RestingStateStats.bat
Lin Cai
Unable to read file '/mnt/data2/derivatives/HCPpipeline/sub-K1908061200/MNINonLinear/Results/PA_run-01_epi/PA_run-01_epi_hp0.ica/.fix'. No such file or
directory.
Error in RestingStateStats (line 115)
Inoise=load(noiselist);
OrigHighPass="0" #Specified in Sigma
Caret7_Command="wb_command"
#RegName="MSMRSNOrig3_d26_DR_DeDrift"
#RegName="MSMAll_2_d41_WRN_DeDrift"
RegName="NONE"
LowResMesh="32"
FinalfMRIResolution="2"
BrainOrdinatesResolution="2"
SmoothingFWHM="2"
OutputProcSTRING="_hp0_clean"
dlabelFile="/mnt/data2/cai_practice/Covid_Project/code/Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii"
MatlabRunMode="1"
BCMode="NONE" #One of REVERT (revert bias field correction), NONE (don't change biasfield correction), CORRECT (revert original bias field correction and apply new one, requires ??? to be present)
OutSTRING="stats"
WM="$HCPPIPEDIR/global/config/FreeSurferWMRegLut.txt"
Lin Cai
RestingStateStats - About to remove fakeNIFTI fileRestingStateStats - Finished fslmaths filtering of cifti input
Error using load
Unable to read file '/mnt/data2/cai_practice/Covid_Project/derivatives/HCPpipeline/sub-K1908061200/MNINonLinear/Results/run12_PA_AP/Movement_Regressors.txt'. No such file or
directory.
Error in RestingStateStats (line 171)
confounds=load([motionparameters '.txt']);
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Harms, Michael
Hi,
I’m not sure if RestingStateStats has been updated to work with MR-FIX. Matt is on vacation, so you may have to repost in a couple weeks for a more definitive response.
Cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Lin Cai <bertr...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Wednesday, July 27, 2022 at 3:25 AM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Subject: Re: [hcp-users] RestingStateStats.bat
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Glasser, Matt
The released version of RestingStateStats does not work with MR+FIX. RestingStateStats overall is in need of a bit of a rewrite. It needs to partition variance into:
*Original
*Detrend Structured Noise
*sICA+FIX Structured Noise
*tICA Structured Noise
*BOLD Signal
*Unstructured Noise
Things like MGTR/WM/CSF/Motion/Physio regressors if still provided should be shown as what they do to the data above and beyond the above recommended denoising steps. The effect of Wishart Filtering might also be useful to show. If there are specific measures you need now from RestingStateStats, it might be best to have a look at the code and compute them yourself.
Matt.
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