[Freesurfer] normalization of hippocampal volume

Hi, FS Experts, I’m using version 5.3 and have performed hippo-subfields analysis. To perform the statistics, shall I get the normalized volumes of each hippo-subfields? or just to do correction for ICV is enough ? thanks.. Hyon ___ Freesurfer

Re: [Freesurfer] How to compute the measures on the average brain?

Great, thanks for your answer. Le 22/10/2015 17:42, Douglas N Greve a écrit : > No, we will continue to support it > > On 10/21/2015 11:13 PM, Mathieu Dubois wrote: >> Hi again, >> >> Another advantage of using qcache in my case is that the file names are >> automatically generated and therefore

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Re: [Freesurfer] Sulcal depth units

Hi Bruce, I chose a random subject from the ADNI dataset and computed the mean and variance for the left and right hemispheres separately. It looks like the mean is close to 0, however the variance is not 1. Do you think it is possible that the surfaces are demeaned, but the units are still

Re: [Freesurfer] How to compute the measures on the average brain?

Great, thanks for your answer. Le 22/10/2015 17:08, Bruce Fischl a écrit : Hi Mathieu I don't see any reason we wouldn't continue to support it Bruce On Thu, 22 Oct 2015, Mathieu Dubois wrote: Hi again, Another advantage of using qcache in my case is that the file names are automatically

[Freesurfer] Issue opening .dmg file for installing freesurfer patch/code addition for brainstem. Error is "image not recognized"

Hello, I'm trying to segment the brainstem into subparts. I found online for freesurfer 5.3 you can use the following link to install the need codes: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ which was from the following freesurfer question/solution:

Re: [Freesurfer] FSFAST -per-run question

Just that the middle would be expected to have the least amount of motion with the rest of the run and so result in less interpolation On 10/22/2015 05:15 PM, dgw wrote: > Hi, > > I know that -per-run is the recommended motion correction option, and > that it uses the middle frame as the

[Freesurfer] FSFAST -per-run question

Hi, I know that -per-run is the recommended motion correction option, and that it uses the middle frame as the reference for motion correction for each run. I was wondering, if there is a reference, or explanation as to why that was chosen and not some other timepoint. Thanks, d

Re: [Freesurfer] Sulcal depth units

H I Simon Do you need the unnormalized sulc? It would be pretty easy to put something in to generate it Bruce > On Oct 22, 2015, at 3:23 PM, Simon Vandekar wrote: > > Hi Bruce, > > I chose a random subject from the ADNI dataset and computed the mean and > variance

Re: [Freesurfer] Sulcal depth units

Hi Simon they are originally mm, but I believe we z-score normalize them so that the sulc file is 0 mean and unit variance. cheers Bruce On Wed, 21 Oct 2015, Simon Vandekar wrote: > Dear Freesurfer experts, > > I am reading the manuscript "Cortical Surface-Based Analysis II: Inflation, >

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Re: [Freesurfer] How to compute the measures on the average brain?

No, we will continue to support it On 10/21/2015 11:13 PM, Mathieu Dubois wrote: > Hi again, > > Another advantage of using qcache in my case is that the file names are > automatically generated and therefore standard. > > Is there any risk (particularly for future compatibility) in using >

Re: [Freesurfer] normalization of hippocampal volume

I'm not sure what you mean by either of those options. can you explain? On 10/22/2015 04:18 AM, geschwind2013 wrote: > Hi, FS Experts, > > I’m using version 5.3 and have performed hippo-subfields analysis. > > To perform the statistics, shall I get the normalized volumes of each >

Re: [Freesurfer] mris_expand - problem reading thickness file?

Hi Alex if you upload the subject that is causing this problem I'll take a look. What version are you running and what OS? cheers Bruce On Thu, 22 Oct 2015, Alex Puckett wrote: Hello! I'm having trouble with mris_expand using the -thickness flag. ​If I expand by a fixed distance

Re: [Freesurfer] per analysis with covariates

what do you mean to control age and gender on both lGI and thickness? If you have thickness = f(gender,age,lGI), then you control for gender, age, and lGI on thickness. On 10/20/2015 06:20 AM, marica.pad...@libero.it wrote: > > Hi, > > I am running a vertex-wise correlation analysis between

Re: [Freesurfer] How to compute the measures on the average brain?

Hi Mathieu I don't see any reason we wouldn't continue to support it Bruce On Thu, 22 Oct 2015, Mathieu Dubois wrote: Hi again, Another advantage of using qcache in my case is that the file names are automatically generated and therefore standard. Is there any risk (particularly for future

Re: [Freesurfer] Talairach_afd error

Hi Anna are the talairach.xfm files generated by the two machines similar? Bruce On Wed, 21 Oct 2015, Anna I. Garcia Diaz wrote: Dear all, I am having problems running the recon-all process. The error log is attached to this e-mail.  This error appears only when I run recon-all in a