Update README.md

README.md

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-# fMRI-cleanup
+ABCD Release 2.0.1 fMRI-cleanup README
+
+Issue:
+Due to incorrect post-processing, all task and resting-state fMRI data obtained on Phillips scanners should be excluded from all analyses. This includes tabulated and minimally processed data. This issue does not affect other modalities (sMRI, dMRI) or raw DICOM data (Fast Track). In DEAP and RDS, Philips fMRI data has been removed. They will be corrected and made available with Data Release 3.0. The field map direction for these data was mistakenly flipped, which led to increased distortion in processed fMRI images. 1512 participants are affected by this issue, which is 13% of baseline MRI visits.
+
+Recommendations: 
+We recommend that all users re-run fMRI related analyses without the Philips fMRI data. For published studies, we encourage users to confirm findings without the Philips fMRI data and provide a corrigendum with the updated results. 
+
+Instructions:
+This R script is to parse the ABCD Release 2.0.1 fMRI tabulated data to remove subjects that have incorrect post-processing distortion correction. 
+
+1. Open the fMRI-cleanup.R in R, RStudio or preferred text editor.'
+2. Edit the working directory (line 2: setwd) to point to a location that contains the ABCD Release 2.0.1 tabulated fMRI text files downloaded from NDA. The full list of affected fMRI instruments is list below. Instruments from previous releases may have different names:
+
+abcd_betnet02.txt
+abcd_midabwdp01.txt
+abcd_midabwdp202.txt
+abcd_midasemdp101.txt
+abcd_midasemdp202.txt
+abcd_midasemp102.txt
+abcd_midasemp202.txt
+abcd_midr1bwdp101.txt
+abcd_midr1bwdp202.txt
+abcd_midr1bwp102.txt
+abcd_midr1bwp202.txt
+abcd_midr2semp102.txt
+abcd_midr2semp202.txt
+abcd_midsemp102.txt
+abcd_midsemp202.txt
+abcd_tfabwdp101.txt
+abcd_tfabwdp201.txt
+abcd_tfnbr1semdp101.txt
+abcd_tfnbr1semdp201.txt
+abcd_tfnbr2bwdp101.txt
+abcd_tfnbr2bwdp201.txt
+abcd_tfnbr2dp101.txt
+abcd_tfnbr2dp201.txt
+abcd_tfncr1bwdp101.txt
+abcd_tfncr1bwdp201.txt
+abcd_tfsstabwdp101.txt
+abcd_tfsstabwdp201.txt
+abcd_tfsstasemdp101.txt
+abcd_tfsstasemdp201.txt
+abcd_tfsstr1bwdp101.txt
+abcd_tfsstr1bwdp201.txt
+abcd_tfsstr1semdp101.txt
+abcd_tfsstr1semdp201.txt
+abcd_tfsstr2bwdp101.txt
+abcd_tfsstr2bwdp201.txt
+abcd_tfsstr2semdp101.txt
+abcd_tfsstr2semdp201.txt
+abcd_tmidr1semdp101.txt
+abcd_tmidr1semdp202.txt
+abcd_tnbasemdp101.txt
+abcd_tnbasemdp201.txt
+abcd_tr2bwdp01.txt
+abcd_tr2bwdp202.txt
+abcd_tr2semdp101.txt
+abcd_tr2semdp202.txt
+midaparc03.txt
+midaparcp203.txt
+midr2bwp102.txt
+midr2bwp202.txt
+mrirscor02.txt
+mrisst02.txt
+mrisstr1bw01.txt
+mrisstr1sem01.txt
+mrisstr2bw01.txt
+mrisstr2bwsem01.txt
+mrisstsem01.txt
+nback_bwroi02.txt
+nbackallsem01.txt
+nbackr101.txt
+nbackr1sem01.txt
+nbackr201.txt
+nbackr2sem01.txt
+
+3. This folder also requires the MRI Info instrument (abcd_mri01.txt).
+4. Edit the output format (line  3: output_format) to export as either a csv file "CSV" or the original text format "TXT".
+Run the R script. As the files are large it can take a few minutes per table. Updated tables are created in the working directory with a "new_" prefix. Ensure there is enough disk space to create a copy of all the data to be processed.  
+
+Alternative datasets available:
+Additionally, a secondary release of processed ABCD fMRI data not affected by this issue will be shared shortly in NDA collection #3165 (https://nda.nih.gov/edit_collection.html?id=3165).  These data have been processed through the ABCD-BIDS pipelines (https://github.com/ABCD-STUDY/abcd-hcp-pipeline). This collection will provide minimally processed data, but not tabulated data.