##2 Step 2: Specify the FreeSurfer subject directory
setenv SUBJECTS_DIR /home/CB/Skrivebord/subjects

##3 Step 3: Specify the TRACULA output directory (default $SUBJECTS_DIR)
set dtroot = /home/CB/Skrivebord/diff_output

##4 Step 4: Specify the list of subject IDs
set subjlist = (100_diab_t1 101_diab_t1 103_diab_t1 106_diab_t1 107_diab_t1 108_diab_t1 111_diab_t1 113_diab_t1 115_diab_t1 116_diab_t1 117_diab_t1 118_diab_t1 119_diab_t1 120_diab_t1 121_diab_t1 122_diab_t1 123_diab_t1 125_diab_t1 126_diab_t1 127_diab_t1 128_diab_t1 129_diab_t1 130_diab_t1 131_diab_t1 132_diab_t1 133_diab_t1 134_diab_t1 135_diab_t1 136_diab_t1 137_diab_t1 138_diab_t1 139_diab_t1 140_diab_t1 141_diab_t1 142_diab_t1 143_diab_t1 144_diab_t1 145_diab_t1 147_diab_t1 149_diab_t1 151_diab_t1 152_diab_t1 154_diab_t1 155_diab_t1 156_diab_t1 157_diab_t1 158_diab_t1 159_diab_t1 160_diab_t1 161_diab_t1 162_diab_t1 163_diab_t1 164_diab_t1 165_diab_t1 166_diab_t1 167_diab_t1 169_diab_t1 170_diab_t1 171_diab_t1 172_diab_t1 173_diab_t1 174_diab_t1 175_diab_t1 176_diab_t1 177_diab_t1 178_diab_t1 179_diab_t1 180_diab_t1 181_diab_t1 182_diab_t1 183_diab_t1 184_diab_t1 185_diab_t1 186_diab_t1 187_diab_t1 188_diab_t1 189_diab_t1 190_diab_t1 191_diab_t1 192_diab_t1 193_diab_t1 194_diab_t1 195_diab_t1 196_diab_t1 197_diab_t1 198_diab_t1 199_diab_t1 200_diab_t1 300_kontrol_t1 302_kontrol_t1 303_kontrol_t1 304_kontrol_t1 305_kontrol_t1 306_kontrol_t1 307_kontrol_t1 308_kontrol_t1 309_kontrol_t1 310_kontrol_t1 311_kontrol_t1 312_kontrol_t1 313_kontrol_t1 314_kontrol_t1 315_kontrol_t1 316_kontrol_t1 317_kontrol_t1 318_kontrol_t1 319_kontrol_t1 320_kontrol_t1 321_kontrol_t1 323_kontrol_t1 324_kontrol_t1 325_kontrol_t1 326_kontrol_t1 327_kontrol_t1 328_kontrol_t1 329_kontrol_t1 330_kontrol_t1 331_kontrol_t1 333_kontrol_t1 334_kontrol_t1 335_kontrol_t1 336_kontrol_t1 337_kontrol_t1 338_kontrol_t1 339_kontrol_t1 340_kontrol_t1 341_kontrol_t1 342_kontrol_t1 343_kontrol_t1 344_kontrol_t1 345_kontrol_t1 346_kontrol_t1 347_kontrol_t1 348_kontrol_t1 349_kontrol_t1 350_kontrol_t1 351_kontrol_t1 352_kontrol_t1 353_kontrol_t1 355_kontrol_t1 356_kontrol_t1 357_kontrol_t1 358_kontrol_t1 359_kontrol_t1 360_kontrol_t1 361_kontrol_t1 362_kontrol_t1 363_kontrol_t1 364_kontrol_t1 365_kontrol_t1 366_kontrol_t1 367_kontrol_t1 368_kontrol_t1 369_kontrol_t1 370_kontrol_t1 371_kontrol_t1 372_kontrol_t1 373_kontrol_t1 374_kontrol_t1 375_kontrol_t1 376_kontrol_t1 377_kontrol_t1 379_kontrol_t1 380_kontrol_t1 381_kontrol_t1 382_kontrol_t1 383_kontrol_t1 384_kontrol_t1 385_kontrol_t1 386_kontrol_t1 387_kontrol_t1 389_kontrol_t1 390_kontrol_t1 391_kontrol_t1 392_kontrol_t1 393_kontrol_t1 394_kontrol_t1 395_kontrol_t1 396_kontrol_t1 397_kontrol_t1 398_kontrol_t1 399_kontrol_t1)

##5 Step 5: Specify the location of diffusion DICOM files
set dcmroot = /home/CB/Skrivebord/Impact

##6 Step 6: Specify the list of input DWIs
set dcmlist = ( diab/100_diab/dwi/06410004 \
                diab/101_diab/dwi/06550004 \
                diab/103_diab/dwi/07210004 \
                diab/106_diab/dwi/06700004 \
                diab/107_diab/dwi/07180004 \
                diab/108_diab/dwi/07280004 \
                diab/111_diab/dwi/06800004 \
                diab/113_diab/dwi/06650004 \
                diab/115_diab/dwi/06510004 \
                diab/116_diab/dwi/04620004 \
                diab/117_diab/dwi/06600004 \
                diab/118_diab/dwi/06460004 \
                diab/119_diab/dwi/06750004 \
                diab/120_diab/dwi/06980004 \
                diab/121_diab/dwi/06880004 \
                diab/122_diab/dwi/04570004 \
                diab/123_diab/dwi/04520004 \
                diab/125_diab/dwi/04470004 \
                diab/126_diab/dwi/00880004 \
                diab/127_diab/dwi/04370004 \
                diab/128_diab/dwi/04320004 \
                diab/129_diab/dwi/04270004 \
                diab/130_diab/dwi/00430004 \
                diab/131_diab/dwi/04220004 \
                diab/132_diab/dwi/00730004 \
                diab/133_diab/dwi/00130004 \
                diab/134_diab/dwi/04420004 \
                diab/135_diab/dwi/04060004 \
                diab/136_diab/dwi/04170004 \
                diab/137_diab/dwi/02130004 \
                diab/138_diab/dwi/01930004 \
                diab/139_diab/dwi/00380004 \
                diab/140_diab/dwi/00180004 \
                diab/141_diab/dwi/01570004 \
                diab/142_diab/dwi/04110004 \
                diab/143_diab/dwi/03990004 \
                diab/144_diab/dwi/03940004 \
                diab/145_diab/dwi/03890004 \
                diab/147_diab/dwi/03840004 \
                diab/149_diab/dwi/03530004 \
                diab/151_diab/dwi/03480004 \
                diab/152_diab/dwi/03800004 \
                diab/154_diab/dwi/03700004 \
                diab/155_diab/dwi/01880004 \
                diab/156_diab/dwi/03620004 \
                diab/157_diab/dwi/06200004 \
                diab/158_diab/dwi/03580004 \
                diab/159_diab/dwi/06300004 \
                diab/160_diab/dwi/03660004 \
                diab/161_diab/dwi/06250004 \
                diab/162_diab/dwi/03410004 \
                diab/163_diab/dwi/01980004 \
                diab/164_diab/dwi/04970004 \
                diab/165_diab/dwi/01330004 \
                diab/166_diab/dwi/06800004 \
                diab/167_diab/dwi/00830004 \
                diab/169_diab/dwi/01030004 \
                diab/170_diab/dwi/00980004 \
                diab/171_diab/dwi/02960004 \
                diab/172_diab/dwi/01730004 \
                diab/173_diab/dwi/03200004 \
                diab/174_diab/dwi/00230004 \
                diab/175_diab/dwi/01380004 \
                diab/176_diab/dwi/02580004 \
                diab/177_diab/dwi/01480004 \
                diab/178_diab/dwi/01180004 \
                diab/179_diab/dwi/00630004 \
                diab/180_diab/dwi/00930004 \
                diab/181_diab/dwi/01430004 \
                diab/182_diab/dwi/01280004 \
                diab/183_diab/dwi/00030004 \
                diab/184_diab/dwi/04740004 \
                diab/185_diab/dwi/03140004 \
                diab/186_diab/dwi/04680004 \
                diab/187_diab/dwi/04920004 \
                diab/188_diab/dwi/04860004 \
                diab/189_diab/dwi/04800004 \
                diab/190_diab/dwi/03260004 \
                diab/191_diab/dwi/02850004 \
                diab/192_diab/dwi/02330004 \
                diab/193_diab/dwi/03030004 \
                diab/194_diab/dwi/02910004 \
                diab/195_diab/dwi/02460004 \
                diab/196_diab/dwi/02970004 \
                diab/197_diab/dwi/02520004 \
                diab/198_diab/dwi/02640004 \
                diab/199_diab/dwi/03380004 \
                diab/200_diab/dwi/02420004 \
                kontrol/300_kontrol/dwi/03620004 \
                kontrol/302_kontrol/dwi/01630004 \
                kontrol/303_kontrol/dwi/05650004 \
                kontrol/304_kontrol/dwi/03560004 \
                kontrol/305_kontrol/dwi/05530004 \
                kontrol/306_kontrol/dwi/02380004 \
                kontrol/307_kontrol/dwi/06150004 \
                kontrol/308_kontrol/dwi/03020004 \
                kontrol/309_kontrol/dwi/06100004 \
                kontrol/310_kontrol/dwi/05180004 \
                kontrol/311_kontrol/dwi/03230004 \
                kontrol/312_kontrol/dwi/00280004 \
                kontrol/313_kontrol/dwi/05700004 \
                kontrol/314_kontrol/dwi/06000004 \
                kontrol/315_kontrol/dwi/06050004 \
                kontrol/316_kontrol/dwi/05950004 \
                kontrol/317_kontrol/dwi/05850004 \
                kontrol/318_kontrol/dwi/05800004 \
                kontrol/319_kontrol/dwi/05900004 \
                kontrol/320_kontrol/dwi/03180004 \
                kontrol/321_kontrol/dwi/05600004 \
                kontrol/323_kontrol/dwi/05480004 \
                kontrol/324_kontrol/dwi/05430004 \
                kontrol/325_kontrol/dwi/05380004 \
                kontrol/326_kontrol/dwi/05330004 \
                kontrol/327_kontrol/dwi/03130004 \
                kontrol/328_kontrol/dwi/03280004 \
                kontrol/329_kontrol/dwi/05280004 \
                kontrol/330_kontrol/dwi/02080004 \
                kontrol/331_kontrol/dwi/01780004 \
                kontrol/333_kontrol/dwi/05230004 \
                kontrol/334_kontrol/dwi/00030004 \
                kontrol/335_kontrol/dwi/05750004 \
                kontrol/336_kontrol/dwi/00340001 \
                kontrol/337_kontrol/dwi/02230004 \
                kontrol/338_kontrol/dwi/00780004 \
                kontrol/339_kontrol/dwi/02540004 \
                kontrol/340_kontrol/dwi/00080004 \
                kontrol/341_kontrol/dwi/00530004 \
                kontrol/342_kontrol/dwi/02030004 \
                kontrol/343_kontrol/dwi/03080004 \
                kontrol/344_kontrol/dwi/05020004 \
                kontrol/345_kontrol/dwi/00280004 \
                kontrol/346_kontrol/dwi/01680004 \
                kontrol/347_kontrol/dwi/00580004 \
                kontrol/348_kontrol/dwi/02180004 \
                kontrol/349_kontrol/dwi/00330004 \
                kontrol/350_kontrol/dwi/01080004 \
                kontrol/351_kontrol/dwi/01830004 \
                kontrol/352_kontrol/dwi/02280004 \
                kontrol/353_kontrol/dwi/00480004 \
                kontrol/355_kontrol/dwi/03320004 \
                kontrol/356_kontrol/dwi/03080004 \
                kontrol/357_kontrol/dwi/01530004 \
                kontrol/358_kontrol/dwi/02780004 \
                kontrol/359_kontrol/dwi/02840004 \
                kontrol/360_kontrol/dwi/02660004 \
                kontrol/361_kontrol/dwi/02900004 \
                kontrol/362_kontrol/dwi/02720004 \
                kontrol/363_kontrol/dwi/02600004 \
                kontrol/364_kontrol/dwi/02480004 \
                kontrol/365_kontrol/dwi/00150001 \
                kontrol/366_kontrol/dwi/01890004 \
                kontrol/367_kontrol/dwi/00690004 \
                kontrol/368_kontrol/dwi/02360004 \
                kontrol/369_kontrol/dwi/02240004 \
                kontrol/370_kontrol/dwi/01110004 \
                kontrol/371_kontrol/dwi/00570004 \
                kontrol/372_kontrol/dwi/02010004 \
                kontrol/373_kontrol/dwi/01290004 \
                kontrol/374_kontrol/dwi/02070004 \
                kontrol/375_kontrol/dwi/01410004 \
                kontrol/376_kontrol/dwi/02300004 \
                kontrol/377_kontrol/dwi/01470004 \
                kontrol/379_kontrol/dwi/02130004 \
                kontrol/380_kontrol/dwi/00630004 \
                kontrol/381_kontrol/dwi/01350004 \
                kontrol/382_kontrol/dwi/01590004 \
                kontrol/383_kontrol/dwi/01950004 \
                kontrol/384_kontrol/dwi/00090004 \
                kontrol/385_kontrol/dwi/01230004 \
                kontrol/386_kontrol/dwi/01170004 \
                kontrol/387_kontrol/dwi/00990004 \
                kontrol/389_kontrol/dwi/00040004 \
                kontrol/390_kontrol/dwi/01050004 \
                kontrol/391_kontrol/dwi/00930004 \
                kontrol/392_kontrol/dwi/00870004 \
                kontrol/393_kontrol/dwi/00810004 \
                kontrol/394_kontrol/dwi/00750004 \
                kontrol/395_kontrol/dwi/00340004 \
                kontrol/396_kontrol/dwi/00220004 \
                kontrol/397_kontrol/dwi/00160004 \
                kontrol/398_kontrol/dwi/00280004 \
                kontrol/399_kontrol/dwi/00100004 )


##7 Step 7: Specify which subjects to analyze
set runlist = (1)

##8 Step 8: Specify the diffusion-encoding gradient table
set bvecfile = /home/CB/Skrivebord/Impact/bvecs.txt

#set bveclist = ( /path/to/elmo.2005/bvecs.txt \
#                 /path/to/elmo.2008/bvecs.txt \
#                 /path/to/elmo.2012/bvecs.txt )

##9 Step 9: Specify the b-value table
set bvalfile = /home/CB/Skrivebord/Impact/bvals.txt

##10 Step 10: Specify if eddy-current compensation will be performed
set doeddy = 1

##11 Step 11: Specify if the gradients will be rotated to match eddy-current compensation
set dorotbvecs = 1

##12 Step 12: Specify if an anatomical brain mask will be used
set usemaskanat = 1

##13 Step 13: Set the threshold for DWI-based brain mask extraction
set thrbet = 0.3

##16 Step 16: Specify which white-matter pathways to reconstruct
set pathlist = ( lh.cst_AS rh.cst_AS \
                 lh.ilf_AS rh.ilf_AS \
                 lh.unc_AS rh.unc_AS \
                 fmajor_PP fminor_PP \
                 lh.atr_PP rh.atr_PP \
                 lh.cab_PP rh.cab_PP \
                 lh.ccg_PP rh.ccg_PP \
                 lh.slfp_PP rh.slfp_PP \
                 lh.slft_PP rh.slft_PP )
#Use this variable to specify which of the 18 pathways included in the TRACULA tract atlas to reconstruct. The default is to reconstruct all 18 pathways, defined below:
#
#    lh.cst_AS: Left corticospinal tract
#    rh.cst_AS: Right corticospinal tract
#    lh.ilf_AS: Left inferior longitudinal fasciculus
#    rh.ilf_AS: Right inferior longitudinal fasciculus
#    lh.unc_AS: Left uncinate fasciculus
#    rh.unc_AS: Right uncinate fasciculus
#    fmajor_PP: Corpus callosum - forceps major
#    fminor_PP: Corpus callosum - forceps minor
#    lh.atr_PP: Left anterior thalamic radiations
#    rh.atr_PP: Right anterior thalamic radiations
#    lh.ccg_PP: Left cingulum - cingulate gyrus endings
#    rh.ccg_PP: Right cingulum - cingulate gyrus endings
#    lh.cab_PP: Left cingulum - angular bundle
#    rh.cab_PP: Right cingulum - angular bundle
#    lh.slfp_PP: Left superior longitudinal fasciculus - parietal endings
#    rh.slfp_PP: Right superior longitudinal fasciculus - parietal endings
#    lh.slft_PP: Left superior longitudinal fasciculus - temporal endings
#    rh.slft_PP: Right superior longitudinal fasciculus - temporal endings 


##17 Step 17: Specify the number of path control points
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)