Dear FreeSurfer experts,
I am reaching out to kindly ask for some clarification on how to set up
mris_pmake to achieve the following:
1. Calculate the distance between pairs of peak vertices on the inflated
fsaverage surface using the Dijkstra's algorithm
2. Create fixed-radius ROIs arou
on behalf of Douglas N. Greve
<mailto:dgr...@mgh.harvard.edu>
Sent: Friday, November 13, 2020 9:58 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_pmake error - freadFloat:
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Friday, November 13, 2020 9:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_pmake error - freadFloat: fread failed
Can you open the smoothwm with another application? Eg, mris_info
Can you open the smoothwm with another application? Eg, mris_info or
freeview -f
On 11/12/2020 9:52 AM, Nasr, Shahin,Ph.D. wrote:
Hi Surfers,
For one subject, when I run mris_pmake as below:
mris_pmake --subject --hemi lh --surface smoothwm
--mpmProg pathFind --mpmArgs vertexStart:,vert
Hi Surfers,
For one subject, when I run mris_pmake as below:
mris_pmake --subject --hemi lh --surface smoothwm --mpmProg
pathFind --mpmArgs vertexStart:,vertexEnd:
--mpmOverlay euclidean
I get the following error:
mris_pmake error - freadFloat: fread failed
This error appears irrespecti
The in-line help in version 6.0 of FreeSurfer is incorrect
unfortunately. Please try the following for example:
mris_pmake --subjecttestSubject \
--hemi lh \
--surfacepial\
Hi,
I’m trying to calculate Dijkstra distance between startVertex and endVertex on
the inflated surface (fsaverage, lh.inflated) using mris_pmake.
I see several options: --surface0, --surface1, --curv0, --curv1
I think I can use ‘--surface0 inflated’, but not sure about other options e.g.
OK -- looked again -- and I need to fix the in-line help obviously.
Anyway, this works:
mris_pmake --subjecttestSubject \
--hemi lh \
--surfacepial\
--curv
External Email - Use Caution
Dear Rudolph,
Thank you for following up.
I changed flags and tried it again with this command line:
mris_pmake --subject cvs_avg35_inMNI152_temp --hemi lh --surfaceFile pial
--curvatureFile
sulc --mpmOverlayArgs euclidean --mpmProgID pathFind --m
Apology if this is a repeat email. I used the wrong email address in my
reply. I was one of the original
authors of `mris_pmake` although it's been (quite) a few years now. I
do remember that at some point the CLI changed, and given the FS
release cycle it took a while for this to make it into pro
External Email - Use Caution
Dear Freesurfers,
I am trying to calculate distances using mris_pmake with Freesurfer Version
6.0.0. When using the command line the following error appears:
mris_pmake: unrecognized option '—surface0'
In January the similar question
(https://www.
Dear FreeSurfers,
I am trying to update an mris_pmake command line that works with the pub v5.3.0
version with a new command line that works with pub v6.0.0 version. The purpose
is to compute the distance between two vertex points on the pial surface using
the cvs_avg35_inMNI152 brain. We are
Dear Surfer & Rudolph,
Hi,
I tried to run mris_pmake, but only got this message:
I'm sorry, but an error condition has occurred.
While I was checking on the options file,
I couldn't access the options file. Does it exist?
How can I use mris_pmake?
I'm working with Vitaly Napadow, and I would l
Dear freesurfer experts,
I want to calculate the distance between two vertices which are
located on different hemispheres. I was wondering how I could do this
with mris_pmake because a hemisphere is required within the analysis.
Is there any possibility to obtain the distance between a verti
Hi Surfers,
I am using mris_pmake (in nmr-dev-env) to measure the distance between
two vertices. Everything is fine as long as I use just one terminal. But,
to accelerate my analysis, I have divided my analysis into multiple parts
and run each part in one terminal. It means, I may run multip
Hi,
Is it also possible to get an updated version for the mris_pmake binary?
This is freesurfer-i386-apple-darwin11.4.2-stable5-20130514 version.
Thanks!
Sarah
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Thank you!
I have Ubuntu 14.04.1 LTS, 64 bit.
Best
Francesca
2015-01-08 16:45 GMT+02:00 Rudolph Pienaar :
> I can send you the updated binary. What Linux are you running on?
> CentOS? 32 bit? 64 bit?
>
> Best
> -=R
>
> On 1/8/15 09:23 , Francesca Strappini wrote:
> > Dear Freesurfer experts,
>
I can send you the updated binary. What Linux are you running on?
CentOS? 32 bit? 64 bit?
Best
-=R
On 1/8/15 09:23 , Francesca Strappini wrote:
> Dear Freesurfer experts,
>
> I'm currently working with Freesurfer 5.3-stable and I would like to
> calculate the geodesic distance between two points
Dear Freesurfer experts,
I'm currently working with Freesurfer 5.3-stable and I would like to
calculate the geodesic distance between two points.
I red in the support main-list that in this Freesurfer's version
'mris_pmake' might be outdated. How can I get the updated version?
Thanks
Francesca
Hi Andrew --
First the good news:
Indeed, there is a much simpler (and quicker way):
mris_pmake --subj --hemi --surface
--mpmProg autodijk --mpmArgs vertexPolar:0 --mpmOverlay euclidean
If called with hemi=lh and surface=smoothwm, it will create an output
overlay called lh.autodijk.crv.
Dear all,
I am trying to calculate the distance from a reference vertex to all other
vertices in a surface mesh (or ideally to a subset of vertices), moving
along the actual surface (e.g. smoothwm).
I am able to loop through the pairs of vertices in which I'm interested,
using mris_pmake in each
Hi Octavian --
On Wed Oct 3 17:43:51 2012, octavian lie wrote:
> mris_pmake --subject A --hemi rh --surface0 sphere.reg --curv0 sulc
> --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs
> startVertex:1,endVertex:2
That seems about right if you want to use the spherical surface.
>
Dear all,
I need to measure the distance between 2 points on the same hemisphere for
subject A, in the common surface space as I have to compare it with the
distance between other 2 points for subjects B, C...
I used
mris_pmake --subject A --hemi rh --surface0 sphere.reg --curv0 sulc --curv1
sulc
On 10/25/11 17:38 , Steph Bickel wrote:
> Hi Rudolph and Bruce,
>
> thanks for your responses.
>
> rudolph, your example works great. just 2 questions:
> what dimension is the total path cost in the mris_pmake output?
> is there a way to input a file with several vertex point pairs to
> compute the
find the angle between the vectors connecting each point with (0,0,0).
compute the fraction of the circle that it represents, and multiply it by:
K * PI * D
where
D = diameter of ?h.sphere
K = sqrt(surface area of surface you are interested in)
-
Hi Rudolph and Bruce,
thanks for your responses.
rudolph, your example works great. just 2 questions:
what dimension is the total path cost in the mris_pmake output?
is there a way to input a file with several vertex point pairs to compute
the distance between, or do I have to loop through the pa
On 10/25/11 10:57 , Steph Bickel wrote:
> Hi Rudolph,
>
> thanks for your speedy response.
> I want to get distance along vertices (the surface) between two vertex
> points.
OK -- 'mris_pmake' works for this. Say you have a subject called 'test'
and you want to calculate the distance on the lh 's
an easy way to do this to within 15% or so is to compute the great circle
distance between the two vertices on the ?h.sphere file.
On Tue, 25 Oct
2011, Steph Bickel wrote:
Hi Rudolph,
thanks for your speedy response.
I want to get distance along vertices (the surface) between two vertex point
Hi Rudolph,
thanks for your speedy response.
I want to get distance along vertices (the surface) between two vertex
points. Is there maybe a matlab function doing this?
Thanks,
Stephan
On Tue, Oct 25, 2011 at 10:54 AM, Rudolph Pienaar <
rudo...@nmr.mgh.harvard.edu> wrote:
> 'mris_pmake' is sti
'mris_pmake' is still very experimental. It's not run as part of the
standard recon-all stream, and is more of a post-processing surface
tool. It has a somewhat complicated set of dependencies at this stage
(among them, a file called 'options.txt' that controls its behavior).
What are you looki
Hi,
when trying to use mris_pmake I get error messages:
when I run:mris_pmake
I get:
sh: cannot create lock: Permission denied
mris_pmake
I'm sorry, but an error condition has occurred.
While I was checking on the options file,
I couldn't access the options file. Does it exist?
Exiting to system
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