Re: [Freesurfer] mri/orig File naming requirements
I think that would be ok, but perhaps Nick or Doug can confirm Bruce On Sat, 9 Oct 2010, Matt Russell wrote: > Hello All, > > I'm currently working an automation program to setup a > FreeSurfer file system for processing. I was wondering > if I put a quality check pipeline in the code, deleting files > that fail an inspection, would I have problems if the > file name order ceased to be 001.mgz, 002.mgz, 003.mgz > and was changed to just 002.mgz, 003.mgz? > > Best, > Matthew Russell > ___ 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] mri/orig File naming requirements
yes, that's fine On 10/10/10 8:11 AM, Bruce Fischl wrote: > I think that would be ok, but perhaps Nick or Doug can confirm > Bruce > On Sat, 9 Oct > 2010, Matt Russell wrote: > >> Hello All, >> >> I'm currently working an automation program to setup a >> FreeSurfer file system for processing. I was wondering >> if I put a quality check pipeline in the code, deleting files >> that fail an inspection, would I have problems if the >> file name order ceased to be 001.mgz, 002.mgz, 003.mgz >> and was changed to just 002.mgz, 003.mgz? >> >> Best, >> Matthew Russell >> > ___ > 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.
[Freesurfer] Side swapped results?
Hi Experts, I have experienced a possible problem with sided-ness within Freesurfer. I have 2 groups which have been processed through the pipeline without error. I have used the lh.aparc and rh.aparc files to extract parcellated cortex volumes, and analysed the mean differences with SPSS. >From this I get significantly different volumes in the RIGHT fusiform gyrus >(amongst others). I then used QDEC to look at vertex based volume differences and found a large significant clusters at the LEFT fusiform gyrus, but not the RIGHT. I'm certain I haven't mixed up the analysis. Can anyone comment on this? ThanksJ___ 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] Cluster Multiple Comparison Correction
Hi Experts, Which option is best to use: mc-z or perm? I have read that perm gives more accurate results than mc-z, as it uses the actual data rather than fake data to estimate the null distribution. When I use perm, I get no significant clusters. When I use mc-z, almost all clusters are significant. Thanks..J___ 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] Cluster Multiple Comparison Correction
Hi Jay, Permutation testing will give the most accurate results. cheers, -MH > Hi Experts, > > Which option is best to use: mc-z or perm? > I have read that perm gives more accurate results than mc-z, as it uses > the actual data rather than fake data to estimate the null distribution. > When I use perm, I get no significant clusters. > When I use mc-z, almost all clusters are significant. > > Thanks..J___ > 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] {Disarmed} Re: Cluster Multiple Comparison Correction
Hi Micheal, Thanks. Looks like I will have to dump all my results done with mc-z! Unfortunately the Freesurfer Wiki is mute on the use of permutation, unless there is some tutorial I haven't found. How many permutations should one run? Any other helpful hints? Cheers...J On Mon Oct 11 9:05 , "Michael Harms" sent: Hi Jay, Permutation testing will give the most accurate results. cheers, -MH > Hi Experts, > > Which option is best to use: mc-z or perm? > I have read that perm gives more accurate results than mc-z, as it uses > the actual data rather than fake data to estimate the null distribution. > When I use perm, I get no significant clusters. > When I use mc-z, almost all clusters are significant. > > Thanks..J___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > MailScanner has detected a possible fraud attempt from "parse.pl" claiming to be 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 > MailScanner has detected a possible fraud attempt from "parse.pl" claiming to be 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 MailScanner has detected a possible fraud attempt from "parse.pl" claiming to be 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.
