[Freesurfer] contrast

Thank you very much Dough! I need to check 4 contrasts. I made them based on the freesurfer page, but cant decide if i interpreted them right! Are my contrasts Ok? If classes are: Patients, healthy control and variables are: Age, TIV, father age, mother age. Are these contrasts ok?

[Freesurfer] tutorial data

Hello, I am trying to download the light tutorial dataset from this page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data The file link is titled: tutorial_data.tar.gz I have tried clicking on the link as well as using

Re: [Freesurfer] Coordinate system in mris_convert

Thanks ! I tried on the left pial surface and I got the expected result. 2016-06-08 15:38 GMT+02:00 Douglas Greve : > > Try the group analysis tutorial > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > > > On 6/8/16 2:39 AM, Dave Yas wrote: > >

[Freesurfer] Older Freesurfer Version with Freesurfer v. 6 HSF & Brainstem Modules

Hello Freesurfer experts, I have two questions regarding the use of old (version 5.1) processed Freesurfer data with the new hippocampal subfields (HSF) and brainstem modules in Freesurfer version 6: 1) Is it possible to use data processed in Freesurfer v. 5.1 and run it directly though the

Re: [Freesurfer] FS volume estimates

1. This is based on Randy Buckner's paper showing that the tal xform gives you a pretty accurate estimate of the TIV (which is hard to compute directly from a T1 image since you can't distinguish bone from CSF). 2. I think including it as a covariate is a better approach, but perhaps

Re: [Freesurfer] latest freeview

Latest freeview is just what comes with the developement version of freesurfer. You can download the latest development verion from the following page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download -Zeke On 06/08/2016 01:11 PM, Jason Tourville wrote: > Hi there, > Looking over the

Re: [Freesurfer] Longitudinal Studies Question

So if these aren't useful for only 1 subject, what would be the best way to look at data over multiple scans for just the one subject? On Mon, Jun 6, 2016 at 2:12 PM, Martin Reuter wrote: > Hi Carolyn, > > not sure what you are asking. You want to do statistics on

[Freesurfer] latest freeview

Hi there, Looking over the freeview development page, it looks like there are some (relatively) new features that would come in handy. Could I get a link to download the latest freeview beta? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language,

Re: [Freesurfer] cespct in FS 5.3

The built-in Intensity normalization is a constant multiplied to each run's data based on the per-run mean, right? It thus normalizes global intensity variation across subjects, but not regional, right? Whereas my approach would normalize regional variation in signal strength (good), at the risk

[Freesurfer] FS volume estimates

Greetings, I have two questions regarding FS volume measurements. I intend to use the volume information of .stats files but I got some doubts regarding the methods used. 1) I read that eTIV estimation is based on the TAL transformation, but what about the volumes of cortical and

Re: [Freesurfer] SAVE REG in tkregister2

tkregister2 --mov template.nii --s fbirn-anat-101.v4 \ --regheader --reg myregister.dat --surf ok, here it is De : freesurfer-boun...@nmr.mgh.harvard.edu de la part de Hao wen Envoyé :

Re: [Freesurfer] aseg.stats and aparc.stats reliability

Johnathan, can you point us to source of the issues you are concerned about? Is there a paper or website? thanks doug On 6/8/16 9:46 AM, Bruce Fischl wrote: > Hi Jonathan > > as far as we know, FreeSurfer is the most reliable and robust > longitudinal brain morphometry tool that is publicly

[Freesurfer] output file from running mri_glmfit-sim

Hi, all, While working on gyrification data using Freesurfer, I have a question to confirm one of output files. First, I did run mri_glmfit using age x IQ itneraction. fsgd file in which I included intracranial volume and gender to covary out. then, I am running mri_glmfit-sim for age x IQ

Re: [Freesurfer] aseg.stats and aparc.stats reliability

Hi Jonathan as far as we know, FreeSurfer is the most reliable and robust longitudinal brain morphometry tool that is publicly available. We are working to improve it (always!), but the answer to your question is yes, certainly 5.3 and the upcoming 6.0 are both excellent longitudinal tools

Re: [Freesurfer] selxavg3-sess error

Do you have both polar and eccen data? If so, can you send the Xtmp.mat file? On 6/8/16 6:08 AM, Francesca Strappini wrote: Hi Freesurfer experts, I'm re-posting this message because I think it got lost. I'm trying to analyze some phase-encoded data with the eccentricity protocol for

Re: [Freesurfer] Coordinate system in mris_convert

Try the group analysis tutorial http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis On 6/8/16 2:39 AM, Dave Yas wrote: Hello all, I'm new to surface analysis. I have 2 groups (patient and healthy control) that i want to check differences between. I want to perform cortical

Re: [Freesurfer] Coordinate system in mris_convert

Try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert Not sure where the issue with the cras came from On 6/7/16 4:25 PM, Alexandre Routier wrote: I have the following error: unknown option --cras_correction. I am using FreeSurfer 5.3, I don't known if it

Re: [Freesurfer] Break 3D volume

Thank you Bruce... This is very helpful!   Bests, John Sent: Wednesday, June 08, 2016 at 9:32 AM From: "Bruce Fischl" To: "Freesurfer support list" Subject: Re: [Freesurfer] Break 3D volume the help is old! should be . (x0,y0,z0)

Re: [Freesurfer] SAVE REG in tkregister2

when you run tkregister, you have a command line. I want you to send me that command line On 6/8/16 4:02 AM, Hao wen wrote: Sorry, I sent you the wrong site, I followed the multimodal registration with three ways to do the regi, Freeview, tkregister2, and bbregister, so with tkregister is

Re: [Freesurfer] Break 3D volume

the help is old! should be . (x0,y0,z0) is the starting point of your bounding box, and (dx,dy,dz) is the extent of it (in voxels) On Wed, 8 Jun 2016, John Anderson wrote: Hi Bruce,  Thank you for the quick response. it is really highly appreciated! I have 3D mask in the form of nifti

Re: [Freesurfer] Break 3D volume

Hi Bruce,  Thank you for the quick response. it is really highly appreciated! I have 3D mask in the form of nifti file and it has the shape of large square( the black big square in my figure). I wanted to divid it to a smaller and equale volumes. It iseems that mri_extract can support my

Re: [Freesurfer] Break 3D volume

Hi John I'm not exactly sure what you mean, but you can use mri_extract to pull out rectangular subvolumes. cheers Bruce On Wed, 8 Jun 2016, John Anderson wrote: Dear FS Experts, Are there any tools in Freesurfer or Matlab scripts that can help to break down a 3D volume ( created using

[Freesurfer] Break 3D volume

Dear FS Experts, Are there any tools in Freesurfer or Matlab scripts that can help to break down a 3D volume ( created using mri_volsynth) to a multiple equal sub volumes ( like the attached figure ) Thanks in a dvance for any suggestion! John Anderson Senior Research Associate Psychological

[Freesurfer] aseg.stats and aparc.stats reliability

Hello Are the volume and thickness measures in FreeSurfer's aseg.stats and aparc.stats accurate and reliable enough to assess changes in volume and thickness longitudinally? I have heard there have been some accuracy/reliability issues in these files in older versions of FreeSurfer. Is the

[Freesurfer] selxavg3-sess error

Hi Freesurfer experts, I'm re-posting this message because I think it got lost. I'm trying to analyze some phase-encoded data with the eccentricity protocol for retinotopic data and I'm having troubles with selxavg3-sess. I run the following commands: mkanalysis-sess -analysis

Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

Hi, so i changed my design matrix, let the gender*group(AD,Contrrol), so this time the design matrix is like this, which i think it is ok AgeSubjects Female*AD Male*AD Female*Control Male*Control +74.3 +0.0 +0.0 +0.0 +1.0 +73.7 +0.0 +0.0 +0.0 +1.0

Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

Also, as far as I know, in Surfstat, we can treat the categorized factor as the covirates, but in FS, the categorized factor should be treated as a class? is that because of this? De : freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

Ok, So in FS, you can not define your design matrix like this? cuz in Surfstat, i can define the design matrix like this, the five columns represent AD, Control, Age, female and male, because in FS, I know we can do the DODS & DOSS, but I want to design some more flexible design matrix, and for

Re: [Freesurfer] SAVE REG in tkregister2

Sorry, I sent you the wrong site, I followed the multimodal registration with three ways to do the regi, Freeview, tkregister2, and bbregister, so with tkregister is not cmdline, its a GUI, but I can not save the result with SAVE REG button, here is the link

Re: [Freesurfer] Freesurfer program for 7 Tesla

Hi Prasad, for me FreeSurfer worked pretty nicely with 7T data. Most critical parts are skull-stripping and surface alignment if intensities of the cortex vary a lot (e.g. darker cortex in temporal lobes). However, I haven’t tried the hippocampal subfields yet and have usually processed small

Re: [Freesurfer] Coordinate system in mris_convert

Hello all, I'm new to surface analysis. I have 2 groups (patient and healthy control) that i want to check differences between. I want to perform cortical thickness/ surface analysis. My categories are Patients, healthy control, age, TIV, father age, mother age. Where age & TIV are