When I look at the README, this is the contents. Are you looking at
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/README ?
Download make_average_subject and the platform-specific version of
mri_aparc2aseg
from this directory and move them to your freesurfer bin directory
External Email - Use Caution
The patch (see text below) only directed me to replace a file in the
freesurfer/gcc/lib directory, which I did. Do I also need to replace the
make_average_subject and mri_aparc2aseg files in my freesurfer bin?
*To patch the existing 6.0.0 release you
It looks like you are still using the old make_average_subject as the
time stamp is from Jan 19, 2017 (same for mri_aparc2aseg). Can you
confirm that those are really the patches?
On 3/29/2021 12:52 PM, Jordan Mullins wrote:
External Email - Use Caution
Hi Douglas,
Just following
External Email - Use Caution
Hi Douglas,
Just following up on this. Thanks!
On Wed, Mar 17, 2021 at 6:12 PM Jordan Mullins
wrote:
> Yes! Results attached.
>
> On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve
> wrote:
>
>>
>> Can you run
>> ls -l
External Email - Use Caution
Yes! Results attached.
On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve
wrote:
>
> Can you run
> ls -l $FREESURFER_HOME/bin/mri_aparc2aseg
> $FREESURFER_HOME/bin/make_average_subject
> and send the result?
>
> Also, the result of
> which
Can you run
ls -l $FREESURFER_HOME/bin/mri_aparc2aseg
$FREESURFER_HOME/bin/make_average_subject
and send the result?
Also, the result of
which mri_aparc2aseg
which make_average_subject
On 3/17/2021 8:36 PM, Jordan Mullins wrote:
External Email - Use Caution
Yes, I had seen that
External Email - Use Caution
Yes, I had seen that report and had downloaded the patch, but still got the
same error. Are there any other steps I can take?
On Wed, Mar 17, 2021 at 2:59 PM Douglas N. Greve
wrote:
> This problem is documented (along with a fix) on our release
This problem is documented (along with a fix) on our release notes
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
On 3/16/2021 3:39 PM, Jordan Mullins wrote:
External Email - Use Caution
Yes, I used the make_average_subject command. I've attached a text
file below of the
What command are you using? make_average_subject? Send the command line
and terminal output
On 3/10/2021 3:53 PM, Jordan Mullins wrote:
External Email - Use Caution
Hello,
I am trying to create an average subject from a set of subjects, but
keep getting an error that says
External Email - Use Caution
Hello,
I am trying to create an average subject from a set of subjects, but keep
getting an error that says "mghRead(mri/norm.mgz, -1): could not open
file". I've read that several others have solved this issue by installing
the patch available at
lf of Maxime Perron <maxime.perro...@ulaval.ca>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, September 6, 2019 at 5:08 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] make_average_subject error
External Email - Us
at 5:08 PM
To: FS Help
Subject: Re: [Freesurfer] make_average_subject error
External Email - Use Caution
Hi Douglas,
I'm sorry for the misunderstanding! Thanks for the command.
I attached the mas.log.
Cheers,
Maxime
De : freesurfer-boun
surfer_S156"
"Freesurfer_S158" "Freesurfer_S164" --out BrainaverageN72
cd
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72
mkdir ori
cd
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_I
"Freesurfer_S151" "Freesurfer_S152"
>> "Freesurfer_S153" "Freesurfer_S154" "Freesurfer_S155" "Freesurfer_S156"
>> "Freesurfer_S158" "Freesurfer_S164" --out BrainaverageN72
>>
>> cd
>> /V
quot;
> "Freesurfer_S144" "Freesurfer_S145" "Freesurfer_S146" "Freesurfer_S147"
> "Freesurfer_S148" "Freesurfer_S150" "Freesurfer_S151" "Freesurfer_S152"
> "Freesurfer_S153" "Freesurfer_S
ot; "Freesurfer_S152"
"Freesurfer_S153" "Freesurfer_S154" "Freesurfer_S155" "Freesurfer_S156"
"Freesurfer_S158" "Freesurfer_S164" --out BrainaverageN72
cd
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM
Is BrainaverageN72 in the subjects list?
On 9/3/19 12:39 PM, Maxime Perron wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Experts,
>
>
> I have the following issue when running the make_average_subject command (
>
> make_average_subject --subjects (Subjid) --out
External Email - Use Caution
Dear Freesurfer Experts,
I have the following issue when running the make_average_subject command (
make_average_subject --subjects (Subjid) --out BrainaverageN72) :
Building hash of lh white
Building hash of lh pial
Building hash of
External Email - Use Caution
Dear all,
I have seen this error mentioned several times on the list but I have never
seen a solution posted. It is claimed that there is a patch and a README
that explains the patch at:
I think it is crashing outside of make_average_surface and make_average_volume,
so the log files are not telling me what is going on. Can you capture the full
terminal output? Also, you can try it with two subjects so that it runs faster
(but it might not crash).
On 7/10/2019 5:39 AM, Mads
Can you send the full terminal output of make_average_subject? There should
also be some log files (make_average_volume.log and make_average_surface.log)
in the average subject that would be helpful
On 7/4/2019 4:36 AM, Mads Jensen wrote:
External Email - Use Caution
HI FreeSurfer
External Email - Use Caution
HI FreeSurfer Developers,
I'm attempting to create an average subject make_average_subject but I
get the error message the following error when I run the
make_average_command:
Loading aseg from REMOVED-PATH/avg_elder/mri/aseg.presurf.hypos.mgz
ASeg
External Email - Use Caution
Hi Douglas,
Yes - attached here is the make_average_subject.log file. The command
used was:
make_average_subject --out average_v2 --subjects $(cat subjects.txt)
subjects.txt also attached.
Thanks again for your help
Colleen
setenv SUBJECTS_DIR
Can you send the make_average-subject command and log file?
On 9/21/18 7:03 AM, C.P.E. Rollins wrote:
External Email - Use Caution
Hello Freesurfer Developpers,
I'm attempting to make a study specific template using all of my subjects as
input using the make_average_subject command, but
External Email - Use Caution
Hello Freesurfer Developpers,
I'm attempting to make a study specific template using all of my
subjects as input using the make_average_subject command, but am
receiving the following error:
Building hash of lh white
Building hash of lh pial
Hi Xiaoyu
how are you trying to create an average subject? It looks like you are
running recon-all on something. Typically we use the script
make_average_subject for this
cheers
Bruce
On Wed, 11 Jul 2018, Wang, Xiaoyu wrote:
External Email - Use Caution
Hello
External Email - Use Caution
Hello FreeSurfer Developers,
I am attempting to perform group analysis on a group of subjects. However, When
I am trying to create an average subject I get the following error.
mghRead(mri/norm.mgz, -1) could not open file
I went into the average
Please see the attached log file.
Thanks,
Tugce
On 11/16/17, 11:35 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve" wrote:
can you send the entire log file?
On
can you send the entire log file?
On 11/16/2017 11:32 AM, Duran, Tugce wrote:
>
> Dear FreeSurfer Experts,
>
> I’m recently getting an error in make_average_subject and can’t find
> the reason.
>
> Please see the following for the error log from recon-all.log:
>
> *Loading aseg from
>
Dear FreeSurfer Experts,
I’m recently getting an error in make_average_subject and can’t find the reason.
Please see the following for the error log from recon-all.log:
Loading aseg from
Hi all,
Did you encounter the error message talairach.m3z does not start as 'MNI
Transform File' when making average of subjects?
I checked all the recon-all.log file and did not find error, but when
running make_average_subject after recon-all, then this error shoot.
To repeat the error
This error may come from regio_read_mincxfm function in registerio.c.
Does this mean something wrong in recon-all?
I forgot to mention that FreeSurfer version is
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song dawnwei.s...@gmail.com wrote:
Hi
sorry, I don't understand. What was the error? I don't see one in this
email. Can you send us the actual screen output?
cheers
Bruce
On Thu, 7 Mar 2013, Xiaowei Song wrote:
This error may come from regio_read_mincxfm function in registerio.c.Does
this mean something wrong in recon-all?
I
Sorry, I did not make it clear.
In make_average_volume.log, the error message is:
1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013
mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ
/usr/local/freesurfer/average/mni305.cor.mgz --xfm
/data/lis9/fs/x/1173622/mri/transforms/talairach.m3z
what was your command line?
On Thu, 7 Mar 2013, Xiaowei Song wrote:
Sorry, I did not make it clear.
In make_average_volume.log, the error message is:
1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013
mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ
Thanks for your help.
My command line is
make_average_subject --out avgGrp139 --subjects `cat
script/subjects.id` --xform
talairach.m3z
On Thu, Mar 7, 2013 at 6:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
what was your command line?
On Thu, 7 Mar 2013, Xiaowei Song wrote:
The xform has to be linear in the xfm format. The m3z cannot be used.
doug
On 03/07/2013 06:44 PM, Xiaowei Song wrote:
Thanks for your help.
My command line is
make_average_subject --out avgGrp139 --subjects `cat
script/subjects.id http://subjects.id` --xform talairach.m3z
On Thu, Mar 7,
Thank you, doug, I will try xfm!
On Thu, Mar 7, 2013 at 7:03 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
The xform has to be linear in the xfm format. The m3z cannot be used.
doug
On 03/07/2013 06:44 PM, Xiaowei Song wrote:
Thanks for your help.
My command line is
Hi all
Could anyone help me with this error:
MRISreadAnnotationIntoArray: vertex index out of range: 1499028058
i=5A595959, in_array_size=133467
annot file:
/home/virtualuser/apps/freesurfer/subjects/s1/surf/../label/lh.aparc.annot
This appeared after trying to average my subject data. It says
Hi Leo, check to see if that subject's analysis is up-to-date. This
usually happens when it was only partially re-run.
doug
leonardo kay wrote:
Hi all
Could anyone help me with this error:
MRISreadAnnotationIntoArray: vertex index out of range: 1499028058
i=5A595959, in_array_size=133467
in advance
Best
JLH
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, June 13, 2011 11:01 PM
To: t...@ms36.hinet.net
Cc: freesurfer
Subject: Re: [Freesurfer] make_average_subject error in T1.mgz and t1.mgz
Do you mean your individual subject after
Do you mean your individual subject after running through FS has a file
called t1.mgz and not T1.mgz? Something is definitely wrong there. Can
you send the log file?
doug
t...@ms36.hinet.net wrote:
Dear FS experts,
I use FS5.1 and previous data run on other machine. When I try to
lt;pgt;Dear FS experts,lt;br /gt;I use FS5.1 and previous data run on other
machine. When I try to make_average_subjects program, I get error message that
it can not get T1.mgz data from subject folder. When I check my dataset,
actually it has t1.mgz rather than T1.mgz. how could I change the
Hi,
Thank you for your response! I solve this problem of mris_preproc.
The next step is to do mri_glmfit.
And, when I type the following command:
mri_glmfit --y lh.noise_0.5-1-5.thickness.10.mgh --fsgd noise_0.5-1-5.fsgd
dods --C noise_0.5-1.mtx --surf fsaverage lh --cortex --glmdir
You probably have an older version that does not recoginze --cortex. Try
--label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label instead
Feng-Xian wrote:
Hi,
Thank you for your response! I solve this problem of mris_preproc.
The next step is to do mri_glmfit.
And, when I type the
Hi,
I copied the default average subject from $FREESURFER_HOME/subjects dir
to my analysis dir.
Then, I make a FSGD file and some contrast matrices and put them into my
analysis dir.
After that, I start to run group analysis.
But, when I type the following commands:
mris_preproc
Is there a space between -- and hemi?
caching is just a way to speed some analyses by pre-smoothing and
sampling to the standard space.
doug
Feng-Xian wrote:
Hi,
I copied the default average subject from $FREESURFER_HOME/subjects dir
to my analysis dir.
Then, I make a FSGD file and
Hi,
I have a problem with make_average_subject.
After running all commands (including ln -s
$FREESURFER_HOME/subjects/fsaverage
and recon-all -s subjid -qcache for all my subjects) about running QDEC, I
found that QDEC could not analysis my group.
Because the group have 1 factor and
Feng-Xian,
It appears that you do not have permission on your system to change the
limits. So you will have to edit the scripts make_average_volume,
make_average_surface and make_average_subject to comment out the 'limit'
line, so that it looks like this:
#limit descriptors unlimited
Nick
Feng-xian,
I should also mention that i dont think creating your own average
subject will solve the problem you describe, where you need to work with
three levels in your group. for that, you wont be able to use qdec, but
will need to run things manually. these pages give examples:
You don't *have to* to run make_average_subject to do your analysis,
only if you want to view the results on a map with the curvature
patterns averaged over your subjects. As for the limit error, how old is
your version of freesurfer? That line was removed about 1.5 years ago...
doug
to
take per subject?
Best wishes
Carolyn
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Wed 5/9/2007 6:21 PM
To: Furlong, Carolyn
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Make_average_subject error
you may be using a version that does not have
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Wed 5/9/2007 6:21 PM
To: Furlong, Carolyn
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Make_average_subject error
you may be using a version that does not have
Hi all
I have run the script make_average_subject and the error message at the end is:
ln: creating symbolic link `rh.sphere' to `rh.sphere.reg': Operation not
permitted
only rh* files have been created.
Can you help?
Best wishes
Carolyn
___
Hi all,
I tried running it again with --no-symlink but this error came up
ERROR: Flag --no-symlink unrecognized.
any advice?
Best wishes
Carolyn
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
I have been able to run it with --no-symlink (the flag has to go last),
but I get errors like this:
mris_make_average_surface: could not read surface file
/Volumes/data/NL-GCS/subjects/freesurfer_3.0.1/GCS_adults/--no-symlink/surf/rh.sphere.reg
Thanks.
Anthony
Furlong, Carolyn wrote:
Hi
you may be using a version that does not have this option. Try using these
doug
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_subject
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
Furlong, Carolyn wrote:
Hi all,
I tried
Title: Re: [Freesurfer] make_average_subject error?
Hi Doug,
I changed the flags to efxv as you recommend, and here is the output for make_average_subject, make_average_volume and make_average_surface. The script doesnt seem to be accepting my command line arguments. I am using the current dev
h.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] make_average_subject error?
try running it with --debug and send us the output
Brian Schweinsburg, Ph.D. wrote:
Hi Folks,
I tried running the latest make_average_subject script (and the
make_average
Title: Re: [Freesurfer] make_average_subject error?
Hi Doug,
The same thing happens when I try to run them separately. It exits to the prompt with no messages.
Brian
--
Brian C. Schweinsburg, Ph.D.
Assistant Adjunct Professor of Psychiatry
University of California, San Diego
Office: 858-552
Try editing those scripts so that the first line is:
#!/bin/tcsh -efxv
ie, adding "xv"
This turns on all kinds of debugging
Brian Schweinsburg, Ph.D. wrote:
Re: [Freesurfer] make_average_subject error?
Hi
Doug,
The same thing happens when I try to run them separately
Hi Folks,
I tried running the latest make_average_subject script (and the
make_average_surface/volume scripts) using the expected command line syntax
and after hitting enter it immediately exits to the csh without error, but
does not produce anything.
make_average_subject --subjects SC010 SC011
try running it with --debug and send us the output
Brian Schweinsburg, Ph.D. wrote:
Hi Folks,
I tried running the latest make_average_subject script (and the
make_average_surface/volume scripts) using the expected command line syntax
and after hitting enter it immediately exits to the csh
Brian
From: Doug Greve [EMAIL PROTECTED]
Date: Mon, 26 Sep 2005 16:40:48 -0400
To: Brian Schweinsburg, Ph.D. [EMAIL PROTECTED]
Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] make_average_subject error?
try running it with --debug and send us
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