[Freesurfer] How does Optseq2 arrange order of conditions?

Hello all, I'm a new user of Optseq2, and I have 2 questions about optseq2 after I got some sequences and read Dale (1999). I'll be grateful to anyone can provide help. 1. I'm curious about why optseq2 arranged the order of conditions, does anyone can provided some references to me?

Re: [Freesurfer] significance overlay in freeview

Hi Caroline, Are you running FS 5.3? The command on the webpage is based on the upcoming 6.0, I believe. So some of the command line options are not available in 5.3. Best, Ruopeng > On Jul 29, 2016, at 9:11 AM, Caroline Beelen > wrote: > > Dear FS team, > >

[Freesurfer] significance overlay in freeview

Dear FS team, Apologies in advance for perhaps again a rather basic question. I attempted to load the aparc overlay in freeview by using the written command from the group analysis page, however it failed to load correctly. I used the following command: freeview -f

[Freesurfer] mri_normalize, 110 is too dark

Dear community and developers, I am experiencing issues during the normalization step, converting NU.mgz to T1.mgz. Gray matter is falsely recognized as white matter and high intensity WM is ignored. The resulting T1.mgz collapses the wrong voxels into the 110 bin. It seems that what

Re: [Freesurfer] brain mask and T1 are not the same size

So you're saying that the dimension changed after you ran freeview and saved the volume? Can you replicate it? ie, if you make a copy of the brainmask.mgz, then edit the copy, does it do the same thing every time you make a copy and edit it? On 7/29/16 12:09 PM, Isabelle Deschamps wrote:

Re: [Freesurfer] mri_normalize, 110 is too dark

Hi Tom it's tough for us to tell without some images or the data. If you upload the entire subject dir of a subject that failed we will take a look. You can't just change which peak is the WM - lots of things downstream would fail cheers Bruce On Fri, 29 Jul 2016, tvg[fs] wrote: > Dear

Re: [Freesurfer] How does Optseq2 arrange order of conditions?

On 7/29/16 3:17 AM, 連 志浩 wrote: Hello all, I'm a new user of Optseq2, and I have 2 questions about optseq2 after I got some sequences and read Dale (1999). I'll be grateful to anyone can provide help. 1. I'm curious about why optseq2 arranged the order of conditions, does anyone can

[Freesurfer] brain mask and T1 are not the same size

Dear FreeSurfer experts, I am trying to fix the skull strip manually for a group of participants. For all participants except 4, I get an error when running recon-all -autorecon-pial -subjid S07_FS, after editing manually in Freeview the brainmask.  In freeview, I followed the instruction

Re: [Freesurfer] error during longitudinal -long stream

Hi Martin, I checked all data are completed except the link to fsaverage, lh.EC_average and rh.EC_average. I run one analysis from the terminal. it works. if I run multiple analysis at the same time, it failed. When I manually linked the 3 files, then run multiple analysis at the same time, it

Re: [Freesurfer] error during longitudinal -long stream

Hi Jinsong, can you give an example of what exactly does not work. Thanks, Martin On 07/29/2016 12:26 PM, Jinsong Tang wrote: Hi Martin, I checked all data are completed except the link to fsaverage, lh.EC_average and rh.EC_average. I run one analysis from the terminal. it works. if I

[Freesurfer] MNI coordinates of all the vertices of fsaverage

Hi Doug, I tried to pick up from the thread below to get MNI coordinates of each destrieux parcellation region. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html I created label files from mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation

[Freesurfer] Running Retinotopy in FSFAST, Design Matrix has Empty Regressors

Hello, I am trying to run a retinotopy analysis in fsfast, using only polar angle. However, when I try to run it, I am getting the error "Input to SVD must not contain NaN or Inf." I have traced this error and it looks like the design matrix X has 12 regressors (the first 12) that consist solely