Something weird is happening with mri_vol2surf - even though the data looks great, the values are odd which carries over when I try to average with mri_concat. I would just like to get percentage values with mri_concat.
thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Mon, Oct 17, 2016 at 5:21 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wrote: > Hi Doug > > *Here is what I ran:* > > *trisanna@kaplan:~$ mri_vol2surf --mov > /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.mnc --o > /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz --hemi lh > --surf pial --regheader icbm-113* > srcvol = /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.mnc > srcreg unspecified > srcregold = 0 > srcwarp unspecified > surf = pial > hemi = lh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > Computing registration from header. > Using /data-01/trisanna/freesurfer/icbm-113/mri/orig.mgz as target > reference. > Reading surface /data-01/trisanna/freesurfer/icbm-113/surf/lh.pial > Done reading source surface > Mapping Source Volume onto Source Subject Surface > 1 0 0 0 > using old > Done mapping volume to surface > Number of source voxels hit = 53960 > Writing to /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz > Dim: 159741 1 1 > > When I open this in Freeview, the values are either 0 or 255 (see attached > image). However, they were binary (0 or 1) in the label_aalf.mnc input > file... > > Trisanna > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Wed, Oct 12, 2016 at 2:09 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> Hmmm, I don't know what could be going on. Can you send the command line >> and all terminal output? >> >> >> On 10/06/2016 10:37 PM, Trisanna Sprung-Much wrote: >> > Hi Doug >> > >> > So the pixel values are 0 and 1 *in the original .mnc*. It seems that >> > after performing mri_vol2surf they become 0 and 255, and stay this way >> > after mri_surf2surf as well. So, why would mri_vol2surf be changing >> > the values? >> > >> > Trisanna >> > >> > >> > >> > -- >> > Ph.D. Candidate >> > McGill University >> > Integrated Program in Neuroscience >> > Psychology >> > >> > >> > On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> > >> > What are the pixel values in the mgz file? They should be binary, >> > ie, 1=in a label, 0 = out of label >> > >> > >> > On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote: >> >> Overlays in .mgz format using mri_vol2surf >> >> >> >> -- >> >> Ph.D. Candidate >> >> McGill University >> >> Integrated Program in Neuroscience >> >> Psychology >> >> >> >> >> >> On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve >> >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> >> wrote: >> >> >> >> what is a labeled vertex? What file format? mgz? annot? >> >> >> >> >> >> On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote: >> >> > the source files are labelled vertices from 20 subjects: >> >> > >> >> > -T1s were labelled using an MNI software >> >> > -Surfaces were created in FreeSurfer and surface overlays >> >> of the >> >> > labels were created using mri_vol2surf >> >> > -Surface overlays were registered to fsaverage using >> >> mri_surf2surf and >> >> > then averaged to create a probability map, originally using >> >> "mri_average" >> >> > >> >> > So, essentially the overlays are binary files of my labels >> >> I believe >> >> > - I can send one over if you wish. >> >> > >> >> > Trisanna >> >> > >> >> > >> >> > -- >> >> > Ph.D. Candidate >> >> > McGill University >> >> > Integrated Program in Neuroscience >> >> > Psychology >> >> > >> >> > >> >> > On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve >> >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu >> > >> >> <mailto:gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >> >> > >> >> > what are the source files ("all files"). What data >> >> type, value range, >> >> > where did they come from? >> >> > >> >> > >> >> > On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote: >> >> > > Hi Doug >> >> > > >> >> > > So, of course now it works without --keep-filetype... >> >> :p it looks >> >> > > pretty much the same was when I use --keep-filetype. >> >> > > >> >> > > However, the values of Min and Max are still odd (out >> >> of 256) - see >> >> > > snapshot >> >> > > >> >> > > Trisanna >> >> > > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > > -- >> >> > > Ph.D. Candidate >> >> > > McGill University >> >> > > Integrated Program in Neuroscience >> >> > > Psychology >> >> > > >> >> > > >> >> > > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve >> >> > > <gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu>> >> >> > <mailto:gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu> >> >> > <mailto:gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote: >> >> > > >> >> > > Depending upon the type of the data, the >> >> --keep-datatype may >> >> > mess >> >> > > things >> >> > > up quite a bit. What happens if you don't include >> >> that? It >> >> > will not >> >> > > create an annotation. maybe you mean some other >> >> file type? >> >> > > >> >> > > >> >> > > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote: >> >> > > > >> >> > > > Hi Doug >> >> > > > >> >> > > > I spoke with you at the Freesurfer tutorial >> >> last week >> >> > about using >> >> > > > mri_average to average my sulcal labels and get a >> >> > probability map on >> >> > > > fsaverage. You had suggested using "mri_concat" >> >> instead, >> >> > which is a >> >> > > > newer command. So, I performed the following >> >> command: >> >> > > > >> >> > > > *mri_concat all files --o output.mgz --mean >> >> --keep-datatype* >> >> > > > >> >> > > > I had to put --keep-datatype or else it tried >> >> to create an >> >> > annot >> >> > > file. >> >> > > > >> >> > > > This worked just fine. >> >> > > > >> >> > > > My question then is concerning *the min and max >> >> values >> >> > *when this >> >> > > > average is overlayed in Freeview. See the >> snapshot >> >> > attached. The >> >> > > > values seem to be based on 256 instead of >> >> percentage and >> >> > this is >> >> > > what >> >> > > > happens when I used "mri_average" without >> >> specifying the >> >> > "-p". Is >> >> > > > there a way to illustrate the values in >> >> percentage in a >> >> > similar way >> >> > > > with mri_concat? >> >> > > > >> >> > > > Many thanks! >> >> > > > >> >> > > > Trisanna >> >> > > > >> >> > > > >> >> > > > -- >> >> > > > Ph.D. Candidate >> >> > > > McGill University >> >> > > > Integrated Program in Neuroscience >> >> > > > Psychology >> >> > > > >> >> > > > >> >> > > > >> >> > > > _______________________________________________ >> >> > > > Freesurfer mailing list >> >> > > > Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> > > <mailto:Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >> >> > > > >> >> > >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> > >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> > >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>> >> >> > > >> >> > > -- >> >> > > Douglas N. Greve, Ph.D. >> >> > > MGH-NMR Center >> >> > > gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu>> >> >> > <mailto:gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu>>> >> >> > > Phone Number:617-724-2358 <tel:617-724-2358> <tel: >> 617-724-2358 >> >> <tel:617-724-2358>> >> >> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 >> >> <tel:617-724-2358>>> >> >> > > Fax: 617-726-7422 <tel:617-726-7422> >> >> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 >> >> <tel:617-726-7422> >> >> > <tel:617-726-7422 <tel:617-726-7422>>> >> >> > > >> >> > > Bugs: >> >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> >> > > >> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> >> >> > > FileDrop: >> >> https://gate.nmr.mgh.harvard.edu/filedrop2 >> >> <https://gate.nmr.mgh.harvard.edu/filedrop2> >> >> > <https://gate.nmr.mgh.harvard.edu/filedrop2 >> >> <https://gate.nmr.mgh.harvard.edu/filedrop2>> >> >> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 >> >> <https://gate.nmr.mgh.harvard.edu/filedrop2> >> >> > <https://gate.nmr.mgh.harvard.edu/filedrop2 >> >> <https://gate.nmr.mgh.harvard.edu/filedrop2>>> >> >> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> > >> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> >> > > >> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> > <http://www.nmr.mgh.harvard.e >> du/facility/filedrop/index.html >> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >>> >> >> > > Outgoing: >> >> > > >> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gr >> eve/> >> >> > >> >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >> ve/ >> >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gr >> eve/>> >> >> > > >> >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >> ve/ >> >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gr >> eve/> >> >> > >> >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >> ve/ >> >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gr >> eve/>>> >> >> > > >> >> > > _______________________________________________ >> >> > > Freesurfer mailing list >> >> > > Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >> >> > > >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> > >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > >> >> > >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> > >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> <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 >> >> <http://www.partners.org/complianceline> >> >> > <http://www.partners.org/complianceline >> >> <http://www.partners.org/complianceline>> >> >> > > <http://www.partners.org/complianceline >> >> <http://www.partners.org/complianceline> >> >> > <http://www.partners.org/complianceline >> >> <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. >> >> > > >> >> > > >> >> > > >> >> > > >> >> > > _______________________________________________ >> >> > > Freesurfer mailing list >> >> > > Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> > > >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> > >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > >> >> > -- >> >> > Douglas N. Greve, Ph.D. >> >> > MGH-NMR Center >> >> > gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu>> >> >> > Phone Number: 617-724-2358 <tel:617-724-2358> >> >> <tel:617-724-2358 <tel:617-724-2358>> >> >> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 >> >> <tel:617-726-7422>> >> >> > >> >> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> >> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> >> <https://gate.nmr.mgh.harvard.edu/filedrop2> >> >> > <https://gate.nmr.mgh.harvard.edu/filedrop2 >> >> <https://gate.nmr.mgh.harvard.edu/filedrop2>> >> >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> > >> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> >> > Outgoing: >> >> > >> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gr >> eve/> >> >> > >> >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >> ve/ >> >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gr >> eve/>> >> >> > >> >> > _______________________________________________ >> >> > Freesurfer mailing list >> >> > Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> > >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> > >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > >> >> > >> >> > >> >> > >> >> > _______________________________________________ >> >> > Freesurfer mailing list >> >> > Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >> -- >> >> Douglas N. Greve, Ph.D. >> >> MGH-NMR Center >> >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> >> <https://gate.nmr.mgh.harvard.edu/filedrop2> >> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> Outgoing: >> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gr >> eve/> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > _______________________________________________ Freesurfer mailing >> > list Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > <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 >> > <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. >> > >> > _______________________________________________ >> > 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.
