[Freesurfer] Unpacking Philips scans work-around... should this work?

Hi, I have scans from a Philips scanner I want to process with FreeSurfer. Previously, the scans have been downloaded in the Philips PAR/REC format and converted into niftis, and those niftis have been used as the raw inputs in other imaging pipelines. Instead of dredging up the original

Re: [Freesurfer] slice timing correction with mulit-band

I tried to use preprocess-sess with -sdf, here is the error message: ERROR: Flag -sdf unrecognized. I attach here the slice timing. I saved it in a .txt file and tried “-sdf slicetimingfile” but got the above error message. Instead of using preproc-sess directly, I tried to use stc-sess to

Re: [Freesurfer] slice timing correction with mulit-band

You will need to know how many slice groups were used in the acquisition, fsfast will not know that. preproc-sess should accept a slice-timing with with -sdf (though this is not listed in the help). What is the error that you are getting? There is no way to do STC before MC in fsfast. When you

[Freesurfer] Fwd: FW: Resting-State and Brain Connectivity, 2018, in Montreal: programs are available

External Email - Use Caution Dear Community, *The Sixth Biennial Conference on Resting-State and Brain Connectivity* *Conference**:** September 26 - 28, 2018* *Educational workshop: September 24 - 25, 2018* *Montreal, QC, Canada* - Early abstract submission deadline:

Re: [Freesurfer] Question on MRI_surf2vol

I'm not sure what you mean. For a given vertex, mri_vol2surf finds the closest voxel in the volume to that vertex and asigns the vertex the value from that voxel (interpolation possible too). On 6/1/18 3:39 PM, Nicholas Heugel wrote: I have some questions regarding how MRI_vol2surf works.

[Freesurfer] Vertex-wise Cortical Thickness BA_exvivo.thresh label

External Email - Use CautionHi,    I would like to obtain a list of each vertex and its cortical thickness of the BA_exvivo.thresh labels (e.g. lh.BA1_exvivo.thresh.label). The stats files (e.g. lh.BA_exvivo.thresh.stats) only provide mean and standard deviations of all vertices

[Freesurfer] Question on MRI_surf2vol

External Email - Use Caution I have some questions regarding how MRI_vol2surf works. More specifically, how does it handle the vertices when performing the process. If the same vertex is the closest to multiple locations on the surface file, is it projected to all those

Re: [Freesurfer] Problem in subfields development version (T2 mode)

External Email - Use Caution And the El Capitan dev is now fixed, too! Thanks to Andrew Hoopes for this. -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

Re: [Freesurfer] Lookup table to surface overlay

External Email - Use Caution Freesurfer Experts, thanks for the response! There was no command for projabs, but looking through the help I think projdist was about what I needed? I was also curious though if there were a way to get it into an annotation--like the one

[Freesurfer] "WARNING: Image geometries differ across time" upon running base step of longitudinal pipeline

External Email - Use Caution Dear all, I have pre and post-intervention data for a single group of subjects, and I'd like to extract the cortical thickness pre and post, for all standard regions in the atlas, and use those in subsequent analyses. Following the standard approach

Re: [Freesurfer] creating a mask for the thalamus parcellations

External Email - Use Caution Thanks Bruce and Eugenio. it will be great to have so looking forward to it. Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: 31 May 2018 17:53:26 To:

Re: [Freesurfer] FSGD design for multi-centre study

External Email - Use Caution Hi again, What about for DODS? I tried to create the contrast for this but got the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check