Re: [Freesurfer] Question about OptSeq

No, there is not. optseq assumes you will be doing an FIR analysis (=finite impulse response = not assuming a shape to the hemodynamic response). In this analysis, this must be the relationship. If you assume a shape, then this relationship is not necessary. In your case, you can set the

[Freesurfer] Surfaces with different numbers of vertices.

Hello Freesurfer users/developers, I have surface with ~73,400 vertices generated from the Freesurfer version 6 fsaverage brain, left hemisphere. I have a surface map that was created by mapping a volume to the fsaverage white surface. Is there a way to map the surface map to the new surface

Re: [Freesurfer] Surfaces with different numbers of vertices.

Hi Ryan I'm not sure why you would have a surface with 73K vertices on fsaverage. Why not use one of the ico representations (40K or 160K vertices)? In any case, mri_surf2surf should do the trick, although you will probably need to create a new subject with a set of 73K vertex surfaces

Re: [Freesurfer] Surfaces with different numbers of vertices.

Hi Bruce, We wanted to map values from a previous analysis to a representation of the brain with the sulci filled — something that resembles the output lh.pial-outer-smoothed from the recon-all -localGI. I tried using mri_surf2surf, but I get the error: ERROR: dimension inconsistency in

Re: [Freesurfer] Surfaces with different numbers of vertices.

Who did you create lh.test.nii? On 7/1/2019 1:47 PM, Nillo, Ryan Michael R wrote: Hi Bruce, We wanted to map values from a previous analysis to a representation of the brain with the sulci filled — something that resembles the output lh.pial-outer-smoothed from the recon-all -localGI. I tried

[Freesurfer] Error opening Freeview

?Hi all, I'm having issues opening Freeview (The most recent version): it loads .mgz and labels correctly, but then after 5 seconds it shuts off, giving off this error: qt_xcb_createCursorXRender: query_pict_formats failed [0]PETSC ERROR:

Re: [Freesurfer] mri_gtmpvc -- Failed tissue type check

Hi Cristina, can you send more info? Eg, your command line and terminal output. Do you do anything special (eg, your own annotation)? On 7/1/2019 5:57 PM, Lois Gomez, Cristina wrote: Hi Freesurfers, I am having trouble with one subject's PVC (we process many cases and never had this issue

Re: [Freesurfer] Surfaces with different numbers of vertices. {Disarmed} {Disarmed}

That is the problem. It is not a cortical surface (ie, white or pial); isn't this LGI surface just a surface shrink wrapped around cortex? Not sure how to map that across subject. On 7/1/2019 2:53 PM, Nillo, Ryan Michael R wrote: Pial-outer-smoothed was a surface created from recon-all

Re: [Freesurfer] Surfaces with different numbers of vertices. {Disarmed}

how was pial-outer-smoothed create? On 7/1/2019 2:33 PM, Nillo, Ryan Michael R wrote: Hi Doug, lh.test.nii was created with: mri_vol2surf --mov ./misc/lh.probability.nii --trgsubject fsaverage_1 --regheader fsaverage_1 --hemi lh --fwhm 30 --surf pial-outer-smoothed --o ./lh.test.nii Where

Re: [Freesurfer] Surfaces with different numbers of vertices. {Disarmed} {Disarmed}

Pial-outer-smoothed was a surface created from recon-all -localGI. Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging > On Jul 1, 2019, at 11:41 AM, Greve, Douglas N.,Ph.D. > wrote: > > how was

[Freesurfer] Citing the development version for use of hippocampal/amygdala sub-field segmentation

External Email - Use Caution Hello, I used the longitudinal HippocampalSubfieldsAndNucleiOfAmygdala pipeline to create

Re: [Freesurfer] Surfaces with different numbers of vertices.

can you send the entire output? On Mon, 1 Jul 2019, Nillo, Ryan Michael R wrote: Hi Bruce, We wanted to map values from a previous analysis to a representation of the brain with the sulci filled — something that resembles the output lh.pial-outer-smoothed from the recon-all -localGI. I

Re: [Freesurfer] Surfaces with different numbers of vertices. {Disarmed}

Hi Doug, lh.test.nii was created with: mri_vol2surf --mov ./misc/lh.probability.nii --trgsubject fsaverage_1 --regheader fsaverage_1 --hemi lh --fwhm 30 --surf pial-outer-smoothed --o ./lh.test.nii Where lh.probability.nii is a probability mask created from about 63 subjects. Thanks in

Re: [Freesurfer] Error opening Freeview

Hi Victor, Would it be possible to send me the data files and the freeview command you ran? You can upload them from here: https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks, Ruopeng On 7/1/19 4:29 PM, Zeng,Victor (BIDMC - Psychiatry) wrote: ​Hi all, I'm having issues opening

[Freesurfer] mri_gtmpvc -- Failed tissue type check

Hi Freesurfers, I am having trouble with one subject's PVC (we process many cases and never had this issue before). When running mri_gtmpvc I get a 'Failed tissue type check' error. I've seen that other people have reported similar errors in the past, but I haven't found any advice on how to

[Freesurfer] LME - Monte Carlo

External Email - Use Caution Dear FreeSurfers, I was reading the wiki documents about how to run LME analyses in FreeSurfer. I found that one of the disadvantages is that, at the moment, it only allows FDR corrections to be applied for multiple comparisons. I have 2 patient