Hi Matt,
Thank you for your reply. I have downloaded the ICA+FIX cleaned data (FIX-Denoised Extended) and found it much more stable than the Minimum-preprocessed one. Thank you a lot! However, regarding to the FIX-Denoised data, I have some further doubts for my proposed 3 steps. 1. Regression on CSF, WM and Whole Brain. I found your discussions last month regarding to the FIX-Denoised related problems. (https://www.mail-archive.com/hcp-users@humanconnectome.org/msg02111.html). There Joelle wrote the following sentence on regressing CSF and WM: In which case, all you need to do is use those simultaneously in a regression to remove the noise space spanned by those two already supplied "*_Cleaned{WM,CSF}tc.txt" files from the hp2000_clean.nii.gz volume data or hp2000_clean.dtseries.nii CIFTI data. (See e.g., Lines 330-334 in RestingStateStats.m for what I mean by using them in a "simultaneous" regression). %Create data if regressing out cleaned WM and CSF timecourses if ~strcmp(WM,'NONE') && ~strcmp(CSF,'NONE') betaWMCSF = pinv([WMtcClean CSFtcClean]) * CleanedTCS'; WMCSFCleanedTCS = CleanedTCS - ([WMtcClean CSFtcClean] * betaWMCSF)'; [WMCSFCleanedMGTRtcs,WMCSFCleanedMGT,WMCSFCleanedMGTbeta,WMCSFCleanedMGTVar,WMCSFCleanedMGTrsq] = MGTR(WMCSFCleanedTCS); WMCSFVar = var((CleanedTCS - WMCSFCleanedTCS),[],tpDim); end I have located the files (e.g.. rfMRI_REST1_LR_Atlas_CleanedWMtc.txt, rfMRI_REST1_LR_Atlas_CleanedCFStc.txt). However, it seems that I need one more cleanTCS file to perform the 'simultaneous' regression? If so, where can I find it? And for the Whole Brain regression, can you suggest which one could I use？Is it rfMRI_REST1_RL_Atlas_CleanedMGT.txt ？(Or the FIX-Denoised data has already dealt with this part well?). I also noticed that you had discussed about the "non-aggressive" and "aggressive" regressions for WM and CSF, and the effectiveness of removing them. Based on my situations, would you suggest me to regress them out or keep it? 2. Smoothing with 4-mm FWHM. Can I use the wb_command -volume-smoothing ? And normally for HCP data, is it more suitable to use 6-mm or 4-mm? 3. Bandpass filtering (0.01 Hz - 0.08 Hz). It seems that you used fslmath to perform some kind of filtering. (I might be wrong). Can you suggest a way for me to perform the bandpass filtering? As so far it seems all other jobs can be done in Matlab+wb_command, I prefer not to use another software/tools only for this operation... I am extremely sorry that I had a lot of questions, some are too technical, some of them are naive and might be stupid. However I have been struggling on those steps and have searched a lot online, and the best way I found is still to ask you through this email list. Your previous reply has helped me a lot, and I truly appreciate your help and patience. Best Regards, Hongquan ________________________________ From: Glasser, Matthew <glass...@wustl.edu> Sent: Thursday, 7 January 2016 19:40 To: #LONG HONGQUAN#; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] How to perform the standard functional connectivity preprocessing on the "Preprocessed" HCP data The minimally preprocessed data have gone through motion correction. The ICA+FIX cleaned data have gone through 24 movement parameter regression (and noise component regression). I would recommend you use the ICA+FIX cleaned data as the basis for your analyses. We don’t do any of those other steps in our processing except for demeaning and detrending (detrending is also already done in the ICA+FIX cleaned data). We don’t do motion censoring with HCP data (and I don’t recommend it, as it doesn’t work very well on high temporal resolution data and you don’t really need it if you are using ICA+FIX cleaned data). I don’t think you need to use FreeSurfer commands for this. You should be able to write most of it in matlab (perhaps occasionally calling wb_command from matlab). Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of #LONG HONGQUAN# <long0...@e.ntu.edu.sg<mailto:long0...@e.ntu.edu.sg>> Date: Thursday, January 7, 2016 at 1:43 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] How to perform the standard functional connectivity preprocessing on the "Preprocessed" HCP data I would like to add on one more question: In the “Minimum Pre-processing Pipeline”, has the data gone through Motion Correction/Head Movement regression? If so, how many parameters have been applied? I ask so because I found two papers, one saying that Motion Correction has been applied in the “Minimum Pipeline”. One saying that Motion Censoring is left out of the “Minimum Pipeline”. (Are they different from each other?) Thank you. On 7 Jan 2016, at 2:46 PM, #LONG HONGQUAN# <long0...@e.ntu.edu.sg<mailto:long0...@e.ntu.edu.sg>> wrote: Hi HCP team, I am very new to this field. I am an undergraduate student doing Final Year Project based on HCP dataset. My topic is to analyse the functional connectivities for some ROIs in “pre-processed” rs-fMRI data. Recently I realised that in HCP database, the “preprocessed” data has only gone though the “Minimum Pre-processing Pipeline”. In order to perform further investigation on those data, I need to perform the following operations: (i) demeaning and detrending across each run, (ii) bandpass filtering (0.01-0.08Hz), (iii) linear regression on CSF, Whole-Brain, White Matter signals along with signal derivatives (iv) smoothing with a 6-mm FWHM smoothing kernel in the surface space May I ask what tools/softwares you would recommend me to use to perform the above 4 operations? I would like to directly apply those functions on the 4-D .nii images. (e.g .../100307_3T_rfMRI_REST1_preproc/100307/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz). After some research online, I have a few possible options (REST+SPM, AFNI, RESTplus, FSL, DPABI, .etc). I would like to ask for your suggestions on what tools/softwares to use, and I would much appreciate if you could give me suggestions on what specific functions to use for each of the four steps. As my project is very small and straightforward, I would appreciate if you can give me suggestions which are the most naive and simplest to implement in Matlab. (If possible, I would prefer to avoid using Freesurfer+shell script). (However it seems that step(iii) will certainly use FreeSurfer? Can we make use of wb_command to separate the masks? Or is there another easy way/tool to do it without creating masks?). I would truly appreciate if you could provide me with some hints. Best Regards, Hongquan Long Undergraduate of School of Computer Engineering Nanyang Technological University _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. 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