Re: [Freesurfer] ReRunning Subjects in Newer FreeSurfer Versions and ICV Differences
Hi Jeff, in most cases that won't run anything. -make all will check the timestamps on the various volumes/surface and only rerun things in cases where something further back in the stream has a newer timestamp than something newer. You need to run it with -all cheers Bruce On Thu, 16 Jun 2011, Jeff Sadino wrote: > Hello Bruce, > > Thank you for your reply. I used recon-all -make all -s subject. > > Thanks, > Jeff > > On Thu, Jun 16, 2011 at 3:11 PM, Bruce Fischl > wrote: > >> Hi Jeff >> >> what command did you run to run them over? >> >> cheers >> Bruce >> >> On Thu, 16 Jun 2011, Jeff Sadino wrote: >> >> Hello, >>> >>> When FS5 came out, I copied over my FS4 reconstructions to my FS5 Subjects >>> Directory, and then reran them using the FS5 recon-all stream. This >>> updated >>> their subject folders with the FS5 changes, but not in as many places as I >>> would have thought. For example, on 6 test subjects, I created their FS5 >>> folders from FS4 folders that I copied over and then ran the FS5 recon-all >>> stream. I also created another copy of their FS5 folders from scratch. >>> The >>> average difference in their ICV values was -12,000 mm^3. Is it to be >>> expected that FS5 reconstructions running on FS4 folders will not include >>> all possible improvements? If I want to get an accurate an ICV >>> measurement >>> as possible, is it advisable to rerun all of my subjects in FS5, starting >>> from scratch? >>> >>> As always, thank you for your valuable assistance! >>> Jeff Sadino >>> >>> >> >> 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] ReRunning Subjects in Newer FreeSurfer Versions and ICV Differences
Hello Bruce, Thank you for your reply. I used recon-all -make all -s subject. Thanks, Jeff On Thu, Jun 16, 2011 at 3:11 PM, Bruce Fischl wrote: > Hi Jeff > > what command did you run to run them over? > > cheers > Bruce > > On Thu, 16 Jun 2011, Jeff Sadino wrote: > > Hello, >> >> When FS5 came out, I copied over my FS4 reconstructions to my FS5 Subjects >> Directory, and then reran them using the FS5 recon-all stream. This >> updated >> their subject folders with the FS5 changes, but not in as many places as I >> would have thought. For example, on 6 test subjects, I created their FS5 >> folders from FS4 folders that I copied over and then ran the FS5 recon-all >> stream. I also created another copy of their FS5 folders from scratch. >> The >> average difference in their ICV values was -12,000 mm^3. Is it to be >> expected that FS5 reconstructions running on FS4 folders will not include >> all possible improvements? If I want to get an accurate an ICV >> measurement >> as possible, is it advisable to rerun all of my subjects in FS5, starting >> from scratch? >> >> As always, thank you for your valuable assistance! >> Jeff Sadino >> >> > > 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.
Re: [Freesurfer] ReRunning Subjects in Newer FreeSurfer Versions and ICV Differences
Hi Jeff what command did you run to run them over? cheers Bruce On Thu, 16 Jun 2011, Jeff Sadino wrote: > Hello, > > When FS5 came out, I copied over my FS4 reconstructions to my FS5 Subjects > Directory, and then reran them using the FS5 recon-all stream. This updated > their subject folders with the FS5 changes, but not in as many places as I > would have thought. For example, on 6 test subjects, I created their FS5 > folders from FS4 folders that I copied over and then ran the FS5 recon-all > stream. I also created another copy of their FS5 folders from scratch. The > average difference in their ICV values was -12,000 mm^3. Is it to be > expected that FS5 reconstructions running on FS4 folders will not include > all possible improvements? If I want to get an accurate an ICV measurement > as possible, is it advisable to rerun all of my subjects in FS5, starting > from scratch? > > As always, thank you for your valuable assistance! > Jeff Sadino > ___ 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.
