[Freesurfer] Pediatric Cortical Thickness Normalization by ICV
External Email - Use Caution Hi, I am running an analysis in a group of pediatric subjects (4-6 years old) and want to correct cortical thickness values by ICV before running the statistical model, since we have limited degrees of freedom. While I know this is not recommended for adults, I believe it is routinely done in pediatrics but I cannot find the implementation in freesurfer. Is there a straightforward way to normalize cortical thickness by ICV before running the glm? Thanks, Brady Williamson ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Pediatric Cortical Thickness Normalization by ICV
External Email - Use Caution Got it, that exactly what I was looking for! Thank you very much. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, February 14, 2019 1:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Pediatric Cortical Thickness Normalization by ICV There is not something that will plug-and-play for this. But you can do something like cd subject/surf fscalc lh.thickness div ETIV -o lh.thickness.etiv.mgz where ETIV is from the aseg.stats file Then specify --meas thickness.etiv.mgz when running mris_preproc On 2/14/19 12:50 PM, Williamson, Brady wrote: > > External Email - Use Caution > > Hi, > > I am running an analysis in a group of pediatric subjects (4-6 years > old) and want to correct cortical thickness values by ICV before > running the statistical model, since we have limited degrees of > freedom. While I know this is not recommended for adults, I believe it > is routinely done in pediatrics but I cannot find the implementation > in freesurfer. Is there a straightforward way to normalize cortical > thickness by ICV before running the glm? > > Thanks, > > Brady Williamson > > > ___ > 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Pediatric Cortical Thickness Normalization by ICV
External Email - Use Caution Fantastic! I look forward to the next release. Thank you again for your responsiveness. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, February 14, 2019 1:32 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Pediatric Cortical Thickness Normalization by ICV btw, I just added this feature to mris_preproc, so, in the next version you will only need to add --etiv to the command line. On 2/14/19 1:17 PM, Williamson, Brady wrote: > External Email - Use Caution > > Got it, that exactly what I was looking for! Thank you very much. > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas > N.,Ph.D. > Sent: Thursday, February 14, 2019 1:15 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Pediatric Cortical Thickness Normalization > by ICV > > There is not something that will plug-and-play for this. But you can > do something like cd subject/surf fscalc lh.thickness div ETIV -o > lh.thickness.etiv.mgz where ETIV is from the aseg.stats file > > Then specify --meas thickness.etiv.mgz when running mris_preproc > > > On 2/14/19 12:50 PM, Williamson, Brady wrote: >> External Email - Use Caution >> >> Hi, >> >> I am running an analysis in a group of pediatric subjects (4-6 years >> old) and want to correct cortical thickness values by ICV before >> running the statistical model, since we have limited degrees of >> freedom. While I know this is not recommended for adults, I believe >> it is routinely done in pediatrics but I cannot find the >> implementation in freesurfer. Is there a straightforward way to >> normalize cortical thickness by ICV before running the glm? >> >> Thanks, >> >> Brady Williamson >> >> >> ___ >> 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 > > > ___ > 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problem with freeview in linux subsystem for windows
External Email - Use Caution Hi, I am trying to run freeview in the linux subsystem (Ubuntu 18.04) for windows 10 but keep getting the following error: failed to get the current screen resources QXcbConnection: XCB error: 170 (Unknown), sequence: 170, resource id: 90, major code: 146 (Unknown), minor code: 20 QXcbConnection: XCB error: 170 (Unknown), sequence: 170, resource id: 90, major code: 146 (Unknown), minor code: 20 Freeview opens but there is no image. Is there a fix for this issue? Thanks, Brady ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with freeview in linux subsystem for
External Email - Use Caution Hi Falk, Thank you for the reply. Yes, I am running Xming and have set this option in the .bashrc file. I still get the same error. I have tried to research this issue extensively but cannot seem to find the answer. Thanks, Brady ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_glmfit in custom ROI
External Email - Use Caution Hi, I have a couple of specific questions about mri_glmfit that I could not quite find the answers to in the tutorials or message boards. 1. How would I run mri_glmfit in a custom ROI (or set of ROIs) and then correct for multiple comparisons? I have found information on how to use the freesurfer predefined labels but not a custom regions. Just for some background, I have a set of 50 regions that make up our network of interest and I would like to limit the glm to these regions. 2. How do I extract and use the results from a whole-brain glm, above a specified corrected threshold, and use those in subsequent analyses? I am doing a whole-brain, between groups analysis and then trying to use the significant results from that in within-subjects analyses. Thank you very much for your time, Brady ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Parcellation to FS surface annotation
External Email - Use Caution Hello, I am trying to convert parcellations in MNI space (BrainNetome and Craddock 200) to a surface annotation file in fsaverage space. I have seen several posts that seem to talk about steps that may be applicable but none of them are very efficient. Is there an easy/direct way to do this conversion? It seems like I am missing something really obvious, like a one line command, that would do the trick. Thank you for any assistance, Brady ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
