[Freesurfer] Segmentation fault

[Donatienne Van Weehaeghe]

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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 remained. I also 
redid the segmentation step
gtmseg --s $word --xcerseg without fixing the problem. Can anyone help me with 
this problem?

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.suvrcerebellum.spmreg --no-rescale --threads 8

Kind regards
Donatienne
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[Freesurfer] Segmentation fault

[Whitney, Jon]

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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 differences in MRI image brightness and mapping between
adult and children's brains may be throwing Tracula off.  In many cases the
typical pathlist of files ( lh.cst_AS, rh.cst_AS, etc) are not fully
populated in the bedp step.  We have therefore started submitting the job
with the set pathlist and set ncpts to only point to files which are
generated during the bedp step.  Nonetheless, we are still getting
segmentation fault errors during the final path step.  I'm using freesurfer
version 6.0.0-2beb96c, but I'm not sure what version of Tracula I'm using.
This is a log of the error:

Initial proposal SD file:
/data/Abeona/W4WUM/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt
/data/Abeona/W4WUM/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt
/data/Abeona/W4WUM/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt
/data/Abeona/W4WUM/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt
/data/Abeona/W4WUM/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt
/data/Abeona/W4WUM/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt
/data/Abeona/W4WUM/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt
/data/Abeona/W4WUM/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt
/data/Abeona/W4WUM/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt
/data/Abeona/W4WUM/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt
/data/Abeona/W4WUM/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt
/data/Abeona/W4WUM/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt
/data/Abeona/W4WUM/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt
/data/Abeona/W4WUM/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt
/data/Abeona/W4WUM/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt
/data/Abeona/W4WUM/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt
/data/Abeona/W4WUM/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt
/data/Abeona/W4WUM/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt
Loading DWIs from /data/Abeona/W4WUM/dmri/dwi.nii.gz
Loading mask from /data/Abeona/W4WUM/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter samples from /data/Abeona/W4WUM/dmri.bedpostX
Loading b-values from /data/Abeona/W4WUM/dmri/bvals
Loading gradients from /data/Abeona/W4WUM/dmri/bvecs
INFO: Found 1 baseline images (b = 0) out of a total of 31 frames
Segmentation fault (core dumped)
Linux ip-10-0-0-222 4.4.0-137-generic #163-Ubuntu SMP Mon Sep 24 13:14:43
UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Wed Oct 24 01:22:16 UTC 2018

The Freesurfer help I've looked at previous suggested that it could be a
memory error, but we're using a remote drive that has lots of disk space
and 26 GB RAM, so I doubt that's it.  Checked the LANG, we are using
en_US.UTF-8.  I've run this on at least 8 different patients so far, and
only one of them has not had this kind of error.  Some of the different
patients have different numbers of the normal path files exported into
/dlabel/diff/, so it seems like there is patient-to-patient variability in
how well the bedp phase is able to map things out.

Thanks for your help!
-Jon

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[Freesurfer] Segmentation fault

[Nicole Espinosa Zarlenga]

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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  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"

I Freeview closes automatically.


Do you know how I can fix this error?

Thanks!
 Nicole Espinosa
Research Assistant | School of Psychology | Faculty of Science

THE UNIVERSITY OF SYDNEY
Healthy Brain Ageing Program
Brain and Mind Centre & Charles Perkins Centre

E: nesp6...@uni.sydney.edu.au



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[Freesurfer] segmentation fault

[Wei Koo]

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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-darwin-macOS-7.1.1.

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[Freesurfer] Segmentation Fault

[Allie Rosen]

Hi All,

Upon trying to assembly my subjects into a single surface space, I got the
following error:

*ERROR: number of vertices in
/media/AMMONIS/fsSubjects/AR_normals/C42/surf/lh.thickness does not match
surface (142271,140585)
ERROR: reading curvature file
*
I then tried to perform recon-all -make all, but got this error:

*ERROR: mpr2mni305 failed, see transforms/talairach_avi.log*

In the .log, I got this:

*-7.5000   22.5000   15. 2793.2134   1Segmentation fault
ERROR: 'imgreg_4dfp /usr/rapps/freesurfer/average/711-2C_as_mni_average_305
/usr/rapps/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11
none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=139
ERROR: mpr2mni305 execution aborted*

Which is a segmentation fault. Can anyone help me fix this?

Thanks,
Allie Rosen, MSc Candidate
Graduate Student, Department of Neurosurgery
Toronto Western Hospital 14-327
399 Bathurst St.
University of Toronto
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[Freesurfer] Segmentation Fault

[Chindhuri Selvadurai]

Hi all,

We are trying to run individual analyses on several subjects, and we keep
getting a 'Segmentation Fault.'  We have run other subjects with the same
command a while ago, and the command worked fine at that time.  Do you
have any idea what would be causing this error?  The output is included
below:

Command: selxavg3-sess -analysis mandyrh3 -fwhm -s PBMCT15
Subjects Dir: /cluster/manoach/milton/subjects
FreeSurfer v. Stable 5


Session: /autofs/cluster/manoach/milton/subjects/PBMCT15 
Fri May 13 12:21:58 EDT 2011
  Run: 012 
Fri May 13 12:21:58 EDT 2011
Update not needed
Fri May 13 12:21:58 EDT 2011
register-sess completed
PBMCT15 MC -
mc-sess -fstem f -fmcstem fmcpr -s PBMCT15 -d
/autofs/cluster/manoach/milton/subjects -fsd bold -rlf task -per-run
-nolog -update
Logfile is /dev/null
---
/autofs/cluster/manoach/milton/subjects/PBMCT15
RunList: 012
  --- ** ---
  --- Motion Correcting Run 012 ---
  --- ** ---
sess = PBMCT15
Fri May 13 12:21:58 EDT 2011
mc-afni2 --i 012/f.nii --t 012/template.nii --o 012/fmcpr.nii.gz --mcdat
012/fmcpr.mcdat
/autofs/cluster/manoach/milton/subjects/PBMCT15/bold
mri_info --nframes --o /tmp/mriinfo.3377 012/template.nii
log file is 012/fmcpr.nii.gz.mclog
mcdat file is 012/fmcpr.mcdat
tmp dir is 012/tmp.mc-afni2.3377
#@# 
/autofs/cluster/manoach/milton/subjects/PBMCT15/bold
mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip
0 --ndrop 0 -odt float
mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip
0 --ndrop 0 -odt float
nskip = 0
ndrop = 0
$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
reading from 012/template.nii...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998297, -0.0395807, 0.0428535)
j_ras = (0.0411249, -0.998513, 0.0357732)
k_ras = (0.0413739, 0.0374746, 0.998441)
changing data type from short to float (noscale = 0)...
writing to 012/tmp.mc-afni2.3377/tempvol.nii.gz...
#@# 
/autofs/cluster/manoach/milton/subjects/PBMCT15/bold
mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float
mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float
Segmentation fault


Thanks!

Best,

Chindhuri Selvadurai

Psychiatric Neuroimaging, Manoach Lab
Martinos Center for Biomedical Imaging, MGH
Phone: (617)726-0307
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[Freesurfer] segmentation fault

[Kirk Gregory R.]

Hi all,
 
I got in the recon-all log
 
#...@# Cortical ribbon mask Tue May 12 17:56:52 CDT 2009
/home/gkirk/freesurfer/freesurfer/subjects/P21/mri
 mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 
--label_right_ribbon 42 --save_ribbon --save_distance P21 
SUBJECTS_DIR is /home/gkirk/freesurfer/freesurfer/subjects
Segmentation fault
Linux debian01 2.6.26-1-amd64 #1 SMP Mon Dec 15 17:25:36 UTC 2008 x86_64 
GNU/Linux
recon-all exited with ERRORS at Tue May 12 18:10:33 CDT 2009
 
running
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0
Linux debian01 2.6.26-1-amd64 #1 SMP Mon Dec 15 17:25:36 UTC 2008 x86_64 
GNU/Linux
 
 
i have gotten 4 of these out of 21 ADNI data sets, I saw Nurunisa at Barry 
Kosofsky's site reported
this also and Nick ask here to send the data set. 11 Nov 2008,
 
got any info on this one ?, i am guessing it is a data quality issue that is 
breaking something
in an uncontrolled way.
 
thanks
 
Greg.

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[Freesurfer] Segmentation fault

[Ritobrato Datta]

Hello All,

I got this error when I ran recon-all -all. I changed machines and the same 
dataset went all the way through without any errors. I ran another dataset with 
the machine "taxi" and it ran fine. 

Any suggestions will be helpful.
_
SUBJECTS_DIR is /jet/kadivar/freesurfer
Segmentation fault
Linux taxi.penn.edu 2.8.10-128.1.1.e5 #1 SMP Thu May 7 10:35:59 EDT 2009 x86_64 
x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Sat Aug  1 06:20:17 EDT 2009
_

Thanks

Ri

Ritobrato Datta, Ph.D.
Post Doctoral Fellow
Department of Neurology
Center for Functional Neuroimaging
University of Pennsylvania School of Medicine
3rd Floor Gates Building
3400 Spruce St. 
Philadelphia
Pa 19104


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[Freesurfer] Segmentation fault ...

[Erick Jorge Canales]

Dear experts,

The recon-all process of some of my subjects (15 from 100) exited with
ERRORS ...

I got in the recon-all file of one of them the following report:

...

Reporting on  49 segmentations
#
#...@# Cortical ribbon mask Sat Aug 29 13:09:43 CEST 2009
/mnt/HDD1/FreeSurfer_Cortical/Results/Prueba/Cont_FreeSurf_BMJGR19839SC/mri

mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white
41 --label_right_ribbon 42 --save_ribbon --save_distance
Cont_FreeSurf_BMJGR19839SC

SUBJECTS_DIR is /mnt/HDD1/FreeSurfer_Cortical/Results/Prueba
Segmentation fault
Linux uifsl5 2.6.26-1-amd64 #1 SMP Thu Oct 9 14:16:53 UTC 2008 x86_64
GNU/Linux

recon-all exited with ERRORS at Sat Aug 29 13:19:32 CEST 2009

...

Is there any way to fix this problem?

My computer have 8 cores and 16 Gb of RAM, in general I have been running 6
recon-all jobs concurrently. I'm  running this version:
freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0

Many thanks in advance,

Regards,

Erick
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[Freesurfer] Segmentation fault?

[Raghav Puranmalka]

Hi all,

I am running recon-all as follows:

recon-all -subjid subj1 -all

and (after about 4 hours of running,) get this error:

0516: dt=0.00, rms=0.507 (0.000%), neg=0, invalid=766
Segmentation fault
ERROR: mri_ca_register with non-zero status 139
but continuing despite the error
#--
#...@# CA Reg Inv Sat Feb  6 02:56:03 EST 2010
/usr/local/freesurfer/subjects/be496/mri

  mri_ca_register -invert-and-save transforms/talairach.m3z

Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z
ERROR: cannot find or read transforms/talairach.m3z
ERROR: mri_ca_register with non-zero status 0

It seems that perhaps this is because it cannot find 
"transforms/talairach.m3z" - indeed, this file doesn't exist. But should 
this be something generated by recon-all? Should I be running recon-all 
differently?

Thanks for your help,

Raghav
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[Freesurfer] Segmentation fault

[De La Llave Teddy]

Hi all,

I am running recon-all as follows:

recon-all -subjid subjectTest -all

and get this error:

Segmentation fault
ERROR: mri_ca_register with non-zero status 139

I can't continue the rest of the process because the file
talairach.m3z not exist.

I saw that others have the same problem but there are no solutions?

freesurfer runs on the virtualbox available in the website. It run
with 1,4Go of RAM.


Thanks for your help,


Teddy

-- 
Teddy De La Llave
Ingénieur développement R&D

te...@eye-brain.com

e(ye)BRAIN
www.eye-brain.com
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[Freesurfer] Segmentation fault

[Nurunisa Neyzi]

Hi I am getting the following error while running auto-recon2.

...

Reporting on  49 segmentations
#
[EMAIL PROTECTED] Cortical ribbon mask Tue Nov 11 01:32:03 EST 2008
/localA/nneyzi/MLS2/PedBirnPipeline_20081103_014127/mri

 mris_volmask --label_left_white 2 --label_left_ribbon 3
--label_right_white 41 --
label_right_ribbon 42 --save_ribbon --save_distance
PedBirnPipeline_20081103_01412
7

SUBJECTS_DIR is /localA/nneyzi/MLS2
Segmentation fault
Linux ped-birn.med.cornell.edu 2.6.18-53.1.13.el5xen #1 SMP Mon Feb 11
13:41:50 ES
T 2008 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Tue Nov 11 01:45:44 EST 2008

What does it mean?
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Re: [Freesurfer] Segmentation fault

[Whitney, Jon]

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 we
were given having empty header data.  We have been able to locate the
original bvec values and it appears as though everything is working now.

Thanks for your help!!

On Wed, Oct 31, 2018 at 10:55 AM Whitney, Jon  wrote:

> 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!
>


-- 

*Jon Whitney*
Image Analysis Engineer
ERT | 26801 Miles Rd | Cleveland, OH 44128 | USA
ert.com




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Re: [Freesurfer] Segmentation fault

[Tim Schäfer]

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> 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.suvrcerebellum.spmreg --no-rescale --threads 8
> 

Is that slash in the part '--seg /gtmseg.mgz' a copy & paste error? If not: it 
is very likely that the file does not exist in that location.

I'm not sure though whether that is the cause of the error. I would rather 
expect a "file not found" error message instead of a seg fault in that case. 
But it's worth checking.

-- 
Tim

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Re: [Freesurfer] Segmentation fault

[Donatienne Van Weehaeghe]

External Email - Use Caution

Dear,


Apologies, this is a copy and paste error the full command was:


#mri_gtmpvc --i 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUVR_cerebellum.nii.gz
 --reg 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/suv.reg.lta
 --psf 5 --seg 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz
 --default-seg-merge --auto-mask 5 0.01 --rbv --o 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/PVC/gtmpvc.output.suvrcerebellum.spmreg
 --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: Freesurfer support list
Onderwerp: Re: [Freesurfer] 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-mask 5 0.01 --rbv --o 
> gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8
>

Is that slash in the part '--seg /gtmseg.mgz' a copy & paste error? If not: it 
is very likely that the file does not exist in that location.

I'm not sure though whether that is the cause of the error. I would rather 
expect a "file not found" error message instead of a seg fault in that case. 
But it's worth checking.

--
Tim

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Re: [Freesurfer] Segmentation fault

[Greve, Douglas N.,Ph.D.]

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:
>
> External Email - Use Caution
>
> Dear,
>
>
> Apologies, this is a copy and paste error the full command was:
>
>
> #mri_gtmpvc --i 
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUVR_cerebellum.nii.gz
>  
> --reg 
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/suv.reg.lta
>  
> --psf 5 --seg 
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz
>  
> --default-seg-merge --auto-mask 5 0.01 --rbv --o 
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/PVC/gtmpvc.output.suvrcerebellum.spmreg
>  
> --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:* Freesurfer support list
> *Onderwerp:* Re: [Freesurfer] 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-mask 5 0.01 --rbv --o 
> gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8
> >
>
> Is that slash in the part '--seg /gtmseg.mgz' a copy & paste error? If 
> not: it is very likely that the file does not exist in that location.
>
> I'm not sure though whether that is the cause of the error. I would 
> rather expect a "file not found" error message instead of a seg fault 
> in that case. But it's worth checking.
>
> -- 
> Tim
>
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Re: [Freesurfer] Segmentation fault

[Donatienne Van Weehaeghe]

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We just found the mistake. I created the SUVR images already in T1 space so I 
remade the lta files using the SUVR images and now it works.


Kind regards

Donatienne


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 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:
>
> External Email - Use Caution
>
> Dear,
>
>
> Apologies, this is a copy and paste error the full command was:
>
>
> #mri_gtmpvc --i
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUVR_cerebellum.nii.gz
> --reg
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/suv.reg.lta
> --psf 5 --seg
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz
> --default-seg-merge --auto-mask 5 0.01 --rbv --o
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/PVC/gtmpvc.output.suvrcerebellum.spmreg
> --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:* Freesurfer support list
> *Onderwerp:* Re: [Freesurfer] 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-mask 5 0.01 --rbv --o
> gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8
> >
>
> Is that slash in the part '--seg /gtmseg.mgz' a copy & paste error? If
> not: it is very likely that the file does not exist in that location.
>
> I'm not sure though whether that is the cause of the error. I would
> rather expect a "file not found" error message instead of a seg fault
> in that case. But it's worth checking.
>
> --
> Tim
>
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>
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[Freesurfer] Segmentation fault mri_em_register

[Loucao, Ricardo]

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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 (watershed is failing but I managed to work around it 
using FSL’s BET combined with mri_convert to create the brainmask.mgz file).

Now I’m running into a segmentation fault error in mri_em_register.
Here’s the relevant portion of the log file:

#@# EM Registration Fri Dec 13 10:55:07 GMT 2019
/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/subjects/PM1/mri

 mri_em_register -rusage 
/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/subjects/PM1/touch/rusage.mri_em_register.dat
 -uns 3 -mask brainmask.mgz nu.mgz 
/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/average/RB_all_2016-05-10.vc700.gca
 transforms/talairach.lta

setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_em_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach.log
reading 
'/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3   using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 6.3 or > 503.7
total sample mean = 78.8 (1011 zeros)

spacing=8, using 2830 sample points, tol=1.00e-05...

register_mri: find_optimal_transform
find_optimal_transform: nsamples 2830, passno 0, spacing 8
Segmentation fault (core dumped)
Linux btupc09 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s PM1 exited with ERRORS at Fri Dec 13 10:55:35 GMT 2019


I’m also sending you the log from the skull striping step, in case the two 
errors might be connected:

#@# Skull Stripping Fri Dec 13 10:23:26 GMT 2019
/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/subjects/PM1/mri

 mri_em_register -rusage 
/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/subjects/PM1/touch/rusage.mri_em_register.skull.dat
 -skull nu.mgz 
/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca
 transforms/talairach_with_skull.lta

aligning to atlas containing skull, setting unknown_nbr_spacing = 5

== Number of threads available to mri_em_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach_with_skull.log
reading 
'/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'...
average std = 22.9   using min determinant for regularization = 52.6
0 singular and 9002 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.7 or > 569.1
total sample mean = 77.6 (1399 zeros)

spacing=8, using 3243 sample points, tol=1.00e-05...

register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=25.1
skull bounding box = (67, 34, 13) --> (199, 162, 201)
using (111, 77, 107) as brain centroid...
mean wm in atlas = 108, using box (95,61,84) --> (127, 92,130) to find MRI wm
before smoothing, mri peak at 106
robust fit to distribution - 107 +- 5.6
after smoothing, mri peak at 106, scaling input intensities by 1.019
scaling channel 0 by 1.01887
initial log_p = -4.775

First Search limited to translation only.

max log p =-4.469154 @ (-9.091, 27.273, 9.091)
max log p =-4.310065 @ (4.545, -4.545, -4.545)
max log p =-4.294819 @ (-2.273, 2.273, -2.273)
max log p =-4.269301 @ (1.136, -1.136, -1.136)
max log p =-4.255560 @ (-0.568, 0.568, 0.568)
max log p =-4.255560 @ (0.000, 0.000, 0.000)
Found translation: (-6.3, 24.4, 1.7): log p = -4.256

Nine parameter search.  iteration 0 nscales = 0 ...

Result so far: scale 1.000: max_log_p=-4.200, old_max_log_p =-4.256 
(thresh=-4.3)
 1.07500   0.0   0.0  -

Re: [Freesurfer] Segmentation fault

[fsbuild]

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 code is exiting..


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Re: [Freesurfer] Segmentation fault

[fsbuild]

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 written somewhere, but I will try and find out if there is a location for it.

When the program exits you could try looking at the end of the system log to 
see if their is any info logged there, e.g.,

$ tail -50 /var/log/syslog

- and look for events that match the timestamp of when the program ran/stopped 
running.

If you can reproduce running a trac* command from the terminal that causes the 
crash, then you could try running that same command with gdb, e.g.,

$ gdb /usr/local/freesurfer/bin/trac-all  -debug -allowcoredump -path 
-c /data/Abeona/648TT/run_648TT_path.txt

 gdb will output some text then at the gdb prompt type run...

(gdb)  run

 then wait for the program to stop and try to get the backtrace with the 
back trace command  

(gdb)  bt  full

 which may yield some more info about the crash .

On Oct 29, 2018, at 16:59, Whitney, Jon  
wrote:External Email - Use 
CautionI got someone to help 
me, and based on what they told me the trac-all.log is where the debug 
information gets stored (I tried using -x +x in my bash command script and it 
only gave me upper level debugging information), so I have attached the 
trac-all.log file.  I also was able to get help from someone who was able 
to save the core dump for when the system crashed, but it is extremely large 
(1.7GB). I can upload the core dump file if that would be helpful.  I 
watched the system resources while the program ran, and I noticed that the 
memory usage only got up to 4% while the CPU usage was 100%, so I don't think 
I'm running out of memory.  We looked at the core dump file, and my linux 
expert friend suggested that it may be a memory overflow error because it 
references memory at 0x000etc.unfortunately, without the 
source code to help us interpret the core dump, I don't think I can provide 
much more in the way of specific information.  Please let me know if 
there's somewhere I can upload the core dump if you want to look at it.Thanks!
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Re: [Freesurfer] Segmentation fault

[fsbuild]

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 binary 
command.  Or if you can find in the output of the trac-all script where it 
runs the binary command that fails, then you could cut and paste that binary 
command line and try running it directly from the terminal.  If you can 
reproduce the error from running the binary command line on the terminal, then 
you could run it in gdb - which might give some more info than just hex output 
if the binary has symbolic info.  Sometimes scripts run other scripts 
before they exec and binaries, so the first level output may not show anything 
useful, but it could be worth a try..

A segfault can be caused by a memory error, but meanwhile I will try to get in 
touch with the developer since the trace we have so far does not contain any 
useful symbolic info. 

On Oct 30, 2018, at 11:02, Whitney, Jon  
wrote:External Email - Use 
CautionAlso, I have located the 
core dump file if that helps.Thanks!On Tue, Oct 30, 2018 at 11:01 AM Whitney, 
Jon  wrote:Hey!  Thanks for your 
help. Looking at the end of the system log:It's a bunch 
of mysterious hex. using gdb on trac-all doesn't work because gdb claims 
it will only work on executable files, not scripts.  However, my 
Linux guru was able to get the backtrace for the crash.which 
is also in inscrutable hex.  He says that the only way to really identify 
the error is by combining data (such as the core dump) with the original code 
to decode this hex data.Thoughts?
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Re: [Freesurfer] Segmentation fault

[Yendiki, Anastasia]

Hi Jon – This log file also has output only from trac-all –path, and not from 
trac-all –prep. I’ll have to see the output from all steps. Thanks!

a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Whitney, Jon" mailto:jon.whit...@ert.com>>
Reply-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

Yes, here is the log file.

Thanks for your help!

 -Jon

On Tue, Oct 30, 2018 at 5:34 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Jon - I suspect that the source of the problem is before the -path step, but 
your trac-all.log only has output from that step. Did you by any chance move 
the original trac-all.log file somewhere else? Typically with every new 
invocation of trac-all the new output is just appended at the end of the log 
file.


a.y


From:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Whitney, Jon mailto:jon.whit...@ert.com>>
Sent: Monday, October 29, 2018 4:59:17 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: Walia, Piyush
Subject: Re: [Freesurfer] Segmentation fault


External Email - Use Caution

I got someone to help me, and based on what they told me the trac-all.log is 
where the debug information gets stored (I tried using -x +x in my bash command 
script and it only gave me upper level debugging information), so I have 
attached the trac-all.log file.  I also was able to get help from someone who 
was able to save the core dump for when the system crashed, but it is extremely 
large (1.7GB). I can upload the core dump file if that would be helpful.  I 
watched the system resources while the program ran, and I noticed that the 
memory usage only got up to 4% while the CPU usage was 100%, so I don't think 
I'm running out of memory.  We looked at the core dump file, and my linux 
expert friend suggested that it may be a memory overflow error because it 
references memory at 0x000etc.

[image.png]
unfortunately, without the source code to help us interpret the core dump, I 
don't think I can provide much more in the way of specific information.  Please 
let me know if there's somewhere I can upload the core dump if you want to look 
at it.

Thanks!

On Mon, Oct 29, 2018 at 1:32 AM fsbuild 
mailto:fsbu...@contbay.com>> wrote:

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 code is exiting.

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--

Jon Whitney
Image Analysis Engineer
ERT | 26801 Miles Rd | Cleveland, OH 44128 | USA
ert.com

<https://www.ert.com/>
[http://signature.ert.com/uc/5ae1cd7003abc93ec2b1d227/img]<http://signature.ert.com/uc/5ae1cd7003abc93ec2b1d227>



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information of ERT that may be confidential, proprietary copyrighted and/or 
legally privileged, and is intended solely for the use of the individual or 
entity named on this message. If you are not the intended recipient, and have 
received this message in error, please immediately return this by e-mail and 
then delete it.
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--

Jon Whitney
Image Analysis Engineer
ERT | 26801 Miles Rd | Cleveland, OH 44128 | USA
ert.com

<https://www.ert.com/>
[http://signature.ert.com/uc/5ae1cd7003abc93ec2b1d227/img]<http://signature.ert.com/uc/5ae1cd7003abc93ec2b1d227>



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information of ERT that may be confidential, proprietary copyrighted and/or 
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Re: [Freesurfer] Segmentation fault

[Whitney, Jon]

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!

-- 
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entity named on this message. If you are not the intended recipient, and 
have received this message in error, please immediately return this by 
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Re: [Freesurfer] segmentation fault

[Greve, Douglas N.,Ph.D.]

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 intersections
Segmentation fault

FreeSurfer version: freesurfer-darwin-macOS-7.1.1.




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[Freesurfer] Segmentation fault: 11

[priya padma]

External Email - Use Caution

Hello Team,

I just installed freesurfer and freeview using the methods mentioned in
https://secure-web.cisco.com/1oeEk1V3fGDlcuYEIm1RFYCYdQcU2m3TJysRGz7NAzZIOMDfxJiOPbas0gR6C45O_k9X6OvLE4pS75bwDoZy4yIzpxK5rduxKwxnHn7m8NEYSw4zXC5joOtwNk5Ms6X54nQoAn7rrCj9BiT1MW3U0nvSPBWGAHn1-KKiJGeORXiIxTTaJU2IhmN_cryZ288yejqNjTtt-OGUhFKw0-g8EuAc_NNBv7FyYimFnE60vT3lXwRS9S8OoUQOq9smu1FATiEsgK1lbDVds_iBqLgQy9QAccg056gs1_IXcIHxwX41K6s2GOsaYfmb4qiLkMLgB/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2F%2FFS7_mac
the installation was successful and after creating the environment the
freeview also opened but whenever I open any volume, freeview crashes and I
get an error saying line 2:  6736 Segmentation fault: 11
$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview
"$@"

I followed the thread
https://secure-web.cisco.com/1Xm7JHZ-l0iAQ6540xdJyuY8nR4ldJU2U31IejPX9O93yncEj0bj1Zlci1unp989Xa1G5UcsaEluZenniTs3pmbfVzbWdlTyRGxygKzrb86U7QdD-UXmQdHNkER0_iq0KmQ_4wz4BHdolR7Lhflv_Rxbki0GzeYFxpyj_cErj7IlEK3dJVVzP9fzpqIzF4tv3uZ9aTOO-VftQSyntsUFB5ytO4PQK0prMhfzK6qoiwvruqin7GEO3_XveaXxgqgHNYMkkZ1IvWRmWhHlIHUPYlPZXOjAN_VUTk0YUgZSBCFd6bEAzZ1UhLOXddXOAOyEQ/https%3A%2F%2Fneurostars.org%2Ft%2Fproblem-installing-freesurfer-in-mac%2F20552%2F2
and tried to move the terminal to the main laptop screen but still I get
the same error. I am unable to open the sample data given along with
freesurfer.

Could you help me with this issue?

-- 
Best Regards
Padma Priya
*AI Developer *

*PhenoMx, Inc.*
*pr...@phenomx.ai  | (+82)10-5405-2685*
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[Freesurfer] Segmentation Fault (Ventura)

[Joann Stewart]

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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 
am using :

 

recon-all -subject 1306_A -i 1306/T1w/T1w_MPR.nii.gz -T2 
1306/T2w/T2w_SPC.nii.gz -T2pial -all -qcache  

 

On the server, when I run this command, it continues until I get to the 
segmentation portion. I have the full output of this command attached to the 
email in a word document titled “Recon-all output on server”. Attached I also 
have a copy of the recon-all.log file.

 

There is another member in my lab who was able to use this command successfully 
with the same files and exact same code. He was using the same server that I 
was on, and we have exactly the same permissions on the server. The only 
difference is that I have updated my mac to Ventura and he has not yet updated 
his mac (he is using macOS Monterey 12.6). 

 

We tried moving my files onto my desktop to see if the recon-all worked there 
as compared to the server. I simply moved the T1w & T2w NIfTI files onto my 
desktop from the server. When I run recon all sourcing from the NIfTI files on 
my desktop rather than the server, it works fine without error. 

 

Therefore, we are wondering if it is an issue with the new Ventura update in 
conjunction with shared network folders. Do you have any suggestions or ideas 
based on the information I have provided?

 
   
   - FreeSurfer version: freesurfer-darwin-macOS-7.3.2-20220804-6354275
   - Platform: MacOS Ventura 13.0

 

Let me know if there is any more information that you need. 

 

Thank you!





Recon-all output on server.docx
Description: MS-Word 2007 document


recon-all.log
Description: Binary data
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[Freesurfer] FreeSurfer Segmentation Fault

[Bartlett, Rob]

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-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
Terminal Output:
Segmentation fault
Syslog Output:
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863337] ThreadIOWorker[390903]: 
segfault at ad0 ip 5613a159eb5d sp 7fb580f68d00 error 4 in 
freeview[5613a0ee8000+bc1000]
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863358] Code: ef c9 f2 0f 5c 14 24 
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 
c9 48 8d 14 96 48 8d 0c 8e  0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863380] ThreadIOWorker[390885]: 
segfault at fe1a641 ip 5613a159eb5d sp 7fb589f7ad00 error 4
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863393] Code: ef c9 f2 0f 5c 14 24 
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 
c9 48 8d 14 96 48 8d 0c 8e  0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863400] traps: 
ThreadIOWorker[390898] general protection fault ip:5613a159ebe0 sp:7fb58376dd00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863410] traps: 
ThreadIOWorker[390890] general protection fault ip:5613a159ebe0 sp:7fb587775d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863450] traps: 
ThreadIOWorker[390901] general protection fault ip:5613a159eb5d sp:7fb581f6ad00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863478] traps: 
ThreadIOWorker[390875] general protection fault ip:5613a159eb5d sp:7fb58ef84d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863499] traps: 
ThreadIOWorker[390905] general protection fault ip:5613a159eb5d sp:7fb57ff66d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863542] traps: 
ThreadIOWorker[390884] general protection fault ip:5613a159eb5d sp:7fb58a77bd00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863566] traps: 
ThreadIOWorker[390886] general protection fault ip:5613a159ebe0 sp:7fb589779d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863579] traps: 
ThreadIOWorker[390881] general protection fault ip:5613a159eb5d sp:7fb58bf7ed00 
error:0


Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
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[Freesurfer] Segmentation Fault Question

[Allie Rosen]

Hi,

I am accessing my subject directory on a network attached drive. When I run
mri glmfit it segfaults. However, it works if the subject directory is on my
own computer. Do you have any way to do this with the subject directory on
the network drive?

Below is a sample output.

Thanks,
Allie

Caduceus:~/ammonis/fsSubjects/subjects_archive> mri_glmfit --y
lh.smoothed.thickness.6.mgz --fsgd GDF1.txt doss --glmdir
lh.smoothed.thickness.6.glmdir --surf fsaverage lh --C ContrastAge.txt
gdfReadHeader: reading GDF1.txt
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 40.0625
1 PCS 9.875
2 Neuro 17.8125
3 Extro 30
4 Open 28.875
5 Agree 32.4375
6 Consc 34.625
Class Means of each Continuous Variable
1 Control 40.0625   9.8750  17.8125  30.  28.8750  32.4375  34.6250
INFO: gd2mtx_method is doss
Reading source surface
/media/AMMONIS/fsSubjects/subjects_archive/fsaverage/surf/lh.white
reading group avg surface area 822 cm^2 from file
Reading in average area
/media/AMMONIS/fsSubjects/subjects_archive/fsaverage/surf/lh.white.avg.area.mgh
Number of vertices 163842
Number of faces327680
Total area 65416.648438
AvgVtxArea   0.399267
AvgVtxDist   0.721953
StdVtxDist   0.195470

$Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $
cwd /media/AMMONIS/fsSubjects/subjects_archive
cmdline mri_glmfit --y lh.smoothed.thickness.6.mgz --fsgd GDF1.txt doss
--glmdir lh.smoothed.thickness.6.glmdir --surf fsaverage lh --C
ContrastAge.txt
sysname  Linux
hostname Caduceus
machine  x86_64
user arosen
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/media/AMMONIS/fsSubjects/subjects_archive/lh.smoothed.thickness.6.mgz
logyflag 0
usedti  0
FSGD GDF1.txt
glmdir lh.smoothed.thickness.6.glmdir
IllCondOK 0
DoFFx 0
Creating output directory lh.smoothed.thickness.6.glmdir
Segmentation fault
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Re: [Freesurfer] Segmentation Fault

[Bruce Fischl]

Hi Allie,

what do you mean by "trying to assemble my subjects into a single surface 
space"?

thanks
Bruce
On Tue, 12 Apr 2011, Allie Rosen wrote:

> Hi All,
>
> Upon trying to assembly my subjects into a single surface space, I got the
> following error:
>
> *ERROR: number of vertices in
> /media/AMMONIS/fsSubjects/AR_normals/C42/surf/lh.thickness does not match
> surface (142271,140585)
> ERROR: reading curvature file
> *
> I then tried to perform recon-all -make all, but got this error:
>
> *ERROR: mpr2mni305 failed, see transforms/talairach_avi.log*
>
> In the .log, I got this:
>
> *-7.5000   22.5000   15. 2793.2134   1Segmentation fault
> ERROR: 'imgreg_4dfp /usr/rapps/freesurfer/average/711-2C_as_mni_average_305
> /usr/rapps/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11
> none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=139
> ERROR: mpr2mni305 execution aborted*
>
> Which is a segmentation fault. Can anyone help me fix this?
>
> Thanks,
> Allie Rosen, MSc Candidate
> Graduate Student, Department of Neurosurgery
> Toronto Western Hospital 14-327
> 399 Bathurst St.
> University of Toronto
>
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Re: [Freesurfer] Segmentation Fault

[Allie Rosen]

Hi Bruce,

I mean the "mris_preproc" step.

Thanks,
Allie

(forgot to reply to all)

On Tue, Apr 12, 2011 at 11:35 AM, Bruce Fischl
wrote:

> Hi Allie,
>
> what do you mean by "trying to assemble my subjects into a single surface
> space"?
>
> thanks
> Bruce
>
> On Tue, 12 Apr 2011, Allie Rosen wrote:
>
>  Hi All,
>>
>> Upon trying to assembly my subjects into a single surface space, I got the
>> following error:
>>
>> *ERROR: number of vertices in
>> /media/AMMONIS/fsSubjects/AR_normals/C42/surf/lh.thickness does not match
>> surface (142271,140585)
>> ERROR: reading curvature file
>> *
>> I then tried to perform recon-all -make all, but got this error:
>>
>> *ERROR: mpr2mni305 failed, see transforms/talairach_avi.log*
>>
>> In the .log, I got this:
>>
>> *-7.5000   22.5000   15. 2793.2134   1Segmentation fault
>> ERROR: 'imgreg_4dfp
>> /usr/rapps/freesurfer/average/711-2C_as_mni_average_305
>> /usr/rapps/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11
>> none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=139
>> ERROR: mpr2mni305 execution aborted*
>>
>> Which is a segmentation fault. Can anyone help me fix this?
>>
>> Thanks,
>> Allie Rosen, MSc Candidate
>> Graduate Student, Department of Neurosurgery
>> Toronto Western Hospital 14-327
>> 399 Bathurst St.
>> University of Toronto
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Segmentation Fault

[Douglas N Greve]

It usually means that you have a subject whose surfaces are 
out-of-synch. This usually happens when you've made edits, launched 
recon-all, but then then recon-all does not finish for some reason. 
Check the time stamps on that subject or try running recon-all -make all 
-s subject

doug

btw, a "Segmentation Fault" is a computer term and does not have 
anything to do with brain segmentation.

Allie Rosen wrote:
> Hi Bruce,
>
> I mean the "mris_preproc" step.
>
> Thanks,
> Allie
>
> (forgot to reply to all)
>
> On Tue, Apr 12, 2011 at 11:35 AM, Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Allie,
>
> what do you mean by "trying to assemble my subjects into a single
> surface space"?
>
> thanks
> Bruce
>
> On Tue, 12 Apr 2011, Allie Rosen wrote:
>
> Hi All,
>
> Upon trying to assembly my subjects into a single surface
> space, I got the
> following error:
>
> *ERROR: number of vertices in
> /media/AMMONIS/fsSubjects/AR_normals/C42/surf/lh.thickness
> does not match
> surface (142271,140585)
> ERROR: reading curvature file
> *
> I then tried to perform recon-all -make all, but got this error:
>
> *ERROR: mpr2mni305 failed, see transforms/talairach_avi.log*
>
> In the .log, I got this:
>
> *-7.5000   22.5000   15. 2793.2134   1Segmentation fault
> ERROR: 'imgreg_4dfp
> /usr/rapps/freesurfer/average/711-2C_as_mni_average_305
> /usr/rapps/freesurfer/average/711-2B_as_mni_average_305_mask
> talsrcimg_g11
> none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed!
> status=139
> ERROR: mpr2mni305 execution aborted*
>
> Which is a segmentation fault. Can anyone help me fix this?
>
> Thanks,
> Allie Rosen, MSc Candidate
> Graduate Student, Department of Neurosurgery
> Toronto Western Hospital 14-327
> 399 Bathurst St.
> University of Toronto
>
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
> 
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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Re: [Freesurfer] Segmentation Fault

[Allie Rosen]

Hi Doug,

I read this on a previous email, and I already tried to run recon-all -make
all. I included it in my original email, but I'll copy it here:


"I then tried to perform recon-all -make all, but got this error:

*ERROR: mpr2mni305 failed, see transforms/talairach_avi.log*

In the .log, I got this:

*-7.5000   22.5000   15. 2793.2134   1Segmentation fault
ERROR: 'imgreg_4dfp /usr/rapps/freesurfer/average/711-2C_as_mni_average_305
/usr/rapps/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11
none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=139
ERROR: mpr2mni305 execution aborted*"

Thanks,
Allie

On Tue, Apr 12, 2011 at 1:35 PM, Douglas N Greve
wrote:

> It usually means that you have a subject whose surfaces are out-of-synch.
> This usually happens when you've made edits, launched recon-all, but then
> then recon-all does not finish for some reason. Check the time stamps on
> that subject or try running recon-all -make all -s subject
>
> doug
>
> btw, a "Segmentation Fault" is a computer term and does not have anything
> to do with brain segmentation.
>
> Allie Rosen wrote:
>
>> Hi Bruce,
>>
>> I mean the "mris_preproc" step.
>>
>> Thanks,
>> Allie
>>
>> (forgot to reply to all)
>>
>> On Tue, Apr 12, 2011 at 11:35 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu > wrote:
>>
>>Hi Allie,
>>
>>what do you mean by "trying to assemble my subjects into a single
>>surface space"?
>>
>>thanks
>>Bruce
>>
>>On Tue, 12 Apr 2011, Allie Rosen wrote:
>>
>>Hi All,
>>
>>Upon trying to assembly my subjects into a single surface
>>space, I got the
>>following error:
>>
>>*ERROR: number of vertices in
>>/media/AMMONIS/fsSubjects/AR_normals/C42/surf/lh.thickness
>>does not match
>>surface (142271,140585)
>>ERROR: reading curvature file
>>*
>>I then tried to perform recon-all -make all, but got this error:
>>
>>*ERROR: mpr2mni305 failed, see transforms/talairach_avi.log*
>>
>>In the .log, I got this:
>>
>>*-7.5000   22.5000   15. 2793.2134   1Segmentation fault
>>ERROR: 'imgreg_4dfp
>>/usr/rapps/freesurfer/average/711-2C_as_mni_average_305
>>/usr/rapps/freesurfer/average/711-2B_as_mni_average_305_mask
>>talsrcimg_g11
>>none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed!
>>status=139
>>ERROR: mpr2mni305 execution aborted*
>>
>>Which is a segmentation fault. Can anyone help me fix this?
>>
>>Thanks,
>>Allie Rosen, MSc Candidate
>>Graduate Student, Department of Neurosurgery
>>Toronto Western Hospital 14-327
>>399 Bathurst St.
>>University of Toronto
>>
>>
>>
>>The information in this e-mail is intended only for the person to
>>whom it is
>>addressed. If you believe this e-mail was sent to you in error and
>>the e-mail
>>contains patient information, please contact the Partners
>>Compliance HelpLine at
>>http://www.partners.org/complianceline . If the e-mail was sent to
>>you in error
>>but does not contain patient information, please contact the
>>sender and properly
>>dispose of the e-mail.
>>
>>
>> 
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
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Re: [Freesurfer] Segmentation Fault

[Douglas N Greve]

Hi Chinduri, is this still happening? I can't replicate.

doug

Chindhuri Selvadurai wrote:
> Hi all,
>
> We are trying to run individual analyses on several subjects, and we keep
> getting a 'Segmentation Fault.'  We have run other subjects with the same
> command a while ago, and the command worked fine at that time.  Do you
> have any idea what would be causing this error?  The output is included
> below:
>
> Command: selxavg3-sess -analysis mandyrh3 -fwhm -s PBMCT15
> Subjects Dir: /cluster/manoach/milton/subjects
> FreeSurfer v. Stable 5
>
>
> Session: /autofs/cluster/manoach/milton/subjects/PBMCT15 
> Fri May 13 12:21:58 EDT 2011
>   Run: 012 
> Fri May 13 12:21:58 EDT 2011
> Update not needed
> Fri May 13 12:21:58 EDT 2011
> register-sess completed
> PBMCT15 MC -
> mc-sess -fstem f -fmcstem fmcpr -s PBMCT15 -d
> /autofs/cluster/manoach/milton/subjects -fsd bold -rlf task -per-run
> -nolog -update
> Logfile is /dev/null
> ---
> /autofs/cluster/manoach/milton/subjects/PBMCT15
> RunList: 012
>   --- ** ---
>   --- Motion Correcting Run 012 ---
>   --- ** ---
> sess = PBMCT15
> Fri May 13 12:21:58 EDT 2011
> mc-afni2 --i 012/f.nii --t 012/template.nii --o 012/fmcpr.nii.gz --mcdat
> 012/fmcpr.mcdat
> /autofs/cluster/manoach/milton/subjects/PBMCT15/bold
> mri_info --nframes --o /tmp/mriinfo.3377 012/template.nii
> log file is 012/fmcpr.nii.gz.mclog
> mcdat file is 012/fmcpr.mcdat
> tmp dir is 012/tmp.mc-afni2.3377
> #@# 
> /autofs/cluster/manoach/milton/subjects/PBMCT15/bold
> mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip
> 0 --ndrop 0 -odt float
> mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip
> 0 --ndrop 0 -odt float
> nskip = 0
> ndrop = 0
> $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
> reading from 012/template.nii...
> TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.998297, -0.0395807, 0.0428535)
> j_ras = (0.0411249, -0.998513, 0.0357732)
> k_ras = (0.0413739, 0.0374746, 0.998441)
> changing data type from short to float (noscale = 0)...
> writing to 012/tmp.mc-afni2.3377/tempvol.nii.gz...
> #@# 
> /autofs/cluster/manoach/milton/subjects/PBMCT15/bold
> mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float
> mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float
> Segmentation fault
>
>
> Thanks!
>
> Best,
>
> Chindhuri Selvadurai
>
> Psychiatric Neuroimaging, Manoach Lab
> Martinos Center for Biomedical Imaging, MGH
> Phone: (617)726-0307
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>   

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Segmentation Fault

[Marcus Belke]

Hi,
I am experiencing the same problem. When I try to do the motion 
correction on fmri data it stops with a segmentation fault in 
mri_convert. This used to work until this week.

Best

Marcus

On 13.05.2011 12:48, Chindhuri Selvadurai wrote:
> Hi all,
>
> We are trying to run individual analyses on several subjects, and we keep
> getting a 'Segmentation Fault.'  We have run other subjects with the same
> command a while ago, and the command worked fine at that time.  Do you
> have any idea what would be causing this error?  The output is included
> below:
>
> Command: selxavg3-sess -analysis mandyrh3 -fwhm -s PBMCT15
> Subjects Dir: /cluster/manoach/milton/subjects
> FreeSurfer v. Stable 5
>
>
> Session: /autofs/cluster/manoach/milton/subjects/PBMCT15 
> Fri May 13 12:21:58 EDT 2011
>Run: 012 
> Fri May 13 12:21:58 EDT 2011
> Update not needed
> Fri May 13 12:21:58 EDT 2011
> register-sess completed
> PBMCT15 MC -
> mc-sess -fstem f -fmcstem fmcpr -s PBMCT15 -d
> /autofs/cluster/manoach/milton/subjects -fsd bold -rlf task -per-run
> -nolog -update
> Logfile is /dev/null
> ---
> /autofs/cluster/manoach/milton/subjects/PBMCT15
> RunList: 012
>--- ** ---
>--- Motion Correcting Run 012 ---
>--- ** ---
> sess = PBMCT15
> Fri May 13 12:21:58 EDT 2011
> mc-afni2 --i 012/f.nii --t 012/template.nii --o 012/fmcpr.nii.gz --mcdat
> 012/fmcpr.mcdat
> /autofs/cluster/manoach/milton/subjects/PBMCT15/bold
> mri_info --nframes --o /tmp/mriinfo.3377 012/template.nii
> log file is 012/fmcpr.nii.gz.mclog
> mcdat file is 012/fmcpr.mcdat
> tmp dir is 012/tmp.mc-afni2.3377
> #@# 
> /autofs/cluster/manoach/milton/subjects/PBMCT15/bold
> mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip
> 0 --ndrop 0 -odt float
> mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip
> 0 --ndrop 0 -odt float
> nskip = 0
> ndrop = 0
> $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
> reading from 012/template.nii...
> TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.998297, -0.0395807, 0.0428535)
> j_ras = (0.0411249, -0.998513, 0.0357732)
> k_ras = (0.0413739, 0.0374746, 0.998441)
> changing data type from short to float (noscale = 0)...
> writing to 012/tmp.mc-afni2.3377/tempvol.nii.gz...
> #@# 
> /autofs/cluster/manoach/milton/subjects/PBMCT15/bold
> mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float
> mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float
> Segmentation fault
>
>
> Thanks!
>
> Best,
>
> Chindhuri Selvadurai
>
> Psychiatric Neuroimaging, Manoach Lab
> Martinos Center for Biomedical Imaging, MGH
> Phone: (617)726-0307
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] Segmentation Fault

[Douglas N Greve]

OK, I've verified and fixed this. It will be in dev in the next build 
(probably overnight). Are you using dev?
doug

Marcus Belke wrote:
> Hi,
> I am experiencing the same problem. When I try to do the motion 
> correction on fmri data it stops with a segmentation fault in 
> mri_convert. This used to work until this week.
>
> Best
>
> Marcus
>
> On 13.05.2011 12:48, Chindhuri Selvadurai wrote:
>   
>> Hi all,
>>
>> We are trying to run individual analyses on several subjects, and we keep
>> getting a 'Segmentation Fault.'  We have run other subjects with the same
>> command a while ago, and the command worked fine at that time.  Do you
>> have any idea what would be causing this error?  The output is included
>> below:
>>
>> Command: selxavg3-sess -analysis mandyrh3 -fwhm -s PBMCT15
>> Subjects Dir: /cluster/manoach/milton/subjects
>> FreeSurfer v. Stable 5
>>
>>
>> Session: /autofs/cluster/manoach/milton/subjects/PBMCT15 
>> Fri May 13 12:21:58 EDT 2011
>>Run: 012 
>> Fri May 13 12:21:58 EDT 2011
>> Update not needed
>> Fri May 13 12:21:58 EDT 2011
>> register-sess completed
>> PBMCT15 MC -
>> mc-sess -fstem f -fmcstem fmcpr -s PBMCT15 -d
>> /autofs/cluster/manoach/milton/subjects -fsd bold -rlf task -per-run
>> -nolog -update
>> Logfile is /dev/null
>> ---
>> /autofs/cluster/manoach/milton/subjects/PBMCT15
>> RunList: 012
>>--- ** ---
>>--- Motion Correcting Run 012 ---
>>--- ** ---
>> sess = PBMCT15
>> Fri May 13 12:21:58 EDT 2011
>> mc-afni2 --i 012/f.nii --t 012/template.nii --o 012/fmcpr.nii.gz --mcdat
>> 012/fmcpr.mcdat
>> /autofs/cluster/manoach/milton/subjects/PBMCT15/bold
>> mri_info --nframes --o /tmp/mriinfo.3377 012/template.nii
>> log file is 012/fmcpr.nii.gz.mclog
>> mcdat file is 012/fmcpr.mcdat
>> tmp dir is 012/tmp.mc-afni2.3377
>> #@# 
>> /autofs/cluster/manoach/milton/subjects/PBMCT15/bold
>> mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip
>> 0 --ndrop 0 -odt float
>> mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip
>> 0 --ndrop 0 -odt float
>> nskip = 0
>> ndrop = 0
>> $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
>> reading from 012/template.nii...
>> TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.998297, -0.0395807, 0.0428535)
>> j_ras = (0.0411249, -0.998513, 0.0357732)
>> k_ras = (0.0413739, 0.0374746, 0.998441)
>> changing data type from short to float (noscale = 0)...
>> writing to 012/tmp.mc-afni2.3377/tempvol.nii.gz...
>> #@# 
>> /autofs/cluster/manoach/milton/subjects/PBMCT15/bold
>> mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float
>> mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float
>> Segmentation fault
>>
>>
>> Thanks!
>>
>> Best,
>>
>> Chindhuri Selvadurai
>>
>> Psychiatric Neuroimaging, Manoach Lab
>> Martinos Center for Biomedical Imaging, MGH
>> Phone: (617)726-0307
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>   

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Segmentation Fault

[Chindhuri Selvadurai]

Not happening anymore, thanks!

> Hi Chinduri, is this still happening? I can't replicate.
>
> doug
>
> Chindhuri Selvadurai wrote:
>> Hi all,
>>
>> We are trying to run individual analyses on several subjects, and we
>> keep
>> getting a 'Segmentation Fault.'  We have run other subjects with the
>> same
>> command a while ago, and the command worked fine at that time.  Do you
>> have any idea what would be causing this error?  The output is included
>> below:
>>
>> Command: selxavg3-sess -analysis mandyrh3 -fwhm -s PBMCT15
>> Subjects Dir: /cluster/manoach/milton/subjects
>> FreeSurfer v. Stable 5
>>
>>
>> Session: /autofs/cluster/manoach/milton/subjects/PBMCT15
>> 
>> Fri May 13 12:21:58 EDT 2011
>>   Run: 012 
>> Fri May 13 12:21:58 EDT 2011
>> Update not needed
>> Fri May 13 12:21:58 EDT 2011
>> register-sess completed
>> PBMCT15 MC -
>> mc-sess -fstem f -fmcstem fmcpr -s PBMCT15 -d
>> /autofs/cluster/manoach/milton/subjects -fsd bold -rlf task -per-run
>> -nolog -update
>> Logfile is /dev/null
>> ---
>> /autofs/cluster/manoach/milton/subjects/PBMCT15
>> RunList: 012
>>   --- ** ---
>>   --- Motion Correcting Run 012 ---
>>   --- ** ---
>> sess = PBMCT15
>> Fri May 13 12:21:58 EDT 2011
>> mc-afni2 --i 012/f.nii --t 012/template.nii --o 012/fmcpr.nii.gz --mcdat
>> 012/fmcpr.mcdat
>> /autofs/cluster/manoach/milton/subjects/PBMCT15/bold
>> mri_info --nframes --o /tmp/mriinfo.3377 012/template.nii
>> log file is 012/fmcpr.nii.gz.mclog
>> mcdat file is 012/fmcpr.mcdat
>> tmp dir is 012/tmp.mc-afni2.3377
>> #@# 
>> /autofs/cluster/manoach/milton/subjects/PBMCT15/bold
>> mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz
>> --nskip
>> 0 --ndrop 0 -odt float
>> mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz
>> --nskip
>> 0 --ndrop 0 -odt float
>> nskip = 0
>> ndrop = 0
>> $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
>> reading from 012/template.nii...
>> TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.998297, -0.0395807, 0.0428535)
>> j_ras = (0.0411249, -0.998513, 0.0357732)
>> k_ras = (0.0413739, 0.0374746, 0.998441)
>> changing data type from short to float (noscale = 0)...
>> writing to 012/tmp.mc-afni2.3377/tempvol.nii.gz...
>> #@# 
>> /autofs/cluster/manoach/milton/subjects/PBMCT15/bold
>> mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float
>> mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float
>> Segmentation fault
>>
>>
>> Thanks!
>>
>> Best,
>>
>> Chindhuri Selvadurai
>>
>> Psychiatric Neuroimaging, Manoach Lab
>> Martinos Center for Biomedical Imaging, MGH
>> Phone: (617)726-0307
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>


Best,

Chindhuri Selvadurai

Psychiatric Neuroimaging, Manoach Lab
Martinos Center for Biomedical Imaging, MGH
Phone: (617)726-0307
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Re: [Freesurfer] segmentation fault

[Nick Schmansky]

Greg,

How much memory does the system have available at the time mris_volmask
is run?  It will consume about 1GB within a minute or two of starting,
and I know that the underlying code (VTK library) doesnt handle memory
alloc failures very gracefully.

If running this stage (-cortribbon) fails consistently on a subject,
perhaps i can supply you with a debug-built version of mris_volmask so
that it generates a core file with info on exactly where this is
segfaulting.  We've never been able to replicate this problem locally.

Nick

On Wed, 2009-05-13 at 14:42 -0500, Kirk Gregory R. wrote:
> Hi all,
>  
> I got in the recon-all log
>  
> #...@# Cortical ribbon mask Tue May 12 17:56:52 CDT 2009
> /home/gkirk/freesurfer/freesurfer/subjects/P21/mri
>  mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 
> 41 --label_right_ribbon 42 --save_ribbon --save_distance P21 
> SUBJECTS_DIR is /home/gkirk/freesurfer/freesurfer/subjects
> Segmentation fault
> Linux debian01 2.6.26-1-amd64 #1 SMP Mon Dec 15 17:25:36 UTC 2008 x86_64 
> GNU/Linux
> recon-all exited with ERRORS at Tue May 12 18:10:33 CDT 2009
>  
> running
> build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0
> Linux debian01 2.6.26-1-amd64 #1 SMP Mon Dec 15 17:25:36 UTC 2008 x86_64 
> GNU/Linux
>  
> 
> i have gotten 4 of these out of 21 ADNI data sets, I saw Nurunisa at Barry 
> Kosofsky's site reported
> this also and Nick ask here to send the data set. 11 Nov 2008,
>  
> got any info on this one ?, i am guessing it is a data quality issue that is 
> breaking something
> in an uncontrolled way.
>  
> thanks
>  
> Greg.
> 
> ___
> Freesurfer mailing list
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> 
> 

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RE: [Freesurfer] segmentation fault

[Kirk Gregory R.]

Nick,
 
I have 8 Gig of mem 2 quad cores, but I have been running 6 or more freesurfer 
jobs concurrently, ill
run them by themselves and see if it persists and let you know.
 
thankx
 
G.



From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Nick Schmansky
Sent: Wed 5/13/2009 3:39 PM
To: Kirk Gregory R.
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] segmentation fault



Greg,

How much memory does the system have available at the time mris_volmask
is run?  It will consume about 1GB within a minute or two of starting,
and I know that the underlying code (VTK library) doesnt handle memory
alloc failures very gracefully.

If running this stage (-cortribbon) fails consistently on a subject,
perhaps i can supply you with a debug-built version of mris_volmask so
that it generates a core file with info on exactly where this is
segfaulting.  We've never been able to replicate this problem locally.

Nick

On Wed, 2009-05-13 at 14:42 -0500, Kirk Gregory R. wrote:
> Hi all,
> 
> I got in the recon-all log
> 
> #...@# Cortical ribbon mask Tue May 12 17:56:52 CDT 2009
> /home/gkirk/freesurfer/freesurfer/subjects/P21/mri
>  mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 
> 41 --label_right_ribbon 42 --save_ribbon --save_distance P21
> SUBJECTS_DIR is /home/gkirk/freesurfer/freesurfer/subjects
> Segmentation fault
> Linux debian01 2.6.26-1-amd64 #1 SMP Mon Dec 15 17:25:36 UTC 2008 x86_64 
> GNU/Linux
> recon-all exited with ERRORS at Tue May 12 18:10:33 CDT 2009
> 
> running
> build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0
> Linux debian01 2.6.26-1-amd64 #1 SMP Mon Dec 15 17:25:36 UTC 2008 x86_64 
> GNU/Linux
> 
>
> i have gotten 4 of these out of 21 ADNI data sets, I saw Nurunisa at Barry 
> Kosofsky's site reported
> this also and Nick ask here to send the data set. 11 Nov 2008,
> 
> got any info on this one ?, i am guessing it is a data quality issue that is 
> breaking something
> in an uncontrolled way.
> 
> thanks
> 
> Greg.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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Re: [Freesurfer] Segmentation fault

[Pedro Paulo de Magalhães Oliveira Junior]

I think you need to send more info about where it crashed
---
Pedro Paulo de M. Oliveira Junior




2009/8/3 Ritobrato Datta 

> Hello All,
>
> I got this error when I ran recon-all -all. I changed machines and the same
> dataset went all the way through without any errors. I ran another dataset
> with the machine "taxi" and it ran fine.
>
> Any suggestions will be helpful.
>
> _
> SUBJECTS_DIR is /jet/kadivar/freesurfer
> Segmentation fault
> Linux taxi.penn.edu 2.8.10-128.1.1.e5 #1 SMP Thu May 7 10:35:59 EDT 2009
> x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all exited with ERRORS at Sat Aug  1 06:20:17 EDT 2009
>
> _
>
> Thanks
>
> Ri
>
> Ritobrato Datta, Ph.D.
> Post Doctoral Fellow
> Department of Neurology
> Center for Functional Neuroimaging
> University of Pennsylvania School of Medicine
> 3rd Floor Gates Building
> 3400 Spruce St.
> Philadelphia
> Pa 19104
>
>
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Re: [Freesurfer] Segmentation fault ...

[Nick Schmansky]

a memory leak in mris_volmask was fixed in v4.5.  this leak is very
likely the source of the segfault you are seeing.  either upgrade to
v4.5, or you can get a fixed mris_volmask.bin here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc

copy it to your $FREESURFER_HOME/bin dir.

nick



On Fri, 2009-10-16 at 12:42 +0200, Erick Jorge Canales wrote:
> Dear experts,
> 
> The recon-all process of some of my subjects (15 from 100) exited with
> ERRORS ...
> 
> I got in the recon-all file of one of them the following report:
> 
> ...
> 
> Reporting on  49 segmentations
> #
> #...@# Cortical ribbon mask Sat Aug 29 13:09:43 CEST 2009
> /mnt/HDD1/FreeSurfer_Cortical/Results/Prueba/Cont_FreeSurf_BMJGR19839SC/mri
> 
> mris_volmask --label_left_white 2 --label_left_ribbon 3
> --label_right_white 41 --label_right_ribbon 42 --save_ribbon
> --save_distance Cont_FreeSurf_BMJGR19839SC 
> 
> SUBJECTS_DIR is /mnt/HDD1/FreeSurfer_Cortical/Results/Prueba
> Segmentation fault
> Linux uifsl5 2.6.26-1-amd64 #1 SMP Thu Oct 9 14:16:53 UTC 2008 x86_64
> GNU/Linux
> 
> recon-all exited with ERRORS at Sat Aug 29 13:19:32 CEST 2009
> 
> ...
> 
> Is there any way to fix this problem?
> 
> My computer have 8 cores and 16 Gb of RAM, in general I have been
> running 6 recon-all jobs concurrently. I'm  running this version:
> freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0
> 
> Many thanks in advance,
> 
> Regards,
> 
> Erick
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Re: [Freesurfer] Segmentation fault?

[Bruce Fischl]

Hi Raghav,

how much RAM do you have in this machine? Have you successfully run other 
recons?

cheers
Bruce
On Sun, 7 Feb 2010, Raghav Puranmalka wrote:

> Hi all,
>
> I am running recon-all as follows:
>
> recon-all -subjid subj1 -all
>
> and (after about 4 hours of running,) get this error:
>
> 0516: dt=0.00, rms=0.507 (0.000%), neg=0, invalid=766
> Segmentation fault
> ERROR: mri_ca_register with non-zero status 139
> but continuing despite the error
> #--
> #...@# CA Reg Inv Sat Feb  6 02:56:03 EST 2010
> /usr/local/freesurfer/subjects/be496/mri
>
>  mri_ca_register -invert-and-save transforms/talairach.m3z
>
> Loading, Inverting, Saving, Exiting ...
> Reading transforms/talairach.m3z
> ERROR: cannot find or read transforms/talairach.m3z
> ERROR: mri_ca_register with non-zero status 0
>
> It seems that perhaps this is because it cannot find
> "transforms/talairach.m3z" - indeed, this file doesn't exist. But should
> this be something generated by recon-all? Should I be running recon-all
> differently?
>
> Thanks for your help,
>
> Raghav
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>
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Re: [Freesurfer] Segmentation fault

[Bruce Fischl]

Hi Teddy,

we need more info than this. Can you send us the recon-all.log and the 
output of bugr.

cheers
Bruce


On Mon, 26 Apr 2010, De La Llave Teddy wrote:

> Hi all,
>
> I am running recon-all as follows:
>
> recon-all -subjid subjectTest -all
>
> and get this error:
>
> Segmentation fault
> ERROR: mri_ca_register with non-zero status 139
>
> I can't continue the rest of the process because the file
> talairach.m3z not exist.
>
> I saw that others have the same problem but there are no solutions?
>
> freesurfer runs on the virtualbox available in the website. It run
> with 1,4Go of RAM.
>
>
> Thanks for your help,
>
>
> Teddy
>
>
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Re: [Freesurfer] segmentation fault

[Nick Schmansky]

Cameron,

I am able to replicate this segfault, and we are working on solution.
It looks to be a bug in the code, and not something to do with the
subject.  Hopefully, a fix will be forthcoming.

Nick

On Tue, 2007-01-16 at 11:23 -0500, Cameron Ellis wrote:
> Hi,
> I attached a text file of the reconall log for a subject which lists a
> segmentation fault that I have received. I have corrected the talairach
> transform for this subject, checked the inorm and skull strip and continue
> to receive this error. There are some minor bumps on the inflated surface
> that correspond to some locations in the wm.mgz where the wm extends very
> slightly beyond the pial surface. How can I tell if this is leading to the
> segmentation fault and if it is worth correcting? Can I tell from the
> error message or do i just have to correct this and rerun recon2 and 3? I
> also included a tiff of lh.inflated and one of a defect in the wm.mgz that
> can be seen on the surface. Any advice is greatly appreciated!
> Thanks,
> Cameron
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Re: [Freesurfer] Segmentation fault

[Nick Schmansky]

Nurunisa,

Can you send me that subject data via the file drop?

https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Nick


On Tue, 2008-11-11 at 10:24 -0500, Nurunisa Neyzi wrote:
> Hi I am getting the following error while running auto-recon2.
> 
> ...
> 
> Reporting on  49 segmentations
> #
> [EMAIL PROTECTED] Cortical ribbon mask Tue Nov 11 01:32:03 EST 2008
> /localA/nneyzi/MLS2/PedBirnPipeline_20081103_014127/mri
> 
>  mris_volmask --label_left_white 2 --label_left_ribbon 3
> --label_right_white 41 --
> label_right_ribbon 42 --save_ribbon --save_distance
> PedBirnPipeline_20081103_01412
> 7
> 
> SUBJECTS_DIR is /localA/nneyzi/MLS2
> Segmentation fault
> Linux ped-birn.med.cornell.edu 2.6.18-53.1.13.el5xen #1 SMP Mon Feb 11
> 13:41:50 ES
> T 2008 x86_64 x86_64 x86_64 GNU/Linux
> 
> recon-all exited with ERRORS at Tue Nov 11 01:45:44 EST 2008
> 
> What does it mean?
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> 

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[Freesurfer] Segmentation fault - mris_make_surfaces

[Adrian Williams]

Dear all

Came across a segmentation fault while running recon-all, specifically
during mris_make_surfaces... Output pasted below...

Any ideas/help greatly appreciated!

Adrian.
-- 
Adrian L. Williams, PhD
Centre for Cognition & Neuroimaging
Brunel University
Uxbridge
Middlesex
UB8 3PH


#
#...@# Make Final Surf rh Sun Jan 11 09:11:39 GMT 2009
/Volumes/DataDisk/freesurf/adrian/scripts
\n mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs adrian rh \n
not using aparc to prevent surfaces crossing the midline
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.99.2.5 2008/08/21 22:48:22 nicks Exp $
$Id: mrisurf.c,v 1.557.2.15 2008/07/30 17:54:19 greve Exp $
reading volume /Volumes/DataDisk/freesurf/adrian/mri/filled.mgz...
reading volume /Volumes/DataDisk/freesurf/adrian/mri/brain.finalsurfs.mgz...
reading volume /Volumes/DataDisk/freesurf/adrian/mri/wm.mgz...
19879 bright wm thresholded.
4 bright non-wm voxels segmented.
reading original surface position from
/Volumes/DataDisk/freesurf/adrian/surf/rh.orig...
computing class statistics...
border white:277588 voxels (1.65%)
border gray  287750 voxels (1.72%)
WM (103.0): 103.2 +- 5.6 [70.0 --> 110.0]
GM (88.0) : 86.5 +- 9.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 75.9 (was 70)
setting MAX_BORDER_WHITE to 111.6 (was 105)
setting MIN_BORDER_WHITE to 85.0 (was 85)
setting MAX_CSF to 66.8 (was 40)
setting MAX_GRAY to 100.4 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 80.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 57.7 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.21 (0.02-->6.25) (max @ vno 57593 --> 140123)
face area 0.28 +- 0.12 (0.00-->4.95)
mean absolute distance = 0.84 +- 1.11
3662 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
smoothing contralateral hemisphere...
intensity peaks found at WM=106,GM=85
using class modes intead of means
mean inside = 100.7, mean outside = 89.6
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=92.7, 106 (106) missing vertices, mean dist 0.2 [0.8
(%36.9)->0.8 (%63.1))]
%59 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=ALW-A, nav=4, nbrs=2, l_repulse=5.000,
l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50

vertex spacing 0.90 +- 0.24 (0.10-->7.73) (max @ vno 57593 --> 140123)
face area 0.28 +- 0.12 (0.00-->4.09)
vertex spacing 0.91 +- 0.25 (0.08-->8.87) (max @ vno 57593 --> 140123)
face area 0.28 +- 0.13 (0.00-->4.04)
smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.06-->8.92) (max @ vno 57593 --> 140123)
face area 0.28 +- 0.13 (0.00-->4.04)
mean absolute distance = 0.46 +- 0.83
3512 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0., sse=3631140.5, rms=6.62
001: dt: 0.5000, sse=4303983.5, rms=4.71
002: dt: 0.5000, sse=4324421.5, rms=3.47
003: dt: 0.5000, sse=4337002.0, rms=2.68
004: dt: 0.5000, sse=4291947.5, rms=2.21
005: dt: 0.5000, sse=4263108.5, rms=1.94
006: dt: 0.5000, sse=4212978.0, rms=1.80
007: dt: 0.5000, sse=4200574.0, rms=1.72
rms = 1.68, time step reduction 1 of 3 to 0.250...
008: dt: 0.5000, sse=4191339.5, rms=1.68
009: dt: 0.2500, sse=3181011.8, rms=1.44
rms = 1.42, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=3087899.5, rms=1.42
rms = 1.41, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=3061586.0, rms=1.41
positioning took 75.5 minutes
inhibiting deformation at non-cortical midline structures...
mean border=94.2, 141 (49) missing vertices, mean dist -0.2 [0.6
(%61.8)->0.3 (%38.2))]
%65 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=ALW-A, nav=2, nbrs=2, l_repulse=5.000,
l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50

vertex spacing 0.90 +- 0.24 (0.03-->9.51) (max @ vno 57593 --> 140123)
face area 0.34 +- 0.16 (0.00-->5.05)
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.24 (0.07-->9.67) (max @ vno 57593 --> 140123)
face area 0.34 +- 0.16 (0.00-->5.09)
mean absolute distance = 0.39 +- 0.57
4028 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0., sse=3383843.2, rms=3.03
012: dt: 0.5000, sse=3668512.5, rms=2.02
013: dt: 0.5000, sse=3762432.5, rms=1.65
014: dt: 0.5000, sse=3746829.0, rms=1.49
015: dt: 0.5000, sse=3832901.5, rms=1.41
rms = 1.41, time step reduction 1 of 3 to 0.250...
016: dt: 0.5000, sse=3843775.0, rms=1.41
017: dt: 0.2500, sse=3401710.2, rms=1.27
rms = 1.26, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=3332062.8, rms=1.26
rms = 1.26, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=3308422.0, rms=1.26
positioning took 36.1 minutes
inhi

[Freesurfer] "segmentation fault" - recon-all

[Mark Plantz]

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 wm, xrange [-1, 257]*

*searching rotation angles z=[-7  7], y=[83 97]*

*searching scale 1 Z rot 6.8  global minimum found at slice 0.0, rotations
(90.00, -0.00)*

*final transformation (x=0.0, yr=90.000, zr=-0.000):*

*-0.000   0.000   1.000   128.000;*

*-0.000   1.000  -0.000   128.000;*

*-1.000   0.000   0.000   128.000;*

* 0.000   0.000   0.000   1.000;*

*Segmentation fault*

*Darwin dhcp-165-124-23-248.prevmed.northwestern.edu 12.4.0 Darwin Kernel
Version 12.4.0: Wed May  1 17:57:12 PDT 2013;
root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64*

*recon-all -s avgseg_seg_test exited with ERRORS at Mon Aug 19 13:32:28 CDT
2013*

*
*

I don't know if this error is directly related to the actual brain
segmentation, but recon-all was run with a different gca atlas. The command
was:

recon-all -gca atlas.gca -all -s 


My best guess is that the .gca file is the source of the problem, but I am
not sure why recon-all would make it to the final transformation and then
throw an error.

Any ideas?

Thanks in advance.

MP
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[Freesurfer] Segmentation Fault with mri_convert

[Christopher Finuf]

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 is the output and error that I get. I'm running the latest
version v 5.3.0 of freesurfer. Any suggestions on what the problem is? What
is strange that it works with half my data set but the other has this
error. I've run this command in the exact way many times before and have
never had this issue.





bash-3.2$ recon-all -i
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
-subjid Bigler_Repeatability_0005Ad_M1


Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects

Actual FREESURFER_HOME /Applications/freesurfer

Darwin NS112201PSY2.byu.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep  1
21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1

\n mri_convert
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz
\n

mri_convert
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm...

Getting Series No

INFO: Found 178 files in
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1

INFO: Scanning for Series Number 2

Scanning Directory

INFO: found 176 files in series

INFO: loading series header info.


RunNo = 1

INFO: sorting.

INFO: (224 256 176), nframes = 1, ismosaic=0

PE Dir ROW ROW

AutoAlign matrix detected

AutoAlign Matrix -

 1.000   0.000   0.000   0.000;

 0.000   1.000   0.000   0.000;

 0.000   0.000   1.000   0.000;

 0.000   0.000   0.000   1.000;


FileName
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm

Identification

NumarisVersyngo MR B17

ScannerModel  TrioTim

PatientName   Bigler_Repeatability_AD_M

Date and time

StudyDate 20160512

StudyTime 075942.531000

SeriesTime081401.859000

AcqTime   080647.62

Acquisition parameters

PulseSeq  *tfl3d1_ns

Protocol  t1_mpr_sag_iso_ave2_ipat2_(mprage)

PhEncDir  ROW

EchoNo1

FlipAngle 9

EchoTime  2.26

InversionTime 900

RepetitionTime1900

PhEncFOV  218.75

ReadoutFOV250

Image information

RunNo 1

SeriesNo  2

ImageNo   1

NImageRows256

NImageCols224

NFrames   1

SliceArraylSize   1

IsMosaic  0

ImgPos 75.8389 136.8499 125.

VolRes  0.9766   0.9766   1.

VolDim224  256  176

Vc  0.0767  -0.9971   0.

Vr -0.   0.  -1.

Vs -0.9971  -0.0767   0.

VolCenter  -3.5106  21.0460   0.

TransferSyntaxUID 1.2.840.10008.1.2.1

UseSliceScaleFactor 0 (slice 0: 1)

Segmentation fault

Darwin NS112201PSY2.byu.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep  1
21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64


recon-all -s Bigler_Repeatability_0005Ad_M1 exited with ERRORS at Wed Jun
8 13:39:08 MDT 2016


For more details, see the log file
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/scripts/recon-all.log

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Segmentation fault in mri_convert

[Christopher Finuf]

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 is the output and error that I get. I'm running the latest
version v 5.3.0 of freesurfer. Any suggestions on what the problem is? What
is strange that it works with half my data set but the other has this
error. I've run this command in the exact way many times before and have
never had this issue.





bash-3.2$ recon-all -i
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
-subjid Bigler_Repeatability_0005Ad_M1


Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects

Actual FREESURFER_HOME /Applications/freesurfer

Darwin NS112201PSY2.byu.edu  14.5.0 Darwin
Kernel Version 14.5.0: Tue Sep  1 21:23:09 PDT 2015;
root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1

\n mri_convert
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz
\n

mri_convert
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm...

Getting Series No

INFO: Found 178 files in
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1

INFO: Scanning for Series Number 2

Scanning Directory

INFO: found 176 files in series

INFO: loading series header info.


RunNo = 1

INFO: sorting.

INFO: (224 256 176), nframes = 1, ismosaic=0

PE Dir ROW ROW

AutoAlign matrix detected

AutoAlign Matrix -

 1.000   0.000   0.000   0.000;

 0.000   1.000   0.000   0.000;

 0.000   0.000   1.000   0.000;

 0.000   0.000   0.000   1.000;


FileName
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm

Identification

NumarisVersyngo MR B17

ScannerModel  TrioTim

PatientName   Bigler_Repeatability_AD_M

Date and time

StudyDate 20160512

StudyTime 075942.531000

SeriesTime081401.859000

AcqTime   080647.62

Acquisition parameters

PulseSeq  *tfl3d1_ns

Protocol  t1_mpr_sag_iso_ave2_ipat2_(mprage)

PhEncDir  ROW

EchoNo1

FlipAngle 9

EchoTime  2.26

InversionTime 900

RepetitionTime1900

PhEncFOV  218.75

ReadoutFOV250

Image information

RunNo 1

SeriesNo  2

ImageNo   1

NImageRows256

NImageCols224

NFrames   1

SliceArraylSize   1

IsMosaic  0

ImgPos 75.8389 136.8499 125.

VolRes  0.9766   0.9766   1.

VolDim224  256  176

Vc  0.0767  -0.9971   0.

Vr -0.   0.  -1.

Vs -0.9971  -0.0767   0.

VolCenter  -3.5106  21.0460   0.

TransferSyntaxUID 1.2.840.10008.1.2.1

UseSliceScaleFactor 0 (slice 0: 1)

Segmentation fault

Darwin NS112201PSY2.byu.edu  14.5.0 Darwin
Kernel Version 14.5.0: Tue Sep  1 21:23:09 PDT 2015;
root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64


recon-all -s Bigler_Repeatability_0005Ad_M1 exited with ERRORS at Wed Jun
8 13:39:08 MDT 2016


For more details, see the log file
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/scripts/recon-all.log

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Segmentation fault using mri_label2vol

[Syeda Maryam]

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 countless times but nothing has 
worked. I also checked my "aseg.mgz" to make sure it's not corrupted but that 
isn't the issue either. Any help would be highly appreciated!! Thanks in advance

mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz --seg 
/tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp 
/scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o 
/tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Number of labels: 0
Annot File:  (null)
Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol:  1
ProjType:   (null)
ProjTypeId: 0
ProjStart:  0
ProjStop:   0
ProjDelta:  0.1
Subject:  (null)
Hemi: (null)
UseNewASeg2Vol:  1
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
-0.000  -0.000  -0.985   128.000;
-0.000   0.833  -0.000   98.000;
 0.000   0.000   0.000   1.000;
Template Voxel Volume: 1.23773
nHits Thresh: 0
Computing registration based on header
RegMat: 
 1.000   0.000   0.000  -0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;
Label RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
 0.000   0.000  -0.985   128.000;
 0.000   0.833   0.000   98.000;
 0.000   0.000   0.000   1.000;
ASeg2Vol: Building LUT
Segmentation fault

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[Freesurfer] Segmentation fault using mri_label2vol

[Syeda Wajiha Maryam]

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 countless times but
nothing has worked. I also checked my "aseg.mgz" to make sure it's not
corrupted but that isn't the issue either. Any help would be highly
appreciated!! Thanks in advance

mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
--seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
/scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
/tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Number of labels: 0
Annot File:  (null)
Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol:  1
ProjType:   (null)
ProjTypeId: 0
ProjStart:  0
ProjStop:   0
ProjDelta:  0.1
Subject:  (null)
Hemi: (null)
UseNewASeg2Vol:  1
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
-0.000  -0.000  -0.985   128.000;
-0.000   0.833  -0.000   98.000;
 0.000   0.000   0.000   1.000;
Template Voxel Volume: 1.23773
nHits Thresh: 0
Computing registration based on header
RegMat: 
 1.000   0.000   0.000  -0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;
Label RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
 0.000   0.000  -0.985   128.000;
 0.000   0.833   0.000   98.000;
 0.000   0.000   0.000   1.000;
ASeg2Vol: Building LUT
Segmentation fault
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[Freesurfer] segmentation fault (core dumped)

[Fengji Geng]

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!

---
Message: 1
Date: Mon, 21 Dec 2015 10:38:08 -0500 (EST)
From: Bruce Fischl 
Subject: Re: [Freesurfer] FW: segmentation fault (core dumped)
To: Freesurfer support list 
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Hi Fengji

hmmm, I don't remember ever seeing a core dump in mri-segstats before. If
you upload the entire subject dir (tarred and gzipped) to our ftp site we
will fix it.

cheers
Bruce



-
Fengji

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[Freesurfer] segmentation fault with mri_label2vol

[Martha Shiell]

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 trouble
viewing the label in question on the inflated surface with freeview, and no
problem viewing the brain.mgz files.

Ideas?
Thank you,
Martha

Command:

mri_label2vol --label d16/roi_lh_man3/lh.behav-full-sig2-transformed.label
--temp ~/project_deaf_anatomy/analysis_nifti_freesurfer/d16/mri/brain.mgz
--reg d16/reg/surf2conf.dat --subject d16 --hemi lh --proj abs -1 -1 0.1
--o d16/roi_lh_man3/roi_lh_man3_conf.nii.gz; done

Output:

Number of labels: 1
d16/roi_lh_man3/lh.behav-full-sig2-transformed.label
Annot File:  (null)
Template Volume:
/home/martha/project_deaf_anatomy/analysis_nifti_freesurfer/d16/mri/brain.mgz
Outut Volume: d16/roi_lh_man3/roi_lh_man3_conf.nii.gz
Registration File: d16/reg/surf2conf.dat
Fill Threshold: 0
Label Vox Vol:  1
ProjType:   abs
ProjTypeId: 1
ProjStart:  -1
ProjStop:   -1
ProjDelta:  0.1
Subject:  d16
Hemi: lh
UseNewASeg2Vol:  1
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR
/home/martha/project_deaf_anatomy/analysis_nifti_freesurfer
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox: 
-1.000   0.000   0.000   128.000;
-0.000  -0.000  -1.000   128.000;
-0.000   1.000  -0.000   128.000;
 0.000   0.000   0.000   1.000;
Template Voxel Volume: 1
nHits Thresh: 0
Loading registration from d16/reg/surf2conf.dat
RegMat: 
 1.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;
Label RAS-to-Vox: 
-1.000   0.000   0.000   128.000;
 0.000   0.000  -1.000   128.000;
 0.000   1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
  INFO: loading surface
 /home/martha/project_deaf_anatomy/analysis_nifti_freesurfer/d16/surf/lh.white
nvertices = 114782
Reading thickness
/home/martha/project_deaf_anatomy/analysis_nifti_freesurfer/d16/surf/lh.thickness
nlabels = 1
Allocating Hit Volume (16777216) voxels
Loading d16/roi_lh_man3/lh.behav-full-sig2-transformed.label
Segmentation fault


-- 
Martha M. Shiell, PhD
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[Freesurfer] Segmentation fault: Core dumped

[Sahil Bajaj]

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 segmentation of anatomical data (generated using recon-all),
and it looks fine to me.
Here I am also attaching the log file created when I run this command.

Any help would be really appreciated.

Thanks,
Sahil
-- 
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 


dat.log
Description: Binary data
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[Freesurfer] Segmentation fault with mri_ca_train

[Mark Plantz]

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 different
environments and can't avoid it. The output is below:

sh-3.2# mri_ca_train -T1 withSkull.mgz -seg seg_edited.mgz atlas_test
/hearingbrain/Desktop/atlas_withSkull.gca
reading T1 data from subject's mri/withSkull.mgz directory
reading segmentation from subject's mri/seg_edited.mgz directory
training on 1 subject and writing results to /Volumes/Macintosh
HD/Users/hearingbrain/Desktop/atlas_withSkull.gca
***
processing subject atlas_test, 1 of 1...
   reading input 0:
/Applications/freesurfer/subjects/atlas_test/mri/withSkull.mgz
gca width modified from 256 to 181
gca height modified from 256 to 217
gca depth modified from 256 to 181
Segmentation fault: 11


Any ideas?

-MP
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Re: [Freesurfer] Segmentation fault mri_em_register

[Bruce Fischl]

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 that fixes your problem

cheers
Bruce


On Fri, 13 Dec 2019, Loucao, Ricardo wrote:



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
(watershed is failing but I managed to work around it using FSL’s BET combined 
with mri_convert to
create the brainmask.mgz file).

Now I’m running into a segmentation fault error in mri_em_register.  
Here’s the relevant portion of the log file:

#@# EM Registration Fri Dec 13 10:55:07 GMT 2019
/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/subjects/PM1/mri

 mri_em_register 
-rusage/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/subjects/PM1/touch/rusage.mri_em_registe
r.dat -uns 3 -mask brainmask.mgz nu.mgz
/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/average/RB_all_2016-05-10.vc700.gca
transforms/talairach.lta 

setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_em_register for OpenMP = 1 == 
reading 1 input volumes...
logging results to talairach.log
reading'/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3   using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 6.3 or > 503.7 
total sample mean = 78.8 (1011 zeros)

spacing=8, using 2830 sample points, tol=1.00e-05...

register_mri: find_optimal_transform
find_optimal_transform: nsamples 2830, passno 0, spacing 8
Segmentation fault (core dumped)
Linux btupc09 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 
x86_64 x86_64 x86_64
GNU/Linux

recon-all -s PM1 exited with ERRORS at Fri Dec 13 10:55:35 GMT 2019


I’m also sending you the log from the skull striping step, in case the two 
errors might be connected:
 
#@# Skull Stripping Fri Dec 13 10:23:26 GMT 2019
/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/subjects/PM1/mri

 mri_em_register 
-rusage/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/subjects/PM1/touch/rusage.mri_em_registe
r.skull.dat -skull 
nu.mgz/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/average/RB_all_withskull_2016-05-10.vc70
0.gca transforms/talairach_with_skull.lta 

aligning to atlas containing skull, setting unknown_nbr_spacing = 5

== Number of threads available to mri_em_register for OpenMP = 1 == 
reading 1 input volumes...
logging results to talairach_with_skull.log
reading'/data/MR/mr_user/rloucao/Scriptery/freesurferCentOS/freesurfer/average/RB_all_withskull_2016-05-10.vc7
00.gca'...
average std = 22.9   using min determinant for regularization = 52.6
0 singular and 9002 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.7 or > 569.1 
total sample mean = 77.6 (1399 zeros)

spacing=8, using 3243 sample points, tol=1.00e-05...

register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=25.1
skull bounding box = (67, 34, 13) --> (199, 162, 201)
using (111, 77, 107) as brain centroid...
mean wm in atlas = 108, using box (95,61,84) --> (127, 92,130) to find MRI wm
before smoothing, mri peak at 106
robust fit to distribution - 107 +- 5.6
after smoothing, mri peak at 106, scaling input intensities by 1.019
scaling channel 0 by 1.01887
initial log_p = -4.775

First Search limited to translation only.

max log p =    -4.469154 @ (-9.091, 27.273, 9.091)
max log p =    -4.310065 @ (4.545, -4.545, -4.545)
max log p =    -4.294819 @ (-2.273, 2.273, -2.273)
max log p =    -4.269301 @ (1.136, -1.136, -1.136)
max log p = 

Re: [Freesurfer] Segmentation fault: 11

[fsbuild]

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-imCCfHdpe0i9n7VbHnkOmApVqwXLBFsNTr00VNAx6komIIAOhuIRk6xXYWHGaglPYJchE8a9lzlAQT29GiC1raPpbWVbt94mHKkuJR3TiY-OFK_tCBU51VFFu9uewTnFXNckvsZOBZI1xinXrvWXo4w5sVl8oWlaqCnq6Y7DwKhnZA1W8tAh_0WR1Dd5kz8GcHoj9sFXFkVoDX7T9CJHyRmQLOsEBtrXXnYLMPFFrjKkqrgu3pegmOSzp28R-xM-z7A1a1dzarbK0-CzqxWJ0cOGPevrxtZTKgyk40s-Py98MTA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads-
 if you used the pkg installer 
file, https://secure-web.cisco.com/1kDieI9mdZudxJbpCFL6WFWngUIQhFugSuxCTUgxkN4I7zm6B97n6zFOzOXu7d603xiHK8yloksQA-mavSlbntpXNUVUyEt2IxFBqjbp6OUtHz3SjeZS5qpUI6EggsHyDvJJtjDS4pbNTfvUdNJlUnJJnH_mRxv60AkjaADCX8b9l-VmjWA3FG7JYhgzwTRLXm9GPZsPTIU-e5UnobSwIR9tS1dOYAboIUCHNkEogDt9FoYYVBGSIsQo9Jee3atsYxSR64iJe60_iQ-NzWOFWqlewHJJ8H1DmEDFe3TDApSJWsPGzPXJUgiyGdPNG5elZR4By4jQUjMJHrLLS8l6s6Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2%2Ffreesurfer-darwin-macOS-7.3.2.pkg-
 what version of MacOS you are running- if you are on an Intel Mac or a new Mac 
with an M1 or M2 chip.
Please make sure you have registered and obtained the freesurfer license.txt 
file by filling out the 
form, https://secure-web.cisco.com/1fpZEOUr_MAQGgEoaIOkzRF-3qUqa6N-GPoNFHsbrnuctCNmhc9id24leJoz6l_qPb6qchGVB28sc5TdXgeSKmsRlhcbWOsDymDubYiXzgDxPTbwBQjIbrztHG0NYp5bU7EFt6dP2ZtmHAXPyqGmnwaB3Ffo_ZayGhQjWhRKFoRyemOSV5sgNJ9PUqhmJ84MunQN_cVhc3ybjFpZSYLbvDcRyhWw-w3b9eFhc1I4S0QIOzL9x0y1bZXRQWztyGsc1epLYYkbUkt1_L7uLnyjQK1KVwy8jmpipmkQM3_wIYDODTLe2QlG_g039fO_c9J4D_EV7DNibbDR4B4r32eJrYQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
The thread you 
referenced, https://secure-web.cisco.com/1D0s4CKkxCu5d6CQKJUyf4knHMaxqpw-OaFbdce0DVPAKaX9_RQ-4wDkshtLmkg81ku3ximPzzeVVQkKFd7oGBdTVb2vtcZKh97LrioXea3Sz7D3G5Pov9ZvUq-qaDE3hFFPtBrQOQwC2rNLEnqex3OEbopWB9_cxjliyD0lsJD6JPEIUCAnAjnjNFy2fxfQC77hKBoDRLqa3hs_HlnwLqMJdlTujxDGrzj9cL59p24ppVlrzg64XgLi3-jAZwc4-HXyYaUIB0t3Smao8B7yPSzb6gHxA5UZhrjOsGMKZBBdPqiHG9pkVDZEftp3zgOIK/https%3A%2F%2Fneurostars.org%2Ft%2Fproblem-installing-freesurfer-in-mac%2F20552%2F21,
 showed the crash went away for a user with a MacBook Pro if they unplugged 
their external monitor.  This is - or at least was - a known problem with 
a 2nd monitor causing a segfault when trying to run some graphics programs. 
 So try unplugging any external monitor if you are using a Mac laptop.
I would try explicitly running the bash shell in your terminal window, but 
typing “bash” at the terminal prompt.  You should then see the output,
$ bash
The default interactive shell is now zsh.
To update your account to use zsh, please run `chsh -s /bin/zsh`.
For more details, please visit 
https://secure-web.cisco.com/1weI0CySFCptz62exS6gCfA2Ymaa7qVQzIZURPdDJ1Yz2dGxXIspkZGB_bUF7bkIFa3SThCs1dYsJwb0g_pcZW825OZ72WiPjcT6_-lQk7bCxJRkhJqF31WXDnFEUusUDjyR6j2iYFIkYSDykxrl9xXbk1ccoVsyf1kR1ElUppfBf-JiSRggqQdhsUMq_wCisCD-Do1HGhK1NeljTcTx6m9iT5Q8W0rwhyXf1GzLdQb9Ln8jMKhV-UNUtiy2QQii88TUkIIZBENPD5fchnBWfZOBAj58YzZ90EhP8nLAIusrH8tMKpmIjHAkpyhETYSCdKCc_3CAybPXYV_ONJ33YkQ/https%3A%2F%2Fsupport.apple.com%2Fkb%2FHT208050.userid%40hostname%3A%7E%26gt;
You can then set FS_LICENSE in your environment to point to the license.txt 
file.  You can put license.txt in your home directory, e.g., wherever that 
path is,

userid@hostname:~> echo $HOME/Users/priya
userid@hostname:~> export 
FS_LICENSE=$HOME/license.txtuserid@hostname:~> cat $FS_LICENSE< output 
deleted - just make sure the environment variable points to license.txt >
Then setup the fressurfer environment, e.g., for the 7.3.2 release installed 
with the .pkg file,
userid@hostname:~> export 
FREESURFER_HOME=/Applications/freesurfer/7.3.2userid@hostname:~> source 
$FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-darwin-macOS-7.3.2-20220803-878457d 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.3.2
FSFAST_HOME       /Users/developer/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Users/developer/freesurfer/subjects
TUTORIAL_DATA     /Users/developer/tutorial_data
MNI_DIR         
  /Users/developer/freesurfer/mni
WARNING: /Users/developer/freesurfer/fsl_507/bin does not exist.
FSL_DIR         
  /Users/developer/freesurfer/fsl_507

userid@hostname:~> which freeview/Applications/freesurfer/7.3.2/bin/freeview
… try running freeview with no argument to see if it brings up an 
empty window …
userid@hostname:~> freeview
… try displaying a simple volume …
userid@hostname:~> freeview $SUBJECTS_DIR/bert/mri/brain.mgz
Let us know how it goes.
- R.
On Oct 5, 2022, at 03:11, priya padma  
wrote:External Email - Use 
CautionHello Team,I just 
installed freesurfer and freeview using the methods mentioned 
in MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.

Re: [Freesurfer] Segmentation Fault (Ventura)

[fsbuild]

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 processed to see if 
there are log files with any more info.  A segmentation fault can happen 
for various reasons, but we might be able to tell something if you can get a 
hold of the core dump file.
There could be differences w.r.t  how Ventura maintains a connection to 
and interacts with a remote file system compared to Monterey, e.g., timeouts, 
authentication, file caching, etc .  If recon-all was proceeding normally 
and then no longer could see or access the remote file system when it needed to 
read or write a file, then the recon-all would fail.  But I would expect 
to see some message w.r.t file not found, permission denied and not just a 
segfault message.

We have have not done any testing with MacOS Ventura and we don’t generally 
test on MacOS using remotely mounted file systems.  Many Mac users I know 
always stay one operating system release behind the latest version of MacOS. 
 They are only now upgrading from BigSur to Monterey since Ventura was 
officially released last month.   If I have test the latest release I try 
to wait until the first .1 release is out as the initial .0 releases are often 
the most buggy (for Ventura that would mean waiting for 13.1).
- R.

On Nov 7, 2022, at 17:27, Joann Stewart  
wrote:External Email - Use 
CautionHello, 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 am 
using : recon-all -subject 1306_A -i 1306/T1w/T1w_MPR.nii.gz -T2 
1306/T2w/T2w_SPC.nii.gz -T2pial -all -qcache   On the server, 
when I run this command, it continues until I get to the segmentation portion. 
I have the full output of this command attached to the email in a word document 
titled “Recon-all output on server”. Attached I also have a copy of the 
recon-all.log file. There is another member in my lab who was able to use 
this command successfully with the same files and exact same code. He was using 
the same server that I was on, and we have exactly the same permissions on the 
server. The only difference is that I have updated my mac to Ventura and he has 
not yet updated his mac (he is using macOS Monterey 12.6).  We tried 
moving my files onto my desktop to see if the recon-all worked there as 
compared to the server. I simply moved the T1w & T2w NIfTI files onto 
my desktop from the server. When I run recon all sourcing from the NIfTI files 
on my desktop rather than the server, it works fine without 
error.  Therefore, we are wondering if it is an issue with the new 
Ventura update in conjunction with shared network folders. Do you have any 
suggestions or ideas based on the information I have provided? FreeSurfer 
version: freesurfer-darwin-macOS-7.3.2-20220804-6354275Platform: MacOS Ventura 
13.0 Let me know if there is any more information that you 
need.  Thank you!___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
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[Freesurfer] Segmentation fault (core dumped)

[Tracy Riggins]

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]

--
#@# 1/1 HMN080 Fri Mar  3 12:14:44 EST 2023 --
---
mri_surf2surf --srcsubject HMN080 --srchemi lh --srcsurfreg sphere.reg
--trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval
./tmp.mris_preproc.51930/HMN080.1.mgh --sval
/export/data/seahorse_ncdl/HMN/data/HMN080/surf/lh.thickness --sfmt curv
--noreshape --no-cortex
Segmentation fault (core dumped)
Linux seahorse.umd.edu 3.10.0-1160.80.1.el7.x86_64 #1 SMP Sat Oct 8
18:13:21 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s HMN080 exited with ERRORS at Fri Mar  3 12:14:48 EST 2023

Can you assist?  OR perhaps tell us where to find the core dump file, which
may have more information?

-- 
Tracy Riggins, Ph.D.
Pronouns 
:
 she/her/hers
Associate Professor of Psychology
4094 Campus Drive, Biology/Psychology Building 2147J
University of Maryland, College Park, MD 20742
Zoom Meeting ID: 6751666548 

*
Research info:  
http://secure-web.cisco.com/1JWrYfqglbLMQuNvUkCI3__mdHJZE-j2I4GZAMwxbYavfuRQfdHTN8Fb8O-hN07nqDsGoHPJbXTMhVpJJQcb_CkXCFgW_Spl6deT8olpw0za5mcWw_IMIBc4ip0tJ-V316-47g1p79Y9ifrfUwiU00KKudbClq_eezPmENt9UeEUmKIafocXLCRHHAjpqvBF87TaCJmkKB55WvpT25kbIZOd_ztdYNYcvAqF9Ynpd0GVjJZBH0MkVdbTiwzOXxXOEGXGUPI6OIU8fyNW3MkA0Czgf4W8BWQ-jrI8lRBCii8iNhOlgQf2kR1KAMjM5VWKgyK6NYVLmdGQ-2n9vUBdZ3A/http%3A%2F%2Fncdl.umd.edu
 and 
https://secure-web.cisco.com/1gMMoT_3zpTn_EJwufCskhV5rA9d3a3dfl-3blyeCnoRvfBV7IOLXCKFjnjtNgy9plsB4KPUM6PJnffPRwzHhudjzlZdUtkSr6tT8Ll8K0IqNRTnxxw1FHkZWYdn2X8MeEIJE8m0IRGMGz9QNeHoRGBLZPWXfpxB1BANB37541RqCqISXkibM62PuhEvmbwxgowSX5h3XquBQeQz56_aWDBc0JZlygwU9AzLlI_K90JGuRb6pOPtxVH8phbxilsQjf-emecx5wT5EScisBR9FYg7i71C-1pp03fSZVxcpulQpJEGECtYqg9p7nab0sNPMuZoUrCfBHjZdl58NRn9qtw/https%3A%2F%2Fwww.facebook.com%2FNCDLumd
Black lives matter in academia

LGBTQIA+ Ally

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Re: [Freesurfer] FreeSurfer Segmentation Fault

[Wang, Ruopeng]

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 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-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
Terminal Output:
Segmentation fault
Syslog Output:
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863337] ThreadIOWorker[390903]: 
segfault at ad0 ip 5613a159eb5d sp 7fb580f68d00 error 4 in 
freeview[5613a0ee8000+bc1000]
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863358] Code: ef c9 f2 0f 5c 14 24 
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 
c9 48 8d 14 96 48 8d 0c 8e  0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863380] ThreadIOWorker[390885]: 
segfault at fe1a641 ip 5613a159eb5d sp 7fb589f7ad00 error 4
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863393] Code: ef c9 f2 0f 5c 14 24 
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 
c9 48 8d 14 96 48 8d 0c 8e  0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863400] traps: 
ThreadIOWorker[390898] general protection fault ip:5613a159ebe0 sp:7fb58376dd00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863410] traps: 
ThreadIOWorker[390890] general protection fault ip:5613a159ebe0 sp:7fb587775d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863450] traps: 
ThreadIOWorker[390901] general protection fault ip:5613a159eb5d sp:7fb581f6ad00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863478] traps: 
ThreadIOWorker[390875] general protection fault ip:5613a159eb5d sp:7fb58ef84d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863499] traps: 
ThreadIOWorker[390905] general protection fault ip:5613a159eb5d sp:7fb57ff66d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863542] traps: 
ThreadIOWorker[390884] general protection fault ip:5613a159eb5d sp:7fb58a77bd00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863566] traps: 
ThreadIOWorker[390886] general protection fault ip:5613a159ebe0 sp:7fb589779d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863579] traps: 
ThreadIOWorker[390881] general protection fault ip:5613a159eb5d sp:7fb58bf7ed00 
error:0


Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
www.exeter.ac.uk
Laver Building, North Park Road, Exeter, EX4 4QE
[http://secure-web.cisco.com/119YVCp1hrsEYkFhq1AwKWgmIcpNnRFPYcQjZ0-xjjxoXAf6UcUYwpLuh88juFgvzCjlQx1E2e5B_ccRw64OO8yofsPIRbtZ9ZtKGOy2pgw20hVbt9xCTUoIk6utGG1K6G_K_-rK0-NG2vdkGkYYSscwlwtxK58zuaMQqmnsUVY_32xHpaU2rsvfIVQHYxnqqPODe0gUXaadMq3BevHC1xXp2hNDNDNnZZZ5mLG7HjLVFPagt_3mjNY2e3_ul7sZN3crwabzwKP7hKWiOynm55ZU0THvS4Uh1u5kl04SCAzsC4JEubOuz7h2C3qB-xqCHIAEnDgpTIAGHvtIWYV5dWg/http%3A%2F%2Fwww.exeter.ac.uk%2Fcodebox%2Femail-sig%2Fstaff-sig.gif]
This email and any attachment may contain information that is confidential, 
privileged, or subject to copyright, and which may be exempt from disclosure 
under applicable legislation. It is intended for the addressee only. If you 
received this message in error, please let me know and delete the email and any 
attachments immediately. The University will not accept responsibility for the 
accuracy/completeness of this email and its attachments.

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The information in this e-mail is intended only for the person to whom it is 
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contains patient information, please contact the Mass General Brigham 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] FreeSurfer Segmentation Fault

[Fischl, Bruce R.,PHD]

Hi Rob

Can you run mri_info on that volume? And just ls -l to see if it is a 
reasonable size?

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bartlett, Rob
Sent: Tuesday, March 21, 2023 6:50 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FreeSurfer 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: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
Terminal Output:
Segmentation fault
Syslog Output:
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863337] ThreadIOWorker[390903]: 
segfault at ad0 ip 5613a159eb5d sp 7fb580f68d00 error 4 in 
freeview[5613a0ee8000+bc1000]
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863358] Code: ef c9 f2 0f 5c 14 24 
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 
c9 48 8d 14 96 48 8d 0c 8e  0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863380] ThreadIOWorker[390885]: 
segfault at fe1a641 ip 5613a159eb5d sp 7fb589f7ad00 error 4
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863393] Code: ef c9 f2 0f 5c 14 24 
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 
c9 48 8d 14 96 48 8d 0c 8e  0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863400] traps: 
ThreadIOWorker[390898] general protection fault ip:5613a159ebe0 sp:7fb58376dd00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863410] traps: 
ThreadIOWorker[390890] general protection fault ip:5613a159ebe0 sp:7fb587775d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863450] traps: 
ThreadIOWorker[390901] general protection fault ip:5613a159eb5d sp:7fb581f6ad00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863478] traps: 
ThreadIOWorker[390875] general protection fault ip:5613a159eb5d sp:7fb58ef84d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863499] traps: 
ThreadIOWorker[390905] general protection fault ip:5613a159eb5d sp:7fb57ff66d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863542] traps: 
ThreadIOWorker[390884] general protection fault ip:5613a159eb5d sp:7fb58a77bd00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863566] traps: 
ThreadIOWorker[390886] general protection fault ip:5613a159ebe0 sp:7fb589779d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863579] traps: 
ThreadIOWorker[390881] general protection fault ip:5613a159eb5d sp:7fb58bf7ed00 
error:0


Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
www.exeter.ac.uk<http://www.exeter.ac.uk>
Laver Building, North Park Road, Exeter, EX4 4QE
[http://secure-web.cisco.com/119YVCp1hrsEYkFhq1AwKWgmIcpNnRFPYcQjZ0-xjjxoXAf6UcUYwpLuh88juFgvzCjlQx1E2e5B_ccRw64OO8yofsPIRbtZ9ZtKGOy2pgw20hVbt9xCTUoIk6utGG1K6G_K_-rK0-NG2vdkGkYYSscwlwtxK58zuaMQqmnsUVY_32xHpaU2rsvfIVQHYxnqqPODe0gUXaadMq3BevHC1xXp2hNDNDNnZZZ5mLG7HjLVFPagt_3mjNY2e3_ul7sZN3crwabzwKP7hKWiOynm55ZU0THvS4Uh1u5kl04SCAzsC4JEubOuz7h2C3qB-xqCHIAEnDgpTIAGHvtIWYV5dWg/http%3A%2F%2Fwww.exeter.ac.uk%2Fcodebox%2Femail-sig%2Fstaff-sig.gif]
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Re: [Freesurfer] FreeSurfer Segmentation Fault

[Bartlett, Rob]

External Email - Use Caution

Hi Bruce, here is the output:

Volume information for 
tutorial_data_20190918_1558/diffusion_recons/Diff001/mri/brainmask.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 12.00 msec, TE: 4.76 msec, TI: 4.76 msec, flip angle: 20.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =  -0., z_r =   0., c_r =-4.5707
  : x_a =   0., y_a =   0., z_a =   1., c_a =40.4204
  : x_s =  -0., y_s =  -1., z_s =   0., c_s = 6.8018

talairach xfm : 
tutorial_data_20190918_1558/diffusion_recons/Diff001/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.  -0.   0.   123.4293
0.   0.   1.   -87.5796
   -0.  -1.   0.   134.8018
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.   0.   123.4293
0.   0.  -1.   134.8018
   -0.   1.  -0.87.5796
   -0.  -0.  -0. 1.

Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
http://secure-web.cisco.com/1T3UxPKF0R9TnBw_2ltCSMTfEH3AvjHM2FInqeG43YNbD7OD0itZmsPW_1S8vtTQoDMMAeJby8Zqgl9nb4m_yLwjeBMDi168NweC6SZzTEObKbV7t-NL4N7sEeH163BzBaKKKlWUDZTrUrxny6ojH9KCi6e2p6kVBz0U0fyO1v1U3KAJcstD5wQafDyf17gEAqCM6Oh-2bmN3f1ZmNQrXymTVERCecg4xfaQP4AgU0QWvcsUodezJ9BOYnFLVlAIR-nt0V_xODXsa29KkWsdFyTy_GpHRnGZ7EQ77RY3b9Ks2PrrOjaBCSF2yUglS60XWj8Ooxpo2RRECHg-C1I4nOw/http%3A%2F%2Fwww.exeter.ac.uk
Laver Building, North Park Road, Exeter, EX4 4QE
[http://secure-web.cisco.com/1qEf3w94plVSPmCQ1FMfRUITvU3KTNbP7UPtrGs_S99-pRbZ55SFEcS7XZZ0XIh4VC_M5EYEfDLw9U7BeTl1tz6kyckI0GFpwzy4ZVmV8NJpbIqjsgwWHBgFZhoJmeV2gPm7zWP5o5SPtP1fNHLOsNA__lNJ3eYA5QiJCQKii7aaly3AA-4AAi6CU9IXYFwKrWt2XjfE44z6Q9aQQ6igCyZ4j5bmidXCyBp2zadwM3EDD8SmIzWwM28cvNKvbVnbEwDMDNXWvPvYE0uyc0dxYwfwy1GpOEf1IGV8-KzLT2B1vf0wFmf4WjQMGitf33TW8_XP61FvUV0atf_FRxof5lg/http%3A%2F%2Fwww.exeter.ac.uk%2Fcodebox%2Femail-sig%2Fstaff-sig.gif]
This email and any attachment may contain information that is confidential, 
privileged, or subject to copyright, and which may be exempt from disclosure 
under applicable legislation. It is intended for the addressee only. If you 
received this message in error, please let me know and delete the email and any 
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accuracy/completeness of this email and its attachments.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fischl, 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.

Hi Rob

Can you run mri_info on that volume? And just ls -l to see if it is a 
reasonable size?

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Bartlett, Rob
Sent: Tuesday, March 21, 2023 6:50 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] FreeSurfer 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: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
Terminal Output:
Segmentation fault
Syslog Output:
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863337] ThreadIOWorker[390903]: 
segfault at ad0 ip 5613a159eb5d sp 7fb580f68d00 error 4 in 
freeview[5613a0ee8000+bc1000]
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863358] Code: ef c9 f2 0f 5c 14 24 
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 
c9 48 8d 14 96 48 8d 0c 8e  0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863380] ThreadIOWorker[390885]: 
segfault at fe1a641 ip 5613a159eb5d sp 7fb589f7ad00 error 4
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863393] Code: ef c9 f2 0f 5c 14 24 
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 
c9 48 8d 14 96 48 8d 0c 8e  0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863400] traps: 
ThreadIOWorker[390898] general protecti

Re: [Freesurfer] FreeSurfer Segmentation Fault

[Bartlett, Rob]

External Email - Use Caution

Hi Ruopeng,

This is the command I have been using: freeview 
tutorial_data_20190918_1558/diffusion_recons/Diff001/mri/brainmask.mgz

I get the same result when I open freeview and select the volume through the 
GUI.

Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
http://secure-web.cisco.com/19LYNNE_BZY4uNXsZT2DPlO-e9qSS7_qSXcEpIdeuO8BHSYdOBEw0tA2Y2mZZS_ESdRsJZNCJniQdZaYX9YOE5br9hharEv5fR6IrKT2H0mnUBuGg-aSNDEgpsyNkwoczYLh-vkPwBM-X6j5kcwpFaWQUIlArVcG8RTMTrwM7SSw3nltF6H51Hcms88_ZF21dFfzmgnjkCKNSvL73NpE-Lp86RnFmaogdT6rXaJnxcmzWfkuptPReL4cExJd5bTWz4dDrkU5ecHXDQtcQHRkxFh28B95pA8ShyL2PtOI2hlrtXZZB7JvuZCFSj5573w9Tr6d0ZxjQYGqLgqsdU1WJ8g/http%3A%2F%2Fwww.exeter.ac.uk
Laver Building, North Park Road, Exeter, EX4 4QE
[http://secure-web.cisco.com/1D8-qFclQeYgdaV0uo-uTrAbM1eCvJUyjIV22w12pF0Q3eQ_S_Mlgb7T3r_w0vxOAw4p78Yx8KkNV9hz4nzEpYmRyBSC0rItAr094f0ftSA4TDMuQXIXnXKSC2TFWnfEOuB5c2DMw8w-BKhQvV2SUUojLRHK9zByMvvmDZl27FP5JnBEUT-E6ZKCbWZfq0We5LG8f4V47lL8NK8MtFmfHGji9h22vnsQxOrUV8sP3hKRQHEXm4u-BH_xZiFoh09oumIHv2E8NuO-9MiJiL2GaK6MhmNu3MyoOtAMdv13SGVsZ_CNa1BBzjLcrlDP6npzevH55ZtmHFALKXugbpJ2U4A/http%3A%2F%2Fwww.exeter.ac.uk%2Fcodebox%2Femail-sig%2Fstaff-sig.gif]
This email and any attachment may contain information that is confidential, 
privileged, or subject to copyright, and which may be exempt from disclosure 
under applicable legislation. It is intended for the addressee only. If you 
received this message in error, please let me know and delete the email and any 
attachments immediately. The University will not accept responsibility for the 
accuracy/completeness of this email and its attachments.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Wang, Ruopeng
Sent: Tuesday, March 21, 2023 1:35 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.

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 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-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
Terminal Output:
Segmentation fault
Syslog Output:
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863337] ThreadIOWorker[390903]: 
segfault at ad0 ip 5613a159eb5d sp 7fb580f68d00 error 4 in 
freeview[5613a0ee8000+bc1000]
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863358] Code: ef c9 f2 0f 5c 14 24 
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 
c9 48 8d 14 96 48 8d 0c 8e  0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863380] ThreadIOWorker[390885]: 
segfault at fe1a641 ip 5613a159eb5d sp 7fb589f7ad00 error 4
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863393] Code: ef c9 f2 0f 5c 14 24 
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 
c9 48 8d 14 96 48 8d 0c 8e  0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863400] traps: 
ThreadIOWorker[390898] general protection fault ip:5613a159ebe0 sp:7fb58376dd00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863410] traps: 
ThreadIOWorker[390890] general protection fault ip:5613a159ebe0 sp:7fb587775d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863450] traps: 
ThreadIOWorker[390901] general protection fault ip:5613a159eb5d sp:7fb581f6ad00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863478] traps: 
ThreadIOWorker[390875] general protection fault ip:5613a159eb5d sp:7fb58ef84d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863499] traps: 
ThreadIOWorker[390905] general protection fault ip:5613a159eb5d sp:7fb57ff66d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863542] traps: 
ThreadIOWorker[390884] general protection fault ip:5613a159eb5d sp:7fb58a77bd00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863566] traps: 
ThreadIOWorker[390886] general protection fault ip:5613a159ebe0 sp:7fb589779d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863579] traps: 
ThreadIOWorker[390881] general protection fault ip:5613a159eb5d sp:7fb58bf7ed00 
error:0


Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
http://secure-web.cisco.com/19LYNNE_BZY4uNXsZT2DPlO-e9qSS7_qSXcEpIdeuO8BHSYdOBEw0tA2Y2mZZS_ESdRsJZNCJniQdZaYX9YOE5br9hharEv5fR6IrKT2H0mnUBuGg-aSNDEgpsyNkwoczYLh-vkPwBM-X6j5kcwpFaWQUIlArVcG8RTMTrwM7SSw3nltF6H51Hcms88_ZF21dFfzmgnjkCKNSvL73NpE-Lp86RnFmaogdT6rXaJnxcmzWfkuptPReL4cExJd5bTWz4dDrkU5ecHXDQtcQHRkxFh28B95pA8ShyL2PtOI2hlrtXZZB7JvuZCFSj5573w9Tr6d0ZxjQYGqLgqsdU1WJ8g/http%3A%2F%2Fwww.exeter.ac.uk<

Re: [Freesurfer] FreeSurfer Segmentation Fault

[Fischl, Bruce R.,PHD]

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 Email - Use Caution
Hi Bruce, here is the output:

Volume information for 
tutorial_data_20190918_1558/diffusion_recons/Diff001/mri/brainmask.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 12.00 msec, TE: 4.76 msec, TI: 4.76 msec, flip angle: 20.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =  -0., z_r =   0., c_r =-4.5707
  : x_a =   0., y_a =   0., z_a =   1., c_a =40.4204
  : x_s =  -0., y_s =  -1., z_s =   0., c_s = 6.8018

talairach xfm : 
tutorial_data_20190918_1558/diffusion_recons/Diff001/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.  -0.   0.   123.4293
0.   0.   1.   -87.5796
   -0.  -1.   0.   134.8018
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.   0.   123.4293
0.   0.  -1.   134.8018
   -0.   1.  -0.87.5796
   -0.  -0.  -0. 1.

Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
www.exeter.ac.uk<http://www.exeter.ac.uk>
Laver Building, North Park Road, Exeter, EX4 4QE
[http://secure-web.cisco.com/1qEf3w94plVSPmCQ1FMfRUITvU3KTNbP7UPtrGs_S99-pRbZ55SFEcS7XZZ0XIh4VC_M5EYEfDLw9U7BeTl1tz6kyckI0GFpwzy4ZVmV8NJpbIqjsgwWHBgFZhoJmeV2gPm7zWP5o5SPtP1fNHLOsNA__lNJ3eYA5QiJCQKii7aaly3AA-4AAi6CU9IXYFwKrWt2XjfE44z6Q9aQQ6igCyZ4j5bmidXCyBp2zadwM3EDD8SmIzWwM28cvNKvbVnbEwDMDNXWvPvYE0uyc0dxYwfwy1GpOEf1IGV8-KzLT2B1vf0wFmf4WjQMGitf33TW8_XP61FvUV0atf_FRxof5lg/http%3A%2F%2Fwww.exeter.ac.uk%2Fcodebox%2Femail-sig%2Fstaff-sig.gif]
This email and any attachment may contain information that is confidential, 
privileged, or subject to copyright, and which may be exempt from disclosure 
under applicable legislation. It is intended for the addressee only. If you 
received this message in error, please let me know and delete the email and any 
attachments immediately. The University will not accept responsibility for the 
accuracy/completeness of this email and its attachments.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Fischl, Bruce R.,PHD
Sent: Tuesday, March 21, 2023 1:58 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 recognise the sender and know the content 
is safe.

Hi Rob

Can you run mri_info on that volume? And just ls -l to see if it is a 
reasonable size?

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Bartlett, Rob
Sent: Tuesday, March 21, 2023 6:50 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] FreeSurfer 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: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
Terminal Output:
Segmentation fault
Syslog Output:
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863337] ThreadIOWorker[390903]: 
segfault at ad0 ip 5613a159eb5d sp 7fb580f68d00 error 4 in 
freeview[5613a0ee8000+bc1000]
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863358] Code: ef c9 f2 0f 5c 14 24 
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 
c9 48 8d 14 96 48 8d 0c 8e  0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863380] ThreadIOWorker[390885]: 
segfault at fe1a641 ip 5613a159eb5d sp 7fb589f7ad00 error 4
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863393] Code: ef c9 f2 0f 5c 14 24 
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 
c9 48 8d 14 96 48 8d 0c 8e  0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 

Re: [Freesurfer] FreeSurfer Segmentation Fault

[Fischl, Bruce R.,PHD]

Oh, sorry, should have read to the end of my inbox before responding.  What 
does ls -l show for that file?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bartlett, Rob
Sent: Tuesday, March 21, 2023 12:18 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault


External Email - Use Caution
Hi Ruopeng,

This is the command I have been using: freeview 
tutorial_data_20190918_1558/diffusion_recons/Diff001/mri/brainmask.mgz

I get the same result when I open freeview and select the volume through the 
GUI.

Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
www.exeter.ac.uk<http://www.exeter.ac.uk>
Laver Building, North Park Road, Exeter, EX4 4QE
[http://secure-web.cisco.com/1D8-qFclQeYgdaV0uo-uTrAbM1eCvJUyjIV22w12pF0Q3eQ_S_Mlgb7T3r_w0vxOAw4p78Yx8KkNV9hz4nzEpYmRyBSC0rItAr094f0ftSA4TDMuQXIXnXKSC2TFWnfEOuB5c2DMw8w-BKhQvV2SUUojLRHK9zByMvvmDZl27FP5JnBEUT-E6ZKCbWZfq0We5LG8f4V47lL8NK8MtFmfHGji9h22vnsQxOrUV8sP3hKRQHEXm4u-BH_xZiFoh09oumIHv2E8NuO-9MiJiL2GaK6MhmNu3MyoOtAMdv13SGVsZ_CNa1BBzjLcrlDP6npzevH55ZtmHFALKXugbpJ2U4A/http%3A%2F%2Fwww.exeter.ac.uk%2Fcodebox%2Femail-sig%2Fstaff-sig.gif]
This email and any attachment may contain information that is confidential, 
privileged, or subject to copyright, and which may be exempt from disclosure 
under applicable legislation. It is intended for the addressee only. If you 
received this message in error, please let me know and delete the email and any 
attachments immediately. The University will not accept responsibility for the 
accuracy/completeness of this email and its attachments.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of 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 recognise the sender and know the content 
is safe.

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 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-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
Terminal Output:
Segmentation fault
Syslog Output:
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863337] ThreadIOWorker[390903]: 
segfault at ad0 ip 5613a159eb5d sp 7fb580f68d00 error 4 in 
freeview[5613a0ee8000+bc1000]
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863358] Code: ef c9 f2 0f 5c 14 24 
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 
c9 48 8d 14 96 48 8d 0c 8e  0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863380] ThreadIOWorker[390885]: 
segfault at fe1a641 ip 5613a159eb5d sp 7fb589f7ad00 error 4
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863393] Code: ef c9 f2 0f 5c 14 24 
66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 
c9 48 8d 14 96 48 8d 0c 8e  0f 5a 09 f2 0f 58 4c >
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863400] traps: 
ThreadIOWorker[390898] general protection fault ip:5613a159ebe0 sp:7fb58376dd00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863410] traps: 
ThreadIOWorker[390890] general protection fault ip:5613a159ebe0 sp:7fb587775d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863450] traps: 
ThreadIOWorker[390901] general protection fault ip:5613a159eb5d sp:7fb581f6ad00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863478] traps: 
ThreadIOWorker[390875] general protection fault ip:5613a159eb5d sp:7fb58ef84d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863499] traps: 
ThreadIOWorker[390905] general protection fault ip:5613a159eb5d sp:7fb57ff66d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863542] traps: 
ThreadIOWorker[390884] general protection fault ip:5613a159eb5d sp:7fb58a77bd00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863566] traps: 
ThreadIOWorker[390886] general protection fault ip:5613a159ebe0 sp:7fb589779d00 
error:0
Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863579] traps: 
ThreadIOWorker[390881] general protection fault ip:5613a159eb5d sp:7fb58bf7ed00 
error:0


Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
www.exeter.ac.uk<https://secure-web.cisco.com/1NQ2zM67bNnfilf7KmYhsWCSnT3aZeW64usyHYR2Ivs-SBNRx2lTktVbSVzAwV6568W0Jcbw2zXjwSZncqczE1Skh1jgRvvGgxH0VJAsfkpl1gy8

Re: [Freesurfer] FreeSurfer Segmentation Fault

[Bartlett, Rob]

External Email - Use Caution

Hi Bruce,

No problem, thanks for getting back to me quickly.

Here is the output of -l against the file:


brainmask.mgz

-rw-rw-rw- 1 rob rob 1363253 Sep 30  2018 brainmask.mgz



Kind regards,

Rob Bartlett
Research IT Officer
University of Exeter
http://secure-web.cisco.com/1yutBkt5hXhgLKg69R5m3lB60Vj9CohXvvYObck-pTgGNEaDA2-3a9UaPwvspO5Su0Ul-G0w_teCqMbsv_um9Z5yBX6vK6k7uaydp2-NH642Od-uJRrVkPKMGmaGKKquSi7Lnt1uGd5DcGoISePP0PYKv-8ZndKX8EZqpgdC-i6_y4xKPABD9i_Z0KURH2C7--Tf42G8KDjjjIFxRp5xPHb7dyCS5MD-8VDKAgT_DNukIo4g9KsebNEMom57Z5_H-H0qgkZLBSLQHP_omhmzpiy2DzpDl0Cwk0fprWCkLosa9Hsub3F3P5ekTEhuQXStD/http%3A%2F%2Fwww.exeter.ac.uk<https://secure-web.cisco.com/195ldMCIMeP9TanL2FO9mHG9s2SmJbStalYWNnxzCdFvde0YZ5ug4DNHQCTumMjhefXxH-537jY9CI5-IDkrGhzuSV6nXdkc6fDwCSbc3eV3QFddPZfoxREyOA6Kcr-zlh-BPqoJNtMd0-vFfdcJF22zwjwvUY4vb_YELAl5YKqPZciVZ-9k6byv4byzX-ChNqKiWYGsVet3DWRXKrk5Fm_Rx6lHunnZccMh_Lg270pAJ6GZPKORoDUxooeMejHnJ9KmEi1Fj24jx7UQVa8pC_Wbvws5h1YjPt5LnOhI0ZYirJ241TwiXqpuVmdE77HUR/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.exeter.ac.uk%252F%26data%3D05%257C01%257CR.Bartlett2%2540exeter.ac.uk%257Cab38191defec41cba9f908db29ee295f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638149875083781919%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DB0%252B7hoeo%252Bfa%252BUgSXzduACwplHUD9z52ah%252B1AegiL4vo%253D%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: 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, should have read to the end of my inbox before responding.  What 
does ls -l show for that file?



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bartlett, Rob
Sent: Tuesday, March 21, 2023 12:18 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault



External Email - Use Caution

Hi Ruopeng,



This is the command I have been using: freeview 
tutorial_data_20190918_1558/diffusion_recons/Diff001/mri/brainmask.mgz



I get the same result when I open freeview and select the volume through the 
GUI.



Kind regards,

Rob Bartlett
Research IT Officer
University of Exeter
http://secure-web.cisco.com/1yutBkt5hXhgLKg69R5m3lB60Vj9CohXvvYObck-pTgGNEaDA2-3a9UaPwvspO5Su0Ul-G0w_teCqMbsv_um9Z5yBX6vK6k7uaydp2-NH642Od-uJRrVkPKMGmaGKKquSi7Lnt1uGd5DcGoISePP0PYKv-8ZndKX8EZqpgdC-i6_y4xKPABD9i_Z0KURH2C7--Tf42G8KDjjjIFxRp5xPHb7dyCS5MD-8VDKAgT_DNukIo4g9KsebNEMom57Z5_H-H0qgkZLBSLQHP_omhmzpiy2DzpDl0Cwk0fprWCkLosa9Hsub3F3P5ekTEhuQXStD/http%3A%2F%2Fwww.exeter.ac.uk<https://secure-web.cisco.com/1g1hjiS2Mk0w4WAXTFAehecMyo1M5XLjw8QyQ6jvPVwjyZ9hCJX4YqYcGjQ4uFzmDNux3a1l0fdvXb5ge7STRj9srcjKbjnRP4tiepAKJPhHP_fu_Vqce60hyh6YNWqElDqW7zczlzWCC--JheIToryfLuMqy1nWgALp3JTpG2hG3Rc2WirX5KZmgGys8LHTZqsAPylA02hZXoDUj1OCmap4kHDUo7j7DNQu9EcDKKf6IzOnXmK7U4IZCEkGRb3qcPHEnJK0Tbi6W8XDZ1ulanz1XGNWMwBL7NgYaQ2C7lAzcwwixCImzMfcCbJiatrzY/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.exeter.ac.uk%252F%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257C627ae2f2d00e4535c78d08db2a3dc38f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150216985257453%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DsPN1LwBsgTbvVcmyqSOITEZHkuPxtoe4m%252Fsj%252F2DE57k%253D%26reserved%3D0>
Laver Building, North Park Road, Exeter, EX4 4QE

[http://secure-web.cisco.com/1D8-qFclQeYgdaV0uo-uTrAbM1eCvJUyjIV22w12pF0Q3eQ_S_Mlgb7T3r_w0vxOAw4p78Yx8KkNV9hz4nzEpYmRyBSC0rItAr094f0ftSA4TDMuQXIXnXKSC2TFWnfEOuB5c2DMw8w-BKhQvV2SUUojLRHK9zByMvvmDZl27FP5JnBEUT-E6ZKCbWZfq0We5LG8f4V47lL8NK8MtFmfHGji9h22vnsQxOrUV8sP3hKRQHEXm4u-BH_xZiFoh09oumIHv2E8NuO-9MiJiL2GaK6MhmNu3MyoOtAMdv13SGVsZ_CNa1BBzjLcrlDP6npzevH55ZtmHFALKXugbpJ2U4A/http%3A%2F%2Fwww.exeter.ac.uk%2Fcodebox%2Femail-sig%2Fstaff-sig.gif]

This email and any attachment may contain information that is confidential, 
privileged, or subject to copyright, and which may be exempt from disclosure 
under applicable legislation. It is intended for the addressee only. If you 
received this message in error, please let me know and delete the email and any 
attachments immediately. The University will not accept responsibility for the 
accuracy/completeness of this email and its attachments.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Wang, Ruopeng
Sent: Tuesday, March 21, 2023 1:35 PM
To:

Re: [Freesurfer] FreeSurfer Segmentation Fault

[Wang, Ruopeng]

Have you tried loading a different volume in the same folder? Such as 
brain.mgz. Will you get the same error?

On Mar 22, 2023, at 6:50 AM, Bartlett, Rob 
mailto:r.bartle...@exeter.ac.uk>> wrote:

External Email - Use Caution

Hi Bruce,

No problem, thanks for getting back to me quickly.

Here is the output of -l against the file:

brainmask.mgz
-rw-rw-rw- 1 rob rob 1363253 Sep 30  2018 brainmask.mgz


Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
www.exeter.ac.uk<https://secure-web.cisco.com/195ldMCIMeP9TanL2FO9mHG9s2SmJbStalYWNnxzCdFvde0YZ5ug4DNHQCTumMjhefXxH-537jY9CI5-IDkrGhzuSV6nXdkc6fDwCSbc3eV3QFddPZfoxREyOA6Kcr-zlh-BPqoJNtMd0-vFfdcJF22zwjwvUY4vb_YELAl5YKqPZciVZ-9k6byv4byzX-ChNqKiWYGsVet3DWRXKrk5Fm_Rx6lHunnZccMh_Lg270pAJ6GZPKORoDUxooeMejHnJ9KmEi1Fj24jx7UQVa8pC_Wbvws5h1YjPt5LnOhI0ZYirJ241TwiXqpuVmdE77HUR/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.exeter.ac.uk%252F%26data%3D05%257C01%257CR.Bartlett2%2540exeter.ac.uk%257Cab38191defec41cba9f908db29ee295f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638149875083781919%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DB0%252B7hoeo%252Bfa%252BUgSXzduACwplHUD9z52ah%252B1AegiL4vo%253D%26reserved%3D0>
Laver Building, North Park Road, Exeter, EX4 4QE


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce R.,PHD 
mailto:bfis...@mgh.harvard.edu>>
Sent: 21 March 2023 18:52
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 recognise the sender and know the content 
is safe.

Oh, sorry, should have read to the end of my inbox before responding.  What 
does ls -l show for that file?



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Bartlett, Rob
Sent: Tuesday, March 21, 2023 12:18 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault



External Email - Use Caution
Hi Ruopeng,



This is the command I have been using: freeview 
tutorial_data_20190918_1558/diffusion_recons/Diff001/mri/brainmask.mgz



I get the same result when I open freeview and select the volume through the 
GUI.



Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
www.exeter.ac.uk<https://secure-web.cisco.com/1g1hjiS2Mk0w4WAXTFAehecMyo1M5XLjw8QyQ6jvPVwjyZ9hCJX4YqYcGjQ4uFzmDNux3a1l0fdvXb5ge7STRj9srcjKbjnRP4tiepAKJPhHP_fu_Vqce60hyh6YNWqElDqW7zczlzWCC--JheIToryfLuMqy1nWgALp3JTpG2hG3Rc2WirX5KZmgGys8LHTZqsAPylA02hZXoDUj1OCmap4kHDUo7j7DNQu9EcDKKf6IzOnXmK7U4IZCEkGRb3qcPHEnJK0Tbi6W8XDZ1ulanz1XGNWMwBL7NgYaQ2C7lAzcwwixCImzMfcCbJiatrzY/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.exeter.ac.uk%252F%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257C627ae2f2d00e4535c78d08db2a3dc38f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150216985257453%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DsPN1LwBsgTbvVcmyqSOITEZHkuPxtoe4m%252Fsj%252F2DE57k%253D%26reserved%3D0>
Laver Building, North Park Road, Exeter, EX4 4QE
[http://secure-web.cisco.com/1D8-qFclQeYgdaV0uo-uTrAbM1eCvJUyjIV22w12pF0Q3eQ_S_Mlgb7T3r_w0vxOAw4p78Yx8KkNV9hz4nzEpYmRyBSC0rItAr094f0ftSA4TDMuQXIXnXKSC2TFWnfEOuB5c2DMw8w-BKhQvV2SUUojLRHK9zByMvvmDZl27FP5JnBEUT-E6ZKCbWZfq0We5LG8f4V47lL8NK8MtFmfHGji9h22vnsQxOrUV8sP3hKRQHEXm4u-BH_xZiFoh09oumIHv2E8NuO-9MiJiL2GaK6MhmNu3MyoOtAMdv13SGVsZ_CNa1BBzjLcrlDP6npzevH55ZtmHFALKXugbpJ2U4A/http%3A%2F%2Fwww.exeter.ac.uk%2Fcodebox%2Femail-sig%2Fstaff-sig.gif]
This email and any attachment may contain information that is confidential, 
privileged, or subject to copyright, and which may be exempt from disclosure 
under applicable legislation. It is intended for the addressee only. If you 
received this message in error, please let me know and delete the email and any 
attachments immediately. The University will not accept responsibility for the 
accuracy/completeness of this email and its attachments.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Wang, Ruopeng
Sent: Tuesday, March 21, 2023 1:35 PM
T

Re: [Freesurfer] FreeSurfer Segmentation Fault

[Bartlett, Rob]

External Email - Use Caution

I get the same error when trying to open any files with the .mgz extension that 
I have tried so far.


Kind regards,

Rob Bartlett
Research IT Officer
University of Exeter
http://secure-web.cisco.com/11On7gOdpigOmuygGY56ARMyr9yhP1a_j0p5BeqsZ8OgvVK-3VeBdHzPQkU6g6AujIrlnLXENFNv33eJR93kF6_oY-MKMU9CBIINa3IbasV9RXGSdkS_BVb1aF6cDi6skhqk-2IyXHCwiQ_oZ5N-049leIYaTit-UBX9z9Wljy-qpV1GGIubV17gP648dTQZhNM68P9P6sLmzXi9c2qgemjhciaXuckwIKSChzuICAVox6-l7AepcvApDgBiyBQYWiMbluf9EeKsDQxjhwqQl39klW1L-aZtHSyRNPZ3Ds_9RKAPtlrqRLhyaL7ks1GxgR3wYZ6EEevwN5QPIHIYkOw/http%3A%2F%2Fwww.exeter.ac.uk<https://secure-web.cisco.com/1Ao_nmhMWqLMJ0SApqz0FgGFfr6xrL6fjzJm5-0MmLUs0YDiRm7kfdIlpEAYsrzJfs2UyJiQGCDucny_3mQF-l6JcA_ZBHP5Q2UL1CWFplbYHtHTIqfCBHARFa75kMbdhHbkurMyAvTTcIUs5sJkiumTevGCyOG_dEBCnonPQh3VCUlRmtf4oisqWYysvjoREOBNS_ksLhehgjL1zRcW0JgBOApEsM5Vl63vj3UUnsI_INIrhIKn_ZhckXJDPlXAjIef05KmS1FGt_MUaDnXf8_FwSZLFB3jTcKB_JaOibuE0dZxvnGPB4BiA25JoqN4rq9e_2OFf7flVBzWH17Ufjw/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.exeter.ac.uk%252F%26data%3D05%257C01%257CR.Bartlett2%2540exeter.ac.uk%257Cab38191defec41cba9f908db29ee295f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638149875083781919%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DB0%252B7hoeo%252Bfa%252BUgSXzduACwplHUD9z52ah%252B1AegiL4vo%253D%26reserved%3D0>
Laver Building, North 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 of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.

Have you tried loading a different volume in the same folder? Such as 
brain.mgz. Will you get the same error?

On Mar 22, 2023, at 6:50 AM, Bartlett, Rob 
mailto:r.bartle...@exeter.ac.uk>> wrote:

External Email - Use Caution

Hi Bruce,

No problem, thanks for getting back to me quickly.

Here is the output of -l against the file:

brainmask.mgz
-rw-rw-rw- 1 rob rob 1363253 Sep 30  2018 brainmask.mgz


Kind regards,
Rob Bartlett
Research IT Officer
University of Exeter
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://secure-web.cisco.com/11On7gOdpigOmuygGY56ARMyr9yhP1a_j0p5BeqsZ8OgvVK-3VeBdHzPQkU6g6AujIrlnLXENFNv33eJR93kF6_oY-MKMU9CBIINa3IbasV9RXGSdkS_BVb1aF6cDi6skhqk-2IyXHCwiQ_oZ5N-049leIYaTit-UBX9z9Wljy-qpV1GGIubV17gP648dTQZhNM68P9P6sLmzXi9c2qgemjhciaXuckwIKSChzuICAVox6-l7AepcvApDgBiyBQYWiMbluf9EeKsDQxjhwqQl39klW1L-aZtHSyRNPZ3Ds_9RKAPtlrqRLhyaL7ks1GxgR3wYZ6EEevwN5QPIHIYkOw/http%3A%2F%2Fwww.exeter.ac.uk<https://secure-web.cisco.com/1Wml9lhUT26ZPphpwU0GnmdMmVs2KQzl8N9RhG1zIdq6JetDNCV9xUtgU-ktF1Ye8DdXwEG04fN7UryW-9ljeGo-j5EvfdIHD4Y4psB6I_l2_UHO9G5As1kdNURXLPsCndXFvuBmdUzTmlWdb4JAOmChaVWd0U76KxDE4O4Qrob5bGipgAjPawbpqCJ_SL1lwulZSiC7ZRnTdAKo95GTkqj731rJ8cYwsnVC85AxCThO8PqlBhgR0MG8k8TeIq0Ku-wpWyp7UapbyvaNwFUI1crqpU9UQk9Pp1zrOmmovCFnrVBOqC4nE7YjNlT6yR98y_9h0_yrOOFthcUK2XJK80A/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F195ldMCIMeP9TanL2FO9mHG9s2SmJbStalYWNnxzCdFvde0YZ5ug4DNHQCTumMjhefXxH-537jY9CI5-IDkrGhzuSV6nXdkc6fDwCSbc3eV3QFddPZfoxREyOA6Kcr-zlh-BPqoJNtMd0-vFfdcJF22zwjwvUY4vb_YELAl5YKqPZciVZ-9k6byv4byzX-ChNqKiWYGsVet3DWRXKrk5Fm_Rx6lHunnZccMh_Lg270pAJ6GZPKORoDUxooeMejHnJ9KmEi1Fj24jx7UQVa8pC_Wbvws5h1YjPt5LnOhI0ZYirJ241TwiXqpuVmdE77HUR%252Fhttps%25253A%25252F%25252Feur03.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttp%2525253A%2525252F%2525252Fwww.exeter.ac.uk%2525252F%252526data%25253D05%2525257C01%2525257CR.Bartlett2%25252540exeter.ac.uk%2525257Cab38191defec41cba9f908db29ee295f%2525257C912a5d77fb984eeeaf321334d8f04a53%2525257C0%2525257C0%2525257C638149875083781919%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%2525257C%2525257C%2525257C%252526sdata%25253DB0%2525252B7hoeo%2525252Bfa%2525252BUgSXzduACwplHUD9z52ah%2525252B1AegiL4vo%2525253D%252526reserved%25253D0%26data%3D05%257C01%257Cr.bartlett2%2540exeter.ac.uk%257C6c0e4745448048d471e608db2adb2c4f%257C912a5d77fb984eeeaf321334d8f04a53%257C0%257C0%257C638150893089192774%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DKRUppguaaFWZ9DGc4VAB9V0A731irntFz68jmREY4Hw%253D%26reserved%3D0>
Laver Building, North Park Road, Exeter, EX4 4QE


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce R.,PHD 
mailto:bfis...@mgh

Re: [Freesurfer] Segmentation Fault Question

[Douglas N Greve]

It's dying when creating the output directory. Does the output dir get 
created? If not, do you have write permissions to that dir?

doug

Allie Rosen wrote:
> Hi,
>
> I am accessing my subject directory on a network attached drive. When 
> I run mri glmfit it segfaults. However, it works if the subject 
> directory is on my own computer. Do you have any way to do this with 
> the subject directory on the network drive?
>
> Below is a sample output.
>
> Thanks,
> Allie
>
> Caduceus:~/ammonis/fsSubjects/subjects_archive> mri_glmfit --y 
> lh.smoothed.thickness.6.mgz --fsgd GDF1.txt doss --glmdir 
> lh.smoothed.thickness.6.glmdir --surf fsaverage lh --C ContrastAge.txt
> gdfReadHeader: reading GDF1.txt
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> Continuous Variable Means (all subjects)
> 0 Age 40.0625
> 1 PCS 9.875
> 2 Neuro 17.8125
> 3 Extro 30
> 4 Open 28.875
> 5 Agree 32.4375
> 6 Consc 34.625
> Class Means of each Continuous Variable
> 1 Control 40.0625   9.8750  17.8125  30.  28.8750  32.4375  34.6250 
> INFO: gd2mtx_method is doss
> Reading source surface 
> /media/AMMONIS/fsSubjects/subjects_archive/fsaverage/surf/lh.white
> reading group avg surface area 822 cm^2 from file
> Reading in average area 
> /media/AMMONIS/fsSubjects/subjects_archive/fsaverage/surf/lh.white.avg.area.mgh
> Number of vertices 163842
> Number of faces327680
> Total area 65416.648438
> AvgVtxArea   0.399267
> AvgVtxDist   0.721953
> StdVtxDist   0.195470
>
> $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $
> cwd /media/AMMONIS/fsSubjects/subjects_archive
> cmdline mri_glmfit --y lh.smoothed.thickness.6.mgz --fsgd GDF1.txt 
> doss --glmdir lh.smoothed.thickness.6.glmdir --surf fsaverage lh --C 
> ContrastAge.txt 
> sysname  Linux
> hostname Caduceus
> machine  x86_64
> user arosen
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y
> /media/AMMONIS/fsSubjects/subjects_archive/lh.smoothed.thickness.6.mgz
> logyflag 0
> usedti  0
> FSGD GDF1.txt
> glmdir lh.smoothed.thickness.6.glmdir
> IllCondOK 0
> DoFFx 0
> Creating output directory lh.smoothed.thickness.6.glmdir
> Segmentation fault
> 
>
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[Freesurfer] Segmentation Fault during mri_ca_normalize

[Tali Swisher]

Hi all,

I was having consistent errors with two cases during mri_ca_normalize, and
after using an updated version (mri_ca_normalize_centos), one case went
through smoothly. I'm having trouble with the second case, however; it now
repeatedly reports a segmentation fault partway through mri_ca_normalize
(error message below) - any ideas??

Thanks!
Tali Swisher

#@# CA Normalize Thu Jul 21 12:25:47 EDT 2011
/home/pnlstaff/freesurfer/subjects/umd_V2_20110711/mri

 mri_ca_normalize -mask brainmask.mgz nu.mgz
/share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca
transforms/talairach.lta norm.mgz

using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes
reading atlas from
'/share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 102 --> 107
resetting gm mean[0]: 64 --> 64
input volume #1 is the most T1-like
using real data threshold=19.0
using (122, 88, 141) as brain centroid...
mean wm in atlas = 107, using box (106,72,120) --> (137, 104,162) to find
MRI wm
before smoothing, mri peak at 215
after smoothing, mri peak at 214, scaling input intensities by 0.500
scaling channel 0 by 0.5
using 244171 sample points...
INFO: compute sample coordinates transform
 1.134   0.005   0.006  -38.602;
 0.006   1.132   0.138  -19.653;
 0.004  -0.150   1.048  -20.038;
 0.000   0.000   0.000   1.000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter
found 41584 control points for structure...
bounding box (142, 46, 61) --> (202, 147, 218)
Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 111.0
19 of 76 (25.0%) samples deleted
finding control points in Right_Cerebral_White_Matter
found 40735 control points for structure...
bounding box (87, 48, 60) --> (144, 148, 219)
Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 107.0
27 of 73 (37.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter
found 3012 control points for structure...
bounding box (146, 122, 85) --> (188, 161, 136)
Left_Cerebellum_White_Matter: limiting intensities to 92.0 --> 105.0
5 of 18 (27.8%) samples deleted
finding control points in Right_Cerebellum_White_Matter
found 2764 control points for structure...
bounding box (103, 122, 83) --> (144, 160, 137)
Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 108.0
0 of 7 (0.0%) samples deleted
finding control points in Brain_Stem
found 3520 control points for structure...
bounding box (130, 115, 118) --> (158, 176, 147)
Segmentation fault
Linux compute-2-1.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006
x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Thu Jul 21 12:28:18 EDT 2011



-- 
Talis M. Swisher, BA
Research Assistant
Psychiatry Neuroimaging Laboratory
Harvard Medical School, Brigham and Women's Hospital
1249 Boylston St, 3rd Floor
Boston, MA 02215
Office: (617) 525-6119
Cell: (336) 577-5071
Fax: (617) 525-6150
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[Freesurfer] Segmentation fault during -autorecon1

[Palzes, Vanessa]

Hello,

 

I am continuously getting a "Segmentation fault" error during
-autorecon1 when it's running mri_binarize. I have been running
Freesurfer on a Mac, but now I am trying to implement it using Linux. I
am running this version:
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on Linux
2.6.9-89.0.20.ELsmp x86_64.

 

I this a memory issue, or can there be another explanation? I've tried
multiple times and with different subjects.

 

Here is my log output:

 

home/harshad/data5/Freesurfer/PATHD/process/P2608/mri/] [2011-09-13
16:08:43] running:

  /usr/local/freesurfer//mni/bin/make_template -quiet -shrink 3
./tmp.mri_nu_correct.mni.31037/nu1.mnc
./tmp.mri_nu_correct.mni.31037/1//template.mnc

 

Transforming
slices:.
.Done

Transforming
slices:.
.Done

 

mri_binarize --i ./tmp.mri_nu_correct.mni.31037/nu2.mnc --min -1 --o
./tmp.mri_nu_correct.mni.31037/ones.mgz

Segmentation fault 

Linux vhasfcapp21 2.6.9-89.0.20.ELsmp #1 SMP Mon Jan 18 12:19:33 EST
2010 x86_64 x86_64 x86_64 GNU/Linux

 

recon-all -s P2608 exited with ERRORS at Tue Sep 13 16:10:11 PDT 2011

 

 

Any help would be greatly appreciated.

 

Thanks,

 

Vanessa Palzes

Research Assistant

Brain Imaging & EEG Lab

San Francisco VA Medical Center

4150 Clement Street

San Francisco, CA 94121

Tel: 415-221-4810 ext. 6155

 

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[Freesurfer] Segmentation fault wmparc a2009s

[Lena Palaniyappan]

I am trying to derive wmparc volumes for a2009s which are by default not
available in wmparc (segments read empty) _ is this because Desikan/Killiany
atlas is used in wmparc by default?

So I decided to run

Mri_aparc2aseg for each subject using
mri_aparc2aseg --s  --annot aparc.a2009s --o mri/wmparc.a2009.mgz
--labelwm --rip-unknown --ctxseg aparc.a2009s+aseg.mgz

I thought this would generate a new wmparc which will now include labels for
wm from a2009s

Then I ran 

mri_segstats --seg mri/wmparc.a2009.mgz --sum stats/wmparc.a2009.stats --pv
mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask
mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm
--in-intensity-units MR --etiv --subject MPRAGE04 --surf-wm-vol --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt

Hoping that this would allow me to obtain statistics from this wmparc file

But for some reason I am getting segmentation fault message as below



atlas_icv (eTIV) = 1663710 mm^3(det: 1.170940 )
Loading mri/wmparc.a2009.mgz
Getting Cerebral WM volumes from surface
lh white matter volume 277542
rh white matter volume 284002
Loading mri/norm.mgz
Loading mri/norm.mgz
Loading mri/brainmask.mgz
# nbrainmaskvoxels 1740943
# brainmaskvolume  1740943.0
# nbrainsegvoxels 260991
# brainsegvolume   260991.0
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1190 segmentations
Computing statistics for each segmentation
  1 1  Left-Cerebral-Exterior  0
  2 2  Left-Cerebral-White-Matter  0
 3 3  Left-Cerebral-Cortex  0
  4 4  Left-Lateral-Ventricle 3953  3953
  5 5  Left-Inf-Lat-Vent  142  142
  6 6  Left-Cerebellum-Exterior  0
  7 7  Left-Cerebellum-White-Matter 15484  15484
  8 8  Left-Cerebellum-Cortex Segmentation fault

Could anyone help please?
Cheers
Lena

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Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of
Nottingham) 
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH



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[Freesurfer] Segmentation fault during mri_segment

[Diandra Lucia]

Hi again,

As we process more cases, we've run into four cases that have had the
same problem.  Each has segfaulted during mri_segment during
autorecon2; here is one example:

#...@# Mask BFS Mon Jul 19 23:38:35 EDT 2010
/home/pnlstaff/freesurfer/subjects/case2403/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz

threshold mask volume at 5
Writing masked volume to brain.finalsurfs.mgz...done.
#
#...@# WM Segmentation Mon Jul 19 23:38:41 EDT 2010

 mri_segment brain.mgz wm.seg.mgz

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (105.0): 105.7 +- 6.1 [80.0 --> 125.0]
GM (72.0) : 71.1 +- 8.6 [30.0 --> 96.0]
setting bottom of white matter range to 79.6
setting top of gray matter range to 88.2
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
12443 sparsely connected voxels removed...
thickening thin strands
Segmentation fault
Linux compute-2-7.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST
2006 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Mon Jul 19 23:40:24 EDT 2010


They all segfaulted at exactly the same place.  These were run with
freesurfer-Linux-rh9-stable-pub-v4.2.0 (without the new version of the
mri_ca_normalize you sent me recently). Please let me know if you need
anything else (data, etc) to help troubleshoot this.

Thanks,
Diandra


-- 
Diandra Lucia
Research Assistant
Project Coordinator
INTRuST Neuroimaging Leadership Core
Psychiatry Neuroimaging Lab, BWH
1249 Boylston St., Boston, MA 02115

email:dian...@bwh.harvard.edu
phone:   617-525-6118
cell:   602-332-7013
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[Freesurfer] Segmentation fault at mri_ca_register

[MacDonald, Christine]

Greetings from St.  Louis.  I recently installed Freesurfer version 4.5
on my Windows XP OS PC after attending your training course held at our
institution, Washington University.  The install went fine, and I was
able to make it through all the checks in your setup and installation
series on your wiki page.  I attempted to then run a data set of my own
and ran into the following error during autorecon2 which I have included
the lines of output right before it as well:

setting smoothness coefficient to 2.00

blurring input image with Gaussian with sigma=2.000...

: dt=0.000, rms=0.465, neg=0, invalid=766

0495: dt=0.028000, rms=0.464 (0.163%), neg=0, invalid=766

0496: dt=0.028000, rms=0.463 (0.154%), neg=0, invalid=766

0497: dt=0.024000, rms=0.463 (0.124%), neg=0, invalid=766

0498: dt=0.000438, rms=0.463 (0.002%), neg=0, invalid=766

0499: dt=0.000438, rms=0.463 (0.002%), neg=0, invalid=766

0500: dt=0.000219, rms=0.463 (0.001%), neg=0, invalid=766

0501: dt=0.14, rms=0.463 (0.000%), neg=0, invalid=766

0502: dt=0.00, rms=0.463 (0.000%), neg=0, invalid=766

blurring input image with Gaussian with sigma=0.500...

: dt=0.000, rms=0.463, neg=0, invalid=766

0503: dt=0.00, rms=0.463 (0.000%), neg=0, invalid=766

Segmentation fault

ERROR: mri_ca_register with non-zero status 139

but continuing despite the error

#--

#...@# CA Reg Inv Fri Jul 23 18:12:09 EDT 2010

/data/TB3241W/TB3241W/mri

 mri_ca_register -invert-and-save transforms/talairach.m3z 

Loading, Inverting, Saving, Exiting ...

Reading transforms/talairach.m3z 

ERROR: cannot find or read transforms/talairach.m3z

ERROR: mri_ca_register with non-zero status 0

Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17
01:57:59 UTC 2009 i686 GNU/Linux

recon-all exited with ERRORS at Fri Jul 23 18:12:10 EDT 2010

 

I am running with 4G of RAM and a quad-core processor.  At first I
thought it was because of the 2GB max space limit in VMware so I even
built and mounted a 100GB drive internal to VMware and ran all the data
from there.  Additionally when I check the disk space after this error
it shows it only used ~1% of the 100GB mounted disk in VMware so I know
I have room.   Output from typing 'bugr' per your request on wiki is the
following:

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0

Debian version: 5.0

Kernel info: Linux 2.6.28-11-generic i686

Any thoughts or guidance as to what may be going wrong?  I fully admit
to my novice status with Freesufer and kindly look forward to any and
all advice.  I found one reference to a similar problem searching
through your Freesurfer support Old Archive but the response from your
organization was just a further inquiry for additional information so I
was unsure as to how to proceed.  Thank you in advance for the help!

 

Best Regards,

Christine Mac Donald

Washington University 

Saint Louis, MO

 

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[Freesurfer] segmentation fault during mri_glmfit

[Bum Seok Jeong]

Dear freesurfer users

I got an error message during mri_glmfit. (please see below my error 
message)
I was able to find 'mri_glmfit.log' file in './glm/lh.dx_age.glmdir' 
directory


Thank you for advance
---
These are my constrasts.
: to construct the contrast vector for testing volume change according 
to age = age.mat

 0 0 0 1
: for effect of interest (ANOVA: f test) -> Am I right?
 1 0 0 0
  0 1 0 0
 0 0 1 0
: for difference btw 3 group independent of age -> Am I right?
-1 0 1 0
0 -1 1 0

There are three class and one variable (see below my FSGD file)
# FSGD file
GroupDescriptorFile 1
Title Thickness vs Dx and Age
Class A circle blue
Class B circle green
Class C plus red
Variables Age
Input   61  A  71
Input   54  A  72
Input   12  B  74
Input   33  B  77
Input   63  C  80
Input   01  C  87
..
DefaultVariable Age

# Error message
mri_glmfit --y lh.dx_age.thickness.10.mgh \--fsgd my_dx_age_1_fsgd.txt 
doss \--glmdir lh.dx_age.glmdir \--surf average lh \--C age.mat

gdfReadHeader: reading my_dx_age_1_fsgd.txt
INFO: ignoring tag vs
INFO: gd2mtx_method is doss
Reading source surface /GR/average/surf/lh.white
reading group avg surface area 936 cm^2 from file
Reading in average area /GR/average/surf/lh.white.avg.area.mgh
Number of vertices 163842
Number of faces327680
Total area 62167.195312
AvgVtxArea   0.379434
AvgVtxDist   0.717000
StdVtxDist   0.244431

$Id: mri_glmfit.c,v 1.83 2006/03/10 23:26:51 greve Exp $
cwd /GR/group_analysis/glm
cmdline mri_glmfit --y lh.dx_age.thickness.10.mgh --fsgd 
my_dx_age_1_fsgd.txt doss --glmdir lh.dx_age.glmdir --surf average lh 
--C age.mat

sysname  Linux
hostname ***
machine  x86_64
user ***
FixVertexAreaFlag = 1
OneSampleGroupMean 0
y/GR/group_analysis/glm/lh.dx_age.thickness.10.mgh
FSGD my_dx_age_1_fsgd.txt
glmdir lh.dx_age.glmdir
Creating output directory lh.dx_age.glmdir
Loading y from /GR/group_analysis/glm/lh.dx_age.thickness.10.mgh
Matrix condition is 177.843
search space = 93594.7
Segmentation fault
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[Freesurfer] segmentation fault error, mri_ca_register

[Teddy Youn]

Hi all,

I have a scan of a patient that I've tried troubleshooting via the listserv and 
fswiki, but with no success.  Generally, during mri_ca_register, I end up with 
a segmentation fault of the following:

-
gca peak Unknown = 0.94091 ( 0)
gca peak Left_Inf_Lat_Vent = 0.14709 (39)
gca peak CSF = 0.14344 (47)
gca peak Left_Accumbens_area = 0.20088 (67)
gca peak Left_undetermined = 0.98433 (34)
gca peak Left_vessel = 0.32698 (60)
gca peak Left_choroid_plexus = 0.11007 (56)
gca peak Right_Inf_Lat_Vent = 0.20176 (34)
gca peak Right_Accumbens_area = 0.32293 (69)
gca peak Right_vessel = 0.36466 (58)
gca peak Right_choroid_plexus = 0.09865 (51)
gca peak Fifth_Ventricle = 0.66382 (40)
gca peak WM_hypointensities = 0.12408 (82)
gca peak non_WM_hypointensities = 0.07897 (54)
gca peak Optic_Chiasm = 0.38389 (74)
Segmentation fault
[swmed-xryrdix93:CorrectedBrainsGE/TBI/St43] teresa%  
-

I can forward a recon-all.log of this subject.  I've also had some major issues 
with intensity inhomogeneities where the pial, wm, and orig surfaces will not 
pick up the sulci in certain regions of the cortex (the wm -aux volume just 
looks like one big blob of grey).   I've tried using -nuiterations 4, 150, 
etc., but have not had much success.  

Any suggestions would be greatly appreciated.

Warm Regards,


-t

Doris Duke Clinical Research Fellow '07-'08 
North Texas TBI Research Center
UT Southwestern Medical Center at Dallas 
Warren Alpert School of Medicine at Brown University, MD '09
[EMAIL PROTECTED] 
(401)-714-2847 

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[Freesurfer] segmentation fault (core dumped)

[Zhangyuanchao]

Dear Mr or Ms,
  My computer was installed with Freesurfer v4.0.3,centos4,
  To make an average surface,I launch "make_average_subject" command,
  I come across an error : 
Processing subject 25/52 sh45 ...
  Reading /media/sda5/yczhang/sh45/surf/lh.sphere.reg
  Segmentation fault (core dumped).
  Could you help me? How can I solve the problem? 
  Thanks!
   yczhang
  

   
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Re: [Freesurfer] Segmentation fault - mris_make_surfaces

[Bruce Fischl]

Hi Adrian,

If you run it again can you replicate the crash? If so, can you send us the 
subject so we can fix it?

cheers,
Bruce


On Mon, 12 Jan 2009, Adrian 
Williams wrote:




Dear all

Came across a segmentation fault while running recon-all, specifically
during mris_make_surfaces... Output pasted below...

Any ideas/help greatly appreciated!

Adrian.


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Re: [Freesurfer] Segmentation fault - mris_make_surfaces

[Adrian Williams]

Hi Bruce

I ran the last command issued by recon-all:

mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs adrian rh

And would you believe it ran without error! Presumably if one comes across
segmentation errors in future, the first thing is to try and replicate them?

How do I continue with the recon-all process? Is it just a case of:

recon-all -s adrian -autorecon2-pial -autorecon3

Many thanks,

Adrian.
-- 
Adrian L. Williams, PhD
Centre for Cognition & Neuroimaging
Brunel University
Uxbridge
Middlesex
UB8 3PH



On 12/1/09 12:29, "Bruce Fischl"  wrote:

> Hi Adrian,
> 
> If you run it again can you replicate the crash? If so, can you send us the
> subject so we can fix it?
> cheers,
> Bruce
> 
> 
> On Mon, 12 Jan 2009, Adrian
> Williams wrote:
> 
>> 
>> Dear all
>> 
>> Came across a segmentation fault while running recon-all, specifically
>> during mris_make_surfaces... Output pasted below...
>> 
>> Any ideas/help greatly appreciated!
>> 
>> Adrian.
>> 

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Re: [Freesurfer] Segmentation fault - mris_make_surfaces

[Bruce Fischl]

Hi Adrian,

you can always do:

recon-all -s adrian -make all

and it will redo the steps that it needs. If the bug doesn't replicate it's 
tough to fix, and could be a real bug or some other issue (bad memory chip, 
full disk, etc...).


cheers,
Bruce

On Tue, 13 Jan 2009, Adrian 
Williams wrote:




Hi Bruce

I ran the last command issued by recon-all:

   mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs adrian rh

And would you believe it ran without error! Presumably if one comes across
segmentation errors in future, the first thing is to try and replicate them?

How do I continue with the recon-all process? Is it just a case of:

   recon-all -s adrian -autorecon2-pial -autorecon3

Many thanks,

Adrian.


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[Freesurfer] segmentation fault with mprph_subject

[Chekema Nayasha Prince]

Hello,

I received the following segmentation fault when I ran morph_subject:

mris2rgb -o hr_MPRAGE_040623/.reg -both -c
/home/freesurfer/freesurfer-20040218/freesurfer//subjects/hr_MPRAGE_040623//surf/lh.sulc
-canon
/home/freesurfer/freesurfer-20040218/freesurfer//subjects/hr_MPRAGE_040623//surf/lh.sphere.reg
/home/freesurfer/freesurfer-20040218/freesurfer//subjects/hr_MPRAGE_040623//surf/lh.sphere.reg
/home/freesurfer/freesurfer-20040218/freesurfer//subjects/hr_MPRAGE_040623//rgb
-
using hr_MPRAGE_040623/.reg as output stem
reading canonical coordinates from
/home/freesurfer/freesurfer-20040218/freesurfer//subjects/hr_MPRAGE_040623//surf/lh.sphere.reg.
writing rgb file
/home/freesurfer/freesurfer-20040218/freesurfer//subjects/hr_MPRAGE_040623//rgb/lateral.lh.hr_MPRAGE_040623/.reg.rgb
iopen: can't open output file
/home/freesurfer/freesurfer-20040218/freesurfer//subjects/hr_MPRAGE_040623//rgb/lateral.lh.hr_MPRAGE_040623/.reg.rgb

No such file or directory
Segmentation fault
mris2rgb exited with errors

After checking the message thread I noticed that someone else also had a similar
error and you recommended that they comment out the mris2rgb line. I looked in
the morph_rgb-lh and rh files and the call to mris2rgb was already commented
out.
Is there any other other reason that this error could be appearing. I ran the
subject with recon-all -stage1 and then I did the manual edits and run
fix_subject and make_final_surfaces_subject.

thanks
-keyma
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[Freesurfer] segmentation fault during mri_convert

[Margaret Duff]

Hi,  Is mri_convert setup yet to convert to mgz format?  I have been 
trying it in both the std and dev environment from dicom format and spm 
format and i keep getting a segmentation fault.  it still converts to cor 
format fine but i thought we were trying to get away from that.  i dont 
know exactly whats 
causing it, but here is my command line and the running information.


troy:mduff[84] mri_convert -ot mgz -it dicom 33749275 
$SUBJECTS_DIR/SM2C1_autoreconall/mri/orig/002
mri_convert -ot mgz -it dicom 33749275 
/space/troy/1/users/FREESURFER/SM2C1_autoreconall/mri/orig/002

reading from 33749275...
Getting Series No
Scanning Directory
INFO: Found 131 files in 
/autofs/space/troy_002/users/fmridata/sm2c1_041118/3danat/dicom/028

INFO: Scanning for Series Number 28
INFO: found 128 files in series
INFO: loading series header info.

INFO: sorting.
RunNo = 27
INFO: (256 256 128), nframes = 1, ismosaic=0
FileName 
/autofs/space/troy_002/users/fmridata/sm2c1_041118/3danat/dicom/028/33747925

Identification
NumarisVersyngo MR 2004V 4VB11D
ScannerModel  Avanto
PatientName   sm2c1
Date and time
StudyDate 20041118
StudyTime 180537.015000
SeriesTime190942.968000
AcqTime   190056.292500
Acquisition parameters
PulseSeq  tfl3d1_ns
Protocol  T1_MPRAGE_sag
PhEncDir  ROW
EchoNo0
FlipAngle 7
EchoTime  3.31
InversionTime 1000
RepetitionTime2730
PhEncFOV  256
ReadoutFOV256
Image information
RunNo 27
SeriesNo  28
ImageNo   1
NImageRows256
NImageCols256
NFrames   1
SliceArraylSize   1
IsMosaic  0
ImgPos 71.7733 130.0894 131.5385
VolRes  1.   1.   1.3300
VolDim256 256 128
Vc  0.1238  -0.9687  -0.2150
Vr -0.0454   0.2110  -0.9764
Vs -0.9913  -0.1306   0.0178
VolCenter  -2.5670  21.9742 -19.4516
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: no Siemens slice order reversal detected (good!).
128 DICOM 3.0 files in list
Found 128 DICOM Files
WARNING: NumberOfFrames 0 != Found Count of slices 128.
reading DICOM image...
-
DICOM meta-header

file name 
/autofs/space/troy_002/users/fmridata/sm2c1_041118/3danat/dicom/028/33747925

Date and time
study date  20041118
study time  180537.015000
series time 190942.968000
acquisition time190942.968000
Identification
patient namesm2c1
manufacturerSIEMENS
Dimensions
number of rows  256
number of columns   256
number of frames128
pixel width 1
pixel height1
slice thickness 1.33
field of view   256
image number1 (might be not reliable)
transfer syntax UID 1.2.840.10008.1.2.1
Acquisition parameters
echo time   3.31
repetition time 2730
inversion time  1000
echo number 0
flip angle  0.122173
bits allocated  16
Spatial information
first image position-71.7733 -130.089 131.539
last image position 95.662 -108.024 134.554
image orientation   -0.123794 0.968728 -0.215038 0.0453834 
-0.210951 -0.976442

-

TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00
i_ras = (0.123794, -0.968728, -0.215038)
j_ras = (-0.0453834, 0.210951, -0.976442)
k_ras = (-0.99127, -0.130637, 0.0178497)
writing to 
/space/troy/1/users/FREESURFER/SM2C1_autoreconall/mri/orig/002...

Segmentation fault

i saw a couple other problems on the list but nothing exactly like this. 
thanks for the help.  margaret

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[Freesurfer] segmentation fault during make_average_surface

[Marie Schaer]

Hello,

I'm trying to make an average surface using the latest version of
make_average_surface (2005/08/02 19:14:20 nicks Exp), and I got the same error
as posted in the following message: 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01135.html, with a
segmentation fault when mris_average_surface is called (I get the same
segmentation fault when running mris_average_surface alone):

mris_make_average_surface -i 7 -o orig rh orig_avg sphere.reg average_test subj1
subj2
processing subject subj1...
The following must be revisited***
Segmentation fault


I did not find in the mailing list how to solve this, thank you very much for
your help,

Marie Schaer

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[Freesurfer] segmentation fault for: mris_convert

[Dahlia Sharon]

Hi,

I'm trying to use mris_convert and am getting a segmentation fault error. 
The precise steps are pasted below. Can anyone figure out why this is 
happening now?


Thanks!
Dahlia.

mirabai:dahlia[81] setenv SUBJECTS_DIR ~/structurals/
mirabai:dahlia[82] nmrenv
 freesurfer-Linux-centos4-stable-v3.0.1c-20060329 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer/stable
FSFAST_HOME /usr/local/freesurfer/stable/fsfast
SUBJECTS_DIR/homes/6/dahlia/structurals/
FUNCTIONALS_DIR /usr/local/freesurfer/stable/sessions
MINC_BIN_DIR/usr/local/freesurfer/stable/mni/bin
MINC_LIB_DIR/usr/local/freesurfer/stable/mni/lib
PERL5LIB/usr/local/freesurfer/stable/mni/lib/perl5/5.8.0
GSL_DIR /usr/local/freesurfer/stable/lib/gsl
QTDIR   /usr/local/freesurfer/stable/lib/qt
TCLLIBPATH  /usr/local/freesurfer/stable/lib/tcltktixblt/lib
FSL_DIR /usr/local/freesurfer/stable/fsl
[mirabai:~] (nmr-std-env) cd structurals/subj06_bay2/surf/
[mirabai:surf] (nmr-std-env) mris_convert rh.occip.patch.flat 
rh.occip.patch.flat.asc

Segmentation fault
[mirabai:surf] (nmr-std-env)


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Re: [Freesurfer] "segmentation fault" - recon-all

[Z K]

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 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 wm, xrange [-1, 257]*
>
> *searching rotation angles z=[-7  7], y=[83 97]*
>
> *searching scale 1 Z rot 6.8 global minimum found at slice 0.0,
> rotations (90.00, -0.00)*
>
> *final transformation (x=0.0, yr=90.000, zr=-0.000):*
>
> *-0.000   0.000   1.000 128.000;*
>
> *-0.000   1.000  -0.000 128.000;*
>
> *-1.000   0.000   0.000 128.000;*
>
> * 0.000   0.000 0.000   1.000;*
>
> *Segmentation fault*
>
> *Darwin dhcp-165-124-23-248.prevmed.northwestern.edu
>  12.4.0 Darwin
> Kernel Version 12.4.0: Wed May  1 17:57:12 PDT 2013;
> root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64*
>
> *recon-all -s avgseg_seg_test exited with ERRORS at Mon Aug 19 13:32:28
> CDT 2013*
>
> *
> *
>
> I don't know if this error is directly related to the actual brain
> segmentation, but recon-all was run with a different gca atlas. The
> command was:
>
> recon-all -gca atlas.gca -all -s 
>
>
> My best guess is that the .gca file is the source of the problem, but I
> am not sure why recon-all would make it to the final transformation and
> then throw an error.
>
> Any ideas?
>
> Thanks in advance.
>
> MP
>
>
>
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Re: [Freesurfer] "segmentation fault" - recon-all

[Mark Plantz]

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 atlas must contain the exact same ROI's as the
default atlas? I was under the impression that the values of the
non-included and/or different ROI's would simply be ignored or set to zero;
however, it actually caused recon-all to fail entirely.

-MP


On Tue, Aug 20, 2013 at 1:40 PM, Z K  wrote:

> 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 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 wm, xrange [-1, 257]*
>>
>> *searching rotation angles z=[-7  7], y=[83 97]*
>>
>> *searching scale 1 Z rot 6.8 global minimum found at slice 0.0,
>> rotations (90.00, -0.00)*
>>
>> *final transformation (x=0.0, yr=90.000, zr=-0.000):*
>>
>> *-0.000   0.000   1.000 128.000;*
>>
>> *-0.000   1.000  -0.000 128.000;*
>>
>> *-1.000   0.000   0.000 128.000;*
>>
>> * 0.000   0.000 0.000   1.000;*
>>
>> *Segmentation fault*
>>
>> *Darwin 
>> dhcp-165-124-23-248.prevmed.**northwestern.edu
>> >
>> 12.4.0 Darwin
>>
>> Kernel Version 12.4.0: Wed May  1 17:57:12 PDT 2013;
>> root:xnu-2050.24.15~1/RELEASE_**X86_64 x86_64*
>>
>> *recon-all -s avgseg_seg_test exited with ERRORS at Mon Aug 19 13:32:28
>> CDT 2013*
>>
>> *
>>
>> *
>>
>> I don't know if this error is directly related to the actual brain
>> segmentation, but recon-all was run with a different gca atlas. The
>> command was:
>>
>> recon-all -gca atlas.gca -all -s 
>>
>>
>> My best guess is that the .gca file is the source of the problem, but I
>> am not sure why recon-all would make it to the final transformation and
>> then throw an error.
>>
>> Any ideas?
>>
>> Thanks in advance.
>>
>> MP
>>
>>
>>
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>>
>>
>
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> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] "segmentation fault" - recon-all

[Nick Schmansky]

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 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 atlas must contain the exact same ROI's as
> the default atlas? I was under the impression that the values of the
> non-included and/or different ROI's would simply be ignored or set to
> zero; however, it actually caused recon-all to fail entirely. 
> 
> 
> -MP
> 
> 
> On Tue, Aug 20, 2013 at 1:40 PM, Z K 
> wrote:
> 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 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 wm, xrange [-1, 257]*
> 
> *searching rotation angles z=[-7  7], y=[83 97]*
> 
> *searching scale 1 Z rot 6.8 global minimum found at
> slice 0.0,
> rotations (90.00, -0.00)*
> 
> *final transformation (x=0.0, yr=90.000, zr=-0.000):*
> 
> *-0.000   0.000   1.000 128.000;*
> 
> *-0.000   1.000  -0.000 128.000;*
> 
> *-1.000   0.000   0.000 128.000;*
> 
> * 0.000   0.000 0.000   1.000;*
> 
> *Segmentation fault*
> 
> *Darwin dhcp-165-124-23-248.prevmed.northwestern.edu
> 
> 12.4.0 Darwin
> 
> Kernel Version 12.4.0: Wed May  1 17:57:12 PDT 2013;
> 
> root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64*
> 
> *recon-all -s avgseg_seg_test exited with ERRORS at
> Mon Aug 19 13:32:28
> CDT 2013*
> 
> *
> 
> *
> 
> I don't know if this error is directly related to the
> actual brain
> segmentation, but recon-all was run with a different
> gca atlas. The
> command was:
> 
> recon-all -gca atlas.gca -all -s 
> 
> 
> My best guess is that the .gca file is the source of
> the problem, but I
> am not sure why recon-all would make it to the final
> transformation and
> then throw an error.
> 
> Any ideas?
> 
> Thanks in advance.
> 
> MP
> 
> 
> 
> 
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[Freesurfer] Segmentation fault:11 with mris_anatomical_stats

[Rupa Sabbineni]

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(which created the stats).  Then I reran the mris_anatomical_stats
command and got the segmentation fault again.


The command im using is

mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log
outSUB1_lhVOL2 SUB1 lh


A little background on the new.label. We got the label by doing a
regression in qdec at FDR 0.05 which created cluster and peak cluster label.


Can anyone please provide me some insight on how to trouble shoot this
problem?

Thank you!

Rupa
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Re: [Freesurfer] Segmentation fault in mri_convert

[Z K]

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 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 is the output and error that I get. I'm running the latest
> version v 5.3.0 of freesurfer. Any suggestions on what the problem is?
> What is strange that it works with half my data set but the other has
> this error. I've run this command in the exact way many times before and
> have never had this issue.
>
>
>
>
>
> bash-3.2$ recon-all -i
> /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
> -subjid Bigler_Repeatability_0005Ad_M1
>
>
> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>
> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>
> INFO: SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects
>
> Actual FREESURFER_HOME /Applications/freesurfer
>
> Darwin NS112201PSY2.byu.edu  14.5.0 Darwin
> Kernel Version 14.5.0: Tue Sep  1 21:23:09 PDT 2015;
> root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
>
> /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1
>
> \n mri_convert
> /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
> /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz
> \n
>
> mri_convert
> /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
> /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz
>
>
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>
> reading from
> /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm...
>
> Getting Series No
>
> INFO: Found 178 files in
> /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1
>
> INFO: Scanning for Series Number 2
>
> Scanning Directory
>
> INFO: found 176 files in series
>
> INFO: loading series header info.
>
>
> RunNo = 1
>
> INFO: sorting.
>
> INFO: (224 256 176), nframes = 1, ismosaic=0
>
> PE Dir ROW ROW
>
> AutoAlign matrix detected
>
> AutoAlign Matrix -
>
>   1.000   0.000   0.000   0.000;
>
>   0.000   1.000   0.000   0.000;
>
>   0.000   0.000   1.000   0.000;
>
>   0.000   0.000   0.000   1.000;
>
>
> FileName
> /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
>
> Identification
>
> NumarisVersyngo MR B17
>
> ScannerModel  TrioTim
>
> PatientName   Bigler_Repeatability_AD_M
>
> Date and time
>
> StudyDate 20160512
>
> StudyTime 075942.531000
>
> SeriesTime081401.859000
>
> AcqTime   080647.62
>
> Acquisition parameters
>
> PulseSeq  *tfl3d1_ns
>
> Protocol  t1_mpr_sag_iso_ave2_ipat2_(mprage)
>
> PhEncDir  ROW
>
> EchoNo1
>
> FlipAngle 9
>
> EchoTime  2.26
>
> InversionTime 900
>
> RepetitionTime1900
>
> PhEncFOV  218.75
>
> ReadoutFOV250
>
> Image information
>
> RunNo 1
>
> SeriesNo  2
>
> ImageNo   1
>
> NImageRows256
>
> NImageCols224
>
> NFrames   1
>
> SliceArraylSize   1
>
> IsMosaic  0
>
> ImgPos 75.8389 136.8499 125.
>
> VolRes  0.9766   0.9766   1.
>
> VolDim224  256  176
>
> Vc  0.0767  -0.9971   0.
>
> Vr -0.   0.  -1.
>
> Vs -0.9971  -0.0767   0.
>
> VolCenter  -3.5106  21.0460   0.
>
> TransferSyntaxUID 1.2.840.10008.1.2.1
>
> UseSliceScaleFactor 0 (slice 0: 1)
>
> Segmentation fault
>
> Darwin NS112201PSY2.byu.edu  14.5.0 Darwin
> Kernel Version 14.5.0: Tue Sep  1 21:23:09 PDT 2015;
> root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
>
>
> recon-all -s Bigler_Repeatability_0005Ad_M1 exited with ERRORS at Wed
> Jun  8 13:39:08 MDT 2016
>
>
> For more details, see the log file
> /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/scripts/recon-all.log
>
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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Re: [Freesurfer] Segmentation fault using mri_label2vol

[Bruce Fischl]

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 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 countless times but nothing has worked. I 
also checked my "aseg.mgz" to
make sure it's not corrupted but that isn't the issue either. Any help would be 
highly appreciated!! Thanks in advance

mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz --seg 
/tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
/scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o 
/tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Number of labels: 0
Annot File:  (null)
Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol:  1
ProjType:   (null)
ProjTypeId: 0
ProjStart:  0
ProjStop:   0
ProjDelta:  0.1
Subject:  (null)
Hemi: (null)
UseNewASeg2Vol:  1
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
-0.000  -0.000  -0.985   128.000;
-0.000   0.833  -0.000   98.000;
 0.000   0.000   0.000   1.000;
Template Voxel Volume: 1.23773
nHits Thresh: 0
Computing registration based on header
RegMat: 
 1.000   0.000   0.000  -0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;
Label RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
 0.000   0.000  -0.985   128.000;
 0.000   0.833   0.000   98.000;
 0.000   0.000   0.000   1.000;
ASeg2Vol: Building LUT
Segmentation fault


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Re: [Freesurfer] Segmentation fault using mri_label2vol

[Syeda Maryam]

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, Syeda Maryam  
wrote:
   

 I'm not sure if my last message got delivered or not so I'll resend it.
Thanks very much for looking into this so quickly. Sure thing! I've 
attached the images here. The aseg file opens up with freeview, and the 
mri_label2vol command works fine on my local machine but when I try to 
implement it on our server using nipype, it gives me the error I mentioned. 

Best,Syeda 


 On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam  
wrote:
   

 Thanks very much for looking into this so quickly. Sure thing! I've attached 
the images here. The aseg file opens up with freeview, and the mri_label2vol 
command works fine on my local machine but when I try to implement it on our 
server using nipype, it gives me the error I mentioned. 

Best,Syeda
 


 On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl 
 wrote:
   

 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 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 countless times but nothing 
> has worked. I also checked my "aseg.mgz" to
> make sure it's not corrupted but that isn't the issue either. Any help would 
> be highly appreciated!! Thanks in advance
> 
> mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz --seg 
> /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o 
> /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> Number of labels: 0
> Annot File:  (null)
> Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> Registration File: (null)
> Fill Threshold: 0
> Label Vox Vol:  1
> ProjType:   (null)
> ProjTypeId: 0
> ProjStart:  0
> ProjStop:   0
> ProjDelta:  0.1
> Subject:  (null)
> Hemi: (null)
> UseNewASeg2Vol:  1
> DoLabelStatVol  0
> LabelCodeOffset  0
> setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> Template RAS-to-Vox: 
> -0.985   0.000   0.000   128.000;
> -0.000  -0.000  -0.985   128.000;
> -0.000   0.833  -0.000   98.000;
>  0.000   0.000   0.000   1.000;
> Template Voxel Volume: 1.23773
> nHits Thresh: 0
> Computing registration based on header
> RegMat: 
>  1.000   0.000   0.000  -0.000;
>  0.000   1.000   0.000   0.000;
>  0.000   0.000   1.000   0.000;
>  0.000   0.000   0.000   1.000;
> Label RAS-to-Vox: 
> -0.985   0.000   0.000   128.000;
>  0.000   0.000  -0.985   128.000;
>  0.000   0.833   0.000   98.000;
>  0.000   0.000   0.000   1.000;
> ASeg2Vol: Building LUT
> Segmentation fault
> 
> 
>


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


   

   

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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Segmentation fault using mri_label2vol

[Bruce Fischl]

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 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, Syeda Maryam 
wrote:


I'm not sure if my last message got delivered or not so I'll resend it.

Thanks very much for looking into this so quickly. Sure thing! I've
attached the images here. The aseg file opens up with freeview, and the
mri_label2vol command works fine on my local machine but when I try to
implement it on our server using nipype, it gives me the error I mentioned.

Best,
Syeda



On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam 
wrote:


Thanks very much for looking into this so quickly. Sure thing! I've attached
the images here. The aseg file opens up with freeview, and the mri_label2vol
command works fine on my local machine but when I try to implement it on our
server using nipype, it gives me the error I mentioned.

Best,
Syeda



On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl
 wrote:


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 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 countless times but nothing
has worked. I also checked my "aseg.mgz" to
> make sure it's not corrupted but that isn't the issue either. Any help
would be highly appreciated!! Thanks in advance
>
> mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
--seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
/tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> Number of labels: 0
> Annot File:  (null)
> Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> Registration File: (null)
> Fill Threshold: 0
> Label Vox Vol:  1
> ProjType:   (null)
> ProjTypeId: 0
> ProjStart:  0
> ProjStop:   0
> ProjDelta:  0.1
> Subject:  (null)
> Hemi: (null)
> UseNewASeg2Vol:  1
> DoLabelStatVol  0
> LabelCodeOffset  0
> setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> Template RAS-to-Vox: 
> -0.985   0.000   0.000   128.000;
> -0.000  -0.000  -0.985   128.000;
> -0.000   0.833  -0.000   98.000;
>  0.000   0.000   0.000   1.000;
> Template Voxel Volume: 1.23773
> nHits Thresh: 0
> Computing registration based on header
> RegMat: 
>  1.000   0.000   0.000  -0.000;
>  0.000   1.000   0.000   0.000;
>  0.000   0.000   1.000   0.000;
>  0.000   0.000   0.000   1.000;
> Label RAS-to-Vox: 
> -0.985   0.000   0.000   128.000;
>  0.000   0.000  -0.985   128.000;
>  0.000   0.833   0.000   98.000;
>  0.000   0.000   0.000   1.000;
> ASeg2Vol: Building LUT
> Segmentation fault

>
>
>


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
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dispose of the e-mail.







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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-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Segmentation fault using mri_label2vol

[Syeda Maryam]

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 using. 
But when I checked the freesurfer versions, turns out the same version is 
installed on both machines: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Needless to say, I'm well and truly stumped right now.Really appreciate your 
help in this matter!
Best,Syeda


 


 On Wednesday, October 14, 2015 12:20 PM, Bruce Fischl 
 wrote:
   

 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 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, Syeda Maryam 
> wrote:
> 
> 
> I'm not sure if my last message got delivered or not so I'll resend it.
> 
> Thanks very much for looking into this so quickly. Sure thing! I've
> attached the images here. The aseg file opens up with freeview, and the
> mri_label2vol command works fine on my local machine but when I try to
> implement it on our server using nipype, it gives me the error I mentioned.
> 
> Best,
> Syeda
> 
> 
> 
> On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam 
> wrote:
> 
> 
> Thanks very much for looking into this so quickly. Sure thing! I've attached
> the images here. The aseg file opens up with freeview, and the mri_label2vol
> command works fine on my local machine but when I try to implement it on our
> server using nipype, it gives me the error I mentioned.
> 
> Best,
> Syeda
> 
> 
> 
> On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl
>  wrote:
> 
> 
> 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 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 countless times but nothing
> has worked. I also checked my "aseg.mgz" to
> > make sure it's not corrupted but that isn't the issue either. Any help
> would be highly appreciated!! Thanks in advance
> >
> > mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
> --seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> > /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
> /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > Number of labels: 0
> > Annot File:  (null)
> > Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> > Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > Registration File: (null)
> > Fill Threshold: 0
> > Label Vox Vol:  1
> > ProjType:   (null)
> > ProjTypeId: 0
> > ProjStart:  0
> > ProjStop:   0
> > ProjDelta:  0.1
> > Subject:  (null)
> > Hemi: (null)
> > UseNewASeg2Vol:  1
> > DoLabelStatVol  0
> > LabelCodeOffset  0
> > setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> > $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> > Template RAS-to-Vox: 
> > -0.985   0.000   0.000   128.000;
> > -0.000  -0.000  -0.985   128.000;
> > -0.000   0.833  -0.000   98.000;
> >  0.000   0.000   0.000   1.000;
> > Template Voxel Volume: 1.23773
> > nHits Thresh: 0
> > Computing registration based on header
> > RegMat: 
> >  1.000   0.000   0.000  -0.000;
> >  0.000   1.000   0.000   0.000;
> >  0.000   0.000   1.000   0.000;
> >  0.000   0.000   0.000   1.000;
> > Label RAS-to-Vox: 
> > -0.985   0.000   0.000   128.000;
> >  0.000   0.000  -0.985   128.000;
> >  0.000   0.833   0.000   98.000;
> >  0.000   0.000   0.000   1.000;
> > ASeg2Vol: Building LUT
> > Segmentation fault
> 
> >
> >
> >
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
> 
> 
> 
> 
> 
> 
> 
>
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Re: [Freesurfer] Segmentation fault using mri_label2vol

[Bruce Fischl]

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 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 using. But when I checked the 
freesurfer versions, turns out the same
version is installed on both machines: 
freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

Needless to say, I'm well and truly stumped right now.
Really appreciate your help in this matter!

Best,
Syeda





On Wednesday, October 14, 2015 12:20 PM, Bruce Fischl 
 wrote:


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 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, Syeda Maryam 
> wrote:
>
>
> I'm not sure if my last message got delivered or not so I'll resend it.
> 
> Thanks very much for looking into this so quickly. Sure thing! I've
> attached the images here. The aseg file opens up with freeview, and the
> mri_label2vol command works fine on my local machine but when I try to
> implement it on our server using nipype, it gives me the error I mentioned.
>
> Best,
> Syeda
>
>
>
> On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam 
> wrote:
>
>
> Thanks very much for looking into this so quickly. Sure thing! I've attached
> the images here. The aseg file opens up with freeview, and the mri_label2vol
> command works fine on my local machine but when I try to implement it on our
> server using nipype, it gives me the error I mentioned.
>
> Best,
> Syeda
>
>
>
> On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl
>  wrote:
>
>
> 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 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 countless times but nothing
> has worked. I also checked my "aseg.mgz" to
> > make sure it's not corrupted but that isn't the issue either. Any help
> would be highly appreciated!! Thanks in advance
> >
> > mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
> --seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> > /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
> /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > Number of labels: 0
> > Annot File:  (null)
> > Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> > Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > Registration File: (null)
> > Fill Threshold: 0
> > Label Vox Vol:  1
> > ProjType:   (null)
> > ProjTypeId: 0
> > ProjStart:  0
> > ProjStop:   0
> > ProjDelta:  0.1
> > Subject:  (null)
> > Hemi: (null)
> > UseNewASeg2Vol:  1
> > DoLabelStatVol  0
> > LabelCodeOffset  0
> > setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> > $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> > Template RAS-to-Vox: 
> > -0.985   0.000   0.000   128.000;
> > -0.000  -0.000  -0.985   128.000;
> > -0.000   0.833  -0.000   98.000;
> >  0.000   0.000   0.000   1.000;
> > Template Voxel Volume: 1.23773
> > nHits Thresh: 0
> > Computing registration based on header
> > RegMat: 
> >  1.000   0.000   0.000  -0.000;
> >  0.000   1.000   0.000   0.000;
> >  0.000   0.000   1.000   0.000;
> >  0.000   0.000   0.000   1.000;
> > Label RAS-to-Vox: 
> > -0.985   0.000   0.000   128.000;
> >  0.000   0.000  -0.985   128.000;
> >  0.000   0.833   0.000   98.000;
> >  0.000   0.000   0.000   1.000;
> > ASeg2Vol: Building LUT
> > Segmentation fault
>
> >
> >
> >
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
>
>
>
>
>

__

Re: [Freesurfer] Segmentation fault using mri_label2vol

[Syeda Maryam]

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 Wednesday, October 14, 2015 12:48 PM, Bruce Fischl 
 wrote:
   

 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 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 using. But when I checked 
> the freesurfer versions, turns out the same
> version is installed on both machines: 
> freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> 
> Needless to say, I'm well and truly stumped right now.
> Really appreciate your help in this matter!
> 
> Best,
> Syeda
> 
> 
> 
> 
> 
> On Wednesday, October 14, 2015 12:20 PM, Bruce Fischl 
>  wrote:
> 
> 
> 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 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, Syeda Maryam 
> > wrote:
> >
> >
> > I'm not sure if my last message got delivered or not so I'll resend it.
> > 
> > Thanks very much for looking into this so quickly. Sure thing! I've
> > attached the images here. The aseg file opens up with freeview, and the
> > mri_label2vol command works fine on my local machine but when I try to
> > implement it on our server using nipype, it gives me the error I mentioned.
> >
> > Best,
> > Syeda
> >
> >
> >
> > On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam 
> > wrote:
> >
> >
> > Thanks very much for looking into this so quickly. Sure thing! I've attached
> > the images here. The aseg file opens up with freeview, and the mri_label2vol
> > command works fine on my local machine but when I try to implement it on our
> > server using nipype, it gives me the error I mentioned.
> >
> > Best,
> > Syeda
> >
> >
> >
> > On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl
> >  wrote:
> >
> >
> > 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 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 countless times but nothing
> > has worked. I also checked my "aseg.mgz" to
> > > make sure it's not corrupted but that isn't the issue either. Any help
> > would be highly appreciated!! Thanks in advance
> > >
> > > mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
> > --seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> > > /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
> > /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > > Number of labels: 0
> > > Annot File:  (null)
> > > Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> > > Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > > Registration File: (null)
> > > Fill Threshold: 0
> > > Label Vox Vol:  1
> > > ProjType:   (null)
> > > ProjTypeId: 0
> > > ProjStart:  0
> > > ProjStop:   0
> > > ProjDelta:  0.1
> > > Subject:  (null)
> > > Hemi: (null)
> > > UseNewASeg2Vol:  1
> > > DoLabelStatVol  0
> > > LabelCodeOffset  0
> > > setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> > > $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> > > Template RAS-to-Vox: 
> > > -0.985   0.000   0.000   128.000;
> > > -0.000  -0.000  -0.985   128.000;
> > > -0.000   0.833  -0.000   98.000;
> > >  0.000   0.000   0.000   1.000;
> > > Template Voxel Volume: 1.23773
> > > nHits Thresh: 0
> > > Computing registration based on header
> > > RegMat: 
> > >  1.000   0.000   0.000  -0.000;
> > >  0.000   1.000   0.000   0.000;
> > >  0.000   0.000   1.000   0.000;
> > >  0.000   0.000   0.000   1.000;
> > > Label RAS-to-Vox: 
> > > -0.985   0.000   0.000   128.000;
> > >  0.000   0.000  -0.985   128.000;
> > >  0.000  

Re: [Freesurfer] segmentation fault (core dumped)

[Douglas N Greve]

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 -hippocampal-subfields-T1T2 $s/T2/*.mgz T1T2'.
>
> It would be great if you could keep us updated on how the fixing is 
> going.
>
> Thanks!
>
> ---
> Message: 1
> Date: Mon, 21 Dec 2015 10:38:08 -0500 (EST)
> From: Bruce Fischl 
> Subject: Re: [Freesurfer] FW: segmentation fault (core dumped)
> To: Freesurfer support list 
> Message-ID:
> 
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Fengji
>
> hmmm, I don't remember ever seeing a core dump in mri-segstats before. If
> you upload the entire subject dir (tarred and gzipped) to our ftp site we
> will fix it.
>
> cheers
> Bruce
>
>
>
> -
> Fengji
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Segmentation fault: Core dumped

[Douglas N Greve]

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 default 0.5 (bet 0 and 1).


On 05/27/2016 04:08 PM, Sahil Bajaj wrote:
> 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 segmentation of anatomical data (generated using 
> recon-all), and it looks fine to me.
> Here I am also attaching the log file created when I run this command.
>
> Any help would be really appreciated.
>
> Thanks,
> Sahil
> -- 
> -
> Sahil Bajaj
> Post-doctoral Fellow
> Nantz National Alzheimer's Center, Department of Neurology
> The Houston Methodist Research Institute (THMRI)
> Houston, TX, USA.
> E-mail:sahil.br...@gmail.com 
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Segmentation fault with mri_ca_train

[Bruce Fischl]

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 segmentation volume to create a GCA 
atlas. I keep
getting this "segmentation fault: 11", which is data allocation error. I have 
tried using all
different environments and can't avoid it. The output is below:

sh-3.2# mri_ca_train -T1 withSkull.mgz -seg seg_edited.mgz atlas_test
/hearingbrain/Desktop/atlas_withSkull.gca 
reading T1 data from subject's mri/withSkull.mgz directory
reading segmentation from subject's mri/seg_edited.mgz directory
training on 1 subject and writing results to /Volumes/Macintosh
HD/Users/hearingbrain/Desktop/atlas_withSkull.gca
***
processing subject atlas_test, 1 of 1...
   reading input 0: 
/Applications/freesurfer/subjects/atlas_test/mri/withSkull.mgz
gca width modified from 256 to 181
gca height modified from 256 to 217
gca depth modified from 256 to 181
Segmentation fault: 11


Any ideas?

-MP

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Re: [Freesurfer] Segmentation fault with mri_ca_train

[Mark Plantz]

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 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
>> different environments and can't avoid it. The output is below:
>>
>> sh-3.2# mri_ca_train -T1 withSkull.mgz -seg seg_edited.mgz atlas_test
>> /hearingbrain/Desktop/atlas_withSkull.gca
>> reading T1 data from subject's mri/withSkull.mgz directory
>> reading segmentation from subject's mri/seg_edited.mgz directory
>> training on 1 subject and writing results to /Volumes/Macintosh
>> HD/Users/hearingbrain/Desktop/atlas_withSkull.gca
>> 
>> ***
>> processing subject atlas_test, 1 of 1...
>>reading input 0: /Applications/freesurfer/subjects/atlas_test/mri/
>> withSkull.mgz
>> gca width modified from 256 to 181
>> gca height modified from 256 to 217
>> gca depth modified from 256 to 181
>> Segmentation fault: 11
>>
>>
>> Any ideas?
>>
>> -MP
>>
>>
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[Freesurfer] segmentation fault mri_convert Ubuntu 14.04

[Alessandra Griffa]

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 /folder/resampled 
image.nii.gz //

//$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $//
//reading from /folder/original_image.nii.gz...//
//Segmentation fault (core dumped)/

Any help on this?
(for consistency with an on-going study I would like not to install a 
newer FreeSurfer version)


Thank you very much!
Alessandra


--
--
Alessandra Griffa
Doctoral assistant

Signal Processing Laboratory 5
EPFL STI IEL LTS5
ELD 233 (Bâtiment ELD)
Station 11 CH-1015
Lausanne
Tel.: +41216934807

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Re: [Freesurfer] Segmentation fault (core dumped)

[Uquillas, Federico D'Oleire]

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 qcache with several versions of the fsaverage (e.g., 
fsaverage5, fsaverage6, fsaverage), and have also tried running it in a variety 
of subjects but they all crash.


Thank you so much for you help.


All the best,


Fred


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Uquillas, Federico 
D'Oleire 
Sent: Thursday, December 14, 2017 6:56:56 PM
To: 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 anybody could help 
me find what is going on.


I've tried running qcache with several versions of the fsaverage (e.g., 
fsaverage5, fsaverage6, fsaverage), and have also tried running it in a variety 
of subjects but they all crash.


Thank you so much for you help.


All the best,


Fred
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