[Freesurfer] mne_analyze not dispalying surfaces

Hello, I'm trying to display the inflated surfaces through mne_analyze and all I see is only few pixels of the surfaces. I'm assuming this is a problem with graphics, so I think I have Matrox Graphics (MGA G200ew WPCM450 rev 0a) installed on my host machine and I'm accessing this machine

[Freesurfer] [freesurfer] FS5.1 talairach issue

Hi freesurfers, I'm currently re-processing with FS5.1 some data that i had already processed with FS5.0 and am experiencing some unexpected issues with the linear talairach transform. - While manually checking with Tkregister, I noticed that some off the subjects had quite unsatisfying

Re: [Freesurfer] selxavg-sess outputs

Hi Doug, As the freesurferwiki says, the h.nii contains the estimated hemodynamic response at each voxel, along with the standard deviation of the residual error, and h-offset.nii contains a map of the mean value at each voxel. My expectation is that h.nii should have the same dimension as my

Re: [Freesurfer] Longitudinal Subject/Base name errors

Hi Jeff, this was a known bug in 5.0 and there are fixes on the web (release notes), just download the recon all from there (and did you grab the robust template binary)?. http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes Best, Martin On Mon, 2011-08-08 at 17:43 -1000, Jeff Sadino wrote:

Re: [Freesurfer] selxavg-sess outputs

It is more accurate to say that it has the regression coefficients for the HRF. If you use a gamma or spm hrf, then it just has the amplitude (your case). If you use an FIR, then it has the coefficients for each delay in the FIR, which can be assembled into a waveform. I'm not sure what you

[Freesurfer] FSGDF matrix

Dear Bruce, I am ready to start my GLM group analysis. I am trying to construct the FSGDF by constructing an my_age_fsgd.txt file.  I was reading the tutorial and I am not sure if I need to put together my patients and controls in my FSGDF since my group study will be for patients versus

Re: [Freesurfer] selxavg-sess outputs

I want the time course for each voxel in my ROI. But the time course should be corrected by removing the drift, which I think that is what the -polyfit option does. I know I probably can do it myself, but I am wondering if Freesurfer has this already. Yang On Wed, Aug 10, 2011 at 1:55 PM,

Re: [Freesurfer] FSGDF matrix

Yes, if you need to compare patients and controls, then put them together in the same FSGD file. doug Antonella Kis wrote: Dear Bruce, I am ready to start my GLM group analysis. I am trying to construct the FSGDF by constructing an my_age_fsgd.txt file. I was reading the tutorial and I

Re: [Freesurfer] selxavg-sess outputs

You can't do that with FSFAST. You can do something like that with mri_glmfit, something like: mri_glmfit --y fmc.nii --qa --glmdir qa.glm --save-yhat This will detrend the time series (removing mean, linear, and quadratic trends). With --save-yhat, one of the outputs will be yhat.mgh (the

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Hi Chris, when I bring that one up in freeview it looks like the a/p axis is still reversed (i.e. 'P' is at the front of the head) Bruce On Wed, 10 Aug 2011, Christopher Luna wrote: Okay, I've uploaded them as cdluna_whitematter_002.img and *.hdr. Thanks, Christopher Luna MIT Brain and

Re: [Freesurfer] Longitudinal Subject/Base name errors

Hi- Note, this bug still exists in 5.1. Below is my exchange with Martin and Nick a several months ago. -Wil --- |-Original Message- |From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] |Sent: Wednesday, May 25, 2011 3:52 PM |To: Irwin, William; Martin Reuter |Subject: RE: 5.1.0

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

Hi Bruce, We tried to reverse A/P by reversing it the Talairach transform since recon-all wasn't able to do it automatically. I'm actually not sure how to reverse it in the IMG and HDR files. Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for

Re: [Freesurfer] FSGDF matrix

yes, they both need to be in there On Wed, 10 Aug 2011, Antonella Kis wrote: Dear Bruce, I am ready to start my GLM group analysis. I am trying to construct the FSGDF by constructing an my_age_fsgd.txt file.  I was reading the tutorial and I am not sure if I need to put together my patients

Re: [Freesurfer] FSGDF matrix

Hi Bruce, Thanks again for your  help. I have two more question please: 1). When I need to average my  subjects and controls all together while using make_average_subject  --subjects 1 2... ? 2) When I run the make_average_subject  I need to specify   -xform talairach.lta or

Re: [Freesurfer] Large White Matter Areas Ignored In Surface Detection

One thing you can try is to look at the current orientation with mri_info --orientation f.img This will print out a 3-letter string like LPS or LSA. Create a new string by replacing the A with a P or P with an A. then mri_convert f.img --in_orientation NewString f.new.nii where NewString is

Re: [Freesurfer] Longitudinal Subject/Base name errors

Hi Nick, can you look into this? I think we fixed this bug in 5.0 or is it something different? Is it still not fixed in 5.1? Thanks, Martin On Wed, 2011-08-10 at 11:19 -0700, Irwin, William wrote: Hi- Note, this bug still exists in 5.1. Below is my exchange with Martin and Nick a several

Re: [Freesurfer] mri_glmfit .nii files

I am actually getting an error message when I type my mri_glmfit command: ERROR: fio_pushd: /group_analysis/volume/m1/mstmct_v_base/type_v_rest ERROR: must specify input y file I did specify a y file and I do not know what fio_pushd is. This is controlled by the $FSF_OUTPUT_FORMAT. By

Re: [Freesurfer] Longitudinal Subject/Base name errors

stable 5.1 contains the fix, which is the addition of -w to the grep on line 5428. that particular fix works for the example names given (11 as the basename, 11_S0 and 11_S1 in the base-tps file). can someone give me the basename and base-tps contents so that i can replicate the

[Freesurfer] repeated measures ANOVA

Hello all, We would like to analyise our repeated measures DTI data using an ANOVA. We are wondering if someone might have experience running AVOVA's on 3D data? Is there a particular tool used or did you use MATLAB for this type of analysis? Thank you, Sandra Sandra Woodman Mood and Motor

[Freesurfer] : Memory and CPU Allocation?

Dear FSFAST, I am using the program selxavg3-sess on 3D data for a single session (i.e. selxavg3-sess -s avml07 -analysis $ana_vol -force) and it errors out with the following message: OLS Residual Pass run 1t= 0.0 ??? Error using == unknown Out of memory. Type HELP MEMORY for your

[Freesurfer] Label2label on fsaverage

Dear freesurfer experts I've tried to export my label file from individual space to fsaverage space by using this command: mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg

Re: [Freesurfer] Label2label on fsaverage

Try using fsaverage as the trgsubject Cheers Bruce On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi roohy...@gmail.com wrote: .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like

[Freesurfer] VRML support

Greetings, I have problems exporting the surface data in VRML format. When I load the resulting .wrl file into Blender (a 3D modeling tool), the resulting surface is full of holes (bad/missing polygons) and connectivity of vertices is all wrong -- I see edges where they are not supposed to be. Is

Re: [Freesurfer] VRML support

Dear Andrei, Do you need any specific feature from VRML? If not, and you simply need to import the mesh into Blender, you can do this: 1) Convert the mesh to ASCII format: /mris_convert somesurface somesurface.asc/ 2) Save the attached script somewhere, make it executable with chmod, then