[Freesurfer] Surface Integral Questions

Hi FreeSurfer community, I have several questions regarding FreeSurfer's surface integral measurements. Perhaps there is a documentation page that answers these questions that someone can point me to that I haven't been able to find, or perhaps someone knows the answers to these questions off

Re: [Freesurfer] Volume to Surface mapping looks great for Vols created in FSL but not SPM

If you have a 3mm MNI152 space, then you should run bbregister to fsaverage to create a new register.dat file. Alternatively, you can register it directly to 32k_fs_LR and cut out the middle man (make sure to use --9 to account for scaling). Please ignore my comment about fsaverage. In that cas

Re: [Freesurfer] Qdec effect sizes, correlation coefficient

yes On 4/3/17 1:34 PM, Juan Baldermann wrote: > Is ist correct that the pcc.mgh file give's me pearson's correlation > coeeficient for each vertex? > > Best, Carlos > > > > Dr. med. Juan Carlos Baldermann > Wissenschaftlicher Mitarbeiter, Assistenzarzt > AG Neuro

Re: [Freesurfer] Generate stat file of ROI voxel sizes

You can use mri_segstats to generate a file for each subject (use the ROI volume as the --seg). Then use asegstats2table to create your final table On 04/04/2017 12:18 PM, Ostrowski, Lauren wrote: > Hello experts, > > We are looking to generate a stat file containing the number of voxels > in

Re: [Freesurfer] Changing the Orientation of Scan Slices (Images included)

you can try playing with the --reorder flag in mri_convert On 04/05/2017 10:11 AM, Jeffrey Crawford wrote: > > Hello everyone! > > I have two types of scans of the same participant. One was an Axial > scan (Image 1) and the other is a Cortical Scan (Image 2), both with > the same dimensions (25

[Freesurfer] Ventricle-to-Brain Ratio

Hello all, I want to calculate a Ventricle-to-Brain ratio (VBR) as a measure of parenchymal atrophy using Freesurfer version 5.3.0. I have tried to go about this using the aseg.stats output (using asegstats2table), but am running into inconsistencies. The basic calculation for VBR is: (Total Ven

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

I believe what I am seeing in the long stream is the edits not properly taking effect. I uploaded a subject with two timepoints, and only baseline edits to the wm as dsemanek2.zip about a week and a half ago. There doesn’t seem to be any significant changes to the surfaces in the base or either

Re: [Freesurfer] ROI seed size

Hi Erik I see. I defer to Thomas on this issue Bruce On Wed, 5 Apr 2017, ERIK JAHNER wrote: Hi Bruce, Thanks for the quick response. Sorry, I meant 6mm radius (for regions such as fusiform face area and visual word form area). I am using the same seeds that are suggested to be associated

[Freesurfer] mri_watershed seed point

Hello FreeSurfer Community, I am attempting to use mri_watershed to create BEM surfaces, but for some of my subjects part of the cerebellum is being cut off. Adjusting the threshold was not sufficient, so I attempted to add a seed point in the cerebellum using the following command: mri_water

[Freesurfer] How to generate binary mask image using FreeSurfer's “mri_volsynth”?

Dear Freesurfers, I am trying to implement the methods mentioned in this paper to deal with partial volume effects when quantifying metabolites: https://www.ncbi. nlm.nih.gov/pmc/articles/PMC4849426/#__sec2title The first step it mentions is: A binary mask must first be created, which represen

Re: [Freesurfer] mri_watershed seed point

Dear Kristen, looking at the source code of mri_watershed, the seed point has to be specified in the format: -s i j k and the option can be specified more than once when you want to add more seed points (30 seed points is maximum). i.e., when you want to input seed points in coordinates 50,60,

[Freesurfer] QDEC-volume, thickness and area

Dear Freesurfer Experts, 1) I have 2 groups (A & B), which do not differ in terms of gender ratio. If there were no significant regions for Group-Gender interaction in mean cortical thickness in the QDEC analysis, can I conclude that gender does not influence the effect of group on thickness? T

[Freesurfer] Selxavg3-sess Looking for (and can't find) "fmc.sm0"

Hello, I am getting an odd bug on selxavg3-sess. I am getting the error message, *ERROR: cannot find [rest of file path]/fmc.sm0* I am indicating zero smoothing in mkanalysis-sess ("-fwhm 0"). I am confused because the output of preproc-sess for no smoothing is fmc.nii.gz, *NOT *fmc.sm0.nii.gz w

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

Dear David, I did not see your data, but maybe couple of relevant remarks could be useful: 1. By default the wm.mgz edits are not propagated from cross to the base, but from the cross to long. And surfaces in long are initialized from the base. Therefore the wm.mgz has to be OK both in the cros

[Freesurfer] ERROR: nu_correct

Dear Freesurfer Developers, I was trying to use the recon-all -autorecon1 -subjid bert and got an error. When I checked I found the error was coming while executing the below command: nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc ./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir ./tmp.mr

[Freesurfer] QDEC-volume, thickness and area

Dear Freesurfer Experts, 1) I have 2 groups (A & B), which do not differ in terms of gender ratio. If there were no significant regions for Group-Gender interaction in mean cortical thickness in the QDEC analysis, can I conclude that gender does not influence the effect of group on thickness?

[Freesurfer] R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis

Hi, as you advise I have run selxavg3-sess with the -svres option.I found a folder called "res" which contain "res-001.nii". Is it the f.nii fully processed?ThanksStefano Messaggio originale Da: "Douglas Greve" Data: 14-mar-2017 17.38 A: Ogg: Re: [Freesurfer] R: Re: Whole prepro

Re: [Freesurfer] Petsc Error in Freesurfer v6.0

I get these pincher errors as well in VirtualBox. One thing that may fix it is to disable 3D acceleration for the graphics in the VM settings. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Michael ONeill Sent: Thursday, 23 March 2017 11

Re: [Freesurfer] Re. display SPM results on inflated surface? {Disarmed}

Hi Douglas, I am wondering, where did you find the mini 152 T1 map? :) Regarding this... Would it be better to instead run recon-all on a higher-res MNI atlas? and then run mri_vol2surf for that segmentation? Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonanc

[Freesurfer] long mri_ca_register error

Freesurfer devs, In freesurfer 6 stable I'm having a problem at the careg stage of the long. The relevant recon-all log is pasted below. Could you point me to where to debug this problem? Cheers, Chris. mri_ca_register -rusage 136_S_0426_20070604.long.136_S_0426/touch/rusage.mri_ca_register.

[Freesurfer] MRIread (load_nifti)- Out of memory

Dear All, I'm trying to load a pretty big diffusion MRI dataset (320x320x260x122). I'm running matlab 2015a 64bit on a linux machine. I'm using MRIread, which in turn calls load_nifti. I'm getting the following error: Error using + Out of memory. Type HELP MEMORY for your options. Error in loa

Re: [Freesurfer] long mri_ca_register error

It happens when I use -bigventricles. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson Sent: Thursday, 6 April 2017 12:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] long mri_ca_register error Freesurfer devs,

[Freesurfer] R: R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis

Furthermore, the res-001.nii which is produce in produced in the res folder in not the same dimension of f.nii.I would do the whole FAST preprocessing on f.nii., maintaining the same dimension and open it with FSL.ThanksStefano Messaggio originale Da: std...@virgilio.it Data: 5-apr-