This was fixed in 7.11. You can use that version or copy the attached
file to this location
$FREESURFER_HOME/matlab/freesurfer_read_surf.m
On 5/11/2021 2:28 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
Hi,
I am using Matlab R2014a, and FS7.1.0
and receiving this error when I try
Hi,
I am using Matlab R2014a, and FS7.1.0
and receiving this error when I try to run -localGI. Is there a package I might
be missing? Or am I using an outdated version of Matlab?
=
mris_smooth -nw -n 30
/mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/surf/tmp
External Email - Use Caution
Dear expert
I am trying to calculate LGI for a subject. Now with some of your suggestions
it runs, but after one hour and half it gives me this errors
remeasuring lGI value for vertex iV = 29501. It may take a few minutes.
WARNING -- Problem for vert
Hi Greve,
Thanks for your help. It is that I only use FWMH = 5 to do my study, it is
decided by my data. Can I think it so?
Sincerely,
Zheng
At 2017-12-14 00:06:39, "Douglas Greve" wrote:
The FWHM used in the MC simulation is computed from the data itself. The final
FWHM is a m
The FWHM used in the MC simulation is computed from the data itself. The
final FWHM is a mixture of the applied FWHM and smoothness inherent in
the data. LGI has a lot of inherent smoothness, so the final FWHM is
very large. The MC sim table only goes up to 30mm, after that it
generates an erro
Hi professors,
I am using Freesurfer 6.0 for calculating LGI. I have done 'recon-all' for
it. When I ran Monte Carlo in qdec (FWHM=10), it has errors:
However, when FWHM=5, It was ok. What led to this result? I don't know why.
Thanks in advance !
Zheng
Hello FS users,
I am using FreeSurfer version 5.3 to calculate local verification index and
processing stopped at make_roi_paths. Here, I was given the error below. I
searched in the archives and found a solution to the problem was to edit a few
lines on SearchProjectionOnPial.m. The new script
> aral ahmadi wrote:
> >
> > Dear experts
> >
> > I have a question regarding Freesurfer- LGI error I got during running
> > LGI after all recon steps been ran with no problem. you could see the
> > error below.
> >
> > *reading fill
hanks,
Aral
aral ahmadi wrote:
>
> Dear experts
>
> I have a question regarding Freesurfer- LGI error I got during running
> LGI after all recon steps been ran with no problem. you could see the
> error below.
>
> *reading filled volume...
> *
>
> *??? undefined func
Dear experts,
I have a question regarding Freesurfer- LGI error I got during running LGI
after all recon steps been ran with no problem. Attached you could see the
error.
The error is ...Undefined function or variable 'ismac' - matlab is
expecting that variable to be defined (it&#
Thanks so much Marie. I will check the toolboxes.
best,
Alan
On Wed, Jul 9, 2014 at 2:56 PM, Marie Schaer wrote:
>
> Hi Alan,
>
> You probably don't have the matlab image processing toolbox installed.
>
> Let me know if you can't install it easily.
>
> Best,
>
> Marie
>
> On Jul 9, 2014
Hi Alan,
You probably don't have the matlab image processing toolbox installed.
Let me know if you can't install it easily.
Best,
Marie
On Jul 9, 2014, at 11:51 AM, Alan Francis
mailto:alandarkene...@gmail.com>>
wrote:
Hi Marie & FreeSurfers:
I am running the LGI command on a group of bra
Hi Marie & FreeSurfers:
I am running the LGI command on a group of brains and I am getting an error
message. MATLAB opens up and begins to run when this error appears:
< M A T L A B (R) >
Copyright 1984-2011 The MathWorks, Inc.
R20
Hi Wanda,
You should have this function in $FREESURFER_HOME/matlab, the same way you
should have compute_lgi.m and many other matlab functions there. Are you sure
that you are looking at the correct location and / or that you didn't delete it?
Marie
On Jan 31, 2014, at 11:32 AM, Wanda Truong
Hi Marie,
Yes, I'm using matlab R3013a. In $FREESURFER_HOME/matlab folder I don't
have a file called SearchProjectionOnPial.m. Should I create it and paste
the updated function?
Thanks for your help!!
Wanda
On 30 January 2014 15:09, Marie Schaer wrote:
>
> Hi Wanda,
>
> I'm not sure to u
Hi Wanda,
I'm not sure to understand your problem. Do you get an error because of using
matlab 2013? If yes, I'm not sure to understand whether you modified the
SearchProjectionOnPial.m function properly.
Can you download the updated function there:
http://www.mail-archive.com/freesurfer@nmr.
Hello Marie,
I am trying to conduct a local gyrification index analysis, however I am
getting this error ERROR: make_roi_paths did not complete successfully!
Which is the same as the one posted earlier by someone else:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032203.html
This is bizarre. The only other explanation is that the "you" who
creates a file is not the same "you" who tries to delete it (it all
sounds rather metaphysical:). Can you have that unix call run some unix
commands to see who you are? Another thing is to make a unix command
that creates a dele
Hi Doug,
I already tried changing all the occurrence of "rm" to "rm -f" in load_mgh.m,
but it did not change anything. The error message remains identical.
The other strange thing is that, as the owner of the file, I have read and
write permission on /tmp/tp9204736418620864.load_mgh.681685.mg
OK, if yours had load_mgh in the file name, then it is definitely from
load_mgh.m. Strange that the one below does not have that.
I think know what is going on. The rm command will sometimes ask if you
want to remove a file, esp if you don't have write permissions. In
general, if you create a
Many thanks Doug for your reply!
For me it happened every time the lGI was launched, but none of the other
freesurfer commands that I used on this system ever resulted in a similar
error, everything else is perfectly fine. The process can hang for days without
going further, it will never come
How often does it happen? Does the process just hang or does it produce
the correct results (eventually)? I don't think it is related to
load_mgh.m because the temporary filename would be different. However,
it is consistent with the temp files used with nifti reading and
writing. Does that ha
Hi Kangchen,
I also had the same error recently on a unix machine, but I unfortunately did
not find the solution and some help would be greatly appreciated.
I think that the bug is due to the fact that make_outer_surface.m calls
MRIread.m, which calls load_mgh.m and that something gets wrong a
Dear all，
When I run "recon-all -s ${subject} -localGI", it appear "rm: remove
regular file `/tmp/tmp4653077.mgh'? ". Then, I write yes, however, it
didn't response anyway. How shold I do next? Thank you!
The echo for the process is followed
--
running subject Emotion_xun
Dear List
Just to say that the below error turned out to be a problem with my
pathdef.m file.
Very best,
Lisa
On Mon, Apr 4, 2011 at 4:24 PM, Lisa Ronan wrote:
> Dear List
>
> I have recently come up agains the same problem as described below, namely
> the error when I compute lGI reads
>
>
Hi Lisa
Are you able to see the paths traced from the 'intermediate' files - you can
find them in a tmp folder within the subject's surf directory
Lena
On 04/04/2011 16:24, "Lisa Ronan" wrote:
Dear List
I have recently come up agains the same problem as described below, namely the
error w
Dear List
I have recently come up agains the same problem as described below, namely
the error when I compute lGI reads
>>reading filled volume...
closing volume...
??? Undefined function or method 'fspecial' for input arguments of
type 'char'.
Error in ==> make_outer_surface at 31
Gaussian = fsp
Hi Frédéric,
Do you have the matlab image processing toolbox installed?
Cheers,
Marie
On 17 déc. 09, at 12:03, Frédéric Andersson wrote:
> Hi,
>
> I've got some troubles computing the lGI.
> It seems to be a trouble related to the class.m and strel.m matlab
> functions.
>
> Does anyone meet s
Hi,
I've got some troubles computing the lGI.
It seems to be a trouble related to the class.m and strel.m matlab
functions.
Does anyone meet such problem?
Thanks
Frederic
gray.local:andersson 11:50am [12] recon-all -s MNI_SINGLESUBJ -localGI
-no-isrunning
INFO: FreeSurfer build sta
Hello,
I'm getting an error running a LGI compute.
I'm working on multnomah on the
directory: /autofs/space/multnomah_002/users/Cashlab/MG07
I'm using the following command line:
[multnomah:MG07] (nmr-std-env) mris_compute_lgi --i lh.pial
--close_sphere_size 30 --smooth_iters 60
I'm getting
Looks like my image processing toolbox from matlab was not properly
installed. Now that I have re-installed the image processing toolbox,
LGI appears to be working fine.
Cheers,
Jenifer
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
___
Freesurfer mailing list
Fre
Hi Jenifer,
I don't know what the error exactly means, but sometimes just re-running the
analysis helps.
Best,
Martin
On Wednesday 24 September 2008 19:24:40 Juranek, Jenifer wrote:
> Hi,
> Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB
> v7.6.0.324 (R2008a) install
Hi,
Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB
v7.6.0.324 (R2008a) installed. Subject was processed under fsv405.
Specific error is pasted below:
Any suggestions to correct my error?
Thanks,
Jenifer
>> reading filled volume...
closing volume...
??? Undefined fun
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