Re: [Freesurfer] aseg.mgz altered after auto-recon2?
Hi, Josh, I think you can run the autorecon1, subcortseg and no segstats if you don't want the statistics file (aseg.stats). Also, use -openmp 8 can speed up quite a lot by multi-threading. For a regular T1 brain image, I can the running time to get aseg.mgz in about 4-5 hours. recon-all -i subject autorecon1 -subcortseg -nosegstats -openmp 8 cheers, Natalie On Thu, Mar 28, 2013 at 12:33 PM, Bruce Fischl wrote: > Hi Josh, > > yes, I think that's correct. > > Bruce > On Thu, 28 Mar 2013, Joshua Lee wrote: > > > In fact, couldn't I stop after calabel if all I want is the aseg.mgz? > > - > > Josh > > > > > > On Thu, Mar 28, 2013 at 11:18 AM, Joshua Lee wrote: > > Hi All, > > > > Am I right in reading the dev table that if I just want the > > aseg.mgz, (not the stats output), I only need to run auto-recon1 > > and auto-recon2? > > > > I need to run 250+ brains just to get the aseg volume, so if I > > can shave off 4-10 hours off each that would be huge. > > > > > > > > > ___ > 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. > > ___ 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.
[Freesurfer] aseg.stats ICV question
Hi, all, anyone knows that if the ICV in the aseg.stats means the whole volumes inside the skull or the total volumes of GM and WM? Does it include the CSF between the skull and the cortex? Thanks. Natalie ___ 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] Problems with ICV
Hi, Bruce, I've been using FS5.1 for segmentation analysis, after I updated the mri_segstats, the ICV does not seem to change at all, only the SupraTentorial Volume changed. If I want to use ICV and SupraTenrotial Volume for my analysis, is that OK to use FS5.1, I don't see more updated version than FS 5.1.0. Thanks. Also, is there a commandline to extract other numbers in the header of aseg.stats? Thanks. Natalie On Mon, Aug 13, 2012 at 9:15 AM, Bruce Fischl wrote: > Hi Laura, > > what version of FS are you running? The ICV is estimated using the talairach > xform, and there were some problems with it in 5.1. > > cheers > Bruce > > > On Mon, 13 Aug 2012, Wisse, L.E.M. wrote: > >> Dear freesurfers, >> >> I tried to calculate ICV with FreeSurfer, but I encountered some problems. >> I >> first ran autorecon 1, 2 and 3, but I noticed afterwards that a few ICV >> values were really off. The values were really high and when I looked at >> brain.finalsurfs.mgz, the segmentation also included skull, eyes and >> sometimes even the nose and ears. (I am not sure that I should look at the >> brainfinal.surfs.mgz for ICV segmentation, but the segmentations seemed to >> correlate with the ICV values.) >> >> So, I decided to try adjusting the watershed parameters and I also tried >> using gcut. I noticed that the segmentation brain.finalsurfs improved a >> lot, >> however in aseg.stats the ICV values did not change at all! >> >> Can anyone help me with this problem? >> >> Kind regards, >> Laura Wisse >> >> >> >> >> >> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is >> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht >> ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender >> direct >> te informeren door het bericht te retourneren. Het Universitair Medisch >> Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de >> W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat >> geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. >> 30244197. >> >> Denk s.v.p aan het milieu voor u deze e-mail afdrukt. >> >> >> >> >> >> This message may contain confidential information and is intended >> exclusively for the addressee. If you receive this message >> unintentionally, >> please do not use the contents but notify the sender immediately by return >> e-mail. University Medical Center Utrecht is a legal person by public law >> and is registered at the Chamber of Commerce for Midden-Nederland under >> no. >> 30244197. >> >> Please consider the environment before printing this e-mail. >> >> > > ___ > 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. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_segstats error
Hi, Doug and all, I wonder if the new version of mri_segstats on the ftp site will change both the ICV and the SupraTentorial volume? Nick seems to mention ICV will be different, the ReleaseNotes says the SupraTentorial Volume will be changed to smaller. Can you explain more on the difference of the new version with the original version in FS.5.1.0? Is everything on the morphometry stats website still the same? http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats. I'm interested in several measurements, including the ICV, and the SupraTentorial Volume and all the structures volume, just wondering if the new version will change all the measurements. Thanks. -Natalie On Wed, Aug 22, 2012 at 8:57 AM, Douglas N Greve wrote: > yes, this is a fix that will be in the next release. The new results are > more accurate. > doug > > On 08/22/2012 11:54 AM, Blazey, Tyler wrote: >> Hi Doug, >> >> Thanks for the quickly reply. The new version of mri_segstats works fine. I >> noticed after running it though that all the volumes are slightly different >> than those reported by previous version. I think it might have something to >> do with the partial volume correction, as the results are the same when I do >> not use the --pv flag. Is this expected behavior? And if so, is the new >> version more accurate? >> >> Thanks again, >> >> -Tyler >> >> >> >> >> >> The material in this message is private and may contain Protected Healthcare >> Information (PHI). If you are not the intended recipient, be advised that >> any unauthorized use, disclosure, copying or the taking of any action in >> reliance on the contents of this information is strictly prohibited. If you >> have received this email in error, please immediately notify the sender via >> telephone or return 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > ___ > 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. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tkmedit segmentation color offset
Hi, all, I have a tkmedit display issue when I try to add transformation to the main volume, but the segmentation volume won't conform to Talairach domain accordingly. Here is the commandline tkmedit subject norm.mgz -main-transform talairach.xfm -seg aseg.mgz really appreciate any feedback on how to add transformation on this segmentation results. Thanks. Natalie <>___ 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] tkmedit segmentation color offset
Thanks for the quick reply. Can you elaborate a little bit how to use mri_vol2vol to get what I want? what would be the final scipt for tkmedit then? On Tue, Mar 5, 2013 at 5:31 PM, Bruce Fischl wrote: > Hi Natalie > > sorry, tkmedit won't do what you want. It's old and we are not developing > it anymore. You can apply the transform using mri_vol2vol, just make sure > to use nearest nbr interp for the aseg. > > cheers > Bruce > > On Tue, 5 Mar 2013, Natalie Han wrote: > > Hi, all, >> I have a tkmedit display issue when I try to add transformation to the >> main >> volume, but the segmentation volume won't conform to Talairach domain >> accordingly. Here is the commandline >> >> tkmedit subject norm.mgz -main-transform talairach.xfm -seg aseg.mgz >> >> really appreciate any feedback on how to add transformation on this >> segmentation results. >> >> Thanks. >> Natalie >> >> >> > > 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 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.
[Freesurfer] how to save screen shot (using TCL) without X11
Hi, I have a tcl script to save multiple tkmedit screen shots, but I wonder if there is a way to suppress the pop out tkmedit windows everytime I want to save the tif. Basically, if I don't have a X11 window when ssh, how can I save the tkmedit screen shots with tcl script? Is there an option in tcl script or tkmedit to render virtually instead of display to the screen? Thanks a lot. -Natalie ___ 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.
