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How to edit tractparams.csv

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Garikoitz Lerma-Usabiaga edited this page Nov 28, 2021 · 1 revision

What is tractparams.csv

In the current version of the RTP-pipeline we are providing almost total flexibility for the tract generation. This means that we can generate the tracts we want, with the ROIs we want, and using several different strategies per each individual tract. We can create a couple of tracts or 30 tracts, there is no theoretical limit.

Here we will explain what are the variables in the csv file.

How to use it

For the container version, copy and paste the csv below, and save it as a .csv file in the $basedir/input/tractparams folder.

Flywheel users, upload the tractparams.csv file as an attachment to the project, and then select it in the GUI/with the SDK as any other file.

Variables in each column

  • roi1: name of roi 1 of tract 1. The file needs to be in the fs/ROIs/ folder in the fs.zip file.
  • extroi1: extension of the file (usually .nii.gz)
  • roi2: name of roi 2 of tract 2. The file needs to be in the fs/ROIs/ folder in the fs.zip file.
  • extroi2: extension of the file (usually .nii.gz)
  • roi3: name of roi 3 of tract 3. The file needs to be in the fs/ROIs/ folder in the fs.zip file. If there is no roi3, call it NO
  • extroi3: extension of the file (usually .nii.gz)
  • dilroi1: numero de dilations required for roi1
  • dilroi2: numero de dilations required for roi2
  • dilroi3: numero de dilations required for roi3
  • label: long name for the tract (for example, Left Arcuate_Fasciculus). To avoid problems, do not use spaces
  • fgnum: Usually a consecutive number.
  • hemi: Hemisphere of the tract, long format (Left)
  • slabel: Short label name (for example, LAF)
  • shemi: Short hemi name (for example L)
  • nhlabel: Label without the hemi, it will be usually duplicated (for example, Arcuate_Fasciculus)
  • wbt: Whole Brain Tractography, if we want the tract to be edited from the WBT or tracked directly, it needs to be true/false
  • usecortex: if we want to use the cortex as an end waypoint in the tracking or editing.
  • maxlen: max fiber length in mm, for tracking, only applies when wbt=false.
  • minlen: min fiber length in mm, for tracking, only applies when wbt=false.
  • angle: max angle in deg, for tracking, only applies when wbt=false.
  • algorithm: algorithm used for tracking, only applies when wbt=false (for example, iFOD2)
  • cutoff: FOD cutoff value for tracking, only applies when wbt=false (for example, iFOD2)
  • maxDist: used in tract cleaning, in Std. Dev. (for example, 3)
  • maxLen: used in tract cleaning, in Std. Dev. (for example, 3)
  • numNodes: number of division in the tract (for example, 100)
  • meanmed: used in tract cleaning, mean or median (usually median)
  • maxIter: used in tract cleaning, max number of cleaning iterations (for example, 3)

Examples for copy and paste

As the structure of the csv might change with different version, we sort the csv examples per version.

RTP-pipeline version(s) 4.2.6

roi1,extroi1,roi2,extroi2,roi3,extroi3,dilroi1,dilroi2,dilroi3,label,fgnum,hemi,slabel,shemi,nhlabel,wbt,usecortex,maxlen,minlen,angle,algorithm,cutoff,maxDist,maxLen,numNodes,meanmed,maxIter
 ATR_roi1_L,.nii.gz,ATR_roi2_L,.nii.gz,NO,.nii.gz,0,0,0,Left_Thalamic_Radiation,1,Left,LTR,L,TR,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 ATR_roi1_R,.nii.gz,ATR_roi2_R,.nii.gz,NO,.nii.gz,0,0,0,Right_Thalamic_Radiation,2,Right,RTR,R,TR,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 CST_roi1_L,.nii.gz,CST_roi2_L,.nii.gz,NO,.nii.gz,0,0,0,Left_Corticospinal,3,Left,LCST,L,CST,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 CST_roi1_R,.nii.gz,CST_roi2_R,.nii.gz,NO,.nii.gz,0,0,0,Right_Corticospinal,4,Right,RCST,R,CST,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 CGC_roi1_L,.nii.gz,CGC_roi2_L,.nii.gz,NO,.nii.gz,0,0,0,Left_Cingulum_Cingulate,5,Left,LCC,L,CC,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 CGC_roi1_R,.nii.gz,CGC_roi2_R,.nii.gz,NO,.nii.gz,0,0,0,Right_Cingulum_Cingulate,6,Right,RCC,R,CC,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 HCC_roi1_L,.nii.gz,HCC_roi2_L,.nii.gz,NO,.nii.gz,0,0,0,Left_Cingulum_Hippocampus,7,Left,LCH,L,CH,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 HCC_roi1_R,.nii.gz,HCC_roi2_R,.nii.gz,NO,.nii.gz,0,0,0,Right_Cingulum_Hippocampus,8,Right,RCH,R,CH,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 FP_R,.nii.gz,FP_L,.nii.gz,NO,.nii.gz,0,0,0,Callosum_Forceps_Major,9,Left,CFMaj,L,CFMAJ,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 FA_L,.nii.gz,FA_R,.nii.gz,NO,.nii.gz,0,0,0,Callosum_Forceps_Minor,10,Right,CFMin,R,CFMIN,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 IFO_roi1_L,.nii.gz,IFO_roi2_L,.nii.gz,NO,.nii.gz,0,0,0,Left_IFOF,11,Left,LIFOF,L,IFOF,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 IFO_roi1_R,.nii.gz,IFO_roi2_R,.nii.gz,NO,.nii.gz,0,0,0,Right_IFOF,12,Right,RIFO,R,IFO,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 ILF_roi1_L,.nii.gz,ILF_roi2_L,.nii.gz,NO,.nii.gz,0,0,0,Left_ILF,13,Left,LILF,L,ILF,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 ILF_roi1_R,.nii.gz,ILF_roi2_R,.nii.gz,NO,.nii.gz,0,0,0,Right_ILF,14,Right,RILF,R,ILF,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 SLF_roi1_L,.nii.gz,SLF_roi2_L,.nii.gz,NO,.nii.gz,0,0,0,Left_SLF,15,Left,LSLF,L,SLF,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 SLF_roi1_R,.nii.gz,SLF_roi2_R,.nii.gz,NO,.nii.gz,0,0,0,Right_SLF,16,Right,RSLF,R,SLF,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 UNC_roi1_L,.nii.gz,UNC_roi2_L,.nii.gz,NO,.nii.gz,0,0,0,Left_Uncinate,17,Left,LUF,L,UF,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 UNC_roi1_R,.nii.gz,UNC_roi2_R,.nii.gz,NO,.nii.gz,0,0,0,Right_Uncinate,18,Right,RUF,R,UF,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 SLF_roi1_L,.nii.gz,SLFt_roi2_L,.nii.gz,NO,.nii.gz,0,0,0,Left_Arcuate,19,Left,LAF,L,AF,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 SLF_roi1_R,.nii.gz,SLFt_roi2_R,.nii.gz,NO,.nii.gz,0,0,0,Right_Arcuate,20,Right,RAF,R,AF,1,0,200,10,45,iFOD2,0.1,3,3,100,median,1
 Left-LGN,.nii.gz,Left-V1,.nii.gz,NO,.nii.gz,3,3,0,Left_Optic_Radiation_V1,21,Left,LORV1,L,ORV1,0,0,230,30,45,iFOD2,0.05,3,3,100,median,1
 Right-LGN,.nii.gz,Right-V1,.nii.gz,NO,.nii.gz,3,3,0,Right_Optic_Radiation_V1,22,Right,RORV1,R,ORV1,0,0,230,30,45,iFOD2,0.05,3,3,100,median,1
 Left-LGN,.nii.gz,Left-V1_AND_Left-V2,.nii.gz,NO,.nii.gz,3,3,0,Left_Optic_Radiation_V1V2,23,Left,LORV1V2,L,ORV1V2,0,0,230,30,45,iFOD2,0.05,3,3,100,median,1
 Right-LGN,.nii.gz,Right-V1_AND_Right-V2,.nii.gz,NO,.nii.gz,3,3,0,Right_Optic_Radiation_V1V2,24,Right,RORV1V2,R,ORV1V2,0,0,230,30,45,iFOD2,0.05,3,3,100,median,1
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