[Freesurfer] mean cortical thickness map

Dear Freesurfer community, I want to visualize the mean cortical thickness map of 20 subjects. I ran the command recon-all on the the T1 images. How can I visualize the mean cortical thickness of one group. Thanks for any advice John___ Freesurfer mail

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

Hi Kyung you can load them into matlab or convert them to ascii if you want Bruce On Sun, 12 Nov 2017, 박경일 wrote: Dear FS experts, I could get QDEC image comparing two groups. However, is there a way to get numerical values of cortical thickness in each vertex? Thank you Best, Kyung ___

[Freesurfer] Bug Reporting: recon-all -s 001 exited with ERRORS

​Hello FreeSurfer Developers, I am attempting ​to compute autorecon1 in a subject to see how it works recon-all in a stepwise as described in the tutorial. Sorry if this is a very naive question but it is the first time I am trying to run an analysis with FreeSurfer. After running: *r* *econ-all

Re: [Freesurfer] Bug Reporting: recon-all -s 001 exited with ERRORS

My apologizes, I missed forgot to include the following information: 1. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2. Platform: CentOS release 6.7 3. uname -a: Linux rosalia-PORTEGE-Z930 4.4.0-98-generic #121-Ubuntu SMP Tue Oct 10 14:24:03 UTC 2017 x86_64 x86_64 x86_64

Re: [Freesurfer] mean cortical thickness map

Hi John if you run recon-all -qcache for each of your subjects it will generate a set of smoothed thickness maps at a set of predefined smoothing levels on the fsaverage surface. You can then use e.g. mri_average to average them. I'm pretty sure Doug has tools that can do this in one step... c

Re: [Freesurfer] Creating cached versions of Xhemi registrations

Dear Doug, I'm performing a linear regression over one sample with a design matrix including columns for one continuous-valued predictor whose effect on neural measures I'm interested in testing, several covariates to adjust for (continuous- or binary-valued such as age, sex, total intracranial

[Freesurfer] error hipp subfields

dear Fs experts i have the whole process to get the hipp subfields. But after some mr's that are processed well i get an error (attachment) I have to do the whole process from the beggining And so on Is there an answer? John

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

Hi Bruce, What I want is the values of cortical thickness in each vertex in each subject. Is that possible? Thanks so much. Kyung 2017-11-13 0:43 GMT+09:00 Bruce Fischl : > Hi Kyung > > you can load them into matlab or convert them to ascii if you want > Bruce > > On Sun, 12 Nov 2017, 박경일 wrot

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

yes. You can use mris_convert to make an ascii file, or read_curv.m to read them into matlab. cheers Bruce On Mon, 13 Nov 2017, 박경일 wrote: Hi Bruce,What I want is the values of cortical thickness in each vertex in each subject. Is that possible? Thanks so much. Kyung   2017-11-13 0:43 GMT+

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

p.s. if you want the vertices to correspond, first run recon-all -qcache for each subject. That will generate a set of thickness maps in fsaverage space at predefined smoothing levels (so that the vertex numbers correspond across subjects) On Mon, 13 Nov 2017, 박경일 wrote: Hi Bruce,What I wa

[Freesurfer] [FSL] Microstructural Imaging Jobs in CUBRIC, Cardiff (fwd)

FYI -- Forwarded message -- Date: Mon, 13 Nov 2017 01:38:46 + From: Derek Jones Dear All, Please find below links to three jobs in microstructural imaging at CUBRIC, Cardiff University (available immediately).  Obviously, a large part of this will be exploring the benefi