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.
[Freesurfer] ReRunning Subjects in Newer FreeSurfer Versions and ICV Differences
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.
