[Freesurfer] mri_glmfit error " FSGD file exceeds the maximum allowed 2000"

FreeSurfer List, I am attempting to run an analyses on 2051 participants. However, when I reach the mri_glmfit stage I receive the following error. ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum allowed 2000 Is there a work around for this? Thank you in advance for

Re: [Freesurfer] Dealing with hyper-intensities

Hi Cassie those are the result of low bandwidth and susceptibility artifacts. There's not much that can be done about them post-hoc - the images don't contain enough information to reconstruct accurate models in those regions. In general we recommend higher bandwidth sequences for this reason

[Freesurfer] [FreeSurfer] mri_glmfit with fractional values in contrast file .mtx

Dear experts, Could you indicate me how to specify a contrast vector with fractional values ? I tried the below formats without success in the .mtx file: [0 0 0 0 0 0 1 1 1 -1 -1 -1]/3 |0 0 0 0 0 0 1 1 1 -1 -1 -1|/3 0 0 0 0 0 0 1/3 1/3 1/3 -1/3 -1/3 -1/3 Thank in advance for helping ! Best re

[Freesurfer] [FreeSurfer] Visualize & Compute Overlaps between two significant surface maps

Dear FreeSurer's experts, I used group analysis based on GLM to compute significative surface maps of different characteristics : thickness, CBF,... Now I've got these maps I would like to visualize overlaps between two different maps and compute the overlap ratio. How could I succeed these two

Re: [Freesurfer] MNIX/Y/Z coordinates in mri_glmfit-sim .summary file

They are MNI305 coordinates. When we mention "Talairach" coordinates, it refers to mni305 coordinates that have been transformed according to some work done by Matthew Brett. It used to be documented here http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html, but it is not in that location anymor

Re: [Freesurfer] [FreeSurfer] mri_glmfit with fractional values in contrast file .mtx

you'll need to use .33 On 03/16/2015 11:09 AM, Matthieu Vanhoutte wrote: > Dear experts, > > Could you indicate me how to specify a contrast vector with fractional > values ? I tried the below formats without success in the .mtx file: > > [0 0 0 0 0 0 1 1 1 -1 -1 -1]/3 > > |0 0 0 0 0 0 1 1 1

Re: [Freesurfer] mri_glmfit error " FSGD file exceeds the maximum allowed 2000"

This is hard coded unfortunately. I've bumped it up to 20k in the most recent version. I've put a linux version here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit On 03/16/2015 06:38 AM, Avram Holmes wrote: > FreeSurfer List, > > I am attempting to run an analyses o

Re: [Freesurfer] [FreeSurfer] Visualize & Compute Overlaps between two significant surface maps

For visualizing the overlap, I would probably create a segmentation in which each vertex is either 1 (present in thickness), 2 (present in CBF), or 3 present in both. You can do this in matlab or with a combination of mri_binarize and fscalc. You can then create an annotation from the seg with

[Freesurfer] Drawing ROIs using coordinates in another space?

Hi all, I'm working with BrainVoyager and Freesurfer. I have some Talairach coordinates from BV for a functional ROI, and I'm trying to see if I can use these coordinates in Freesurfer to draw the same ROI on the structural slices. Is this possible? Alternatively, is it possible to draw a sphere

Re: [Freesurfer] [FreeSurfer] mri_glmfit with fractional values in contrast file .mtx

Thank you Douglas. Matthieu Vanhoutte, MSc Research Engineer - Neuroradiology Department Regional University Hospital, Lille, France Le 16 mars 2015 18:17, "Douglas N Greve" a écrit : > you'll need to use .33 > > On 03/16/2015 11:09 AM, Matthieu Vanhoutte wrote: > > Dear experts, > > > > Cou

Re: [Freesurfer] [FreeSurfer] Visualize & Compute Overlaps between two significant surface maps

Thank you Douglas I will try this. Matthieu Vanhoutte, MSc Research Engineer - Neuroradiology Department Regional University Hospital, Lille, France Le 16 mars 2015 19:13, "Douglas N Greve" a écrit : > > For visualizing the overlap, I would probably create a segmentation in > which each vertex i

Re: [Freesurfer] Trac-all error

Thank you so much, Zeke! That helped a lot. Best, Emad > On Mar 10, 2015, at 11:43 PM, zkauf...@nmr.mgh.harvard.edu wrote: > > Hello Emad, > > The download page states that OSX versions of freesurfer require the user > to download and install XQuartz onto their machine. I have updated the > dow

[Freesurfer] segmentation

Dear Freesurfer users, Does anybody knows if the steps after the segmentation have some impact in subcortical structures volume? If it does, how can I have this measurements back even if I had already run recon-all? best, Maurício Anés ___ Freesurfer ma

Re: [Freesurfer] Thin Surface

Hi, Bruce. I tried several thresholds in some subjects and it seems to work reallh well. Thanks for the help! However, I would like to ask whether I should determine the expert values based on the raw image (001.mgz) or the normalized image (T1.mgz)? I am asking this because I believe the normal

[Freesurfer] Reading retinotopy output (eccentricity/polar) into Matlab in correct space for SPM

Hi all, I’m new to both freesurfer and fMRI, and after reading some related posts on the forum I still can't complete this task so would appreciate any help or suggestions. I’m trying to import the eccentricity and polar maps from a freesurfer retinotopy analysis into matlab. My goal is to hav