[Freesurfer] reducing a matrix

Hello Dr. Greve, I ran the program below and got the following errors. Can you help??? I really would appreciate it. What does it mean?. -Linda ? Loading source LTA boldregister003.dat INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. Loading

[Freesurfer] reducing a matrix

Hello Dr. Greve, I ran the program below and got the following errors. Can you help??? I really would appreciate it. What is wrong? -Linda ? Loading source LTA boldregister003.dat INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. Loading GCAM

Re: [Freesurfer] reducing a matrix

Hello Dr. Greve, I ran the program below and got the following errors. Can you help??? I really would appreciate it. -Linda Loading source LTA boldregister003.dat INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. Loading GCAM

[Freesurfer] FSFAST (plot-twf-sess)

Dear Dr Greeve, I am new to FSFAST so I highly appreciate your response. I have resting state fMRI data and I am following the steps as reported in wiki. My questions is regarding motion evaluation. The attached figure is an output of "plot-twf-sess". 1. Given the plotted data can we say that

Re: [Freesurfer] niiRead error

I think this may be fixed in 6.0 On 7/31/17 12:43 PM, Francesca Strappini wrote: Thanks for the reply. freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0. I opened it with fslview and it looks like a normal 3-dimentional file. Thanks Francesca 2017-07-31 16:38 GMT+02:00 Douglas Greve

[Freesurfer] Error: trac-all -prep "Segmentation fault (core dumped)"

Hello FreeSurfer Developers, I am attempting to compute the tracula preprocessing directive (-prep), but for all my subjects I get the following error when it computes the pathway priors from atlas to T1. ... WARN: Turning off overlap check for center streamline INFO: Step is 3 voxels INFO:

Re: [Freesurfer] niiRead error

Thanks for the reply. freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0. I opened it with fslview and it looks like a normal 3-dimentional file. Thanks Francesca 2017-07-31 16:38 GMT+02:00 Douglas Greve : > what version of FS are you running? > > > On 7/30/17 12:37

Re: [Freesurfer] creating mesh with specifications

That makes sense, I still wanted to see if it is possible as the other software I am working with is not flexible. Thank you! Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl

Re: [Freesurfer] creating mesh with specifications

Hi Idil no, you can't specify all those things as they are defined by the topology of the surface. You could reduce the number of vertices, but then that will specify the edges and faces I expect. I'm not aware of any software taht lets you set all 3, and in fact you can't do all 3 as they

[Freesurfer] creating mesh with specifications

Hello freesurfer experts, I am trying to export an inflated surface file and its overlay made in Freesurfer to a different software and it seems like the surface file needs to have a particular number of vertices, triangles and average # of neighbors to be compatible. I have used mris_decimate

Re: [Freesurfer] Total White matter and CSF value Calculation

On 7/31/17 3:12 AM, M Janani wrote: Hi Team, Could you please confirm whether the below mentioned formulas to compute Total WM and ventricular CSF are correct 1.Total White Matter = CerebralWhiteMatterVol + (lh+rh) Cerebellum White Matter looks right, though some

Re: [Freesurfer] niiRead error

what version of FS are you running? On 7/30/17 12:37 PM, Bruce Fischl wrote: > Hi Francesca > > why is the nifti 5-dimensional? The code is complaining that it doesn't > know how to intepret the input volume > > cheers > Bruce > On Sun, 30 Jul 2017, Francesca > Strappini wrote: > >> Hi, I'm

Re: [Freesurfer] Extracting vertex data from thickness maps after masking by sig.mgh

yes, mean across space. for vertex wise, you'll probably have to go into matlab, something like mask = MRIread('mask.mgh'); imask = find(mask.vol == 1); cc = MRIread('concat.mgh'); ccmat = fast_vol2mat(cc); cc_in_mask = ccmat(:,imask); On 7/31/17 10:25 AM, Elijah Mak wrote: Hi Doug,

Re: [Freesurfer] Extracting vertex data from thickness maps after masking by sig.mgh

Hi Doug, Thanks! mri_segstats —i concat.mgh  --seg mask.mgh --avgwf data 1) concat.mgh is the stack of individual surfaces in fsaverage space 2) mask.mgh is the binarised mask from the sig.mgh  3) --avgwf to produce the 2 columns of data (inside and outside) The values from the --avgwf

Re: [Freesurfer] Extracting vertex data from thickness maps after masking by sig.mgh

You can use mri_segstats with either the --sum option (for an input with one time point) or --avgwf (for multiple). Pass your mask with --seg. By default it will give you both outside the mask (first column) and inside the mask (second column). On 7/28/17 10:44 AM, Elijah Mak wrote: Hi

Re: [Freesurfer] negative header after preproc-sess

If this is surface data, then there is nothing that we can do right now. One possibility is to read the data into matlab with the FS MRIread.m, then write it out in nifti2 using some other tool On 7/28/17 10:26 AM, Bai Haohao wrote: Hi, Thanks for your reply, and I get these dims by using

Re: [Freesurfer] extract values for significant cluster

I don't know what the rest of your analysis is about. If you created maps of change in thickness per year and you extracted those values, then that is what you will get. On 7/28/17 4:24 AM, Clara Kühn wrote: > Dear Doug, > > thank you so much. I now have a value for each of my participants.

[Freesurfer] Univariate Linear Mixed Effects

Hi there, I am currently working through the linear mixed effects example for hippocampal volume on the wiki and I can't quite get my head around how the contrast matrix is set up. In the example, the design matrix has 14 columns but the contrast matrix only seems to have 5 (below), could

[Freesurfer] Total White matter and CSF value Calculation

Hi Team, Could you please confirm whether the below mentioned formulas to compute Total WM and ventricular CSF are correct 1. Total White Matter = CerebralWhiteMatterVol + (lh+rh) Cerebellum White Matter 2. Total ventricular CSF = (lh + rh) Lateral-Ventricle + =

Re: [Freesurfer] How to create mask for Total Graymatter and White matter Volume

Thanks Douglas try --gm On 07/25/2017