I have a CD with one session of MRI scans for one person. Under the DICOM folder I have 9 folders. Each folder typically has a series of 25 files and each series is different position (ex. Starts from the Top, starts from the front etc.) When I run dcmunpack I get the result as below
1 LOCALIZER3PLANE 5 20 40 0.546875 ROW 180 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000000/IM000003 2 T1SESAG 8 345 90 0.8984375 ROW 140 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000001/IM000011 3 T2TSEAX 85 4170 180 0.8984375 ROW 110 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000002/IM000011 4 T1SEAX 8 410 90 0.8984375 ROW 140 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000003/IM000011 5 T2FLAIRAX 117 9000 180 0.8984375 ROW 130 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000004/IM000011 6 T2FL2DAXHEMO 27 855 20 0.8984375 ROW 80 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000005/IM000011 7 AXep2d_diff_2scan_trace 98 4100 90 1.796875\1.796875 COL 1260 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000006/IM000011 8 AXep2d_diff_2scan_trace_ADC 98 4100 90 1.796875\1.796875 COL 1260 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000007/IM000011 9 T2TSECOROBL 87 4260 180 0.4296875 ROW 110 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000008/IM000011 I started recon-all on #2 and #4. I went through the stats for #2 and #4 expecting the results to be similar but I am unsure if they are and also which one to consider for further analysis. Thanks Sravan -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, November 17, 2014 9:11 AM To: Freesurfer support list Subject: Re: [Freesurfer] Recon-all on 2 different DCM files is this two different scans of the same person? Was it during the same session or on different days? It would also be easier for us if you just post the percent changes that you are asking about cheers Bruce On Mon, 17 Nov 2014, Mattevada, Sravan wrote: > > Hey Guys, > > > > I did a recon-all on 2 different dcm files the same subject. > > I posted the stats of the 2 recons below (blue and green). > > Can anyone please tell me if both the results are close enough to be > considered as the same person? > > > > Thanks > > > > > > # Title Segmentation Statistics > > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, > 1147149.000000, > mm^3 > > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation > Volume Without Ventricles, 1106755.000000, mm^3 > > # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain > Segmentation Volume Without Ventricles from Surf, 1105797.602179, mm^3 > > # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter > volume, 178265.204424, mm^3 > > # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter > volume, 178573.457404, mm^3 > > # Measure Cortex, CortexVol, Total cortical gray matter volume, > 356838.661828, mm^3 > > # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left > hemisphere cortical white matter volume, 278821.965888, mm^3 > > # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right > hemisphere cortical white matter volume, 288297.974464, mm^3 > > # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical > white matter volume, 567119.940351, mm^3 > > # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, > 51897.000000, mm^3 > > # Measure TotalGray, TotalGrayVol, Total gray matter volume, > 502065.661828, > mm^3 > > # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, > 1014280.602179, mm^3 > > # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, > Supratentorial volume, 979180.602179, mm^3 > > # Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, > Supratentorial volume voxel count, 976438.000000, mm^3 > > # Measure Mask, MaskVol, Mask Volume, 1677160.000000, mm^3 > > # Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of > BrainSegVol to eTIV, 0.771851, unitless > > # Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, > 1.128466, unitless > > # Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh > surfaces prior to fixing, 81, unitless > > # Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh > surfaces prior to fixing, 92, unitless > > # Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in > surfaces prior to fixing, 173, unitless > > # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total > Intracranial Volume, 1486230.461972, mm^3 > > # Excluding Cortical Gray and White Matter > > # ExcludeSegId 0 2 3 41 42 > > # VoxelVolume_mm3 1 > > # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean > normStdDev normMin normMax normRange > > 1 4 12614 12613.8 Left-Lateral-Ventricle > 51.1769 > 11.7938 28.0000 105.0000 77.0000 > > 2 5 706 706.0 Left-Inf-Lat-Vent > 60.9081 > 9.7501 30.0000 83.0000 53.0000 > > 3 7 16205 16205.0 Left-Cerebellum-White-Matter > 94.4526 > 5.0202 36.0000 107.0000 71.0000 > > 4 8 46866 46866.0 Left-Cerebellum-Cortex > 76.8904 > 9.8783 34.0000 117.0000 83.0000 > > 5 10 7843 7843.2 Left-Thalamus-Proper > 103.1140 > 8.5790 59.0000 121.0000 62.0000 > > 6 11 2734 2734.4 Left-Caudate > 90.8078 > 9.9212 61.0000 111.0000 50.0000 > > 7 12 2748 2747.5 Left-Putamen > 98.2484 > 5.0525 79.0000 112.0000 33.0000 > > 8 13 1640 1640.1 Left-Pallidum > 104.2372 > 3.9806 90.0000 115.0000 25.0000 > > 9 14 2022 2022.4 3rd-Ventricle > 57.2360 > 11.2028 33.0000 91.0000 58.0000 > > 10 15 895 895.1 4th-Ventricle > 53.9897 > 7.5234 29.0000 71.0000 42.0000 > > 11 16 20089 20089.4 Brain-Stem > 88.9277 > 11.8940 34.0000 113.0000 79.0000 > > 12 17 4777 4777.2 Left-Hippocampus > 83.7333 > 8.3881 53.0000 106.0000 53.0000 > > 13 18 1245 1245.3 Left-Amygdala > 86.5452 > 6.1434 59.0000 102.0000 43.0000 > > 14 24 2417 2417.3 CSF > 66.2343 > 11.6273 38.0000 105.0000 67.0000 > > 15 26 202 201.7 Left-Accumbens-area > 86.4204 > 6.8440 65.0000 99.0000 34.0000 > > 16 28 4252 4252.3 Left-VentralDC > 98.6040 > 11.8373 50.0000 120.0000 70.0000 > > 17 30 0 0.0 Left-vessel > 0.0000 > 0.0000 0.0000 0.0000 0.0000 > > 18 31 1125 1125.3 Left-choroid-plexus > 63.5452 > 11.2806 37.0000 96.0000 59.0000 > > 19 43 19334 19334.1 Right-Lateral-Ventricle > 47.7236 > 11.9759 26.0000 96.0000 70.0000 > > 20 44 381 380.6 Right-Inf-Lat-Vent > 59.5799 > 9.3492 31.0000 84.0000 53.0000 > > 21 46 22199 22199.2 Right-Cerebellum-White-Matter > 92.4601 > 4.8787 45.0000 109.0000 64.0000 > > 22 47 44564 44564.1 Right-Cerebellum-Cortex > 74.0031 > 9.9533 32.0000 105.0000 73.0000 > > 23 49 6571 6571.4 Right-Thalamus-Proper > 99.6773 > 9.6696 53.0000 116.0000 63.0000 > > 24 50 2979 2978.8 Right-Caudate > 84.3075 > 11.2002 54.0000 112.0000 58.0000 > > 25 51 3272 3271.8 Right-Putamen > 100.6600 > 4.7432 77.0000 114.0000 37.0000 > > 26 52 1471 1470.7 Right-Pallidum > 104.8643 > 3.8221 89.0000 117.0000 28.0000 > > 27 53 4198 4198.0 Right-Hippocampus > 84.3948 > 7.0679 53.0000 108.0000 55.0000 > > 28 54 1463 1463.2 Right-Amygdala > 84.8762 > 6.6090 56.0000 99.0000 43.0000 > > 29 58 308 307.5 Right-Accumbens-area > 93.4572 > 5.3543 78.0000 108.0000 30.0000 > > 30 60 3574 3573.8 Right-VentralDC > 95.2002 > 14.7423 39.0000 122.0000 83.0000 > > 31 62 0 0.0 Right-vessel > 0.0000 > 0.0000 0.0000 0.0000 0.0000 > > 32 63 1380 1379.5 Right-choroid-plexus > 62.8493 > 10.5738 35.0000 101.0000 66.0000 > > 33 72 16 16.3 5th-Ventricle > 63.4444 > 7.9204 49.0000 78.0000 29.0000 > > 34 77 7309 7309.1 WM-hypointensities > 79.9911 > 11.7723 40.0000 108.0000 68.0000 > > 35 78 0 0.0 Left-WM-hypointensities > 0.0000 > 0.0000 0.0000 0.0000 0.0000 > > 36 79 0 0.0 Right-WM-hypointensities > 0.0000 > 0.0000 0.0000 0.0000 0.0000 > > 37 80 10 9.5 non-WM-hypointensities > 71.1667 > 14.5404 53.0000 94.0000 41.0000 > > 38 81 0 0.0 Left-non-WM-hypointensities > 0.0000 > 0.0000 0.0000 0.0000 0.0000 > > 39 82 0 0.0 Right-non-WM-hypointensities > 0.0000 > 0.0000 0.0000 0.0000 0.0000 > > 40 85 339 338.6 Optic-Chiasm > 74.9807 > 16.3591 38.0000 109.0000 71.0000 > > 41 251 832 832.5 CC_Posterior > 105.5668 > 12.5924 67.0000 127.0000 60.0000 > > 42 252 343 342.6 CC_Mid_Posterior > 98.9137 > 10.3627 67.0000 117.0000 50.0000 > > 43 253 267 266.6 CC_Central > 104.3759 > 7.1576 80.0000 113.0000 33.0000 > > 44 254 284 284.1 CC_Mid_Anterior > 106.1203 > 7.2499 80.0000 116.0000 36.0000 > > 45 255 511 511.1 CC_Anterior > 106.4299 > 8.9098 67.0000 119.0000 52.0000 > > > > # Title Segmentation Statistics > > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, > 1141594.000000, > mm^3 > > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation > Volume Without Ventricles, 1101450.000000, mm^3 > > # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain > Segmentation Volume Without Ventricles from Surf, 1100508.937477, mm^3 > > # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter > volume, 191427.646717, mm^3 > > # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter > volume, 193305.757680, mm^3 > > # Measure Cortex, CortexVol, Total cortical gray matter volume, > 384733.404398, mm^3 > > # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left > hemisphere cortical white matter volume, 261874.458124, mm^3 > > # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right > hemisphere cortical white matter volume, 270384.074956, mm^3 > > # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical > white matter volume, 532258.533079, mm^3 > > # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, > 49354.000000, mm^3 > > # Measure TotalGray, TotalGrayVol, Total gray matter volume, > 530741.404398, > mm^3 > > # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, > 1003805.937477, mm^3 > > # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, > Supratentorial volume, 969153.937477, mm^3 > > # Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, > Supratentorial volume voxel count, 966844.000000, mm^3 > > # Measure Mask, MaskVol, Mask Volume, 1653467.000000, mm^3 > > # Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of > BrainSegVol to eTIV, 0.734385, unitless > > # Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, > 1.063672, unitless > > # Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh > surfaces prior to fixing, 137, unitless > > # Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh > surfaces prior to fixing, 149, unitless > > # Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in > surfaces prior to fixing, 286, unitless > > # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total > Intracranial Volume, 1554489.673066, mm^3 > > # Excluding Cortical Gray and White Matter > > # ExcludeSegId 0 2 3 41 42 > > # VoxelVolume_mm3 1 > > # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean > normStdDev normMin normMax normRange > > 1 4 11624 11623.6 Left-Lateral-Ventricle > 50.4191 > 11.8898 26.0000 111.0000 85.0000 > > 2 5 613 613.0 Left-Inf-Lat-Vent > 62.7041 > 8.9657 36.0000 84.0000 48.0000 > > 3 7 17895 17894.7 Left-Cerebellum-White-Matter > 93.5453 > 5.7395 36.0000 176.0000 140.0000 > > 4 8 46848 46847.7 Left-Cerebellum-Cortex > 75.2992 > 10.4832 32.0000 137.0000 105.0000 > > 5 10 7742 7741.9 Left-Thalamus-Proper > 102.7636 > 9.1489 56.0000 122.0000 66.0000 > > 6 11 2282 2281.5 Left-Caudate > 98.5579 > 8.8743 69.0000 123.0000 54.0000 > > 7 12 2832 2831.9 Left-Putamen > 98.5576 > 6.2032 75.0000 114.0000 39.0000 > > 8 13 1341 1341.1 Left-Pallidum > 103.9716 > 5.0861 83.0000 116.0000 33.0000 > > 9 14 2279 2279.2 3rd-Ventricle > 49.9377 > 10.3587 30.0000 89.0000 59.0000 > > 10 15 1058 1058.5 4th-Ventricle > 53.5181 > 8.1795 31.0000 79.0000 48.0000 > > 11 16 21113 21112.6 Brain-Stem > 90.0067 > 11.5625 32.0000 126.0000 94.0000 > > 12 17 4621 4620.9 Left-Hippocampus > 85.4185 > 8.0210 51.0000 108.0000 57.0000 > > 13 18 1288 1287.9 Left-Amygdala > 89.0411 > 5.3142 68.0000 100.0000 32.0000 > > 14 24 2181 2180.9 CSF > 63.2374 > 11.2796 37.0000 103.0000 66.0000 > > 15 26 285 284.5 Left-Accumbens-area > 91.7901 > 6.2213 69.0000 107.0000 38.0000 > > 16 28 4002 4002.0 Left-VentralDC > 98.2775 > 11.9238 53.0000 120.0000 67.0000 > > 17 30 0 0.0 Left-vessel > 0.0000 > 0.0000 0.0000 0.0000 0.0000 > > 18 31 1715 1715.5 Left-choroid-plexus > 62.6751 > 11.3107 31.0000 100.0000 69.0000 > > 19 43 19174 19173.7 Right-Lateral-Ventricle > 46.8736 > 11.6110 27.0000 94.0000 67.0000 > > 20 44 198 197.9 Right-Inf-Lat-Vent > 61.6270 > 6.8874 46.0000 80.0000 34.0000 > > 21 46 21541 21541.4 Right-Cerebellum-White-Matter > 91.7927 > 5.0592 49.0000 107.0000 58.0000 > > 22 47 48243 48243.4 Right-Cerebellum-Cortex > 73.3856 > 10.2191 36.0000 98.0000 62.0000 > > 23 49 6367 6366.8 Right-Thalamus-Proper > 99.7574 > 9.0787 57.0000 118.0000 61.0000 > > 24 50 2594 2594.4 Right-Caudate > 85.5413 > 11.7252 49.0000 116.0000 67.0000 > > 25 51 3463 3463.1 Right-Putamen > 100.7573 > 5.6687 72.0000 116.0000 44.0000 > > 26 52 761 760.5 Right-Pallidum > 96.1806 > 7.6082 70.0000 115.0000 45.0000 > > 27 53 4180 4180.0 Right-Hippocampus > 85.4995 > 8.1312 53.0000 107.0000 54.0000 > > 28 54 1205 1205.2 Right-Amygdala > 86.3778 > 6.1255 61.0000 98.0000 37.0000 > > 29 58 326 326.1 Right-Accumbens-area > 92.3921 > 7.5403 70.0000 112.0000 42.0000 > > 30 60 3659 3659.1 Right-VentralDC > 92.1746 > 15.4662 35.0000 119.0000 84.0000 > > 31 62 0 0.0 Right-vessel > 0.0000 > 0.0000 0.0000 0.0000 0.0000 > > 32 63 1941 1941.4 Right-choroid-plexus > 62.5491 > 9.8952 36.0000 92.0000 56.0000 > > 33 72 1 1.0 5th-Ventricle > 79.0000 > 0.0000 79.0000 79.0000 0.0000 > > 34 77 8877 8877.1 WM-hypointensities > 79.8507 > 12.8359 32.0000 116.0000 84.0000 > > 35 78 0 0.0 Left-WM-hypointensities > 0.0000 > 0.0000 0.0000 0.0000 0.0000 > > 36 79 0 0.0 Right-WM-hypointensities > 0.0000 > 0.0000 0.0000 0.0000 0.0000 > > 37 80 30 29.6 non-WM-hypointensities > 70.0769 > 10.2837 50.0000 88.0000 38.0000 > > 38 81 0 0.0 Left-non-WM-hypointensities > 0.0000 > 0.0000 0.0000 0.0000 0.0000 > > 39 82 0 0.0 Right-non-WM-hypointensities > 0.0000 > 0.0000 0.0000 0.0000 0.0000 > > 40 85 401 401.0 Optic-Chiasm > 63.0072 > 9.7281 42.0000 91.0000 49.0000 > > 41 251 309 308.9 CC_Posterior > 103.6121 > 8.5291 77.0000 123.0000 46.0000 > > 42 252 198 198.4 CC_Mid_Posterior > 91.1027 > 6.3446 78.0000 105.0000 27.0000 > > 43 253 264 263.9 CC_Central > 90.3532 > 6.4921 72.0000 106.0000 34.0000 > > 44 254 120 120.4 CC_Mid_Anterior > 88.3944 > 6.8912 73.0000 108.0000 35.0000 > > 45 255 179 178.7 CC_Anterior > 93.0686 > 10.4366 74.0000 114.0000 40.0000 > > > > > > Sravan Mattevada, MSCS > > Computer Prog. Analyst III > > UNT Health > > Ph . 817 735 0499 > > > > > _______________________________________________ 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.
