in).
Thank you!
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 this e-m
External Email - Use Caution
Hello,
I have a raw anatomical image called raw.mgz, which I have manually
annotated using Freeview; the resulting annotations are saved in a file
called seg.mgz. I want to compare this to the annotations automatically
generated by recon-all, so I ran
ted) options for running the process on
CPU only? Any other suggestions are greatly appreciated.
Regardless of specific suggestions you may have, I wanted to bring this to your
attention as a potential bug that could produce memory leaks or similar issues.
Thanks,
Drew
Andrew R. Bender, P
ficant cluster - however the cluster is now in the
isthmuscingulate.
Am I doing something incorrectly or is this possible? And if so, could you help
me understand what is going on here.
Best,
Andrew
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: Freesurfer support list
Subject: Re: [Freesurfer] WM Hypointensities
External Email - Use Caution
Hi Andrew,
I can’t answer if wm-hypointensity is supported in recon-all-clinical. I’m
assuming that you obtained aseg.stats by running mri_segstats. How does your
command look like
supported by recon-all-clinical?
Best,
Andrew
---
Andrew D. Geoly, MS
Research Data Analyst 1
Brain Stimulation Lab
Department of Psychiatry and Behavioral Sciences
Stanford University School of Medicine
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supported by recon-all-clinical?
Best,
Andrew
---
Andrew D. Geoly, MS
Research Data Analyst 1
Brain Stimulation Lab
Department of Psychiatry and Behavioral Sciences
Stanford University School of Medicine
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ndependent segmentation extractions from those and
bypass the longitudinal stream entirely (not saying I would want to but I am
curious)?
Any and all help here would be greatly appreciated, and I thank you very much
for your time.
Warmest regards,
Andrew
---
Andrew D. Geoly, MS
Res
overthinking it. What is the best way to go about doing this?
Thank you,
Andrew
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The information in this e-mail is intended only for the pers
No such file or directory
error: niiRead(): unsupported datatype 2304 (with scl_slope = 0) in
/Users/andrewmichalak/Desktop/RNS/CURNS8/Imaging/CURNS8_post_CT.nii
Is there a different method to convert TIFFs (or PNG, JPEG, etc.) to DICOM
or .nii for use in the freesurfer ecosystem?
Thank you!!
--
External Email - Use Caution
Hi Yujing,
Thank you very much for clarifying and letting me know of your testing results. I really appreciate all
your help with this issue.
Andrew
*Andrew Beaudin, PhD* | Research Associate
University of Calgary | Cumming School of
matrix, maybe very subtle shearing as the determinant is still
very close to 1, so no scaling). This could be a numerical issue. Anyway
increasing the threshold to 0.001 should fix this. Or did you get another error
after that for this specific case?”
Thanks again.
Andrew
Andrew Beaudin, PhD
External Email - Use Caution
Hi,
I'd like to request access to the Freesurfer VM.
Thanks,
Andrew Mao
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External Email - Use Caution
Hi Yujing,
No problem at all. I really appreciate yours, and now Martin's, help with this issue. If you would like to
start with dicoms, please let me know.
Again, thank you both for your help.
Andrew
----
*Andrew Beaudin, PhD* | Res
6.0 - same MyMatrix::RotationMean Error.
Again, thank you for the help….and please let me know if your need any
additional information or anything clarified.
Andrew
----
Andrew Beaudin, PhD | Postdoctoral Scholar
University of Calgary | Cumming School of Medicine
Department of Clinical Neuroscien
z24_TzO25_ti0wPS3jRLw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg72948.html)
but I still cannot find a solution to this problem.
Any insights are greatly appreciated.
Thanks for the help.
Andrew
Andrew Beaudin, PhD | Postdoctoral Scholar
University of Calgar
nii ? Does recon-all do keep everything in patient space, or does
it register them to fsaverage space automatically? If so, how would I
convert these MRIs and CTs to MNI305 space?
Thank you very much.
Andrew
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Good afternoon, everyone!
My name's Andrew Augustine and I'm a systems group member within Florida State
University's Mathematics department. I'm emailing on behalf of Claire Hickey,
one of our grad students who has been instru
.
Interestingly, while including the -affine flag works for some participants,
for others I get "MatrixLog Error: Result too imaginary to ignore!" error.
Any help/recommendations are greatly appreciated.
Thanks
Andrew
----
Andrew Beaudin, PhD | Research Associate
University of Calgary
To mimic the original matlab implementation, segment_subregions saves stats as
*.txt files in the mri subdirectory of the subject.
But maybe we should just save things in the stats folder to be consistent.
Eugenio/Doug, what do you think?
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
Unfortunately, tensorflow and M1 don’t mix well at the moment. Not sure if
there is a universal fix yet.
Rob, do you remember where the mac-specific TF package can be installed from?
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Abdelkarim, Ahmed
Date: Tuesday
This might be related to a small bug in the previous longitudinal code, which
affected volume rescaling. It should be fixed now. You could try out the new
implementation: https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
c3Nsfek1dX-2ZcfyofJgATm7_3x4dxBVVFXtW3LjQdkXeF5FP0UwRptADFLkDJRHCnLZ0xT8KDhGNfGNJeAsoOkOn_5HQg--PcUyUeQ6bMZMgly3L22SbfL48bjyIQb1ZIEXiJr0S0TEKN5X2H3JHlXqDYXQgNPTsnGyVX4iQl65pbf6ChI/https%3A%2F%2Fsiliconheaven.info%2Fxlaunch-configuration-file%2F%23gsc.tab%3D0) for the steps.
Hope this helps.
Andrew
----
*Andrew Beaudin, PhD* | Postdoctoral Scholar
University of Calgary
| awk
'{print $2; exit;}'):0.0
Remember, when you modify the Xming configuration file through
XLaunch, make sure that Xming is not running or the updated config
file will not be saved.
Hope this helps.
Andrew
Andrew Beaudin, PhD |
fer to use the rigid body
registration but am at a loss for why these images are failing using the rigid
body registration is failing. Any help/insights/recommendations are greatly
appreciated.
Thank you very much.
Andrew
Andrew Beaudin, PhD | Postdoctoral Scholar
University of Calgary | C
why these
images are failing using the rigid body registration is failing. Any
help/insights/recommendations are greatly appreciated.
Thank you very much.
Andrew
Andrew Beaudin, PhD | Postdoctoral Scholar
University of Calgary | Cumming School of M
iated.
Thank you very much.
Andrew
Andrew Beaudin, PhD | Postdoctoral
Scholar
University of Calgary | Cumming School of Medicine
Department of Clinical Neurosciences
HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2
the paths to your
freesurfer installation and your input/output data.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Caitlin R Bowman
Date: Wednesday, March 9, 2022 at 12:57 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal segmentation Matlab crash
your input image to
a supported type, like uint8, int, or float.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Koen Van Leemput
Date: Wednesday, March 9, 2022 at 12:44 PM
To: daedalu...@aol.com
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] run_samseg
Hi Begum,
You could try the just-recently released SynthStrip command `mri_synthstrip`
available in the dev distributions of freesurfer (as of today, march 15th). It
should be more robust than the watershed utility.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
Hi Cait,
Before running the command, can you try unsetting the LD_LIBRARY_PATH variable?
You can do this in bash with:
unset LD_LIBRARY_PATH
or in cshell with:
unsetenv LD_LIBRARY_PATH
best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Caitlin R Bowman
Date: Tuesday
is not much we can do to fix this on our side of things,
because the main solution requires recompiling tensorflow from scratch.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Cerri, Stefano
Date: Monday, February 28, 2022 at 3:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc
Dr. Greve,
I don't believe that file exists--fsaverage folder was empty. We re-ran these
files through v7.2.1 while seeking solutions. Is it going to produce tenable
findings if we run Freesurfer v7.2.1 cross-sectional data through Freesurfer's
v6.0's longitudinal stream
label ./lh.BA1_exvivo.label --hemi lh --regmethod surface
Moreover, with the base template error, it was not possible to go from there to
create the individual longitudinal mri output based on the base template
I'd be really grateful for help with this debugging! Thank you.
Andrew Sunday Wi
Hi Corinna,
Do you happen to have the LD_LIBRARY_PATH environment variable set in your
shell? If so, I would unset it. LD_LIBRARY_PATH tends to mess with any programs
linked to dynamic libraries. In this case, it’s forcing freeview to load the
wrong matlab Qt libraries.
Andrew
From: freesurfer
Are you adding sudo in front of every command? like this:
cd $FREESURFER_HOME/bin && sudo curl
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
-o fs_install_mcr && sudo chmod +x fs_install_mcr
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Junyeon
Yes! And thanks for the reminder – I just pushed 7.2.0 to dockerhub
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Andy Worth
Date: Tuesday, August 31, 2021 at 3:45 PM
To: Freesurfer support list
Subject: [Freesurfer] Shiny new 7.2!
External Email - Use Caution
Is
container instead?
https://hub.docker.com/r/freesurfer/freesurfer
Best
Andrew
From: Iglesias Gonzalez, Juan E.
Date: Thursday, August 12, 2021 at 2:57 PM
To: Freesurfer support list
Cc: Hoopes, Andrew
Subject: Re: [Freesurfer] Hippocampal, thalamus and brainstem subfields: Matlab
crash bump
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Lauri Tuominen
Date: Wednesday, August 18, 2021 at 10:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Issue with tksurfer-sess
External Email - Use Caution
Dear Surfers,
I ran into a problem with tksurfer
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Lab of Autism and
Developmental Neuroscience, Lab of Autism and Developmental Neuroscience
Date: Tuesday, August 17, 2021 at 2:43 PM
To: Freesurfer support list
Subject: [Freesurfer] LGI - output issue
External Email - Use
Hi Xin,
Are you using the QA tools from
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools? Those are specific to FS 5.3
(we should update the wiki). v7.1 includes an executable named `qatools.py`
that functions similarly.
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf
Hi Rito, which freesurfer version are you using here?
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Ritobrato Datta
Date: Wednesday, August 11, 2021 at 3:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] error running samseg on cluster
External Email
most or even all
of the distribution.
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Shruthi Srinivasan
Date: Saturday, July 17, 2021 at 2:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] fsaverage file download
External Email - Use Caution
Good
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
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
The line of code you sent doesn’t seem changed though
best
andrew
From: Kaija Sander
Date: Thursday, July 29, 2021 at 5:40 PM
To: Hoopes, Andrew , Freesurfer support list
Cc: Iglesias Gonzalez, Juan E.
Subject: Re: [Freesurfer] Error in hippocampal subfields longitudinal processing
Hi Kaija,
Not sure I follow. Have you tried making the change I suggested in the last
email?
Best,
Andrew
From: Kaija Sander
Date: Wednesday, July 28, 2021 at 2:30 PM
To: Freesurfer support list
Cc: Hoopes, Andrew , Iglesias Gonzalez, Juan E.
Subject: Re: [Freesurfer] Error in hippocampal
t; | tr -d ' ' ) ;
That seems to have fixed this problem in the past.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Kaija Sander
Date: Monday, June 14, 2021 at 9:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Error in hippocampal subfields lon
run_samseg_long (FreeSurfer v7).
Thank you,
Andrew
Andrew Russo
Clinical Research Coordinator
Multiple Sclerosis Imaging Lab
Massachusetts General Hospital
149 13th Street | Boston, MA 02129
617-726-7531
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Hi Diana,
If there are a lot of obvious holes in the surface topology, it might be worth
doing some manual fixing of the white-matter segmentation. The tutorial at
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 walks
through that process.
Best
Andrew
From: DIANA
/Applications/freesurfer/7.1.1
etc… when installing different distributions. Just make to correctly source the
directories when using different versions.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Boa Sorte Silva, Narlon
Date: Tuesday, May 25, 2021 at 6:17 PM
To
Hi Diana,
Can you send the recon-all.cmd file? Have you tried running without parallel
processing enabled?
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of DIANA ORTEGA CRUZ
<100315...@alumnos.uc3m.es>
Date: Friday, May 21, 2021 at 11:00 AM
To: free
Hi Joe,
Is this the full command output from start to finish? There is usually some
helpful information preceding the “Segmentation violation detected” error.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Xin Qiao
Date: Thursday, May 20, 2021 at 12:44 AM
To
coverage can get me sent to
australia for analysis as there is no way the hundreds of falls and head injury
i have had can leave me “normal” yet barely functional
thank you for any help you may be able to give
Kind Regards
Andrew Raines
> Begin forwarded message:
>
> From: Andr
-specific issue with calling the matlab
runtime library from python. If you’re using anaconda or something, it might be
overwriting matlab-runtime linked libraries. I’m not sure how much we can help
out here, unfortunately.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Joana
Hi Erika,
Can you untar the file you downloaded instead of the "HighSierra" version.
There was a small typo in the UpdateFreeview instructions that mentioned
high-sierra. The freeview you downloaded should work fine for 10.12
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvar
Hi Fabio,
How much memory are you allowing for this process? You might want to just try
increasing the limit on the slurm job to see if that works.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bernardoni, Fabio
Date: Tuesday, May 11, 2021 at 4:22 AM
To: freesurfer
If this is the last message before crashing, it sounds like it’s probably a
memory issue – how much do you have available? CC’ing Stefano who might have an
idea of the total memory requirement for lesions.
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Alberto Del
should verify that the
DYLD_LIBRARY_PATH env var in the python subshell is the same as in the terminal
environment.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Melissa Marie Rundle
Date: Friday, May 7, 2021 at 2:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject
as well:
freeview -v mri/norm.mgz mri/wm.mgz:colormap=heat:opacity=0.5 -f
surf/?h.smoothwm.nofix
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yakupov, Renat /DZNE
Date: Friday, May 7, 2021 at 6:00 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer
If the output directory is missing seg.mgz, then samseg failed. You’ll have to
send us the log or some sort of information about the error for us to debug
this.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Alberto Del Cerro Leon
Date: Friday, May 7, 2021 at 6:49 AM
Hi Giulio,
I’ll follow up off-list.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Giulio Degano
Date: Friday, May 7, 2021 at 3:20 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Multiple Freesurfer(s)
External Email - Use Caution
Hi all,
I am trying
tool in
freesurfer.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Alberto Del Cerro Leon
Date: Wednesday, May 5, 2021 at 11:11 AM
To: Freesurfer support list
Subject: [Freesurfer] help with SAMSEG
External Email - Use Caution
Hello Freesurfer team, my group is
Hi Jewelia,
Can you try running without the -parallel flag to see if that’s the issue?
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Jewelia K. Yao
Date: Tuesday, May 4, 2021 at 11:06 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer version 7
Hi Renat,
That 3rd defect is fairly large – normally it would hang but it’s possible
you’re running out of memory. If you can zip the subject and file drop it to
us, we can take a look:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
best,
Andrew
From: freesurfer-boun
Hi Mudathir,
What freesurfer version are using? I haven’t been able to reproduce this
segfault on our end. Can you run the same command on lh.aparc.annot instead to
narrow down whether this is an issue with your lh.par.annot file or not?
best
Andrew
From: freesurfer-boun
We don't have B0 fieldmap data, would I still be able to perform this
correction? For preprocessing we ran eddy_openmp and dtifit.
The helpdesk has added klawms to your sudo groups for access to the data.
Please let me know if you need any more information.
Thanks so much for your help,
A
Hi Josephine,
It appears that the rh.thickness file is corrupted. I would suggest rerunning
to see if that clears things up.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of 林諐庭
Date: Tuesday, April 20, 2021 at 4:35 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer
Please check out the known issues section of
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes for a fix
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Vishnu S
Date: Monday, April 19, 2021 at 8:05 AM
To: Freesurfer support list
Subject: [Freesurfer] Freeview
Log file is attached.
Thank you,
Andrew
Andrew Russo
Clinical Research Coordinator
Multiple Sclerosis Imaging Lab
Massachusetts General Hospital
149 13th Street | Boston, MA 02129
617-726-7531
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N
Hi Christina,
You’ll need to specify the version tag. You can try:
docker pull freesurfer/freesurfer:7.1.1
best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Chr. Roßmanith
Date: Friday, April 16, 2021 at 8:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer
Hi AJ,
Freesurfer ships its own python distribution, so it doesn’t matter what you
have installed on your system. Can you let us know the specific version of
macOS you are using and send the full error report from pip?
Thanks
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
Hi Max,
You could try downloading an updated, standalone release of freeview from
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Max Korbmacher
Date: Wednesday, April 14, 2021 at 2:05 PM
To: freesurfer
what you suggest.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Saemann, Philipp
Date: Monday, April 12, 2021 at 4:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] addon question perl version needed for FS5.3
External Email - Use Caution
Hi
I’m not totally sure of the answer here. Could be filesystem limitations or a
permissions issue. Have you tried untar’ing without the -p flag, or ensuring
that you can write to /usr/local?
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Pål Gunnar Larsson
Date
Have you made sure that you have read permission to open those files? What is
the output of `ls -l asta.mgh`? And asta.nii doesn’t seem to be a file in your
working directory.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Pierpaolo Croce
Date: Thursday, April 8
Thanks for the details. We’ll look into it a bit and get back to you.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Cook, Philip
Date: Monday, April 5, 2021 at 11:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] "ERROR: crypt() returned null with 4-line
Hi Katja,
Okay good to know. I will follow up off-list.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Zoner, Katja
Date: Tuesday, March 30, 2021 at 1:24 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [External] Re: "ERROR: crypt() returned null wi
to download the
7.1 docker container from https://hub.docker.com/r/freesurfer/freesurfer and
run FS through that. That should fix any system-specific problems.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Ramtilak Gattu
Date: Thursday, March 25, 2021 at 7:20 PM
To
Hi Katja,
I wonder if this is related to possible security settings. I can’t replicate
this, but can you send your license file so that we can narrow down the
possibilities? You can send it directly to my email, off-list.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
Hi Ezequiel,
Just including the FS license in the software as a separate text file is fine.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Ezequiel Mikulan
Date: Monday, March 22, 2021 at 12:48 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] License
Hi Ursula,
I was just reminded that we purposely don’t include MCR in the container due to
redistribution-restrictions by the MCR license. So, it’s up to the user to
install or provide the MCR library if needed.
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Hoopes
Hi Ursula,
Thanks for pointing this out. I think it’s just the case that MCR wasn’t
installed in that container. I’m surprised this hasn’t been brought up before.
We’ll update the container with it.
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Ursula Tooley
Date
Hi Matt,
Hopefully this isn’t specific to M1, but I’m not sure it would be in this case.
Maybe try running fs_install_mcr with sudo in front? Some users are suggesting
it here:
https://www.mathworks.com/matlabcentral/answers/176228-error-message-install_unix-not-found
best
Andrew
From
Hi Philipp,
Okay interesting. So it's failing on centos 8. Do you mind sending the license
file directly to my email (off-list)?
thanks
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Saemann, Philipp
Sent: Monday, March 15, 2
Hi Philipp,
Can you let us know the OS and version you’re running on? The license format
was updated for v6. It should be backwards compatible, but it’s possible it’s
not anymore on newer systems.
thanks
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Saemann, Philipp
rectly, so it’s
required that you have matlab installed on your computer to use it.
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Georgia Kapizioni
Date: Wednesday, March 10, 2021 at 6:35 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Matlab ver
difficult to rebuild a
local package for centos8.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Tobias, Malcolm
Date: Monday, March 8, 2021 at 3:49 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Supporting older versions of FreeSurfer (5.3) on
newer OSs
ni
cp -r $FS_60/mni $FS_53/
Then, customize the 5.3 SetUpFreeSurfer.sh (or whatever you use to source FS)
to ensure that the following variables are set in a 5.3 environment:
export PERL5LIB="$FS_53/mni/share/perl5"
export MNI_PERL5LIB="$FS_53/mni/share/perl5"
Hope that helps,
If you installed freesurfer with admin permissions, you should mv or cp the
file to the destination directory with `sudo` in front of your command to run
as root.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Donato Romano
Date: Monday, March 8, 2021 at 6:52 AM
To
Looks like it downloaded fine. In that case, just move that file to your FS
install:
mv fs_install_mcr $FREESURFER_HOME/bin
and you should be good to go.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Georgia Kapizioni
Date: Monday, March 1, 2021 at 10:57 AM
To
Can you run this instead:
apt-get -y install libncurses5
That should fix it. Also, please do not globally add the MCRv84 path to
LD_LIBRARY_PATH. This shouldn’t be needed to run the subfield code and will
likely cause problems for other freesurfer binaries.
Best
Andrew
From: freesurfer-boun
Hi Bruno,
I’m not sure I fully understand the question. If you want to use freesurfer in
combination with MNE, why not just install FS normally and source it while
you’ve activated your conda environment?
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruno Mansur
of that?
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Georgia Kapizioni
Date: Friday, February 26, 2021 at 1:04 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Matlab version 2012b installation problem
External Email - Use Caution
Hello Andrew
Hi Michele,
It looks like there is a local MNI install in /opt/minc/1.9.16 that is taking
priority over freesurfer. I would suggest rerunning freesurfer without sourcing
this local minc.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Michele Valotti
Date: Monday
-ordered face indices resulting
in bad normal computations. Not sure if this is easy in blender, but it might
be worth visualizing the surface normals to see if they’re pointing in
reasonable directions. I haven’t been able to replicate this issue on our end.
Best
Andrew
From: freesurfer-boun
that
listed in the registration file (1,1,1)
Do you know if this needs to be corrected or if there is a better method?
Thanks for the help,
Andrew
Andrew Russo
Clinical Research Coordinator
Multiple Sclerosis Imaging Lab
Massachusetts General Hospital
149 13th Street | Boston, MA 02129
617-726-7531
Hi Ishi,
What FS version are you using? Can you try installing `apt-get install
libncurses5-dev`?
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Ishi Tandon
Date: Thursday, February 18, 2021 at 12:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampus
incorrectly
computed during the conversion? You could narrow down whether it’s a conversion
issue by converting the same lh.pial file with both v6 and v7 mris_convert and
comparing those STLs.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Wang, Ruopeng
Date: Tuesday
If you send the mri_nu_correct.mni.log we can figure it out for sure.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Michele Valotti
Date: Thursday, February 11, 2021 at 12:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mincRead error
External Email
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