
loading mask error
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 Permalink
Re
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 Permalink
Hi Dr. Yan Thanks a lot for
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 Permalink
Re
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 Wed, 06/01/2011 - 00:35 Permalink
Thanks Dr.Yan Let me try it,
Thanks Dr.Yan
Let me try it, sorry, I was busy with other stuff for last few weeks,
Thanks
Shah
Submitted by Shah on Sun, 06/26/2011 - 05:23 Permalink
Dear Dr. Yan I was able to
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 Permalink
Re
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!
Submitted by chenyuchen1989 on Mon, 06/17/2013 - 23:18 Permalink
Re: Single Slice resting state analysis
Hi Shah:
Do you have the mask of rat? In your attachments, the fun_mask is not complete. Could you send one to me?
Thank you very much!
Best wishes!
chen