h Park Road, Exeter, EX4 4QE
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Wang, Ruopeng
Sent: 22 March 2023 13:38
To: Freesurfer support list
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault
CAUTION: This email originated from outside
eesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault
CAUTION: This email originated from outside of the organisation. Do not click
links or open attachments unless you recognise the sender and know the content
is safe.
Oh, sorry,
53D%26reserved%3D0>
Laver Building, North Park Road, Exeter, EX4 4QE
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fischl, Bruce R.,PHD
Sent: 21 March 2023 18:52
To: Freesurfer support list
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault
CAUTION
Wang, Ruopeng
Sent: Tuesday, March 21, 2023 1:35 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault
CAUTION: This email originated from outside of the organisation. Do not click
links or open attachments unless you recog
Hmm, that all looks fine. And what is your freeview command line that crashes?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Bartlett, Rob
Sent: Tuesday, March 21, 2023 12:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault
External
: Freesurfer support list
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault
CAUTION: This email originated from outside of the organisation. Do not click
links or open attachments unless you recognise the sender and know the content
is safe.
Can you post the full freeview command that you ran
, Bruce R.,PHD
Sent: Tuesday, March 21, 2023 1:58 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault
CAUTION: This email originated from outside of the organisation. Do not click
links or open attachments unless you recognise the sender and know the content
is safe
Segmentation Fault
External Email - Use Caution
Hi, I am using FreeSurfer 7.3.2 with Ubuntu 20.04.4 LTS. I have an issue where
Freeview crashes with a segmentation fault when loading a .mgz volume file. The
files I have been trying to open are part of the tutorial dataset.
Build Stamp
Can you post the full freeview command that you ran?
Ruopeng
On Mar 21, 2023, at 6:50 AM, Bartlett, Rob
mailto:r.bartle...@exeter.ac.uk>> wrote:
External Email - Use Caution
Hi, I am using FreeSurfer 7.3.2 with Ubuntu 20.04.4 LTS. I have an issue where
Freeview crashes with a segment
External Email - Use Caution
Hi, I am using FreeSurfer 7.3.2 with Ubuntu 20.04.4 LTS. I have an issue where
Freeview crashes with a segmentation fault when loading a .mgz volume file. The
files I have been trying to open are part of the tutorial dataset.
Build Stamp: freesurfer-
External Email - Use Caution
As Yujing said, the 5.1.0 release is quite old (dating back to CentOS4) and
binary backwards compatibility cannot be expected to work indefinitely going
forwards to newer versions of the OS. I ran a simple mri_surf2surf
command from 5.1.0 on CentOS7
] Segmentation fault (core dumped)
External Email - Use Caution
Greetings FS experts:
We are trying to run recon-all -s -qcache on a handful of brains processed in
freesurfer v5.1.0. (it's an old dataset...5.1 makes the most sense for our
purpose.)
The error is below:
[cid:image00
External Email - Use Caution
Greetings FS experts:
We are trying to run recon-all -s -qcache on a handful of brains processed
in freesurfer v5.1.0. (it's an old dataset...5.1 makes the most sense for
our purpose.)
The error is below:
[image: image.png]
---
External Email - Use Caution
Hello Joann,
If I read correctly, you are doing a remote mount of a shared network
drive to your Mac to store/read/write the subject files but running the
recon-all using your Mac processors.
You might want to check the directory for the last subject
External Email - Use Caution
Hello,
I am attempting to analyze some structural morphometry data. I am having issues
with the recon-all command that I am using. I am attempting to run this command
on a shared network folder through my institution. Here is the exact command I
External Email - Use Caution
Hello Priya,
It could help to know,- the version of freesurfer you installed, e.g., the
latest 7.3.2 release
from https://secure-web.cisco.com/1zdcvVhqKzcbDdvruGd5f9eNe1UebLwxcHQNPPf-imCCfHdpe0i9n7VbHnkOmApVqwXLBFsNTr00VNAx6komIIAOhuIRk6xXYWHGaglPYJch
External Email - Use Caution
Hello Team,
I just installed freesurfer and freeview using the methods mentioned in
https://secure-web.cisco.com/1oeEk1V3fGDlcuYEIm1RFYCYdQcU2m3TJysRGz7NAzZIOMDfxJiOPbas0gR6C45O_k9X6OvLE4pS75bwDoZy4yIzpxK5rduxKwxnHn7m8NEYSw4zXC5joOtwNk5Ms6X54nQoAn7rrCj
External Email - Use Caution
Hello Yuhui,
Did you try something like the following (from
https://secure-web.cisco.com/1hub7Psr57JCR6YgoGWEJLmEuz6voF9O_4wwW1Ngq-Krek8hQagKNFY9pH9jg_UzrEMFBjBl1Lo36JvBnp02E7HopuMgcNTaG0pTRx-2PR61unk8dCsv-4Gp50vSlBbeEJzjsRZGWS1jqAp0pVmSzDy9Ob23Rg1PB3s
External Email - Use Caution
Hello,
As a beginner, I am trying to run freeview -v using tutorial_data by the code
below.
freeview -v \
good_output/mri/T1.mgz \
good_output/mri/wm.mgz \
good_output/mri/brainmask.mgz \
good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \
-f good_o
External Email - Use Caution
Hi,
I am trying to use Freeview in my MacBook Pro. However, every time I tried to
open it from terminal I get this error:
/Applications/freesurfer/7.2.0/bin/freeview: line 2: 5984 Segmentation fault:
11 $FREESURFER_HOME/Freeview.app/Contents/MacOS
,
Kevin
Date: Tue, 12 Jan 2021 15:45:37 +
From: "Greve, Douglas N.,Ph.D."
mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Segmentation Fault During mri_convert
running FS 5.0
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesu
+
From: "Greve, Douglas N.,Ph.D."
mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Segmentation Fault During mri_convert
running FS 5.0
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
mailto:freesurf
For some reason, it is not capturing the terminal output in the log files. Can
you just run
mri_convert
/autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii
deleteme.mgz
and send me the terminal output?
On 1/2/2021 2:23 PM, Dowling, Kevin Francis wrote:
Hello FreeSur
Please send the recon-all.log file
On 12/25/2020 8:42 PM, Wei Koo wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to run recon2 for a number of subjects, but one of my subjects I
get the following error when I run the mri_tesellate command:
Removing int
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to run recon2 for a number of subjects, but one of my subjects I
get the following error when I run the mri_tesellate command:
Removing intersections
Segmentation fault
FreeSurfer version: freesurfer-darwi
It is seg faulting at the defect correction stage which is before the FLAIR
would be used. At this point it should be identical to the T1-only analysis.
Check your commands to make sure they are the same except for the FLAIR part
On 1/16/2020 9:55 AM, Swanson,Clayton wrote:
External Ema
Hi Ricardo
hmmm, the fact that it says "MRImaskDifferentGeometry" suggests that your
skull stripping didn't end up "conforming", which is probably the error.
Try something like:
cp brainmask.mgz brainmask.bet.mgz
mri_convert -rl orig.mgz brainmask.bet.mgz brainmask.mgz
then rerun and see if
External Email - Use Caution
Dear Freesurfer experts,
I’m trying to run recon-all on "T1-like” data (it is actually a quantitative
MRI map with a contrast very similar to T1).
I managed to put it through recon-all’s autorecon1 stage without any major
tricks or modifications (wat
namens Greve, Douglas N.,Ph.D.
Verzonden: donderdag 14 maart 2019 17:17:54
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] Segmentation fault
Can you send the command line with out variables and the full terminal
output?
On 3/14/19 8:48 AM, Donatienne Van Weehaeghe wrote
t;
> --no-rescale --threads 8
>
> Kind regards
>
> Donatienne
>
>
> //
>
>
> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu
> namens Tim Schäfer
>
> *Verzonden:* woensdag 13 maart 2019 23:22:07
> *Aan:* Frees
] Segmentation fault
External Email - Use Caution
> On March 13, 2019 at 9:18 PM Donatienne Van Weehaeghe
> wrote:
> The code I tried to run:
>
> #mri_gtmpvc --i SUVR_cerebellum.nii.gz --reg suv.reg.lta --psf 5 --seg
> /gtmseg.mgz --default-seg-merge --auto-mas
External Email - Use Caution
> On March 13, 2019 at 9:18 PM Donatienne Van Weehaeghe
> wrote:
> The code I tried to run:
>
> #mri_gtmpvc --i SUVR_cerebellum.nii.gz --reg suv.reg.lta --psf 5 --seg
> /gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o
> gtmpvc.output.su
External Email - Use Caution
Dear,
I encountered the following error when I tried to run mri_gtmpvc -- rbv:
Segmentation fault (core dumped)
First I performed the PET to orig registration using spmregister, secondly I
tried with the registration using mri_coreg but the error
External Email - Use Caution
Update - Segmentation fault
I think I have finally found the issue. The bvec files I uploaded actually
contained only zeroes for each bvec value, and that made it impossible for
Tracula to function properly. This was a result of the original files w
External Email - Use Caution
I probably deleted the log file prior to running the path step so I could
focus on what was going on. I'll re-run it and give you the results when
it finishes.
Thanks!
--
Notice: This e-mail message, together with any attachments, contains
informat
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, October 31, 2018 at 9:57 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Segmentation fault
External Email - Use Caution
Hello Jon,
Since trac-all is a tcsh script, you could try prefacing it with "tcsh -x" to
get extra output about what it is doing, i.e.,
$ tcsh -x trac-all rest of args...
- and then look thru the trac-all output to see where it actually runs a bi
External Email - Use Caution
Hello Jon,
Looks like you are already running with -debug and -allowcoredump option, and
the shell limits do not look like they are too small to allow the coredump to
be written. I don't know offhand if that coredump option causes a file to
be wri
External Email - Use Caution
Hello Jon,
Can you get any stack or backtrace information after the segfault occurs ?,
e.g., Mac OS has the option to display the crash report with a trace. On
Linux you could run thru gdb and get a back trace. This would help
us to see where the
External Email - Use Caution
Hey Freesurfer team,
I'm working on running Tracula, and have been running into segmentation
fault issues. We have consistently been running into segmentation fault
issues. * The data we are working with comes from children*, and I'm
concerned that
External Email - Use Caution
Hello
I notice a systematic segmentation fault with several function that use
a .lta file (lta_convert or mri_vol2vol)
This is due to a too long filename path in the .lta file :
If I manually edit the .lta file and change the file_path associate to
t
N Greve
>
> *Sent:* Monday, December 18, 2017 5:09:25 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Segmentation fault (core dumped)
>
> We need more details. Try looking at this web site
>
>
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
o:* Freesurfer support list [freesurfer@nmr.mgh.harvard.edu]
> *Cc:* Jacobs, Heidi Irma Louisa; Vannini, Patrizia,Ph.D.
> *Subject:* [Freesurfer] Segmentation fault (core dumped)
>
> Dear FreeSurfer experts,
>
>
> I am unable to run the qcache procedure and was wondering if a
freesurfer@nmr.mgh.harvard.edu]
Cc: Jacobs, Heidi Irma Louisa; Vannini, Patrizia,Ph.D.
Subject: [Freesurfer] Segmentation fault (core dumped)
Dear FreeSurfer experts,
I am unable to run the qcache procedure and was wondering if anybody could help
me find what is going on.
I've tried running qcac
to the files
listed in the folder "mri". Maybe the problem is caused here?
I will try to rerun the recon-all analysis of this subject.
Thank you very much for your help!
Regards,
Jens
Gesendet: Montag, 29. Mai 2017 um 16:32 Uhr
Von: "Bruce Fischl"
An: "Freesurfer
matic section. I will report,
if the issue appears there, too.
Regards,
Jens
Gesendet: Montag, 29. Mai 2017 um 07:41 Uhr
Von: "Jens Offenbach"
An: freesurfer@nmr.mgh.harvard.edu
Cc: "Freesurfer support list"
Betreff: Re: [Freesurfer] Segmentation fault (core dumped) error
I
An: freesurfer@nmr.mgh.harvard.edu
Cc: "Freesurfer support list"
Betreff: Re: [Freesurfer] Segmentation fault (core dumped) error
I am facing a similar issue with recon-all in FreeSurfer 6.0.0. on two subjects
from OASIS-Brains.
I will retry the run.
This is the last log entry:
mri_cc -aseg
: Freitag, 26. Mai 2017 um 15:52 Uhr
Von: "Devin Sodums"
An: "Freesurfer support list"
Betreff: Re: [Freesurfer] Segmentation fault (core dumped) error
Sure thing, I’ll send it in a few.
Thanks,
Devin
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr
Sure thing, I'll send it in a few.
Thanks,
Devin
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Friday, May 26, 2017 9:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Segmentation fault (core d
No idea. Can you upload the subject so I can take a closer look?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 5/26/17 9:35 AM, Devin Sodums wrote:
Hello FreeSurfer developers,
I’m attempting to run recon-all on a T1 image and keep getting the
same error message:
Segmentation fault (core d
Hello Christopher,
Perhaps you could upload a data set for which mri_convert is segfaulting
so that we can take a closer look?
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
-Zeke
On 06/13/2016 02:19 PM, Christopher Finuf wrote:
> I'm trying to convert the dicom to the original 00
I'm trying to convert the dicom to the original 001.mgz file using the
following command on a Mac OSX Yosemite version 10.10.5. My
SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/
. My current working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/
. The following i
I'm trying to convert the dicom to the original 001.mgz file using the
following command on a Mac OSX Yosemite version 10.10.5. My
SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/
. My current working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/
. The following i
It did not find any voxels in the ROI. This can happen for several
reasons. First, check your registratoin (tkregister-sess). Second, it
can happen because the size of the ROI is too small and does not occupy
enough space in a voxel. Try changing the -fillthresh to something
smaller than the de
Hello FS experts,
I am running a command "fcseed-sess -s S01 -cfg abc.config" to get *.dat
file for further analysis. I used the same steps to calculate FC for 40
subjects, all steps run fine with 38 subjects but for 2 subjects I am
getting an error: Segmentation fault: Core dumped.
I checked the
There is nothing obvious going wrong. If the exact same command
sometimes fails and sometimes works, then it may be a problem on your
system. In any event, without a reproducible error, I can't really debug it.
On 04/15/2016 08:31 PM, Elijah Mak wrote:
>
> On another note, I am running into a pu
Dear all,
I get a segmentation fault when running mri_convert, FreeSurfer version 5.0.0
on a fresh Ubuntu 14.04 installation.
In the past, and on a different machine, I could fix this problem by copying
the Ubuntu_12.04 file libcrypt-2.*.so to the $FREESURFER_HOME/lib folder of the
Ubuntu_14
Hello Freesurfer list,
I have several different surface labels that I am converting into volume
regions-of-interest in white matter. For 2 out of 11 participants, one of
the labels will not convert. My command has worked for these two
participants with all other labels that I've tried. I have no t
what server did you upload it to? What is the name of the file? Make
sure to include the entire output folder, not just the input files
On 12/21/2015 03:33 PM, Fengji Geng wrote:
> Hi Bruce,
>
> I have uploaded all the data to the server. The command that I run is
> 'recon-all -all -s $s -hippoc
Hi Bruce,
I have uploaded all the data to the server. The command that I run is
'recon-all -all -s $s -hippocampal-subfields-T1T2 $s/T2/*.mgz T1T2'.
It would be great if you could keep us updated on how the fixing is going.
Thanks!
--
So the strangest thing happened. Just on a hunch, I logged out of the server
then logged back in, and now it's running! It's a mystery to me. Thanks again,
I'll check the RAM specs and get back to you. For now though it seems to be
working. Hope it stays that way!
Best,Syeda
On Wednesda
Hi Syeda
it doesn't die when I run it locally. How much RAM do you have on the
machine that it crashes on? If you want a new version we can send you one.
cheers
Bruce
On Wed, 14 Oct 2015, Syeda Maryam wrote:
Hi Bruce,
I just sent you the files on filedrop! I thought it might have something
Hi Bruce,I just sent you the files on filedrop! I thought it might have
something to do with the freesurfer version since the mri_label2vol comman
works fine on my local machine and the segmentation fault I was talking about
only happens when I try to run it on the server our research group is u
it's possible, or something to do with your images. You can use either
our filedrop or ftp site to send them to me if you want
On Wed, 14 Oct 2015,
Syeda Maryam wrote:
So for some reason my mail with the attachments won't get delivered...the
message size exceeds the limits. I was wondering if
So for some reason my mail with the attachments won't get delivered...the
message size exceeds the limits. I was wondering if the segmentation fault
error I'm getting might be do to some problem in the freesurfer version I'm
running?
Thanks,Syeda
On Wednesday, October 14, 2015 12:09 PM,
Hi Syeda
that commnand doesn't segfault when I try it on another subject here. If
you email me the aseg.mgz and the rawavg.mgz I'll take a look
cheers
Bruce
On Wed, 14 Oct 2015, Syeda
Maryam wrote:
Hello Freesurfer experts,
I'm getting a segmentation fault when I use the mri_label2vol co
Hello Freesurfer experts,
I'm getting a segmentation fault when I use the mri_label2vol command to
push aseg labels from freesurfer space to my subject's original T1 space
(using the example given on the freesurfer website). I'm not sure why this
is happening...I've tried changing the parameters c
Hello Freesurfer experts,
I'm getting a segmentation fault when I use the mri_label2vol command to push
aseg labels from freesurfer space to my subject's original T1 space (using the
example given on the freesurfer website). I'm not sure why this is
happening...I've tried changing the parameters
gt; From: "Prabesh Kanel"
> To: "Freesurfer support list"
> Sent: Friday, August 14, 2015 9:05:38 AM
> Subject: Re: [Freesurfer]segmentationfaultwhilerunning
> -hippocampal-subfields-T1 flag
>
> Hi Eugenio,
>
> Thank you for your help.
: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Prabesh Kanel"
To: "Freesurfer support list"
Sent: Friday, August 14, 2015 9:05:38 AM
Subject: Re: [Freesurfer] segmentationfault while running
-hippocampal-subfields-T1 flag
Hi Eugenio,
Thank you
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Eugenio Iglesias
Sent: Friday, August 14, 2015 11:52 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] segmentation fault while running
-hippocampal-subfields-T1 flag
Sorry, I
ort list"
Sent: Friday, August 14, 2015 11:51:54 AM
Subject: Re: [Freesurfer] segmentation faultwhile running
-hippocampal-subfields-T1 flag
Hi again, Prabesh
would you mind trying this? It was a suggestions from a Mathworks
representative.
Please edit
--- Original Message -
From: "Prabesh Kanel"
To: "Freesurfer support list"
Sent: Monday, August 10, 2015 9:01:26 AM
Subject: Re: [Freesurfer] segmentation faultwhile running
-hippocampal-subfields-T1 flag
Hi Eugenio,
I have about 128 GB of RAM memory in both machine. I
list
Subject: Re: [Freesurfer] segmentation fault while running
-hippocampal-subfields-T1 flag
Hi Prabesh,
do you get the same error if you try rerunning the module on the same volume?
Also, how much RAM memory does the machine have?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral
/legal-disclaimer
- Original Message -
From: "Prabesh Kanel"
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, August 7, 2015 9:06:51 PM
Subject: [Freesurfer] segmentation fault while running
-hippocampal-subfields-T1 flag
Hi Freesurfer group,
I am using freesurfer (Linux-cent
Hi Freesurfer group,
I am using freesurfer (Linux-centos6_x86_64 August 3rd) for segmenting subfield
of hippocampus. I followed the instruction written and was able to segment
hippocampus subfields for number of MR images in one of the server. I followed
the same instruction in another server w
t; Subject: Re: [Freesurfer] Segmentation fault in mris_fix_topology when
> compiling with gcc 4.8 + AVX2
>
> Thank you for this information.
>
> -Zeke
>
> On 06/22/2015 02:22 AM, Chris Adamson wrote:
>> Everyone,
>>
>> I know this is a fairly specific issue but nonethe
: Freesurfer support list
Subject: Re: [Freesurfer] Segmentation fault in mris_fix_topology when
compiling with gcc 4.8 + AVX2
Thank you for this information.
-Zeke
On 06/22/2015 02:22 AM, Chris Adamson wrote:
> Everyone,
>
> I know this is a fairly specific issue but nonetheless.
&
Thank you for this information.
-Zeke
On 06/22/2015 02:22 AM, Chris Adamson wrote:
> Everyone,
>
> I know this is a fairly specific issue but nonetheless.
>
> If you compile Freesurfer 5.3.0 with the option –march=core-avx2 with
> gcc 4.8 it can cause mris_fix_topology to segfault at
> utils/mris
Everyone,
I know this is a fairly specific issue but nonetheless.
If you compile Freesurfer 5.3.0 with the option -march=core-avx2 with gcc 4.8
it can cause mris_fix_topology to segfault at utils/mrisurf.c:64770
mrisCopyDefectPatch
gcc 4.9 also does the same thing.
If you still use AVX but dis
Thank you Zeke.
I copied the library from a third computer and now there are no more
segmentation faults. Probelm solved.
Best,
Luigi.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Luigi,
I will be able to assist you in getting this to work but I am away at the
moment and won't be back till mid next week. If no one else provides you with a
solution I will be able to help you at that time.
-Zeke
> On Feb 19, 2015, at 12:14 AM, Luigi Antelmi wrote:
>
> Dear all,
> I'm
Dear all,
I'm facing the same problem of Alessandra, but the solution provided by
Zeke doesn't work for me.
I still get a segmentation fault in converting mnc to nii.
Thanks in advance for your help.
Luigi.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.h
Hello Alessandra,
This is a known issue with pre-freesurfer v5.3 releases and the most
recent version of Ubuntu. To fix the issue, if you have access to a
machine that still runs Ubuntu 12.04, please do the following:
1) On the Ubuntu 12.04 system, find the find the file "libcrypt-2.*.so"
usual
Dear all,
I am running FreeSurfer version [recon-all,v 1.313.2.6 2010/08/04] on an
Ubuntu machine.
After updating my system from Ubuntu 12.04 to Ubuntu 14.04 I get a
segmentation fault when I try to resample images using mri_convert:
/mri_convert -vs 1 1 1 /folder/original_image.nii.gz /folde
Ahh, that did the trick. Thanks!
On Fri, Jul 11, 2014 at 5:30 PM, Bruce Fischl
wrote:
> Hi Mark
>
> have you tried "conforming" the inputs (making them all 256^3, 1mm iso and
> 8 bits/voxel)?
> Bruce
>
> On Fri, 11 Jul 2014, Mark Plantz wrote:
>
> Hello freesurfers,
>>I am running into som
Hi Mark
have you tried "conforming" the inputs (making them all 256^3, 1mm iso
and 8 bits/voxel)?
Bruce
On Fri, 11 Jul 2014, Mark Plantz wrote:
Hello freesurfers,
I am running into some sort of memory allocation issue when running
mri_ca_train. I am
simply using an intensity volume and a
Hello freesurfers,
I am running into some sort of memory allocation issue when running
mri_ca_train. I am simply using an intensity volume and a segmentation
volume to create a GCA atlas. I keep getting this "segmentation fault: 11",
which is data allocation error. I have tried using all differ
Thank you Doug. I was using the same label file for all subjects before. I
will create the labels for each individual and run the
mris_anatomical_stats ( I tested it on one subject that didnt run before,
and it did not give any errors this time)
Thanks again!
Rupa
It looks like this label w
It looks like this label was created on fsaverage. Is that the case? If
so, then you need to run mri_label2label to map it into the space of an
individual, then run mris_anatomical_stats
doug
On 03/18/2014 12:59 PM, Rupa Sabbineni wrote:
> Hi Doug
> Attached is a label file.
> The FS version i
Can you verify that the label does actually have label points in it?
Just open it in a text editor or cat it to a terminal. If it does have
points, send it to me. Also let me know which version of FS you are running.
doug
On 3/17/14 5:35 PM, Rupa Sabbineni wrote:
muen223-105-dhcp:subjects
muen223-105-dhcp:subjects rupasabbineni$ mris_anatomical_stats -l new.label
-a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh
limiting computations to label
/Volumes/DISK/Software/freesurfer/subjects/qdec/Results/new.label.
computing statistics for each annotation in aparc.a2009s.annot.
outputting
Can you send the terminal output?
On 03/17/2014 01:54 PM, Rupa Sabbineni wrote:
>
> Good morning!
>
>
> I was trying to run the mris_anatomical_stats command and for some
> subjects I keep getting Segmentation fault:11 error.
>
> Some of the posts in the archive suggested that I run the recon-all
Good morning!
I was trying to run the mris_anatomical_stats command and for some subjects
I keep getting Segmentation fault:11 error.
Some of the posts in the archive suggested that I run the recon-all command
since it usually means that subjects surfaces are out of sync SO I RERAN
RECON_ALL(whi
Mark,
How was the .gca file created? Can you send us this file?
Nick
On Tue, 2013-08-20 at 14:15 -0500, Mark Plantz wrote:
> Thanks for the responses.
>
>
> I think I have determined the cause of the error. I thought it would
> be OK to run recon-all with a .gca atlas that contained some dif
Thanks for the responses.
I think I have determined the cause of the error. I thought it would be OK
to run recon-all with a .gca atlas that contained some different ROI's from
the default .gca atlas. I think that this may be throwing off the
subcortical segmentation.
Does anyone know if the gca
I think the best way to diagnose the issue would be to run the subject
using the standard atlas provided with freesurfer. If that runs to
completion that the .gca is almost certainly the source of the problem.
-Zeke
On 08/19/2013 03:07 PM, Mark Plantz wrote:
> Hello all,
>
> While running
Hello all,
While running recon-all for a subject, I ran into the following error
message:
*reading aseg from
/Users/IngvalsonLab/Desktop/avgseg_seg_test/mri/aseg.auto_noCCseg.mgz*
*reading norm from /Users/IngvalsonLab/Desktop/avgseg_seg_test/mri/norm.mgz*
*0 voxels in left wm, 0 in right w
Martina,
Can you send me the recon-all.log file?
Nick
On Tue, 2013-05-07 at 17:38 +0200, martina.andell...@fastwebnet.it
wrote:
> Hi Freesurfer experts,
> I've got Ubuntu version 13.04 installed on my computer, and after I saw the
> post
> : "http://www.mail-archive.com/freesurfer@nmr.mgh.harv
Hi Freesurfer experts,
I've got Ubuntu version 13.04 installed on my computer, and after I saw the post
: "http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html"; I d
ecide to install the BETA version freesurfer-Linux-centos6_x86_64-stable-pub-v5.
3.0-BETA.tar.gz as adviced.
I st
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