Re: [Freesurfer] BrainSegVolNotVent
I think you may be using a very old version of mri_segstats. The version 5.3 mri_segstats gives: # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1290472.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1279674.00, mm^3 On 07/18/2016 02:46 PM, Eryilmaz, H. Hamdi wrote: > Hi Doug, > > Thanks for your reply. I just sent you this subject's directory via file > drop. Please note that there are two aseg.stats files under the 'stats' > folder: > > aseg.stats: generated by the mri_segstats command I ran including the > --brainmask mri/brainmask.mgz --brain-vol-from-seg flags. > aseg_original.stats: generated by the original recon-all command. > > Let me know if you need anything else. > > Best, > Hamdi > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Monday, July 18, 2016 1:33 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] BrainSegVolNotVent > > That does look suspicious, esp since BrainSegNotVent should be smaller > than BrainSeg. Can you tar up the subject and send it to me? It may be > some strange incompatibility with v5 > > > On 07/07/2016 03:50 PM, Eryilmaz, H. Hamdi wrote: >> Hello Doug and Freesurfers, >> >> I am trying to compute a structural measure called >> 'BrainSegVolNotVent' as an approximate value of total brain volume. >> 'BrainSegVolNotVent' is now present in aseg.stats files but the >> dataset I'm working on was preprocessed using FS 5.0, which did not >> produce this variable. Per your advice I found in a previous email, I >> reran mri_segstats adding the flags --brainmask mri/brainmask.mgz >> --brain-vol-from-seg. >> >> The new aseg.stats file contains the following lines that were added >> after running this command: >> >> # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1667093, unitless >> # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1667093.00, mm^3 >> # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation >> Volume Without Ventricles, 232145.00, mm^3 >> # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, >> 1410666, unitless >> # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 1410666.00, mm^3 >> >> The numbers look a bit odd. BrainSegVol and BrainSegVolNotVent should >> normally be close to each other, right? Also unitless values such as >> BrainSegNVox and BrainMaskNVox seem to be equal to their corresponding >> volumetric values. >> >> Do you have any idea what might have gone wrong? Here's the command I >> ran: >> >> mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv >> mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent >> --subcortgray --in mri/norm.mgz --in-intensity-name norm >> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol >> --totalgray --ctab /usr/local/freesurfer/stable5_0_0/ASegStatsLUT.txt >> --subject SUBJECT_ID --brainmask mri/brainmask.mgz --brain-vol-from-seg >> >> >> Thanks very much for your help! >> >> Best, >> Hamdi >> >> >> >> >> >> ___ >> 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 > > ___ > 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 Freesu
Re: [Freesurfer] BrainSegVolNotVent
Hi Doug, Thanks for your reply. I just sent you this subject's directory via file drop. Please note that there are two aseg.stats files under the 'stats' folder: aseg.stats: generated by the mri_segstats command I ran including the --brainmask mri/brainmask.mgz --brain-vol-from-seg flags. aseg_original.stats: generated by the original recon-all command. Let me know if you need anything else. Best, Hamdi From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2016 1:33 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] BrainSegVolNotVent That does look suspicious, esp since BrainSegNotVent should be smaller than BrainSeg. Can you tar up the subject and send it to me? It may be some strange incompatibility with v5 On 07/07/2016 03:50 PM, Eryilmaz, H. Hamdi wrote: > Hello Doug and Freesurfers, > > I am trying to compute a structural measure called > 'BrainSegVolNotVent' as an approximate value of total brain volume. > 'BrainSegVolNotVent' is now present in aseg.stats files but the > dataset I'm working on was preprocessed using FS 5.0, which did not > produce this variable. Per your advice I found in a previous email, I > reran mri_segstats adding the flags --brainmask mri/brainmask.mgz > --brain-vol-from-seg. > > The new aseg.stats file contains the following lines that were added > after running this command: > > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, > 1667093, unitless > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1667093.00, mm^3 > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation > Volume Without Ventricles, 232145.00, mm^3 > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, > 1410666, unitless > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, > 1410666.00, mm^3 > > The numbers look a bit odd. BrainSegVol and BrainSegVolNotVent should > normally be close to each other, right? Also unitless values such as > BrainSegNVox and BrainMaskNVox seem to be equal to their corresponding > volumetric values. > > Do you have any idea what might have gone wrong? Here's the command I > ran: > > mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv > mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent > --subcortgray --in mri/norm.mgz --in-intensity-name norm > --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol > --totalgray --ctab /usr/local/freesurfer/stable5_0_0/ASegStatsLUT.txt > --subject SUBJECT_ID --brainmask mri/brainmask.mgz --brain-vol-from-seg > > > Thanks very much for your help! > > Best, > Hamdi > > > > > > ___ > 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 ___ 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.
Re: [Freesurfer] BrainSegVolNotVent
That does look suspicious, esp since BrainSegNotVent should be smaller than BrainSeg. Can you tar up the subject and send it to me? It may be some strange incompatibility with v5 On 07/07/2016 03:50 PM, Eryilmaz, H. Hamdi wrote: > Hello Doug and Freesurfers, > > I am trying to compute a structural measure called > 'BrainSegVolNotVent' as an approximate value of total brain volume. > 'BrainSegVolNotVent' is now present in aseg.stats files but the > dataset I'm working on was preprocessed using FS 5.0, which did not > produce this variable. Per your advice I found in a previous email, I > reran mri_segstats adding the flags --brainmask mri/brainmask.mgz > --brain-vol-from-seg. > > The new aseg.stats file contains the following lines that were added > after running this command: > > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, > 1667093, unitless > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1667093.00, mm^3 > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation > Volume Without Ventricles, 232145.00, mm^3 > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, > 1410666, unitless > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, > 1410666.00, mm^3 > > The numbers look a bit odd. BrainSegVol and BrainSegVolNotVent should > normally be close to each other, right? Also unitless values such as > BrainSegNVox and BrainMaskNVox seem to be equal to their corresponding > volumetric values. > > Do you have any idea what might have gone wrong? Here's the command I > ran: > > mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv > mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent > --subcortgray --in mri/norm.mgz --in-intensity-name norm > --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol > --totalgray --ctab /usr/local/freesurfer/stable5_0_0/ASegStatsLUT.txt > --subject SUBJECT_ID --brainmask mri/brainmask.mgz --brain-vol-from-seg > > > Thanks very much for your help! > > Best, > Hamdi > > > > > > ___ > 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.
