Dear FS gurus,
I just want to give some feedback on an error message that has
bedeviled some of us for the last few months even after running fs_update and
turning off SIP.
I have been getting this error when I ran mri_coreg or mris_convert:
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
In my case there were multiple versions of libgomp.1.dylib. One in the current
Freesurfer 6.0 install, one in the gcc-7.1 compiler library that I recently
installed (after I ran into this error) and the third from an ANFI install from
2013. When I rearranged the order of the PATH as shown, the error went away.
This was my old path:
/usr/local/bioimagesuite35:/usr/local/bioimagesuite35/sbin:/usr/local/bioimagesuite35/bin:/usr/local/bioimagesuite35/bin:/Users/fred/Dropbox/Research_Scripts/EpiSurg-iElvis/iELVis/iELVis_BASH:/Users/fred/Dropbox/Research_Scripts/Linux-Scripts:/Applications/MATLAB_R2015a.app/bin/:/usr/local/cuda/bin:/usr/local/AFNI:/usr/local/fsl/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/git/bin:/usr/local/fsl/bin:/usr/local/afni
This is my new path:
/Users/fred/Dropbox/Research_Scripts/EpiSurg-iElvis/iELVis/iELVis_BASH:/Users/fred/Dropbox/Research_Scripts/Linux-Scripts:/usr/local/gcc-7.1/bin:/Applications/MATLAB_R2015a.app/bin/:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/fsl/bin:/usr/local/AFNI:/usr/local/bioimagesuite35:/usr/local/bioimagesuite35/sbin:/usr/local/bioimagesuite35/bin:/usr/local/bioimagesuite35/bin:/usr/local/cuda/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/git/bin:/usr/local/fsl/bin:/usr/local/afni
Best,
Fred
Fred Lado, MD PhD
Director, Epilepsy - Central and Eastern Regions
Northwell Health
917-608-1881 (mobile)
516-325-7000 (practice)
516-325-7001 (fax)
fl...@northwell.edu
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> On Aug 24, 2017, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>
> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
> freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
> 1. Re: recon-all error (Douglas N Greve)
> 2. Re: Continuous co-variate by continuous co-variate
> interaction effects (Douglas N Greve)
> 3. Re: Hard failure via XNAT pipeline (Freesurfer 6)
> (Rockers, Elijah D.)
> 4. Using Total Cortical White Matter Volume as a "whole brain"
> covariate (Mehta, Chintan)
> 5. Re: mri_coreg (Douglas N Greve)
> 6. Functional Connectivity Motion Regression (Leathem, Logan Daniel)
> 7. Qdec keyboard input error (???)
> 8. Xlib: extension "GLX" missing on display "0.0" when running
> freeview (fengmei fan)
> 9. cudadetect fails: wrong amount of memory and number of cores
> detected (markus.mert...@evkb.de)
> 10. Re: mri_coreg (Joudy.carter)
> 11. Re: QA tools for FS vs 6.0 (Antonietta Pepe)
> 12. sub cortical analysis (John Anderson)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 23 Aug 2017 14:54:29 -0400
> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] recon-all error
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <b83cfed1-8a92-fcc7-8ce5-96ec093e1...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> does this happen every time you run it? The message said that the job
> was killed, which suggests something outside of recon-all (eg, if you
> were running it on a cluster, sometimes a job will get killed if it runs
> out of memory or runs too long).
>
>
> On 08/23/2017 02:30 PM, Cara Bohon wrote:
>> I have a couple of subjects "exited with ERRORS" after running almost 48
>> hours (when my others all took about 13-15 hours on the same server). Both
>> exited during Fix Topology lh.
>>
>> The only time "error" appears is in this line: IFLAG= -1 LINE SEARCH
>> FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH:
>> INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT
>> TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 - which
>> prior messages to this list suggest is not meaningful or problematic.
>>
>> I am brand new to Freesurfer, so I'm not quite sure where to start in
>> troubleshooting. The orig.mgz file looks fine to me, but maybe I'm missing
>> something. Any other tips for things to check? I'm attaching a recon-all.log
>> file in case that is helpful. I am running Freesurfer 5.3.0 on Linux.
>>
>> Thanks for any tips on addressing the error!
>>
>> -Cara
>>
>>
>> _______________________________________________
>> 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: 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/
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 23 Aug 2017 14:57:53 -0400
> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Continuous co-variate by continuous
> co-variate interaction effects
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <e1a5bf46-9c3f-564b-fbe0-ce081f513...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Is that your design matrix or the contrast matrix? To test for the
> interaction between two continuous variables, one usually creates a new
> variable by multiplying them together and then just testing for the
> regressor for that variable being different than zero
>
>
> On 08/23/2017 12:34 PM, Timothy Hendrickson wrote:
>> Freesurfer experts,
>>
>> I have created a design matrix in order to test for whether there is
>> an interaction effect between two continuous co-variates controlling
>> for a categorical variable.
>>
>> So I have one categorical variable with two levels, and two continuous
>> co-variates.
>>
>> My design matrix is as follows:
>>
>> 0 0 1 1 0 0
>> 0 0 0 0 1 1
>>
>> Is this correct?
>>
>> -Tim
>>
>> Timothy Hendrickson
>> Department of Psychiatry
>> University of Minnesota
>> Bioinformatics and Computational Biology M.S. Candidate
>> Office: 612-624-6441
>> Mobile: 507-259-3434 (texts okay)
>>
>>
>> _______________________________________________
>> 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: 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/
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 23 Aug 2017 21:54:20 +0000
> From: "Rockers, Elijah D." <edrock...@houstonmethodist.org>
> Subject: Re: [Freesurfer] Hard failure via XNAT pipeline (Freesurfer
> 6)
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <1503525260.5299.80.ca...@houstonmethodist.org>
> Content-Type: text/plain; charset="utf-8"
>
> We'll try to process it on a blade server tongiht... if it succeeds we can
> edit any incorrect results as needed.
>
> The image is from a separate site, it has OK resolution (1x1x1.5) but has an
> enormous amount of gibbs ringing compared to our on-site images, which is
> probably causing the issue...
>
> Thanks,
> Eli
>
>
>
> Date: Wed, 23 Aug 2017 11:54:06 -0400
> From: Bruce Fischl
> <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] Hard failure via XNAT pipeline (Freesurfer
> 6)
> To: Freesurfer support list
> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
> Message-ID:
> <54b7b7a7-cdc3-46f1-8e1b-098142fd3...@nmr.mgh.harvard.edu<mailto:54b7b7a7-cdc3-46f1-8e1b-098142fd3...@nmr.mgh.harvard.edu>>
> Content-Type: text/plain; charset="us-ascii"
>
> That defect is so big you probably ran out of memory.
>
>> On Aug 23, 2017, at 11:21 AM, Rockers, Elijah D.
>> <edrock...@houstonmethodist.org<mailto:edrock...@houstonmethodist.org>>
>> wrote:
>>
>> We encountered a hard failure, below is the tail of the log. We are
>> currently running Freesurfer 6 again locally to see if it succeeds on a
>> desktop machine (this is the first time encountering a hard failure on the
>> XNAT server). Any suggestions?
>>
>> -merging segment 180 into 178
>> 160 defects to be corrected
>> 0 vertices coincident
>> reading input surface
>> /data/build/nnac/20170818_114535/alamode_MRI08162017/20170818114538/alamode_MRI08162017/surf/lh.qsphere.nofix...
>> reading brain volume from brain...
>> reading wm segmentation from wm...
>> Computing Initial Surface Statistics
>> -face loglikelihood: -8.7982 (-4.3991)
>> -vertex loglikelihood: -6.2982 (-3.1491)
>> -normal dot loglikelihood: -3.5611 (-3.5611)
>> -quad curv loglikelihood: -6.1931 (-3.0965)
>> Total Loglikelihood : -24.8505
>>
>> CORRECTING DEFECT 0 (vertices=40706, convex hull=11265, v0=89)
>> XL defect detected...
>> Segmentation fault (core dumped)
>> Linux hhvrixnatp01 2.6.32-431.el6.x86_64 #1 SMP Sun Nov 10 22:19:54 EST 2013
>> x86_64 x86_64 x86_64 GNU/Linux
>>
>> recon-all -s alamode_MRI08162017 exited with ERRORS at Mon Aug 21 19:27:09
>> CDT 2017
>>
>> To report a problem, see
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting&d=DwIBAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ZUxVIMrFX5hWNR4618Ng1NGK5pswnaS1K8_SrFxDwio&s=UPo-wFt-ACmW_p7FRxtgmbsmsxyiC8zWu4xz_jMpwRM&e=
>>
>> Houston Methodist. Leading Medicine.
>>
>> Houston Methodist is ranked by U.S. News & World Report as the No. 1
>> hospital in Texas for patient care. Houston Methodist is nationally ranked
>> in 8 specialties and is designated as a Magnet hospital for excellence in
>> nursing. Visit us at houstonmethodist.org. Follow us at
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHosp&d=DwIBAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ZUxVIMrFX5hWNR4618Ng1NGK5pswnaS1K8_SrFxDwio&s=OO5cwh0TYxKrHk7C0DiMckR5_f7AfSahK9xF3CSe3Hw&e=
>> and
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__facebook.com_HoustonMethodist&d=DwIBAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ZUxVIMrFX5hWNR4618Ng1NGK5pswnaS1K8_SrFxDwio&s=fT36tQ3TMuZagDYvb4HSxJ3fhMjgib0EdBJluu7uRAY&e=
>> .
>>
>> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston
>> Methodist and/or its relevant affiliates and may contain restricted and
>> privileged material for the sole use of the intended recipient(s). Any
>> review, use, distribution or disclosure by others is strictly prohibited. If
>> you are not the intended recipient (or authorized to receive for the
>> recipient), please contact the sender and delete all copies of the message.
>> Thank you.
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ZUxVIMrFX5hWNR4618Ng1NGK5pswnaS1K8_SrFxDwio&s=STACrwCfPSrQfmQMFLcII3rDEnp66bw5ZgRLLMyVSLs&e=
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> ------------------------------
>
> Message: 4
> Date: Wed, 23 Aug 2017 22:44:34 +0000
> From: "Mehta, Chintan" <chintan.me...@yale.edu>
> Subject: [Freesurfer] Using Total Cortical White Matter Volume as a
> "whole brain" covariate
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
>
> <bn6pr08mb27232e7c14230287dc7a51419d...@bn6pr08mb2723.namprd08.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear FreeSurfer Developers,
>
>
> I am using FreeSurfer 5.3 to analyze whether a risk factor explains variation
> in brain structures related to surface area, mean thickness, and subcortical
> volumes.
>
>
> Documentation suggests using estimated Total Intracranial Volume (eTIV) as a
> covariate to adjust for brain size in analyses of surface area and volumes:
> (https://surfer.nmr.mgh.harvard.edu/fswiki/eTIV). Previous posts have also
> suggested using BrainSegNotVent or Total Gray Matter Volume as covariates as
> a "whole brain" covariate, with the choice of covariates representing
> different hypotheses regarding local vs. global atrophy.
>
>
> However, it seems to me that using BrainSegNotVent or Total Gray Matter
> Volume as covariates could lead to a significant loss in power in detecting
> effects on area/thickness measures from a risk factor associated with atrophy
> across many regions. On the other hand, eTIV may suffer from not accounting
> accounting for local atrophy (in addition to heightened measurement error, as
> frequently alluded into previous posts). But still, a normalization covariate
> is needed to account for differences in brain size need to be accounted
>
>
> In the analysis of cortical surface area or mean cortical thickness among
> normal populations, could it make sense to use cortical white matter volume
> as the "whole brain" covariate? In normal populations, cortical white matter
> volume is significantly correlated with surface area, mean thickness, and
> gray matter volumes but its value is not derived from the gray matter
> structures. My understanding is that FreeSurfer sets cortical surface area as
> the area at the boundary of white and gray matter. As a covariate in models
> of cortical surface area or mean thickness, white matter volume could
> side-step the loss in power in detecting effects lead to both global atrophy
> in gray matter volume while also partly adjusting for total brain differences.
>
>
> Cortical white matter volume is not a standard "whole brain" covariate in the
> literature (in the way eTIV or Total Gray Matter Volume are). However, am I
> misunderstanding how FreeSurfer computes these Cortical White Matter that
> makes it unsuitable as a "whole brain" covariate?
>
>
> Thank you.
>
>
> Best,
>
> Chintan
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> ------------------------------
>
> Message: 5
> Date: Wed, 23 Aug 2017 18:49:59 -0400
> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] mri_coreg
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <534b8894-1b63-a5f1-6373-7d03275a1...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Actually, it is on by default (thanks to Emma for pointing it out). The
> smoothing helps to blur anatomical differences which reduces the chance
> that it will get stuck in a local minimum. It will usually only smooth
> the reference, and only if it is high res; this can help the reference
> look a little more like the moveable. In the end, I don't think it makes
> much of a difference except to make it a little more robust.
>
>
> On 08/21/2017 03:52 PM, Douglas N Greve wrote:
>> I don't think that is turned on by default. There is smoothing of the
>> NMI historgrams, but that is unrelated
>>
>>
>> On 08/21/2017 12:07 PM, John Anderson wrote:
>>> Dear Dr Greve,
>>> Kindly, I wanted to know why "mri_coreg" apples smoothing during
>>> registration. e.g.
>>>
>>> mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta
>>>
>>> Are there any effects on the accuracy of smoothing if I turn off this
>>> default feature (specifically in pet surfer pipeline).
>>>
>>> mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta
>>> --no-smooth
>>>
>>> Thank you for any clarification
>>> John
>>>
>>>
>>> _______________________________________________
>>> 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: 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/
>
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 24 Aug 2017 02:21:31 +0000
> From: "Leathem, Logan Daniel" <lleat...@mgh.harvard.edu>
> Subject: [Freesurfer] Functional Connectivity Motion Regression
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <4ebc097b-5fab-4374-8ba0-d032daca1...@mgh.harvard.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Freesurfer list,
>
> My group is switching to the fsfast functional connectivity pipeline. We
> would like to continue regressing out the six-parameter rigid body head
> motion as a nuisance variable. In order to do this, which file should we
> flag: is it fmcpr.mcdat or mcprextreg?
>
> Thank you!
>
> Best,
> Logan
>
> Logan D. Leathem
> Clinical Research Coordinator
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 13th Street, Rm 2602A
> Charlestown, MA 02129
> Phone: 617-643-4441
>
>
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>
> ------------------------------
>
> Message: 7
> Date: Thu, 24 Aug 2017 17:04:34 +0900
> From: ??? <dryic...@naver.com>
> Subject: [Freesurfer] Qdec keyboard input error
> To: <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <bcaf88847233f755bb8e93fcca52...@cweb02.nm.nhnsystem.com>
> Content-Type: text/plain; charset="utf-8"
>
> I'm studying freesurfer especially, QDEC to execute group analysis.
> In QDEC, I can type in Subjects and Design tap. But I can't type in Display
> tap like threshold p.
> I've seen several question like me but no one give solution.
>
> Here's my environment.
> OS : CentOS 7.0
> Freesurfer : stable 6.0
> QDEC : 1.5
>
> Show me how to solve this problem.
>
> Thank you.
>
> =============================================
> Hyunwoo Kim
>
> Graduate school of Yonsei University
> Biosignal Processing Laboratory
>
> #201 Sanhakgwan, 1 Yonseidaegil, Heungup, Wonju, Gangwon, 220-710, Republic
> of Korea
>
> Tel. +82-33-760-2809
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>
> ------------------------------
>
> Message: 8
> Date: Thu, 24 Aug 2017 08:59:45 +0000
> From: fengmei fan <fanfeng...@live.com>
> Subject: [Freesurfer] Xlib: extension "GLX" missing on display "0.0"
> when running freeview
> To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
>
> <dm5pr17mb11305535c2a1eaf01143c022a1...@dm5pr17mb1130.namprd17.prod.outlook.com>
>
> Content-Type: text/plain; charset="gb2312"
>
> HI,
>
> I installed Freesurfer 6 in CentOS 6.5, when runing freeview, errors occurred:
>
> Xlib: extension "GLX" missing on display "0.0"
> Xlib: extension "GLX" missing on display "0.0"
>
> What's wrong? And how to settle this problem?
>
> Best,
> Fengmei Fan
> Assistant professor,
> Beijing Huilongguan Hospital,
> Beijing Huilongguan Medical College of Peking University
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>
> Message: 9
> Date: Thu, 24 Aug 2017 09:59:23 +0000
> From: <markus.mert...@evkb.de>
> Subject: [Freesurfer] cudadetect fails: wrong amount of memory and
> number of cores detected
> To: <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> <387e7487cd0f4b4f9588c783ccc2ce6505a4b...@vba3exch2.vd.bethel.de>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello FreeSurfer Developers,
>
> I would like to use recon-all with the option "-use-gpu" so I ran cudadetect
> first to see whether the nvidia card on my system will be detected. But at
> least the values for total amount of memory and number of cores are wrong
> (should be 8GB and 2304 cores).
>
> $ cudadetect
> Detecting CUDA... There are 0 devices supporting CUDA:
>
> Device 0: "Quadro K5200"
> CUDA Driver Version: 8.0
> CUDA Runtime Version: 6.50
> CUDA Capability Major revision number: 3
> CUDA Capability Minor revision number: 5
> Total amount of global memory: 4224450560 bytes
> Number of multiprocessors: 12
> Number of cores: -2109039396
> Total amount of constant memory: 65536 bytes
> Total amount of shared memory per block: 49152 bytes
> Total number of registers available per block: 65536
> Warp size: 32
> Maximum number of threads per block: 1024
> Maximum sizes of each dimension of a block: 1024 x 1024 x 64
> Maximum sizes of each dimension of a grid: 2147483647 x 65535 x 65535
> Maximum memory pitch: 2147483647 bytes
> Texture alignment: 512 bytes
> Clock rate: 0.77 GHz
> Concurrent copy and execution: Yes
> Run time limit on kernels: Yes
> Integrated: No
> Support host page-locked memory mapping: Yes
> Compute mode: Default (multiple host
> threads can use this device simultaneously)
> $
>
> What could I try?
>
> Thank you.
>
>
>
> FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
> uname -a: Linux cortex 4.4.74-server-1.mga5 #1 SMP Mon Jun 26 08:34:35
> UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>
> _______________________________________________________________
>
> Evangelisches Klinikum Bethel gGmbH
> Akademisches Lehrkrankenhaus der Universit?t M?nster
>
> Sitz der Gesellschaft
> Kantensiek 11 | 33617 Bielefeld
>
> Amtsgericht Bielefeld HRB 30169
>
> Gesch?ftsf?hrer
> Dr. Rainer Norden (Vorsitz)
> Dr. Matthias Ernst
> Dr. Maren Th?ter
>
> Vorsitzender des Aufsichtsrates
> Pastor Ulrich Pohl
>
> 150 Jahre Bethel - F?r Menschen da sein
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> ------------------------------
>
> Message: 10
> Date: Thu, 24 Aug 2017 06:24:24 -0400
> From: "Joudy.carter" <joudy.car...@protonmail.com>
> Subject: Re: [Freesurfer] mri_coreg
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
>
> <PBYaodFQvA4KI5HGk7ZpGZdSKSNPq2_e6v_IoWGAmB_ObBmvL7PQo8L6N0hBdifCHOL7wjnMgqcR2IJIwuQ2UzSKJ23bAQ96GqvQFv1rKlc=@protonmail.com>
>
> Content-Type: text/plain; charset="utf-8"
>
> Actually thank you for me as well for such a nice question! ;-)
> This great response makes sense. Thank you very much Dr Greve for the follow
> up
>
>> -------- Original Message --------
>> Subject: Re: [Freesurfer] mri_coreg
>> Local Time: August 23, 2017 6:49 PM
>> UTC Time: August 23, 2017 10:49 PM
>> From: gr...@nmr.mgh.harvard.edu
>> To: freesurfer@nmr.mgh.harvard.edu
>>
>> Actually, it is on by default (thanks to Emma for pointing it out). The
>> smoothing helps to blur anatomical differences which reduces the chance
>> that it will get stuck in a local minimum. It will usually only smooth
>> the reference, and only if it is high res; this can help the reference
>> look a little more like the moveable. In the end, I don"t think it makes
>> much of a difference except to make it a little more robust.
>>
>> On 08/21/2017 03:52 PM, Douglas N Greve wrote:
>>> I don"t think that is turned on by default. There is smoothing of the
>>> NMI historgrams, but that is unrelated
>>>
>>>
>>> On 08/21/2017 12:07 PM, John Anderson wrote:
>>>> Dear Dr Greve,
>>>> Kindly, I wanted to know why "mri_coreg" apples smoothing during
>>>> registration. e.g.
>>>>
>>>> mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta
>>>>
>>>> Are there any effects on the accuracy of smoothing if I turn off this
>>>> default feature (specifically in pet surfer pipeline).
>>>>
>>>> mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta
>>>> --no-smooth
>>>>
>>>> Thank you for any clarification
>>>> John
>>>>
>>>>
>>>> _______________________________________________
>>>> 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: 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/
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> 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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> ------------------------------
>
> Message: 11
> Date: Thu, 24 Aug 2017 14:41:45 +0200
> From: Antonietta Pepe <antonietta.p...@u-bordeaux.fr>
> Subject: Re: [Freesurfer] QA tools for FS vs 6.0
> To: Falk L?sebrink <falk.luesebr...@ovgu.de>
> Cc: "yongl...@gmail.com" <yongl...@gmail.com>, Freesurfer support list
> <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <18ef28ed-6645-4eb6-aa8c-2af0810aa...@u-bordeaux.fr>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Falk,
>
> Thanks for your replay.
> I tried getting in contact with him more than a month ago without success,
> this is why I was hoping in a more official release.
> I did use a different email address though, probably not the good one?
>
> Best,
> Antonietta
>
>
>> On 23 Aug 2017, at 17:32, Falk L?sebrink <falk.luesebr...@ovgu.de> wrote:
>>
>> Dear Antonietta,
>>
>> I don?t know of any official statement in that regard, however, Yong Li
>> (CC?ed) seems to have updated the QA tools working with FS 6 in April. He
>> may share his code.
>>
>> Best,
>> Falk
>>
>> Von: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Antonietta
>> Pepe
>> Gesendet: Mittwoch, 23. August 2017 16:47
>> An: freesurfer@nmr.mgh.harvard.edu
>> Betreff: [Freesurfer] QA tools for FS vs 6.0
>>
>> Dear FreeSurfer list,
>> is any of you aware of a new version of the QA (quality assessment) tools
>> <https://surfer.nmr.mgh.harvard.edu/fswiki/QATools
>> <https://surfer.nmr.mgh.harvard.edu/fswiki/QATools>> working for FS vs 6.0?
>> Should I expect a new release in the near feature?
>>
>> Kind regards,
>>
>> Antonietta
>>
>> ANTONIETTA PEPE
>> IMN, Institut des Maladies Neurod?g?n?ratives, UMR 5293
>> Equipe 5 : GIN, Groupe d?Imagerie Neurofonctionnelle, CEA - CNRS -
>> Universit? de Bordeaux
>> Universit? de Bordeaux
>> 146 rue L?o Saignat - CS 61292 - Case 28
>> 33 076 Bordeaux cedex
>> http://www.imn-bordeaux.org/ <http://www.imn-bordeaux.org/>
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> ------------------------------
>
> Message: 12
> Date: Thu, 24 Aug 2017 10:29:37 -0400
> From: John Anderson <john.ande...@protonmail.com>
> Subject: [Freesurfer] sub cortical analysis
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
>
> <vqORNDcJIVpAGpzNpbI7EP9kup0QuUbYAqDF3S8L5aJ5lwaWS_9OdNpCBvd2veRvX_FJsMm3-SKGChqv2eeUk8cX4QrVcb6rrDUzSVmXpQo=@protonmail.com>
>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Dr Greve,
>
> I am using pet surfer to analyze suv images. I followed all the steps in
> wiki, I used the option mgx then I fed the images mgx.{ctxgm,subctxgm,gm}
> into surface based analysis for left and right hemispheres. I want to inquire
> about the sub cortical analysis.
>
> 1. I assume the analysis for sub cortical gray matter (i.e. using the images
> subctxgm) is volumetric. Correct?
>
> 2. Are the following steps correct for sub cortical gray matter analysis
>
> mri_vol2vol --mov subctxgm.nii.gz --reg reg.dat --tal --talres 2 --talxfm
> talairach.xfm --nearest --no-save-reg --o subctxgm.tal2mm.nii.gz
>
> mri_mask subctxgm.tal2mm.nii.gz
> $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
> subctxgm.tal2mm_subc.nii.gz &
>
> Concatenate all subjects together using mri_concat
>
> smooth using mri_fwhm (what is the recommended smoothing for suv)?
>
> Then Group analysis:
>
> mri_glmfit --y all.suvr.tal2mm.subc.sm10.nii --fsgd fsgd.dat --C contrast.mtx
> --glmdir dir
>
> mri_glmfit-sim --glmdir dir --grf 1.3 pos --cwpvalthresh 0.0166
>
> for "mri_glmfit-sim" in subcortical structure is the flag grf correct or
> cache?
>
> Thanks in advance!
> John
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>
> End of Freesurfer Digest, Vol 162, Issue 52
> *******************************************
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