Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding

[Z K]

Hello Jared,

Would it be possible to tar up the subject directory and upload it to our 
server so I can take a look?

 https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

-Zeke 

> On Feb 20, 2017, at 2:47 PM, Jared Saletin  wrote:
> 
> Dear Zeke,
> 
> Thanks for your reply. I can verify that recon-all completes without error on 
> a single thread, but crashes on parallel.
> 
> I thought it may be hippocampus-subfield specific, but the same pattern 
> remerges regardless of the subfield reconstruction.
> 
> Is there something in newer OS X that broke the libraries?
> 
> Thanks!
> Jared
> 
> —
> 
> Jared M. Saletin, PhD
> 
> Assistant Professor of Psychiatry and Human Behavior
> Alpert Medical School of Brown University
> 
> E.P. Bradley Sleep Research Lab
> 300 Duncan Drive
> Providence, RI 02906
> 
> Email: jared_sale...@brown.edu
> Phone: 401-421-9440 
> Fax: 401-453-3578
> 
> 
> 
>> On Feb 17, 2017, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>> 
>> Message: 30
>> Date: Fri, 17 Feb 2017 10:21:03 -0500
>> From: Z K 
>> Subject: Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra:
>>  during mris_smooth. dyld: lazy symbol binding
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID: 
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>> 
>> Hello Jared,
>> 
>> Curious... Can you try processing this particular subject with a single 
>> thread and see what happens? If the problem persists let me know and I 
>> will take a look at the subject.
>> 
>> -Zeke
>> 
>>> On 02/17/2017 08:28 AM, Jared Saletin wrote:
>>> Hi Freesurfer gurus:
>>> 
>>> I recently installed 6.0.0 on MacOS 10.12 and recon-all is exiting with
>>> an error in mris_smooth. It looks like a library issue.
>>> 
>>> A prior post had the same issue and indicated uninstalling the whole
>>> distribution and re-installing 6.0.0 fresh (as opposed to installing
>>> over 5.3). I receive the same error however (pasted below).
>>> 
>>> Does anyone have any thoughts?
>>> 
>>> Thanks!
>>> Jared
>>> 
 #@# Smooth1 rh Thu Feb 16 16:47:23 EST 2017
 /Users/jared/Desktop/fMRITest/test/scripts
 \n mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix
 ../surf/rh.smoothwm.nofix \n
 Waiting for PID 11130 of (11130 11133) to complete...
 /Applications/freesurfer/bin/reconbatchjobs: line 81: 11130 Abort
 trap: 6   exec $JOB >> $LOG 2>&1
 Waiting for PID 11133 of (11130 11133) to complete...
 /Applications/freesurfer/bin/reconbatchjobs: line 81: 11133 Abort
 trap: 6   exec $JOB >> $LOG 2>&1
 
 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix
 ../surf/lh.smoothwm.nofix
 
 setting seed for random number generator to 1234
 dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from:
 /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib
 
 dyld: Symbol not found: ___emutls_get_address
  Referenced from:
 /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib
 
 
 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix
 ../surf/rh.smoothwm.nofix
 
 setting seed for random number generator to 1234
 dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from:
 /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib
 
 dyld: Symbol not found: ___emutls_get_address
  Referenced from:
 /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib
 
 PIDs (11130 11133) completed and logs appended.
 Darwin Jareds-iMac.local 16.4.0 Darwin Kernel Version 16.4.0: Thu Dec
 22 22:53:21 PST 2016; root:xnu-3789.41.3~3/RELEASE_X86_64 x86_64
 
 recon-all -s test exited with ERRORS at Thu Feb 16 16:47:23 EST 2017
>>> 
>>> ?
>>> 
>>> Jared M. Saletin, PhD
>>> 
>>> Assistant Professor of Psychiatry and Human Behavior
>>> Alpert Medical School of Brown University
>>> 
>>> E.P. Bradley Sleep Research Lab
>>> 300 Duncan Drive
>>> Providence, RI 02906
>>> 
>>> Email: jared_sale...@brown.edu 
>>> Phone: 401-421-9440
>>> Fax: 401-453-3578
>>> 
>>> 
>>> 
>>> 
>>> 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
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>>> 
>> 
> 
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The 

Re: [Freesurfer] mri_cvs_register error : PETSC Error

[Bhavana Ganesh]

Hi Lilla,
Is there a work around for this because I would at max be able to allocate
8GB for the tool but I dont have the resource for 35GB.

*Regards,*
*Bhavana*







On Mon, Feb 20, 2017 at 4:43 PM, Lilla Zollei 
wrote:

>
> Hi Bhavana,
>
> We recommend to assign about 35GB of RAM on our cluster nodes for this
> operation. I am not sure how that compares to your VB.
>
> Lilla
>
> On Mon, 20 Feb 2017, Bhavana Ganesh wrote:
>
> Hi Lilla,
>> I have allocated 40GB for my VB and 3GB of RAM space. I am not allocating
>> anything specific to the function.
>>
>> Regards,
>> Bhavana
>>   [linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-website.png]
>>
>>
>>
>> On Mon, Feb 20, 2017 at 12:21 PM, Lilla Zollei <
>> lzol...@nmr.mgh.harvard.edu> wrote:
>>
>>   Hi Bhavana,
>>
>>   How much memory are you allocating to this process?
>>
>>   Lilla
>>
>>   On Mon, 20 Feb 2017, Bhavana Ganesh wrote:
>>
>>   > Hi Developers,
>>   >
>>   > I'm receiving this error while I try to run mri_cvs_register. The
>> same error was received when I reran the same even after increasing the
>> memory allocated to my VB. Can anybody help me with the issue I am facing.
>>   > Below are the details of my system and software configurations.
>>   > PFA error log files.
>>   >
>>   > FreeSurfer version: freesurfer-Linux-centos6_x86_6
>> 4-stable-pub-v6.0.0-2beb96c
>>   > Platform: CentOS7 on VirtualBox
>>   >
>>   > Command Run:
>>   >
>>   > mri_cvs_register --mov bert2
>>   >
>>   >
>>   > 0]PETSC ERROR: - Error Message
>> 
>>   >
>>   > [0]PETSC ERROR: Out of memory. This could be due to allocating
>>   > [0]PETSC ERROR: too large an object or bleeding by not properly
>>   > [0]PETSC ERROR: destroying unneeded objects.
>>   > [0]PETSC ERROR: Memory allocated 0 Memory used by process -
>> 2147483648
>>   > [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for
>> info.
>>   > [0]PETSC ERROR: Memory requested 576224344!
>>   > [0]PETSC ERROR: --
>> --
>>   > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15
>> 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
>>   > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>>   > [0]PETSC ERROR: See docs/faq.html for hints about trouble
>> shooting.
>>   > [0]PETSC ERROR: See docs/index.html for manual pages.
>>   > [0]PETSC ERROR: --
>> --
>>   > [0]PETSC ERROR: surf2vol on a linux-gnu named
>> localhost.localdomain by root Thu Feb 16 09:57:44 2017
>>   > [0]PETSC ERROR: Libraries linked from
>> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/pets
>> c/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
>>   > [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
>>   > [0]PETSC ERROR: Configure options --with-debugging=no
>> --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1
>> --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0
>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
>>   > [0]PETSC ERROR: --
>> --
>>   > [0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c
>>   > [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in
>> src/mat/impls/aij/seq/aij.c
>>   > [0]PETSC ERROR: MatTranspose_SeqAIJ() line 1460 in
>> src/mat/impls/aij/seq/aij.c
>>   > [0]PETSC ERROR: MatTranspose() line 3500 in
>> src/mat/interface/matrix.c
>>   > [0]PETSC ERROR: TSolver::setup_load_sym() line 1130 in
>> unknowndirectory/solver.h
>>   >  after setup_load_mfc
>>   > Linear solve converged due to CONVERGED_ITS iterations 1
>>   >
>>   > Thank You
>>   >
>>   > Regards,
>>   > Bhavana
>> >   [linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-websi
>> te.png]
>> >
>> >
>> >
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>> NFcK8Zziyesd-5JlzLnhEkAycTFrE3zdMqcNdQnXHUM=
>>
>>
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Re: [Freesurfer] Output from mri_cvs_register

[Lilla Zollei]

That is the same. You shoudl be fine.
Lilla

On Mon, 20 Feb 2017, Magnús Ingvi wrote:


Hi!I am running mri_cvs_regsiter, on the cvs_avg35 space. In the dt_recon 
tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion ), 
the expected .m3z output file is called 
combined_tocvs_avg35_elreg_afteraseg-norm.m3z, but the output I get in the cvs 
folder is called
final_CVSmorph_tocvs_avg35.m3z
Is this the same file, or did I mess up somewhere?
Best 
M.Ingvi

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Re: [Freesurfer] apply CVS morph to a list of coordinates

[Lilla Zollei]

Hi Cristian,

The below error message indicates that your morph cannot be read. How much 
memeory do you have on the machine where you are running this operation?


Lilla

On Fri, 10 Feb 2017, Donos, Cristian wrote:


Hi,

I have registered a patient’s MRI over the ColinN27 with mri_cvs_register and 
now i need convert an electrode (or voxel) coordinate from the subject’s space 
to the N27 space. I found an old post in the mailing list, but it did not work 
for me. The coords.txt file is just one line containing 10 10 10.  What am i
doing wrong?


http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39971.html

Here are the commands i used and the results :

> createMorph --out fullCSVmorph.tm3d --template 
/Volumes/Sector2/surfaces/TandonLang/TT_N27/mri/orig.mgz --subject 
/Volumes/Sector2/surfaces/TandonLang/TS076CD/mri/orig.mgz --in gcam 
/Volumes/Sector2/surfaces/TandonLang/TS076CD/TS076CD/csv/combined_toColin27_elreg_aseg.m3z
 

 atlas geometry = 256 , 256 , 256
 image geometry = 256 , 256 , 256
 vox 2 ras atlas = 
-1.000   0.000   0.000   127.000;
 0.000   0.000   1.000  -111.000;
 0.000  -1.000   0.000   147.000;
 0.000   0.000   0.000   1.000;
 ras 2 vox image = 
-1.000   0.000   0.000   128.000;
-0.000  -0.000  -1.000   138.000;
-0.000   1.000  -0.000   143.000;
 0.000   0.000   0.000   1.000;
 product = 
 1.000   0.000   0.000   1.000;
 0.000   1.000   0.000  -9.000;
 0.000   0.000   1.000   32.000;
 0.000   0.000   0.000   1.000;

 transform at origin
 1.000;
-9.000;
 32.000;
 1.000;
 invalid voxel count = 9071323
 saveTransform code
 writing transform size = 49918625
 writing morph to file fullCSVmorph.tm3d


> applyMorph --template 
/Volumes/Sector2/surfaces/TandonLang/TT_N27/mri/orig.mgz --transform 
fullCVSmorph.tm3d point_list coords.txt transformed_coords.txt linear

Template name:/Volumes/Sector2/surfaces/TandonLang/TT_N27/mri/orig.mgz
After loading template
Template name:/Volumes/Sector2/surfaces/TandonLang/TT_N27/mri/orig.mgz
After loading template
 extension = tm3d
 Exception caught while loading transform
VolumeMorph load - failed to open input stream

Thank you,

Cristian Donos, PhD 
Postdoctoral Research Fellow, Department of Neurosurgery               
6431 Fannin Street | Suite G.550D | Houston, Texas 77030
Phone: 979-633-9208
Email:  cristian.do...@uth.tmc.edu



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Re: [Freesurfer] 答复: Longitudinal proceesing for Pediatric data

[Lilla Zollei]

Hi Dong,

What is the age range that you are working with?

Lilla

On Mon, 20 Feb 2017, Martin Reuter wrote:



No, not that I know of.

Also I expect that it also depends on other factors (like image resolution, 
quality, subject anatomy etc) .


Best, Martin


Am 15.02.2017 um 08:21 schrieb Dongnandi:

  Hi Martin

   

  Thanks a lot for your reply!  Is there any reference that the 
longitudinal processing would fail if the difference in head size exceeded any 
certain value?

   

  Best, Dong

   

  发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] 代表 Martin Reuter
  发送时间: 2017年2月15日 2:40
  收件人: Freesurfer support list 
  主题: Re: [Freesurfer] Longitudinal proceesing for Pediatric data

 

Hi Dong, 

 

it can work, if time points are close to each other (so not much head growth). 
Feel free to try, but make sure you are carefully looking at the surfaces, that 
no gray matter is clipped in later time points. 

 

The alternative is to only do cross sectional processing.

 

Best, Martin

 

  On 14 Feb 2017, at 04:56, Dongnandi  wrote:

 

Dear freesurfer exports,

 

As it is mentioned in the documentation that ‘pediatric data violates the fixed 
head size assumption’ for the current longitudinal stream. Is there any 
solution for the issue now?

 

Thanks

Dong

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Re: [Freesurfer] mri_cvs_register error : PETSC Error

[Lilla Zollei]

Hi Bhavana,

We recommend to assign about 35GB of RAM on our cluster nodes for this 
operation. I am not sure how that compares to your VB.


Lilla

On Mon, 20 Feb 2017, Bhavana Ganesh wrote:


Hi Lilla,
I have allocated 40GB for my VB and 3GB of RAM space. I am not allocating 
anything specific to the function.

Regards,
Bhavana
  [linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-website.png]


On Mon, Feb 20, 2017 at 12:21 PM, Lilla Zollei  
wrote:

  Hi Bhavana,

  How much memory are you allocating to this process?

  Lilla

  On Mon, 20 Feb 2017, Bhavana Ganesh wrote:

  > Hi Developers,
  >
  > I'm receiving this error while I try to run mri_cvs_register. The same 
error was received when I reran the same even after increasing the memory 
allocated to my VB. Can anybody help me with the issue I am facing.
  > Below are the details of my system and software configurations.
  > PFA error log files.
  >
  > FreeSurfer version: 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
  > Platform: CentOS7 on VirtualBox
  >
  > Command Run:
  >
  > mri_cvs_register --mov bert2
  >
  >
  > 0]PETSC ERROR: - Error Message 

  >
  > [0]PETSC ERROR: Out of memory. This could be due to allocating
  > [0]PETSC ERROR: too large an object or bleeding by not properly
  > [0]PETSC ERROR: destroying unneeded objects.
  > [0]PETSC ERROR: Memory allocated 0 Memory used by process -2147483648
  > [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
  > [0]PETSC ERROR: Memory requested 576224344!
  > [0]PETSC ERROR: 

  > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 
17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
  > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
  > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
  > [0]PETSC ERROR: See docs/index.html for manual pages.
  > [0]PETSC ERROR: 

  > [0]PETSC ERROR: surf2vol on a linux-gnu named localhost.localdomain by 
root Thu Feb 16 09:57:44 2017
  > [0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
  > [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
  > [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
  > [0]PETSC ERROR: 

  > [0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c
  > [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in 
src/mat/impls/aij/seq/aij.c
  > [0]PETSC ERROR: MatTranspose_SeqAIJ() line 1460 in 
src/mat/impls/aij/seq/aij.c
  > [0]PETSC ERROR: MatTranspose() line 3500 in src/mat/interface/matrix.c
  > [0]PETSC ERROR: TSolver::setup_load_sym() line 1130 in 
unknowndirectory/solver.h
  >  after setup_load_mfc
  > Linear solve converged due to CONVERGED_ITS iterations 1
  >
  > Thank You
  >
  > Regards,
  > Bhavana
>       [linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-website.png]
>
>
>
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Re: [Freesurfer] mri_cvs_register error : PETSC Error

[Bhavana Ganesh]

Hi Lilla,
I have allocated 40GB for my VB and 3GB of RAM space. I am not allocating
anything specific to the function.

*Regards,*
*Bhavana*







On Mon, Feb 20, 2017 at 12:21 PM, Lilla Zollei 
wrote:

>
> Hi Bhavana,
>
> How much memory are you allocating to this process?
>
> Lilla
>
> On Mon, 20 Feb 2017, Bhavana Ganesh wrote:
>
> > Hi Developers,
> >
> > I'm receiving this error while I try to run mri_cvs_register. The same
> error was received when I reran the same even after increasing the memory
> allocated to my VB. Can anybody help me with the issue I am facing.
> > Below are the details of my system and software configurations.
> > PFA error log files.
> >
> > FreeSurfer version: freesurfer-Linux-centos6_x86_
> 64-stable-pub-v6.0.0-2beb96c
> > Platform: CentOS7 on VirtualBox
> >
> > Command Run:
> >
> > mri_cvs_register --mov bert2
> >
> >
> > 0]PETSC ERROR: - Error Message
> 
> >
> > [0]PETSC ERROR: Out of memory. This could be due to allocating
> > [0]PETSC ERROR: too large an object or bleeding by not properly
> > [0]PETSC ERROR: destroying unneeded objects.
> > [0]PETSC ERROR: Memory allocated 0 Memory used by process -2147483648
> > [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
> > [0]PETSC ERROR: Memory requested 576224344!
> > [0]PETSC ERROR: --
> --
> > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15
> 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > [0]PETSC ERROR: See docs/index.html for manual pages.
> > [0]PETSC ERROR: --
> --
> > [0]PETSC ERROR: surf2vol on a linux-gnu named localhost.localdomain by
> root Thu Feb 16 09:57:44 2017
> > [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/
> Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.
> 3-p13/lib/linux-gnu-c-opt
> > [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> > [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> > [0]PETSC ERROR: --
> --
> > [0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c
> > [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in
> src/mat/impls/aij/seq/aij.c
> > [0]PETSC ERROR: MatTranspose_SeqAIJ() line 1460 in
> src/mat/impls/aij/seq/aij.c
> > [0]PETSC ERROR: MatTranspose() line 3500 in src/mat/interface/matrix.c
> > [0]PETSC ERROR: TSolver::setup_load_sym() line 1130 in
> unknowndirectory/solver.h
> >  after setup_load_mfc
> > Linear solve converged due to CONVERGED_ITS iterations 1
> >
> > Thank You
> >
> > Regards,
> > Bhavana
> >   [linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-
> website.png]
> >
> >
> >
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Re: [Freesurfer] issues with -T2pial option in v.5.3

[Antonin Skoch]

Dear Petr,

according to the screenshot, the problem is that there is quite low signal 
intensity in the cut-out parts of gray matter on T2 images.

Apart from HCP pipelines, you can try to increase -nsigma_below parameter of 
mris_make_surfaces to prevent this cut-out. The default value is 3, try 
something higher.

Or you can try dev version of freeSurfer and experiment with explicit setting 
of T2 intensity threshold using -T2_min and -T2_outside_min parameters.

Regards,

Antonin Skoch

You could try with the HCP Pipelines and see if that helps:

https://github.com/Washington-University/PipelinesPeace,

Matt.

From:   on behalf of Petr Bednarik

Reply-To:  Freesurfer support list 
Date:  Monday, February 20, 2017 at 12:26 PM
To:  
Subject:  [Freesurfer] issues with -T2pial option in v.5.3

Hi everyone, 

I am using Freesurfer version 5.3. I tried to refine the pial surfaces by
using  -T2pial option:

recon-all -subjid $SUBJ -T2/SUBJECT_DIR/$SUBJ/mri/orig/T2raw.mgz -T2pial
-autorecon3 

This step was helpful - e.g. it removed nicely residuals of venous sinuses,
but in some subjects it also removed part of the parietal or frontal cortex,
while the white matter is appropriately segmented.

https://www.dropbox.com/s/4gzsvrg85xsfdkn/surfaces_over_brainmask.mgz.png?dl
=0

The T2-space images had the same resolution as T1-MPRAGE (1x1x1mm) and were
acquired in the same session (3T Siemens Trio, standard 32 channel coil).
The problem does not seem to be caused by T2 misregistration :

https://www.dropbox.com/s/a7gdpxom0cqgj1u/surfaces_over_T2.mgz.png?dl=0

Question : What could cause this error and how could I extend pial surfaces
and get correct final segmentation ?

Thanks a lot !

PB
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Re: [Freesurfer] mri_cvs_register error : PETSC Error

[Lilla Zollei]

Hi Bhavana,

How much memory are you allocating to this process?

Lilla

On Mon, 20 Feb 2017, Bhavana Ganesh wrote:

> Hi Developers,
> 
> I'm receiving this error while I try to run mri_cvs_register. The same error 
> was received when I reran the same even after increasing the memory allocated 
> to my VB. Can anybody help me with the issue I am facing.
> Below are the details of my system and software configurations.
> PFA error log files.
> 
> FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> Platform: CentOS7 on VirtualBox
> 
> Command Run:
> 
> mri_cvs_register --mov bert2
> 
> 
> 0]PETSC ERROR: - Error Message 
> 
> 
> [0]PETSC ERROR: Out of memory. This could be due to allocating
> [0]PETSC ERROR: too large an object or bleeding by not properly
> [0]PETSC ERROR: destroying unneeded objects.
> [0]PETSC ERROR: Memory allocated 0 Memory used by process -2147483648
> [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
> [0]PETSC ERROR: Memory requested 576224344!
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: surf2vol on a linux-gnu named localhost.localdomain by root 
> Thu Feb 16 09:57:44 2017
> [0]PETSC ERROR: Libraries linked from 
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c
> [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in 
> src/mat/impls/aij/seq/aij.c
> [0]PETSC ERROR: MatTranspose_SeqAIJ() line 1460 in src/mat/impls/aij/seq/aij.c
> [0]PETSC ERROR: MatTranspose() line 3500 in src/mat/interface/matrix.c
> [0]PETSC ERROR: TSolver::setup_load_sym() line 1130 in 
> unknowndirectory/solver.h
>  after setup_load_mfc
> Linear solve converged due to CONVERGED_ITS iterations 1
> 
> Thank You
> 
> Regards,
> Bhavana
>   [linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-website.png]
> 
> 
>
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Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding

[Jared Saletin]

Dear Zeke,

Thanks for your reply. I can verify that recon-all completes without error on a 
single thread, but crashes on parallel.

I thought it may be hippocampus-subfield specific, but the same pattern 
remerges regardless of the subfield reconstruction.

Is there something in newer OS X that broke the libraries?

Thanks!
Jared

—

Jared M. Saletin, PhD

Assistant Professor of Psychiatry and Human Behavior
Alpert Medical School of Brown University

E.P. Bradley Sleep Research Lab
300 Duncan Drive
Providence, RI 02906

Email: jared_sale...@brown.edu
Phone: 401-421-9440 
Fax: 401-453-3578



> On Feb 17, 2017, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
> 
> Message: 30
> Date: Fri, 17 Feb 2017 10:21:03 -0500
> From: Z K >
> Subject: Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra:
>   during mris_smooth. dyld: lazy symbol binding
> To: freesurfer@nmr.mgh.harvard.edu 
> Message-ID:  >
> Content-Type: text/plain; charset=windows-1252; format=flowed
> 
> Hello Jared,
> 
> Curious... Can you try processing this particular subject with a single 
> thread and see what happens? If the problem persists let me know and I 
> will take a look at the subject.
> 
> -Zeke
> 
> On 02/17/2017 08:28 AM, Jared Saletin wrote:
>> Hi Freesurfer gurus:
>> 
>> I recently installed 6.0.0 on MacOS 10.12 and recon-all is exiting with
>> an error in mris_smooth. It looks like a library issue.
>> 
>> A prior post had the same issue and indicated uninstalling the whole
>> distribution and re-installing 6.0.0 fresh (as opposed to installing
>> over 5.3). I receive the same error however (pasted below).
>> 
>> Does anyone have any thoughts?
>> 
>> Thanks!
>> Jared
>> 
>>> #@# Smooth1 rh Thu Feb 16 16:47:23 EST 2017
>>> /Users/jared/Desktop/fMRITest/test/scripts
>>> \n mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix
>>> ../surf/rh.smoothwm.nofix \n
>>> Waiting for PID 11130 of (11130 11133) to complete...
>>> /Applications/freesurfer/bin/reconbatchjobs: line 81: 11130 Abort
>>> trap: 6   exec $JOB >> $LOG 2>&1
>>> Waiting for PID 11133 of (11130 11133) to complete...
>>> /Applications/freesurfer/bin/reconbatchjobs: line 81: 11133 Abort
>>> trap: 6   exec $JOB >> $LOG 2>&1
>>> 
>>> mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix
>>> ../surf/lh.smoothwm.nofix
>>> 
>>> setting seed for random number generator to 1234
>>> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>>>  Referenced from:
>>> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>>>  Expected in: /usr/lib/libSystem.B.dylib
>>> 
>>> dyld: Symbol not found: ___emutls_get_address
>>>  Referenced from:
>>> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>>>  Expected in: /usr/lib/libSystem.B.dylib
>>> 
>>> 
>>> mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix
>>> ../surf/rh.smoothwm.nofix
>>> 
>>> setting seed for random number generator to 1234
>>> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>>>  Referenced from:
>>> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>>>  Expected in: /usr/lib/libSystem.B.dylib
>>> 
>>> dyld: Symbol not found: ___emutls_get_address
>>>  Referenced from:
>>> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>>>  Expected in: /usr/lib/libSystem.B.dylib
>>> 
>>> PIDs (11130 11133) completed and logs appended.
>>> Darwin Jareds-iMac.local 16.4.0 Darwin Kernel Version 16.4.0: Thu Dec
>>> 22 22:53:21 PST 2016; root:xnu-3789.41.3~3/RELEASE_X86_64 x86_64
>>> 
>>> recon-all -s test exited with ERRORS at Thu Feb 16 16:47:23 EST 2017
>> 
>> ?
>> 
>> Jared M. Saletin, PhD
>> 
>> Assistant Professor of Psychiatry and Human Behavior
>> Alpert Medical School of Brown University
>> 
>> E.P. Bradley Sleep Research Lab
>> 300 Duncan Drive
>> Providence, RI 02906
>> 
>> Email: jared_sale...@brown.edu  
>> >
>> Phone: 401-421-9440
>> Fax: 401-453-3578
>> 
>> 
>> 
>> 
>> 
>> ___
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>> 
>> 
> 

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Re: [Freesurfer] issues with -T2pial option in v.5.3

[Matt Glasser]

You could try with the HCP Pipelines and see if that helps:

https://github.com/Washington-University/Pipelines

Peace,

Matt.

From:   on behalf of Petr Bednarik

Reply-To:  Freesurfer support list 
Date:  Monday, February 20, 2017 at 12:26 PM
To:  
Subject:  [Freesurfer] issues with -T2pial option in v.5.3

Hi everyone, 

I am using Freesurfer version 5.3. I tried to refine the pial surfaces by
using  -T2pial option:

recon-all -subjid $SUBJ -T2/SUBJECT_DIR/$SUBJ/mri/orig/T2raw.mgz -T2pial
-autorecon3 

This step was helpful - e.g. it removed nicely residuals of venous sinuses,
but in some subjects it also removed part of the parietal or frontal cortex,
while the white matter is appropriately segmented.

https://www.dropbox.com/s/4gzsvrg85xsfdkn/surfaces_over_brainmask.mgz.png?dl
=0

The T2-space images had the same resolution as T1-MPRAGE (1x1x1mm) and were
acquired in the same session (3T Siemens Trio, standard 32 channel coil).
The problem does not seem to be caused by T2 misregistration :

https://www.dropbox.com/s/a7gdpxom0cqgj1u/surfaces_over_T2.mgz.png?dl=0

Question : What could cause this error and how could I extend pial surfaces
and get correct final segmentation ?

Thanks a lot !

PB
   
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[Freesurfer] issues with -T2pial option in v.5.3

[Petr Bednarik]

Hi everyone, 

I am using Freesurfer version 5.3. I tried to refine the pial surfaces by using 
 -T2pial option:

recon-all -subjid $SUBJ -T2/SUBJECT_DIR/$SUBJ/mri/orig/T2raw.mgz -T2pial 
-autorecon3 

This step was helpful - e.g. it removed nicely residuals of venous sinuses, but 
in some subjects it also removed part of the parietal or frontal cortex, while 
the white matter is appropriately segmented. 

https://www.dropbox.com/s/4gzsvrg85xsfdkn/surfaces_over_brainmask.mgz.png?dl=0 


The T2-space images had the same resolution as T1-MPRAGE (1x1x1mm) and were 
acquired in the same session (3T Siemens Trio, standard 32 channel coil). 
The problem does not seem to be caused by T2 misregistration :

https://www.dropbox.com/s/a7gdpxom0cqgj1u/surfaces_over_T2.mgz.png?dl=0 


Question : What could cause this error and how could I extend pial surfaces and 
get correct final segmentation ? 

Thanks a lot !

PB
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Re: [Freesurfer] hippocampal subfields in average space

[Iglesias Gonzalez, Eugenio]

Hi Lauri,
it depends on what you mean by template. If you mean an intensity averaged 
image, then no. But if you mean probabilities in a reference space, then yes. 
You can visualize the atlas with (warning: the viewer is a big buggy):
cd $FREESURFER_HOME/average/HippoSF/atlas
kvlViewMeshCollectionWithGUI AtlasMesh.gz
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 20 Feb 2017, at 17:12, Tuominen, Lauri Johannes 
> wrote:

Hi everyone,

Is there a template of the hippocampal subfields in some average space?

Best
Lauri Tuominen

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Re: [Freesurfer] Hippocampus eTIV correction (LONGITUDINAL)

[Martin Reuter]

Hi Sebastian,

the etiv is estimated in the base/subject-template, so it is constant 
for all time points. And if you want to include it into a longitudinal 
design depends on what you want. If you look at percent changes , you 
don't have to, but if you look at yearly rates, it is probably a good idea.

Best, Martin

Am 18.02.2017 um 13:52 schrieb Sebastian Huhn:
> Dear Freesurfer community,
>
> I wondered, how you correct the longitudinal hippocampus segmentation for 
> total intracranial volume.
> Our cross-sectional analysis is corrected for total intracranial volume as 
> described, for example, in Kerti et al. 2013 Neurology ( 
> http://dx.doi.org/10.1212/01.wnl.435561.00234.ee ).
>
> They used this formula: adjusted volume = raw volume - b*(ICV - mean ICV).
> The coefficient b represents the slope of regression of a region-of-interest 
> volume on ICV.
>
> Now I am curious how to perform such a correction for intracraial volume for 
> our longitudinal data.
> Do I correct for example the longitudinal hippocampus volume for timepoint 1, 
> for eTIV found in SUBJECT.long.template/stats/aseg.stats,  or for eTIV of the 
> template, or anything else?
> Or are such corrections even neccessary for longitudinal runs?
>
> Thanks a lot for helping me out of my confusion.
> Best,
> Sebastian
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Re: [Freesurfer] 答复: Longitudinal proceesing for Pediatric data

[Martin Reuter]

No, not that I know of.

Also I expect that it also depends on other factors (like image 
resolution, quality, subject anatomy etc) .



Best, Martin


Am 15.02.2017 um 08:21 schrieb Dongnandi:


Hi Martin

Thanks a lot for your reply!  Is there any reference that the 
longitudinal processing would fail if the difference in head size 
exceeded any certain value?


Best, Dong

*发件人:*freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *代表 *Martin Reuter

*发送时间:*2017年2月15日2:40
*收件人:*Freesurfer support list 
*主题:*Re: [Freesurfer] Longitudinal proceesing for Pediatric data

Hi Dong,

it can work, if time points are close to each other (so not much head 
growth). Feel free to try, but make sure you are carefully looking at 
the surfaces, that no gray matter is clipped in later time points.


The alternative is to only do cross sectional processing.

Best, Martin

On 14 Feb 2017, at 04:56, Dongnandi > wrote:

Dear freesurfer exports,

As it is mentioned in the documentation that ‘pediatric data
violates the fixed head size assumption’ for the current
longitudinal stream. Is there any solution for the issue now?

Thanks

Dong

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[Freesurfer] hippocampal subfields in average space

[Tuominen, Lauri Johannes]

Hi everyone, 

Is there a template of the hippocampal subfields in some average space? 

Best
Lauri Tuominen

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Re: [Freesurfer] Hipposubfield outputs 6.0

[Iglesias Gonzalez, Eugenio]

The volumes are already in cubic mm.
Cheers,
/E

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 20 Feb 2017, at 12:50, std...@virgilio.it wrote:

Hi list,
I wonder whether in the 6.0 the hipposubfield outputs needs for nomalization 
(by diving for 3 the volumes as well as the 5.3) or they are already corrected?
Thanks

Stefano
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[Freesurfer] Hipposubfield outputs 6.0

[stdp82]

Hi list,I wonder whether in the 6.0 the hipposubfield outputs needs for 
nomalization (by diving for 3 the volumes as well as the 5.3) or they are 
already corrected?Thanks
Stefano___
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Re: [Freesurfer] Trying to download FreeSurfer 6

[Jose Enrique Romero Gómez]

I was using Chrome, I tried using Firefox and it works.

Thanks a lot!

Jose

2017-02-17 16:10 GMT+01:00 Z K :

> What browser are you using? My first recommendation would be to try
> downloading using another browser. If the problem persists than its
> probably due to some type of file size limit on the network you are on.
>
> On 02/17/2017 07:25 AM, Jose Enrique Romero Gómez wrote:
> >
> > Hello,
> >
> > I'm trying to download FS6 but always get a timeout error.
> >
> > This is the link I'm using:
> >
> > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
> >  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz>
> >
> > And this is the error message
> >
> > *Connection to 132.183.202.158 failed.*
> >
> > The system returned: /(110) Connection timed out/
> >
> > The remote host or network may be down. Please try the request again.
> >
> >
> > Thanks!
> >
> > Jose
> >
> >
> >
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> dispose of the e-mail.
>
>
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[Freesurfer] Output from mri_cvs_register

[Magnús Ingvi]

Hi!
I am running mri_cvs_regsiter, on the cvs_avg35 space. In the dt_recon
tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion
), the expected .m3z output file is called
combined_tocvs_avg35_elreg_afteraseg-norm.m3z, but the output I get in the
cvs folder is called final_CVSmorph_tocvs_avg35.m3z
Is this the same file, or did I mess up somewhere?
Best
M.Ingvi
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