Hi JeeSu
which surface you use is irrelevant (we only need one with the right topology).
As for converting from ascii back to curv, matlab is probably the easist using read_ascii_curv.m and write_curv.m. You will need to also read in a surface to get the number of faces. Again, any one of the same topology ones should be fine (e.g. lh.inflated for lh.thickness.asc)
cheers Bruce
On Thu, 4 Jul 2019, Jee Su Suh wrote:
External Email - Use Caution
Hi Bruce and Doug, Thanks for your responses. Apologies if my query was unclear. The operation I would like to do is the opposite: instead of converting to ascii, I want to convert from ascii to curv format.
I used the command stated in your replies to do the first conversion to ascii, which I required in order to carry out an algorithm for correcting for site effects on the dataframe of vertex-wise thickness values. Now that I have done that, I was hoping to convert back into the original curv format in order to carry out the normal group comparison pipeline (mri_preproc, mri_glmfit). Is this possible, from your view?
A slightly tangential note: when I did the first conversion to the ascii format, I used lh.inflated as the surface-- would this have had a significant impact on what I am attempting to do now?
Thanks for your help, JeeSu
--
Date: Wed, 3 Jul 2019 18:51:49 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error in mris_convert thickness file from ascii format To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1907031851200.2160@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Hi JeeSu if you look at the help for mris_convert, you'll see this example:
Convert a scalar overlay file in "curv" format to ascii: mris_convert -c lh.thickness lh.white lh.thickness.asc
which you should follow
cheers Bruce
On Wed, 3 Jul 2019, Jee Su Suh wrote:
????????External Email - Use Caution???????? Hello, I am trying to convert ascii files containing vertex-wise thickness data into binary curvature
files
for subsequent smoothing and input into mri_glmfit. The command I used is: mris_convert lh.test.asc lh.test.thickness But then get the following error: ERROR: MRISalloc: nfaces=-5 < 0 No such file or directory I'm not sure what file or directory the error message is referring to, nor what the meaning of nfaces is. I am running version 6.0 on macOS Mojave. I have also attached a truncated version of
the
ascii file for inspection purposes (the whole thing was too big), which was converted from a csv that was generated by a python script correcting for site effects. This script took in as input
the
original ascii converted from the original lh.thickness file using mris_convert. The coordinates correspond to the fsaverage template (~160k vertices in the whole file). Thanks in advance for any guidance,
-- JeeSu Suh, BSc. MSc. Student, Graduate Neuroscience Program McMaster University suhj5@mcmaster.ca