I'm not sure that anyone is maintaining this code any more. However, you can try running
mri_convert --nskip 1 asl.nii asl.skip.nii and then use asl.skip.nii as input. This just removes the 1st frame so that the tag/control will be in the expected order doug On 10/22/2014 10:29 AM, Asif Jamil wrote: > Hello, > > I have pcASL data from a Siemens 3T scanner which I would like to > process using the provided rcbf-prep command. The process completes > smoothly without error. However when I inspect my roi.dat file, I > observe that all the ROI values are actually negative, and seem to be > beyond physiological CBF range (~60-120 ml/100g/min). > > The roi.dat file is pasted below. Would there be any reason to suspect > that the tag-control subtraction might be running inverted? I was > trying to find a way to customize the command, but seems like there’s > no option to specifying the order of tag and control. > > Any help would be appreciated! > > Best, > Asif > > > > > # Title Segmentation Statistics > # > # generating_program mri_segstats > # cvs_version $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ > # cmdline mri_segstats --seg > /www/data/fMRI/subjects/PV/mri/aparc+aseg.mgz --ctab > /www/data/fMRI/ANODAL/PV_2.0_hum_10387/ASL/30/rcbf/roi.table --i > /www/data/fMRI/ANODAL/PV_2.0_hum_10387/ASL/30/rcbf/rcbf.anat.nii --sum > /www/data/fMRI/ANODAL/PV_2.0_hum_10387/ASL/30/rcbf/roi.dat > # sysname Darwin > # hostname MBP-4.local > # machine x86_64 > # user asif > # anatomy_type volume > # > # SegVolFile /www/data/fMRI/subjects/PV/mri/aparc+aseg.mgz > # SegVolFileTimeStamp 2014/10/21 08:43:42 > # ColorTable /www/data/fMRI/ANODAL/PV_2.0_hum_10387/ASL/30/rcbf/roi.table > # ColorTableTimeStamp 2014/10/22 15:52:27 > # InVolFile > /www/data/fMRI/ANODAL/PV_2.0_hum_10387/ASL/30/rcbf/rcbf.anat.nii > # InVolFileTimeStamp 2014/10/22 16:00:34 > # InVolFrame 0 > # Only reporting non-empty segmentations > # VoxelVolume_mm3 1 > # TableCol 1 ColHeader Index > # TableCol 1 FieldName Index > # TableCol 1 Units NA > # TableCol 2 ColHeader SegId > # TableCol 2 FieldName Segmentation Id > # TableCol 2 Units NA > # TableCol 3 ColHeader NVoxels > # TableCol 3 FieldName Number of Voxels > # TableCol 3 Units unitless > # TableCol 4 ColHeader Volume_mm3 > # TableCol 4 FieldName Volume > # TableCol 4 Units mm^3 > # TableCol 5 ColHeader StructName > # TableCol 5 FieldName Structure Name > # TableCol 5 Units NA > # TableCol 6 ColHeader Mean > # TableCol 6 FieldName Intensity Mean > # TableCol 6 Units unknown > # TableCol 7 ColHeader StdDev > # TableCol 7 FieldName Itensity StdDev > # TableCol 7 Units unknown > # TableCol 8 ColHeader Min > # TableCol 8 FieldName Intensity Min > # TableCol 8 Units unknown > # TableCol 9 ColHeader Max > # TableCol 9 FieldName Intensity Max > # TableCol 9 Units unknown > # TableCol 10 ColHeader Range > # TableCol 10 FieldName Intensity Range > # TableCol 10 Units unknown > # NRows 114 > # NTableCols 10 > # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min > Max Range > 1 0 15692031 15692031.0 Unknown -74.0533 149.7173 -409.6000 212.1609 > 621.7609 > 2 2 223002 223002.0 Left-Cerebral-White-Matter -225.7412 41.4942 > -378.4684 43.0771 421.5454 > 3 4 5142 5142.0 Left-Lateral-Ventricle -213.5301 25.6550 -268.4635 > -140.5092 127.9543 > 4 5 210 210.0 Left-Inf-Lat-Vent -250.1857 11.2349 -268.3093 -227.5028 > 40.8065 > 5 7 12201 12201.0 Left-Cerebellum-White-Matter -184.3329 132.5210 > -314.1348 0.0000 314.1348 > 6 8 38822 38822.0 Left-Cerebellum-Cortex -106.5107 126.4406 -397.5404 > 0.0000 397.5404 > 7 10 7802 7802.0 Left-Thalamus-Proper -256.3931 10.4379 -280.3882 > -205.4267 74.9615 > 8 11 4000 4000.0 Left-Caudate -202.6371 20.4855 -256.5304 -151.9264 > 104.6040 > 9 12 6375 6375.0 Left-Putamen -225.6037 14.5390 -274.2597 -175.4577 > 98.8020 > 10 13 1502 1502.0 Left-Pallidum -253.1898 12.3024 -277.3420 -185.7775 > 91.5645 > 11 14 550 550.0 3rd-Ventricle -225.0951 31.5825 -306.7295 -134.6138 > 172.1157 > 12 15 964 964.0 4th-Ventricle -212.5151 112.4167 -288.3225 0.0000 > 288.3225 > 13 16 18186 18186.0 Brain-Stem -234.2281 112.8928 -319.7348 0.0000 > 319.7348 > 14 17 4114 4114.0 Left-Hippocampus -261.7396 17.4063 -339.8024 > -223.4028 116.3996 > 15 18 1513 1513.0 Left-Amygdala -253.4237 8.8525 -288.2225 -232.8777 > 55.3447 > 16 24 847 847.0 CSF -257.5531 13.5256 -300.9257 -212.2279 88.6977 > 17 26 535 535.0 Left-Accumbens-area -227.1246 45.3633 -360.7124 > -138.9498 221.7626 > 18 28 3786 3786.0 Left-VentralDC -270.4991 24.1379 -308.4358 -148.3388 > 160.0970 > 19 30 35 35.0 Left-vessel -239.3001 10.2992 -259.7188 -227.2777 32.4411 > 20 31 1442 1442.0 Left-choroid-plexus -230.4919 15.5479 -280.8550 > -169.9589 110.8961 > 21 41 223786 223786.0 Right-Cerebral-White-Matter -226.0802 45.5920 > -388.7630 99.2566 488.0197 > 22 43 4499 4499.0 Right-Lateral-Ventricle -218.3645 29.3800 -283.5730 > -136.7349 146.8381 > 23 44 124 124.0 Right-Inf-Lat-Vent -224.9743 6.5724 -238.9407 > -213.7236 25.2171 > 24 46 12584 12584.0 Right-Cerebellum-White-Matter -193.3710 131.2612 > -321.5745 0.0000 321.5745 > 25 47 39998 39998.0 Right-Cerebellum-Cortex -115.9971 131.6163 > -397.0068 0.0000 397.0068 > 26 49 7671 7671.0 Right-Thalamus-Proper -257.6761 12.1048 -286.1383 > -201.9509 84.1875 > 27 50 3771 3771.0 Right-Caudate -194.8961 24.1022 -261.2213 -130.2366 > 130.9848 > 28 51 5541 5541.0 Right-Putamen -207.9626 20.2756 -263.4107 -152.3473 > 111.0634 > 29 52 1586 1586.0 Right-Pallidum -240.4646 16.8542 -274.6204 -178.9617 > 95.6588 > 30 53 4340 4340.0 Right-Hippocampus -255.1402 15.5864 -317.2354 > -214.7629 102.4725 > 31 54 1443 1443.0 Right-Amygdala -223.3856 13.5761 -275.9869 -188.8713 > 87.1156 > 32 58 599 599.0 Right-Accumbens-area -233.9969 41.2913 -328.8579 > -130.0125 198.8454 > 33 60 3578 3578.0 Right-VentralDC -265.3871 29.2565 -302.4017 > -137.6554 164.7464 > 34 62 42 42.0 Right-vessel -204.7102 4.3293 -215.7804 -196.4114 19.3690 > 35 63 1778 1778.0 Right-choroid-plexus -234.2253 23.0682 -286.4693 > -173.1205 113.3488 > 36 72 5 5.0 5th-Ventricle -224.2637 0.6994 -224.9757 -223.0969 1.8788 > 37 77 1198 1198.0 WM-hypointensities -237.1980 23.6141 -288.2162 > -124.3671 163.8491 > 38 80 6 6.0 non-WM-hypointensities -219.0157 25.7339 -241.4550 > -178.7211 62.7339 > 39 85 240 240.0 Optic-Chiasm -339.9201 33.8276 -387.3214 -244.3237 > 142.9977 > 40 251 1125 1125.0 CC_Posterior -287.1999 13.0189 -328.2475 -253.4940 > 74.7535 > 41 252 474 474.0 CC_Mid_Posterior -258.9252 7.4909 -275.8824 -243.3831 > 32.4993 > 42 253 466 466.0 CC_Central -243.8036 9.1146 -260.0744 -213.7926 46.2818 > 43 254 506 506.0 CC_Mid_Anterior -220.1470 10.0537 -248.5798 -188.5451 > 60.0347 > 44 255 913 913.0 CC_Anterior -214.1350 20.9075 -243.5242 -150.2715 > 93.2527 > 45 1000 723 723.0 ctx-lh-unknown -268.9304 44.9523 -368.2704 -151.4314 > 216.8390 > 46 1001 2368 2368.0 ctx-lh-bankssts -181.3014 22.6124 -237.0966 > -91.1488 145.9478 > 47 1002 2124 2124.0 ctx-lh-caudalanteriorcingulate -166.5679 24.2600 > -239.7585 -107.8335 131.9250 > 48 1003 5407 5407.0 ctx-lh-caudalmiddlefrontal -138.6242 38.4188 > -223.4834 -4.1240 219.3594 > 49 1005 2805 2805.0 ctx-lh-cuneus -219.2092 24.4863 -307.2400 > -100.9523 206.2876 > 50 1006 1835 1835.0 ctx-lh-entorhinal -313.5578 37.2401 -400.2783 > -245.7666 154.5116 > 51 1007 9297 9297.0 ctx-lh-fusiform -271.4266 44.9975 -403.3750 > -178.3286 225.0465 > 52 1008 11208 11208.0 ctx-lh-inferiorparietal -198.1575 29.6503 > -337.2401 -97.1248 240.1152 > 53 1009 9229 9229.0 ctx-lh-inferiortemporal -292.8779 58.9245 > -402.0195 -139.4616 262.5579 > 54 1010 2200 2200.0 ctx-lh-isthmuscingulate -256.2006 13.6217 > -309.5894 -221.2736 88.3158 > 55 1011 10741 10741.0 ctx-lh-lateraloccipital -241.9617 44.5052 > -387.3303 -134.7086 252.6217 > 56 1012 6759 6759.0 ctx-lh-lateralorbitofrontal -234.8751 55.8340 > -391.7819 -116.4604 275.3214 > 57 1013 5512 5512.0 ctx-lh-lingual -252.9017 15.0886 -364.8814 > -199.6257 165.2558 > 58 1014 3917 3917.0 ctx-lh-medialorbitofrontal -224.2145 76.9983 > -385.2454 -15.3043 369.9411 > 59 1015 10136 10136.0 ctx-lh-middletemporal -215.7101 41.6577 > -379.8396 -89.4147 290.4249 > 60 1016 2054 2054.0 ctx-lh-parahippocampal -288.6394 39.2564 -387.4811 > -235.1773 152.3038 > 61 1017 3422 3422.0 ctx-lh-paracentral -233.0926 13.5023 -263.2673 > -170.3670 92.9003 > 62 1018 4574 4574.0 ctx-lh-parsopercularis -149.2349 39.6032 -217.8855 > 9.6249 227.5103 > 63 1019 1593 1593.0 ctx-lh-parsorbitalis -169.5554 35.9393 -282.0561 > -72.7232 209.3329 > 64 1020 3291 3291.0 ctx-lh-parstriangularis -144.1005 36.0805 > -230.1887 4.5093 234.6980 > 65 1021 1713 1713.0 ctx-lh-pericalcarine -231.6538 8.5455 -255.3997 > -203.6041 51.7957 > 66 1022 10227 10227.0 ctx-lh-postcentral -181.9029 37.4439 -299.1582 > -21.3713 277.7869 > 67 1023 2807 2807.0 ctx-lh-posteriorcingulate -230.5880 18.4718 > -274.6758 -173.2297 101.4461 > 68 1024 12919 12919.0 ctx-lh-precentral -183.6406 39.6604 -306.2378 > -40.3290 265.9088 > 69 1025 9442 9442.0 ctx-lh-precuneus -230.5928 15.9918 -306.5322 > -163.3685 143.1636 > 70 1026 2548 2548.0 ctx-lh-rostralanteriorcingulate -157.6567 39.7513 > -254.3800 -89.2986 165.0814 > 71 1027 13071 13071.0 ctx-lh-rostralmiddlefrontal -83.8164 67.7580 > -394.8940 134.8738 529.7678 > 72 1028 21736 21736.0 ctx-lh-superiorfrontal -122.8224 69.0962 > -316.2417 196.0131 512.2548 > 73 1029 12628 12628.0 ctx-lh-superiorparietal -221.9534 26.6104 > -364.8822 -107.6960 257.1862 > 74 1030 11394 11394.0 ctx-lh-superiortemporal -186.1106 40.3886 > -350.9529 -40.3714 310.5815 > 75 1031 10576 10576.0 ctx-lh-supramarginal -176.2239 42.3754 -354.6027 > -41.8400 312.7627 > 76 1032 595 595.0 ctx-lh-frontalpole -283.6195 82.6117 -394.6566 > -37.1957 357.4609 > 77 1033 2431 2431.0 ctx-lh-temporalpole -277.4131 30.0602 -374.9873 > -178.5805 196.4068 > 78 1034 1232 1232.0 ctx-lh-transversetemporal -210.0555 15.6700 > -241.2193 -159.1772 82.0421 > 79 1035 6246 6246.0 ctx-lh-insula -206.2323 18.6802 -262.2652 > -161.5516 100.7136 > 80 2000 486 486.0 ctx-rh-unknown -235.6483 29.0666 -303.1176 -176.8145 > 126.3031 > 81 2001 1910 1910.0 ctx-rh-bankssts -165.2222 33.7818 -232.1002 > -46.5102 185.5900 > 82 2002 1806 1806.0 ctx-rh-caudalanteriorcingulate -173.3855 25.8466 > -243.1284 -116.1957 126.9327 > 83 2003 5075 5075.0 ctx-rh-caudalmiddlefrontal -164.3494 26.3759 > -240.7866 -75.2611 165.5255 > 84 2005 3408 3408.0 ctx-rh-cuneus -241.5760 20.8712 -370.4695 > -182.1323 188.3371 > 85 2006 1327 1327.0 ctx-rh-entorhinal -291.8428 46.4631 -397.5590 > -204.5806 192.9784 > 86 2007 8621 8621.0 ctx-rh-fusiform -277.8799 38.7263 -398.6075 > -180.0617 218.5457 > 87 2008 12648 12648.0 ctx-rh-inferiorparietal -203.4482 32.5607 > -354.4304 -108.6639 245.7665 > 88 2009 9708 9708.0 ctx-rh-inferiortemporal -264.8841 66.1289 > -400.9079 -77.6510 323.2569 > 89 2010 2341 2341.0 ctx-rh-isthmuscingulate -265.9744 15.0482 > -310.5466 -229.7068 80.8398 > 90 2011 11259 11259.0 ctx-rh-lateraloccipital -249.5812 43.6094 > -392.7505 -137.7381 255.0125 > 91 2012 6527 6527.0 ctx-rh-lateralorbitofrontal -205.4345 57.0364 > -379.2646 -52.3057 326.9589 > 92 2013 6336 6336.0 ctx-rh-lingual -270.3578 14.8451 -375.5747 > -218.0085 157.5662 > 93 2014 4191 4191.0 ctx-rh-medialorbitofrontal -217.2649 76.5895 > -381.2976 -28.7736 352.5240 > 94 2015 12028 12028.0 ctx-rh-middletemporal -166.6064 53.4122 > -370.0519 42.7304 412.7823 > 95 2016 1888 1888.0 ctx-rh-parahippocampal -291.0411 34.0657 -386.3947 > -243.3085 143.0863 > 96 2017 3708 3708.0 ctx-rh-paracentral -239.3826 13.8495 -269.6346 > -180.5456 89.0890 > 97 2018 4159 4159.0 ctx-rh-parsopercularis -124.4858 40.3498 -206.4271 > 34.1722 240.5993 > 98 2019 2191 2191.0 ctx-rh-parsorbitalis -127.3451 51.8375 -295.4905 > 11.9257 307.4162 > 99 2020 3475 3475.0 ctx-rh-parstriangularis -84.7648 53.4594 -190.6588 > 101.4333 292.0922 > 100 2021 2007 2007.0 ctx-rh-pericalcarine -250.7360 12.8022 -325.5542 > -173.3052 152.2490 > 101 2022 9599 9599.0 ctx-rh-postcentral -200.0130 39.5983 -299.2733 > -53.0320 246.2413 > 102 2023 2682 2682.0 ctx-rh-posteriorcingulate -235.8722 18.9181 > -285.3879 -169.6746 115.7133 > 103 2024 13064 13064.0 ctx-rh-precentral -187.4779 45.2968 -282.6149 > -29.0527 253.5621 > 104 2025 9932 9932.0 ctx-rh-precuneus -240.3425 16.8327 -338.1844 > -166.0625 172.1219 > 105 2026 1904 1904.0 ctx-rh-rostralanteriorcingulate -159.2295 47.7504 > -328.0970 -69.7684 258.3285 > 106 2027 13009 13009.0 ctx-rh-rostralmiddlefrontal -76.5586 64.9635 > -388.0326 139.6366 527.6691 > 107 2028 19644 19644.0 ctx-rh-superiorfrontal -136.2872 62.1116 > -250.7094 117.8829 368.5923 > 108 2029 12094 12094.0 ctx-rh-superiorparietal -231.3411 27.9200 > -377.6333 -148.5919 229.0414 > 109 2030 11110 11110.0 ctx-rh-superiortemporal -144.3232 45.9093 > -303.4510 -4.4534 298.9976 > 110 2031 11218 11218.0 ctx-rh-supramarginal -183.9012 36.5165 > -339.1638 -46.8222 292.3416 > 111 2032 735 735.0 ctx-rh-frontalpole -225.4727 127.2478 -388.1892 > 80.9771 469.1663 > 112 2033 1999 1999.0 ctx-rh-temporalpole -237.0710 32.1687 -352.4148 > -168.1622 184.2525 > 113 2034 948 948.0 ctx-rh-transversetemporal -197.8872 24.2673 > -238.0692 -137.0336 101.0356 > 114 2035 6087 6087.0 ctx-rh-insula -179.7504 28.2217 -253.5477 > -103.3342 150.2135 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
