Re: [Freesurfer] Error in mris_convert thickness file from ascii format

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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

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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:

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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,