External Email - Use Caution
Hello,
I’m trying to reconstruct an old pipeline that I don’t completely understand
(so sorry if this is very elementary or out of date), and one step is to
convert the freesurfer T1 segmentation ribbon.mgz to .nii format using
mri_convert.
Through
External Email - Use Caution
Bruce, thank you for this response. In fact I had the T1 path wrong despite
having read it over and over 20 times.. listing directory contents indeed
revealed my error…
-andrew
> On Jul 30, 2021, at 13:38, Fischl, Bruce wrote:
>
> Can
to run something like
aparcstats2table and extract the values? Or, is there a way to utilize the
smoothed concatenated file (from mris_preproc) to get at the same thing?
Thanks!
Andrew Schoen
University of Wisconsin - Madison___
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exact and takes some
time. Is there a simple way I am missing?
-Andrew
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rol points to extend
white matter, or removing some skull/non brain tissue from the brainmask. The
effect of these edits were very minor in terms of regional
thickness/area/volume, on the order of a few percent different.
-Andrew
From: freesurfer-boun...@nmr.
Looks like you just need to download x11 or xquartz to have a x-window program
available. You can google it if you need instructions. If you are using a Mac
they stopped including x11 as standard software on Yosemite, which I think is
kind of stupid.
-Andrew
(mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
123 80243 2.367 0.916 0.144 0.0452 0.2
paracentral_rh_cesdTotal
[aoshea@gator1 ~]$
Any help would be greatly
essed//EX03/surf/rh.white
>
>and/or view it in freeview to make sure it isn't corrupted?
>On
>Wed, 15 Jul 2015, O'Shea,Andrew wrote:
>
>> Hello all,
>> I am having an issue where the mris anatomical stats command is failing
>>and
>> only p
loading the file correctly, or if the transform was indeed erroneous.
Thanks for any help!
Andrew Schoen
Center for Investigating Healthy Minds
at the Waisman Center
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ntered widthwise. However, I am not sure if this has something to do with it
not loading the file correctly, or if the transform was indeed erroneous.
Thanks for any help!
Andrew Schoen
Center for Investigating Healthy Minds
at the Waisman Center
University of Wisconsin - M
from the right side of the head, instead of the
face. We are running on 64-bit linux. Any idea what may be causing this?
All the gca files were downloaded directly from the site.
Let me know if any more information would be helpful!
Thanks!
Andrew Schoen
Center for Investigating Healthy Minds
y idea what may be causing this? All the gca files were downloaded directly
from the site.
Let me know if any more information would be helpful!
Thanks!
Andrew Schoen
Center for Investigating Healthy Minds
Waisman Center
University of Wisconsin - Madison_
ny and all help is greatly appreciated,
Andrew
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Hi Martin,
Excellent, it works just fine without the --initorient. However, I'd be
happy to help test the fixed version. I'm running the stable v5.3 linux
distribution (actual OS is Debian 'jesse' 8.1).
Thanks,
Andrew
On Wed, Sep 23, 2015 at 11:12 PM
wrote:
> Hi Andrew
Hello Freesurfer experts,
I'm having a bit of difficulty running the recon-all command. I recently
downloaded Freesurfer version 6.0.
The command that I'm running is:
recon-all -all -s $name -hippocampal-subfields-T1
However I keep receiving this error:
If: Expression Syntax
I've attached t
surfer@nmr.mgh.harvard.edu&q=date:20160822>
Nothing looks suspicious. Try setting
setenv SUBJECTS_DIR /usr/local/DTI_processed_data/freesurfer_data_dir
ie, removing the trailing "/"
On 08/22/2016 02:12 AM, Elpiniki Andrew wrote:
> Hello Freesurfer experts,
>
> I&#x
AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all error using Freesurfer 6.0
Does this file exist?
$FREESURFER_HOME/subjects/fsaverage/label/lh.BA1_exvivo.label
If not, what version of FS are you using?
On 08/24/2016 08:14 PM, Elpiniki Andrew wrote:
>
> Thanky
be greatly appreciated.
-Andrew
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Direct link:
http://rfmh.iapplicants.com/ViewJob-499585.html
Please email me with any questions.
Best, Andrew
Andrew J. Gerber, M.D., Ph.D.
Interim Director, MRI Unit
Assistant Professor of Clinical Psychiatry
New York State Psychiatric Insitute / Columbia University
Division of Child and
Hello FS experts,
In QDEC when I click on a vertex a scatter plot is generated with each
individuals data for that vertex. Is there a simple way to extract that data
(for each subject) into spreadsheet form for a specific vertex?
-Andrew
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Dear Allison,
You have me down for a slot, right? I don't want to miss it! :-)
Best, Andrew
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Allison Stevens
Sent: Friday, April 18, 2014 3:16 PM
To: frees
FreeSurfer course
Hi Andrew,
Yes you're down for a spot. Yours wasn't one of the two :).
Allison
On Apr 18, 2014, at 3:23 PM, Andrew Gerber wrote:
> Dear Allison,
> You have me down for a slot, right? I don't want to miss it! :-) Best,
> Andrew
>
> -Original M
Hi all,
I'm having a problem similar to Krista's, where I'm getting holes in a few
labels (e.g. V1.label, MT.label, BA44.label, BA45.label) produced by the
recon-all pipeline. Did you ever discover the solution to this issue?
I'm running Freesurfer v5.3.0.
Andrew
On T
ditional info or guidance on this topic would be much appreciated.
-Andrew
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The information in this e-mail is intended only for the p
am looking for whole folders
that contain all the files from the recon-all process. I was thinking outliers
from a group mean in certain ratios (region A thickness/region B thickness,
etc.) may provide some insight.
-Andrew
-
I've looked at the actual editing of voxels (ie, erasi
nding.
-Andrew
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of John Anderson
mailto:j.ander...@publicist.com>>
Reply-To:
"freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date:
alone" is the new process? Does
the new process use any inputs from the recon-all stream which have changed in
the upcoming version? Thanks!
-Andrew
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!
Andrew Schoen
Center for Investigating Healthy Minds
Waisman Center
University of Wisconsin - Madison
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The information in this e-mail is
Try mean centering your ICV values (I.e. Subtract the mean value from each
individual value). This has worked for me to bypass this error.
-Andrew
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Hirsch, Gabriella"
mailto:gabriella_hir...@meei.harvar
I believe your issue is you are trying to do a between group analysis but you
only have 1 subject in group B. There is no way to estimate the variance in the
measure if there is only one subject in the group.
-Andrew
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of &
alone" is the new process? Does
the new process use any inputs from the recon-all stream which have changed in
the upcoming version? Thanks!
-Andrew
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Hi all,
I am receiving the same error, using the same version of Freesurfer (
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0).
Was a solution found?
Andrew
On Mon, Nov 2, 2015 at 3:31 AM, Shani Ben Amitay
wrote:
> Dear Lilla and freesurfers,
>
> I hvae tried to rub the mri_CVS
Hi all,
It turns out this error was due to a lack of memory, increasing to ~15GB of
memory solved the problem.
Andrew
On Wed, Nov 25, 2015 at 2:50 PM, Andrew Bock wrote:
> Hi all,
>
> I am receiving the same error, using the same version of Freesurfer (
> freesurfer-Linux-ce
I ran
with that (same subject as second log, above), it ran to completion fine.
Any idea what might be happening? Let me know if any other info would be
useful!
Thanks!
Andrew Schoen
Center for Healthy Minds
Waisman Center
University of Wisconsin - Madison
d
finishes without error. I do not receive this error when using Freesurfer
5.1.0. I have yet to run 'recon-all -all -subjid ' in 5.3.0.
Any ideas on what produces this error? is it safe to ignore?
Thanks in advance,
Andrew
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Freesurfer mai
, otherwise I'll
update to that version.
Andrew
On Thu, May 30, 2013 at 10:51 AM, Z K wrote:
> Hi Andrew,
>
> It is expected that you would not see this warning with Freesurfer version
> 5.1.
>
> Its just a warning, but tcsh v6.17.06 on Ubuntu always returns exit code
> 0. T
000 -sumconds -o
test/pain-v-rest.mat -wdelay 1 -no-octave
Mon Jul 1 08:51:02 EDT 2013
"
It is not creating a .mat file in the analysis directory. Any suggestions would
be greatly appreciated. Thanks!
-Andrew
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I have been trying to run tracula with a config file but keep getting the same
error message when I use the trac-all command for pre-processing
"set: Variable name must begin with a letter"
Attached is the text from the config file I used.
Hope to hear from you soo
have matlab installed and in your path?
doug
On 07/01/2013 08:55 AM, O'Shea,Andrew wrote:
Hello,
I am trying to work through the FS-FAST tutorial on my data. I am
using OSX 10.6.8 with Freesurfer v. 5.1 When I get to the make
contrast command which I run
' mkcontrast-sess -analy
I have been trying to run tracula with a config file but keep getting the same
error message when I use the trac-all command for pre-processing
"set: Variable name must begin with a letter"
Its become very annoying.
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Fr
I have been trying to run tracula with a config file but keep getting the same
error message when I use the trac-all command for pre-processing
"set: Variable name must begin with a letter"
It has become very, very annoying. PLEASE SOMEONE HELP!!!
Andrew
--
# FreeSurfer SU
That was my problem Doug, thanks! I used
' sudo ln -s /Applications/MATLAB_R2011b.app/bin/matlab /usr/local/bin '
and it fixed it.
-Andrew
Message: 9
Date: Mon, 01 Jul 2013 09:46:39 -0400
From: Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Prob
Helo all,
I was finally able to figure out my configuration file problem. But when I run
the first step of pre-processing I receive an error about freesurfer being
unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz
/Users/Wayn
ld subject ID with the anonymized ID (this option is
preferable)? Ideally, we don't want to have to reconstruct every binary file
using the updated subject ID.
Thanks for the help!
Andrew Ward
Brigham and Women's Hospital (BBNG)
Massachusetts General Hospital (GRU)
Athinoula A. Ma
.
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 12:35 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - My guess is that it's something about the file
that file to complete tracula. I was
hoping someone could help with this or perhaps send me the file?
I am using freesurfer-
Darwin-snowleopard-i686-stable-pub-v5.3.0-
MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0:
Hope to hear from someone soon,
Andrew
label/rh.V1.prob.label
.//label/rh.V1.predict.label
mris_anatomical_stats -l .//label/lh.V1.predict.label
lh >> .//stats/hinds_V1_lh
mris_anatomical_stats -l .//label/rh.V1.predict.label
rh >> .//stats/hinds_V1_rh
Andrew
On Tue, Jun 12, 2012 at 9:48 AM, Bruce Fis
actice."
Crazy, right? Enjoy...
Andrew
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addressed.
. does not look like
a brain). I would expect this file to look like the fsaverage brain, is
that not correct?
Andrew
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The information
you would expect that. what does it look like? how are you
> visualizing it?
>
> On 09/20/2012 06:18 PM, Andrew Bock wrote:
> > Hello,
> >
> > I am attempting to run preproc-sess on my functional data, and am
> > following the tutorial found here:
> >
Hi Doug,
I uploaded two example files, as far as I can tell the raw f.nii and
talairach transform look okay. I obtained these files from the tutorial
data set, so I'm assuming they were processed properly.
Andrew
On Mon, Sep 24, 2012 at 1:03 PM, Douglas N Greve
wrote:
> Actually, be
e previous
post, but could not find it on the ftp site. Any suggestions?
Andrew
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e/mri/?
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 --uchar
transforms/talairach.xfm
mri_ca_normalize -mask brainmask.mgz nu.mgz
$FREESURFER_HOME/average/RB_all_2008-03-26.gca transforms/talairach.lta
norm.mgz
Andrew
On Mon, Oct 1, 2012 at 8:32 PM, Douglas Greve wrote:
>
> I just put a new version he
does work for my other subjects, so I'll be
able to find a solution.
Thanks for your help,
Andrew
On Tue, Oct 2, 2012 at 12:19 PM, Douglas N Greve
wrote:
> when did you update the xhemi scripts last? Do a search on our wiki for
> xhemi to get pointers to the most recent ones
>
&g
subjects.
Instead, I can run xhemireg on all my subjects, and then resample the left
hemisphere overlay of fsaverage to the left and /xhemi (right) hemispheres
for each subject. It will take a bit longer, but it should be fine.
Andrew
On Tue, Oct 2, 2012 at 3:05 PM, Douglas N Greve
wrote:
> why
Hello,
Our data set has two T1 weighted scans for some subjects but only one for
others. Would you recommend running all subjects with no motion correction (1
scan input)? Also can files be mixed in the analysis that have had motion
correction with those who have not? Thanks!
-Andrew
for any help in advance.
-Andrew
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe
the link it says I do not have permission the access.
Thanks for any help in advance.
-Andrew
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The information in this e-mail is
lc --curv1
sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs
startVertex:###,endVertex:###
Any suggestions to cut down my processing time, while still calculating
along the surface, would be greatly appreciated.
Andrew
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results. Does a negative rate
change indicate either a deepening or a shallowing of the sulci? Is the
opposite the case for gyral regions? Any advice would be greatly appreciated.
-Andrew
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https
R" flag in your autorecon3
command will do the job.
best,
Andrew
From: Sneha Pandya
Sent: Tuesday, January 24, 2017 12:49:31 PM
To: Hoopes, Andrew; Freesurfer support list
Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
Thank you
moved. Creates a new
brain.mgz volume*".
My question is: if brain.mgz is meant to be an improved version of
norm.mgz, why not use brain.mgz for partial volume weighting? What
advantages does norm.mgz provide?
Thanks much,
Andrew Davis
[^1]: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconA
his further.
best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of David Semanek
Sent: Monday, March 13, 2017 11:55 AM
To: Bruce Fischl; Freesurfer support list
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
Hello,
We are looking for a Post-doctoral associate with experience and skills in
multimodal neuroimaging. See below for the posting.
Post-doctoral Associate
Woods Lab, Center for Cognitive Aging and Memory
Description:
The Department of Clinical and Health Psychology and Center for Cognitive A
Hi Colleen,
If you source freesurfer, and run:
ls $FREESURFER_HOME/mni/bin
It should output a list of mni tools, including nu_correct. Is this what you
see? There's a possibility that your mni sub-directory isn't sourced.
Andrew
From: frees
After sourcing freesurfer, what comes up if you run the command "which
nu_correct"? If it cannot find nu_correct on your path, do you mind telling me
the method you use to source FS?
Thanks,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
FREESURFER_HOME /usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
which will set some environment variables and make all FS commands available to
you. Sourcing FS like this should fix your issue with nu_correct, if not, this
could be a bug.
best,
Andrew
Hi Bronwyn, I tried to replicate your issue using both v5.3 and the current dev
environment, but I had no luck. I'm guessing the problem has to do with
combining the development binary along with 5.3, so I suggest using the 5.3
version of mris_make_surfaces to fix this.
best,
A
Sure thing, just let me know the filename once it's uploaded.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bronwyn Overs
Sent: Wednesday, August 02, 2017 10:02 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Medial Su
o commands:
cd transfer/incoming
put file.tar.gz
note: to compress a directory before uploading, you can use tar:
tar -zcvf output.tar.gz /path/to/dir
best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Leavitt, Mackenzie
Sent: Friday,
Sure, you should be unsubscribed now.
best,
Andrew
> On Aug 25, 2017, at 11:29 AM, Micah Rhodes wrote:
>
> Please unsubscribe me to this email list.
>
> Thanks.
> ___
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> Freesurfer@nmr
Hi Ritesh,
What operating system and version are you running freesurfer on, ubuntu?
Can you also send the fs version build stamp (you can get this by running
'bugr’)
best
Andrew
> On Aug 29, 2017, at 11:41 AM, Ritesh Mahajan
> wrote:
>
> Hello guys,
>
> I am
Hello,
Is it possible to use cluster-defining thresholds such as p = 0.025 with
mri_glmfit-sim? (This would roughly correspond to a negative log value of 1.6.)
My design doesn't allow the use of permutations for simulating cluster sizes,
so I have to use the mczsim option; however, from what I
elp to get more info
On 09/07/2017 11:05 AM, Jahn, Andrew wrote:
> Hello,
>
> Is it possible to use cluster-defining thresholds such as p = 0.025
> with mri_glmfit-sim? (This would roughly correspond to a negative log
> value of 1.6.) My design doesn't allow the use of permuta
Hi Markus,
What is the output when you run the following: (this will list libraries you
have access to)
/sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep
libvtkverdict.so
best,
Andrew
On Sep 15, 2017, at 3:33 AM, Markus Gschwind
mailto:markus.gschw...@gma
libvtkverdict.so.5.6.0 libvtkverdict.so.5.6
then do you get the same error from freeview?
-Andrew
On Sep 15, 2017, at 12:10 PM, Markus Gschwind
mailto:markus.gschw...@gmail.com>> wrote:
Dear Andrew,
The command gives this result:
[gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <
Hi Markus, okay - I'll directly send you a tar of the vtk library. A reinstall
of vtk might work, because those shared objects that we distribute are usually
sym-linked
Can you also send the fs buildstamp? You can get this by running the command
‘bugr’ after sourcing freesurfer
Andrew
O
Hi Arkadiy,
If you send the buildstamps for your two freesurfer distributions, I can see
what the respective versions are. You can print the buildstamp by running the
command “bugr” in a sourced fs environment
best
Andrew
On Sep 19, 2017, at 2:25 PM, Maksimovskiy, Arkadiy
mailto:amaksimovs
Hi Aziz,
We store non-text files outside of the repository, have you set up a remote
with git annex yet? Instructions are here:
https://surfer.nmr.mgh.harvard.edu/fswiki/Freesurfer_github
best
Andrew
On Sep 28, 2017, at 4:10 AM, Aziz Nanthaamornphong
mailto:azi...@phuket.psu.ac.th>>
Hi Sol,
I don't recognize this error, but will look into it. Have you set up the
required system libraries and library dependencies described in
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page ?
Andrew
On Oct 2, 2017, at 5:55 PM, Sol Jerome
mai
hanks
Andrew
On Oct 3, 2017, at 1:16 PM, Sol Jerome
mailto:s...@utdallas.edu>> wrote:
I think so. I am actually attempting to build an RPM. Here is my spec
file:
Name: freesurfer
Version:6.0.0
Release:1%{?dist}
Summary:FreeSurfer Software Sui
Hi Aziz,
The centos6-built packages seem to cause issues when building on ubuntu,
particularly for tcltk apps. I would ignore this for now, or you could compile
tcltk yourself. As a general fix, I’ll work on building a package distribution
on ubuntu16
best,
Andrew
On Oct 9, 2017, at 2:02 AM
Hi Ramesh,
Freesurfer is built and developed mainly on centos machines, but ubuntu works
fine as well.
Here’s some more info:
https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements
best
Andrew
On Oct 17, 2017, at 7:04 AM, Ramesh Babu
mailto:mgrameshbabu2...@gmail.com>> wrote:
Hi Yawu,
Seems like a graphics driver issue. Does running "glxinfo" give the same error?
What OS are you using?
Andrew
> On Oct 24, 2017, at 3:36 AM, Liu Y wrote:
>
> Dear Experts,
> When I run qdec, it showed me error message, any suggestins?
> qdec
> X Error
Hi Arkadiy,
This might have to do with SIP, which blocks libraries stored in /usr. I would
suggest disabling SIP and rerunning to see if that fixes things:
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
Andrew
On Oct 27, 2017, at 2:13 PM, Maksimovskiy
s/OSX/mris_decimate
to your $FREESURFER_HOME/bin
best,
Andrew
On Oct 30, 2017, at 3:31 AM, Paula Popa
mailto:paula.p...@codemart.ro>> wrote:
Hello FreeSurfer Developers,
I am using the development version of FreeSurfer, both for Mac and Linux.
I have noticed that mris_decimate is not included in
- and overwrite the current $FREESURFER_HOME/bin/recon-all.makefile
mv -f recon-all.makefile ${FREESURFER_HOME}/bin/recon-all.makefile # (sudo
might be required)
Let me know if you still have issues
best,
Andrew
On Oct 31, 2017, at 10:48 PM, Anne Park
mailto:annep...@sas.upenn.edu>>
g your
SUBJECTS_DIR like this:
mkdir test_subjects
export SUBJECTS_DIR=/path/to/test_subjects
then try running a sample recon:
cd ${FREESURFER_HOME}/subjects
recon-all -i sample-001.nii.gz -s bert -all
best,
Andrew
On Nov 7, 2017, at 7:19 PM, Danny Deng
mailto:dannytang...@gmail.com>> wrote:
H
tribution under $FREESURFER_HOME/subjects
Andrew
On Nov 8, 2017, at 3:51 AM, Danny Deng
mailto:dannytang...@gmail.com>> wrote:
Hi Andrew,
I have followed your suggestion and the error pop up like this:
Xues-MacBook-Air:~ DannyDeng$ mkdir test_subjects
mkdir: test_subjects: File ex
install an older version of
perl (5.10 should be old enough):
https://stackoverflow.com/questions/16147120/how-can-i-install-another-version-of-perl-on-top-of-the-default-version-on-cento
or install freesurfer v6.0:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
best,
Andrew
On Nov 13, 2017, at
Hi John,
So you've been able to run some subjects successfully through the subfield
stream? Can you provide some more information like freesurfer
version/buildstamp (run the command ‘bugr') as well as your operating system
and version?
thanks,
Andrew
On Nov 13, 2017, at 7:3
What is the output of:
ldd `which freeview.bin`
thanks,
Andrew
On Nov 10, 2017, at 8:52 AM, Ruopeng Wang
mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
What version of freesurfer did you run? It looks like the issue is related to
incompatible/missing libraries.
Ruopeng
On Nov 10, 2017, a
Hi Carl,
How many lines of text exist in your license file?
Andrew
On Nov 9, 2017, at 8:18 AM, Carl Anderson
mailto:remfr...@gmail.com>> wrote:
Hi Everyone,
I'm running freesurfer-Darwin-OSX-dev-20171107-ec5ce3a
I seem to get the line "error parsing license file, expected 4
Hi Danny,
If you want to cd into SUBJECTS_DIR, just run:
export SUBJECTS_DIR=/downloads/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR
“cd $downloads/buckner_data/tutorial_subjs” isn’t a valid command if you
haven’t set a variable named “downloads"
Andrew
> On Nov 23, 2017, at 4:00 A
Hi Sofia,
Another user seems to be experiencing a similar issue right now. How many
subjects are you trying to average? I haven’t been able to replicate this, so
it might require uploading some subjects. Can you send the
make_average_volume.log?
best,
Andrew
On Nov 27, 2017, at 10:16 AM
Hi Kelly,
This might have to do with SIP being enabled, which blocks libraries stored in
/usr. I would suggest disabling SIP and rerunning to see if that fixes things:
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
best,
Andrew
On Nov 27, 2017, at 6:33 PM
particular subject
that’s causing this)?
best,
Andrew
On Nov 28, 2017, at 12:20 PM, Sofia Rodriguez Penuela
mailto:srod...@upo.es>> wrote:
Hi,
User M del Mar and me belong to same investigation group, so the problem is
common. We have 116 subjects and we detected this trouble. Howev
Hi Stephan,
This probably has to do with SIP being enabled, which blocks libraries stored
in /usr. I would suggest disabling SIP and rerunning to see if that fixes
things:
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
best,
Andrew
On Nov 29, 2017, at 1
try.
best,
Andrew
On Nov 30, 2017, at 3:46 AM, M del Mar Velasco
mailto:melly_2...@hotmail.com>> wrote:
Hi,
We are not using the make_average_subject 6.0.0-patch. Do you think it would be
a possible solution? Where can I find that patch?
On the other hand, we've noticed that recon
Hi Ri,
It looks like there might be an issue with the license saved at
/Applications/freesurfer6/.license. Try overwriting this file with your
license.txt
best,
Andrew
On Nov 29, 2017, at 6:23 PM, Ritobrato Datta
mailto:ridatpennc...@gmail.com>> wrote:
Hi All,
I am using Mac OS X
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