Re: [Freesurfer] Mid point on Freeview

Hi do you mean in the curvature display? If so, it is the "0" point at which red transitions to green (for positive and negative curvature) cheers Bruce On Thu, 13 Jul 2017, Trisanna Sprung-Much wrote: > Hi there > I have a question concerning viewing a surface in Freeview (FS 6.0): What >

[Freesurfer] vertex-wise contra-lateral mapping on an ico surface

Hello, I've created single subject surfaces sampled in ico7 space with make_average_subject --ico with a single input subject. Because of the ico7 sampling, both hemispheres have the same number of vertices. I am interested in the index-to-index mapping between equivalent contra-lateral vertices.

[Freesurfer] Mid point on Freeview

Hi there I have a question concerning viewing a surface in Freeview (FS 6.0): *What does the "mid point" variable refer to?* I can change it and it seems to change the shading within the sulci when I am looking at a white matter surface. Many thanks Trisanna -- Ph.D. Candidate McGill University

Re: [Freesurfer] R: Re: 3G1V.fsgd

those are correct On 07/13/2017 05:44 PM, std...@virgilio.it wrote: > Many thanks! > > In conclusion, you can confirm that the complete list of contrast reported > below is corrected for 3g1v, please? > > Contrast 1) HC-MCI_intercept.mtx > 1 -1 0 0 0 0 > > Contrast 2) HC-MCI_slope.mtx > 0 0 0 1

[Freesurfer] R: R: Re: 3G1V.fsgd

I obtain this error ERROR: dimension mismatch between X and contrast group.effect.intercept. mtx X has 6 cols, C has 3 cols Stefano >Messaggio originale >Da: std...@virgilio.it >Data: 13-lug-2017 23.44 >A: "Freesurfer support list" >Ogg:

[Freesurfer] R: Re: 3G1V.fsgd

Many thanks! In conclusion, you can confirm that the complete list of contrast reported below is corrected for 3g1v, please? Contrast 1) HC-MCI_intercept.mtx 1 -1 0 0 0 0 Contrast 2) HC-MCI_slope.mtx 0 0 0 1 -1 0 Contrast 3) HC-AD_intercept.mtx 1 0 -1 0 0 0 Contrast 4) HC-AD_slope.mtx 0 0 0

[Freesurfer] Regression diagnostic in context of surface-based analysis

Dear experts, I am looking for a way how to effectively run a regression model diagnostic in context of surface-based analysis. My example case is the regression model where response variable is cortical thickness and explanatory variable is continuous (disease duration). The statistical

Re: [Freesurfer] GLM Analysis Number of vertices and Area

I'm not sure what you mean. Do you want stats for every cluster regardless of significance? If so, you can run the monte carlo correction with a clusterwise p-value (--cwp in mri_glmfit-sim) of 1.0 On 07/13/2017 11:52 AM, Aman Montazeri wrote: > Hello Friends, > > Sorry for the simple

Re: [Freesurfer] 3G1V.fsgd

On 07/13/2017 10:37 AM, std...@virgilio.it wrote: > Dear FS group, > > I don't understand how I should build the contrast for 3 groups 1 > covariate. > No specific example is provided within fsgd example and also other > colleagues report the same problem in the mail list. > Please could you

Re: [Freesurfer] PETsurfer AC/TOF

Sorry, I don't know what the difference is. I always use the mean update volume as the template for registration. On 07/13/2017 01:57 PM, Fu, Jason (NIH/NINDS) [F] wrote: > ac/tof is attenuation corrected/time of flight. Ac/hd is attenuation > corrected/head. > > -Original Message- >

Re: [Freesurfer] PETsurfer AC/TOF

ac/tof is attenuation corrected/time of flight. Ac/hd is attenuation corrected/head. -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thursday, July 13, 2017 12:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PETsurfer AC/TOF sorry,

[Freesurfer] Error with glmfit in Qdec

Hello all, I keep running into the following error when attempting to run a qdec analysis: ERROR: matrix is ill-conditioned or badly scaled, condno = 10196.8 Attempting to diagnose further SumSq: Min=2.449490 (col 1), Max=26.457514 (col 7) The scale is much different between columns 1 and

Re: [Freesurfer] PETsurfer AC/TOF

sorry, what is an ac/tof file? On 07/13/2017 12:12 PM, Fu, Jason (NIH/NINDS) [F] wrote: > > Hi, > > I am currently using PETsurfer PVC to determine glucose metabolism > differences in certain structures between the brain hemispheres. I am > currently using ac/tof files to coregister to the

[Freesurfer] 2 post-doc positions available at University of Michigan

*Job Summary* Two postdoctoral research fellow positions are available immediately at the *Functional Neuroimaging, Cognitive, and Mobility Laboratory*, Department of Radiology, University of Michigan, Ann Arbor, MI, USA. Our laboratory specializes in clinical, mobility, cognition, and multimodal

[Freesurfer] PETsurfer AC/TOF

Hi, I am currently using PETsurfer PVC to determine glucose metabolism differences in certain structures between the brain hemispheres. I am currently using ac/tof files to coregister to the anatomy. One of the patients did not have the ac/tof files, would ac/hd files work instead? Thanks,

[Freesurfer] GLM Analysis Number of vertices and Area

Hello Friends, Sorry for the simple question. I am doing GLM analysis using QDEC between two groups (one discrete variable), then I run the Monte-Carlo clustering and got the stats of my cluster. My supervisor asked me to get the Stats of blobs/clusters (area and number of vertices in each

[Freesurfer] Pediatric Atlas/Template

I am wondering whether there are still plans to implement a pediatric atlas/template? I’m working with children aged 3-6 years. Thanks in advance, Jess. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Pediatric Atlas/Template

I am wondering whether there are still plans to implement a pediatric atlas/template? I’m working with children aged 3-6 years. Thanks in advance, Jess. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Pediatric Atlas/Template

I am wondering whether there are still plans to implement a pediatric atlas/template? I’m working with children aged 3-6 years. Thanks in advance, Jess. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] [External] Re: Differences in volume between mri_segstats and mris_anatomical_stats

Unless this is something invoked in the recon-all stage, I haven't run this command. Apologies if I'm misunderstanding your question. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve

Re: [Freesurfer] FS 6.0

Hi Elisabetta we need more information than this if you want our help. What command did you run that failed? What was the screen output? cheers Bruce On Thu, 13 Jul 2017, Del Re, Elisabetta wrote: Dear FS team, we are setting up FS 6.0 and have run one test case. The run went through

[Freesurfer] FS 6.0

Dear FS team, we are setting up FS 6.0 and have run one test case. The run went through but only after we created a 001.mgz image. It seems somewhat strange to us. Thank you so much, best, Elisabetta From: freesurfer-boun...@nmr.mgh.harvard.edu

[Freesurfer] 3G1V.fsgd

Dear FS group, I don't understand how I should build the contrast for 3 groups 1 covariate.No specific example is provided within fsgd example and also other colleagues report the same problem in the mail list.Please could you provide us details on this topic?Especially, how should be the

Re: [Freesurfer] BBRegister + partial FoV fail

So far it isn't anymore. It's more of a problem with ANTs now. BBRegister works with --init-header for partial FoV T1 and mean EPI are more or less in alignment. But if they wouldn't be then one would have a problem with registration. On 07/13/2017 12:35 AM, Douglas N Greve wrote: > Is this still