Pleae resmaple your mask or ROI definition file first!

Submitted by YAN Chao-Gan on
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Hi, Cleofé Peña Gómez!
     1. You need to resample your mask or ROI file to the dimension of your functional images.
          There were three ways: (1) use SONG Xiao-Wei's program, from http://restfmri.net/forum/node/78                              
                                                 (2) use my program, from http://restfmri.net/forum/node/81   (the third one)
                                                 (3) use SPM5:
                                                                       a. Click "Coregister"
                                                                       b. Click "New "Coreg: Reslice""
                                                                       c. "Image Defining Space": choose one of your functional image. e.g. your normalized functional image or image after Detrend and Filter.
                                                                       d. "Images to Reslice": choose the mask file or ROI definition file. e.g. BrainMask_05_61x73x61.img
                                                                       e. "Reslice Options" -> "Interpolation": choose "Nearest neighbour"
                                                                       f. Just click "Run". Then you will get the resmapled mask or ROI file with a surfix of "r".
      

Q&A: "REST error...ReadNiftiImage.m"

Submitted by YAN Chao-Gan on
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Hello,

I am trying to analyze some resting state data using REST, but I cannot load the data in the GUI.  Am I correct to assume we need to enter data in conseqcutive file names of ANALYZE format?  The error message I get in Matlab refers to line 103 of rest_ReadNiftiImage.m

Is this script necessary if we are using ANALYZE not NIFTI?  If it is not necessary how do I skip it.

I do not know how to proceed.  Any assistance would be greatly appreciated.

Thank you,

Carlos

RE: long mixed session of rest and task

Submitted by ZangYF on
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A long session, 22 minutes: Resting state 9 minutes, and then a blocked design (2 minutes task + 30s rest) 13 minutes. The questions are:
(1) Is the head motion a concern?
(2) Can the 9-minutes rest be used as a baseline for the data analysis of the blocked design?

My answer:
(1) Yes. There may be more head motion for such a long session. But occasionally, a long rest is necessary (e.g., epilepsy and sleep study).

Out of memory--Error message for running ReHo and FC tools

Submitted by Haibo on
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Dear REST experters:

      I am new to run REST toolbox. When running ReHO and FC, get the following error messages. I don't know what wrong I did. BTW, do you have some stand along program or easy tools for extracting the time course data. Thanks in advance.

Haibo


error messages:

Two extra seminars (afternoon, April 6) after the RS-fMRI symposium

Submitted by ZangYF on
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From 14:00, April 6th

The meeting room, 2nd floor, Brain Imaging Center, Beijing Normal University

Rest-State fMRI: From Default Mode Network to Cognitive Network
Jen-Chuen Hsieh (謝仁俊), MD, PhD
Professor and Director, Institite of Brain Science, Yang-Ming University, and Director of Brain Center, VA Hospital, Taipei

Granger Causality: Inferring direction of neural interaction
Xue Wang (王雪), PhD,
Clinical Research Associate

Erratum: Scanning parameters of RS-fMRI for 3T SIEMENS

Submitted by ZangYF on
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I am sorry that in the following parameters, I made a type error. The thickness/gap should be 3.5/0.7 mm. If you have used 3.5/0.6, it OK.
Please note that an FOV of 200*200 is sometimes small.

The following parameters are what we are using on a SIEMENS 3T trio scanner. 33 axial slices, thickness/gap = 3.5/0.6 mm, in-plane resolution = 64 × 64, TR = 2000 ms, TE = 30 ms, flip angle = 90, FOV = 200 × 200 mm, volumes = 240 (480 s). I strongly recommend that the RS-fMRI session is placed before the task sessions.

about the resting state fmri workshop

Submitted by y.kong on
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刚看了workshop的介绍，非常好的内容，包括了fMRI, EEG, DTI; ICA, functional connectivity; psychiatric disorder etc. 而且邀请到了biswal和kiviniemi两位专家，一位是先驱，一位是fast ICA专家 (biswal的英语口音比较难懂，大家做好心理准备 ：）....

可惜我4月没有时间去听讲座。可能很多有兴趣的人也有种种原因不能前去。请问组织者能否在会后提供讲座ppt/pdf下载？或者会议录像下载？

谢谢 

Bandpass filtering

Submitted by alex on
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 Hi,

I'm trying to use the rest_bandpass function in your toolkit, but I can't get it to read my data. Specifically, I get the error message below. If I try to use the GUI, I get an error dialog saying "There is no data or non-data files in this directory".

I get the same message for different datatsets. I have made sure that only the volumes and not other files are in that directory. I can use the image files with no problems using other analysis packages.

 

Thanks for your help,

Alex

 

 

Re: "sunshine"'s question: spatially smoothing before or after ReHo

Submitted by ZangYF on
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In a few earlier studies, spatilly smoothing was performed before ReHo analysis. However, Mr. LONG Xiang-Yu found that, for some voxels, the ReHo value is very high because spatially smoothing certainly increase the local similarity. That is why we now recommend to perform spatially smoothing after ReHo calculation. Please note that we are not sure which is "better" for group level analysis, especially between-group studies. I suggest you can compare the results. 

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