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,
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Jee Su Suh