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. 314.1348
> 6 8 38822 38822.0 Left-Cerebellum-Cortex -106.5107 126.4406 -397.5404
> 0. 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.
> 288.3225
> 13 16 18186 18186.0 Brain-Stem -234.2281 112.8928 -319.7348 0.
> 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 -224.9
