[Freesurfer] recon-all error (sample tutorial data)
Dear freesurfer users, I have recently downloaded freesurfer (virtualbox verion) and started testing using the sample data bert. I got the following error (I also tried on my data and the same error occured). Any suggestions? FINAL ITERATIVE TEMPLATE DEFORMATION Compute Local values csf/gray Fine Segmentation...46 iterations mghRead: encountered error executing: 'zcat /usr/local/freesurfer/subjects/bert/mri/T1.mgz',frame -1, errno 12 mri_strip_skull: done peeling brain Brain Size = 1793357 voxels, voxel volume = 1.000 mm3 = 1793357 mmm3 = 1793.357 cm3 mri_watershed Error: read failed Linux freesurfer-virtual 2.6.28-17-generic #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Thu Dec 17 17:20:18 EST 2009 Thank you. Hui Jing Yu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] aseg.stats
Dear Freesurfer Experts, I have ran recon-all on a T1 SPGR image of a control subject without error. The outputs look reasonable (visually). However, the numbers I got from aseg.stats do not make sense (they are way off). Any thoughts? # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject AH --surf-wm-vol --ctab /mrbin/freesurfer.cver/ASegStatsLUT.txt # sysname Linux # machine x86_64 # anatomy_type volume # # SUBJECTS_DIR /freesurfer.v4.50/subjects # subjectname CTRL # BrainMaskFile mri/brainmask.mgz # BrainMaskFileTimeStamp 2009/12/28 13:45:15 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1403481, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1403481.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1021869.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1034494, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1034494.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1218358.332484, mm^3 # SegVolFile mri/aseg.mgz # SegVolFileTimeStamp 2009/12/28 20:51:43 # ColorTable /freesurfer.cver/ASegStatsLUT.txt # ColorTableTimeStamp 2009/08/11 08:24:37 # InVolFile mri/norm.mgz # InVolFileTimeStamp 2009/12/28 14:25:34 # InVolFrame 0 # PVVolFile mri/norm.mgz # PVVolFileTimeStamp 2009/12/28 14:25:34 # surface-based-volume mm3 lh-cerebral-white-matter 192622.906250 # surface-based-volume mm3 rh-cerebral-white-matter 198347.390625 # surface-based-volume mm3 tot-cerebral-white-matter 390970.296875 # ExcludeSegId 0 # 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 normMean # TableCol 6 FieldName Intensity normMean # TableCol 6 Units MR # TableCol 7 ColHeader normStdDev # TableCol 7 FieldName Itensity normStdDev # TableCol 7 Units MR # TableCol 8 ColHeader normMin # TableCol 8 FieldName Intensity normMin # TableCol 8 Units MR # TableCol 9 ColHeader normMax # TableCol 9 FieldName Intensity normMax # TableCol 9 Units MR # TableCol 10 ColHeader normRange # TableCol 10 FieldName Intensity normRange # TableCol 10 Units MR # NRows 49 # NTableCols 10 # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 2187032 187032.0 Left-Cerebral-White-Matter 102.5864 7.894842. 128.86. 2 3216661 216661.0 Left-Cerebral-Cortex 75.4785 9.626220. 120. 100. 3 4 5897 5897.0 Left-Lateral-Ventricle46.5982 12.117821. 103.82. 4 5 111 111.0 Left-Inf-Lat-Vent 53.2529 9.173031.75.44. 5 7 1812418124.0 Left-Cerebellum-White-Matter 86.7241 5.804134. 108.74. 6 8 4897148971.0 Left-Cerebellum-Cortex67.2554 9.067220.94.74. 7 10 5893 5893.0 Left-Thalamus-Proper 94.6949 7.516351. 115.64. 8 11 2861 2861.0 Left-Caudate 89.1393 6.879154. 112.58. 9 12 4485 4485.0 Left-Putamen 92.3673 5.676859. 107.48. 10 13 1403 1403.0 Left-Pallidum 99.4880 9.096938. 117.79. 11 14 848 848.0 3rd-Ventricle 53.1839 14.1313 9.88.79. 12 15 1595 1595.0 4th-Ventricle 43.9798 10.932119.84.65. 13 16 2002220022.0 Brain-Stem87.3585 9.3424 0. 111. 111. 14 17 3923 3923.0 Left-Hippocampus 79.3928 7.251147. 105.58. 15 18 1332 1332.0 Left-Amygdala 75.6713 6.198053.93.40. 16 24 1112 1112.0 CSF 61.4318 13.156810. 115. 105.
[Freesurfer] Subcortical Volume Calculation
Dear Freesurfer users, I am wondering how are the volumes calculated from stats such aseg.stat. When I export the aseg and do a voxel count and multiple the volume per voxel, my total volume is different from that is given by the stats. For example, the hippocampal volume given by aseg.stats for one of my controls is 4000 cm3, but when I export the aseg.mgz into matlab and do a voxel count (my original voxel volume is 1mm3 isotropic) for that labeled mask, the total volume is aorund 3000 cm3. Does freesurfer does some sort of intensity normalization or partial volume correction? Even if so, the magnitude of difference is large that I am puzzled. Thank you very much. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Subcortical Volume Calculation
Thank you for the quick response. If you do a partial volume correction, I would think the volumes from freesurfer would be less than simply counting all voxels, but it seems to be the opposite. Any thoughts? - Original Message - From: Bruce Fischl Date: Monday, February 15, 2010 10:42 am Subject: Re: [Freesurfer] Subcortical Volume Calculation To: Hui J Yu Cc: freesurfer@nmr.mgh.harvard.edu > yes, we do a partial volume correction of the volumes, > accounting for the fraction of the structure in each border voxel. > > cheers > Bruce > On Mon, 15 Feb 2010, Hui J Yu wrote: > > >Dear Freesurfer users, > > > >I am wondering how are the volumes calculated from stats such > aseg.stat. When I export the aseg and do a voxel count and > multiple the volume per voxel, my total volume is different from > that is given by the stats. For example, the hippocampal > volume given by aseg.stats for one of my controls is 4000 cm3, > but when I export the aseg.mgz into matlab and do a voxel count > (my original voxel volume is 1mm3 isotropic) for that labeled > mask, the total volume is aorund 3000 cm3. Does freesurfer > does some sort of intensity normalization or partial volume > correction? Even if so, the magnitude of difference is > large that I am puzzled. > > > >Thank you very much. > > > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] qcache for multiple subjects
Dear freesurfer users, After running recon-all for all subjects, I started running qcache using the following commands: (in the subject directory) foreach i (*) recon-all -s $i -qcache end However, the process was terminated/stopped. Is there a way to resume the process (like what you will have with -make all). Thank you. ___ 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.
