Re: [Freesurfer] Recon-all on 2 different DCM files

Bruce Fischl Mon, 17 Nov 2014 08:42:04 -0800

Hi Sravan

if you only have 25 files or so then neither one is likely to give yougood results. Typically you need at least 96 or 128 slices to get towhole-brain high enough resolution to get reasonable morphometry results


cheers
Bruce

OnMon, 17 Nov 2014, Mattevada, Sravan wrote:

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


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Re: [Freesurfer] Recon-all on 2 different DCM files

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