Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.eduTo 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-request@nmr.mgh.harvard.edu
You can reach the person managing the list at
freesurfer-owner@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.Mertens@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 <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <b83cfed1-8a92-fcc7-8ce5-96ec093e10fc@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
greve@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 <greve@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-ce081f513ae8@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
greve@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." <edrockers@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.camel@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 <fischl@nmr.mgh.harvard.edu<mailto:fischl@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-098142FD3DB2@nmr.mgh.harvard.edu<mailto:54B7B7A7-CDC3-46F1-8E1B-098142FD3DB2@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. <edrockers@houstonmethodist.org<mailto:edrockers@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=
-------------- next part --------------
An HTML attachment was scrubbed...
URL: https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20170823_25408482_attachment-2D0001.html&d=DwIBAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ZUxVIMrFX5hWNR4618Ng1NGK5pswnaS1K8_SrFxDwio&s=0_mTIdxw9CWUx4VItMCJF-bgRCkUw2l7BwLlpWLAvis&e=
------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170823/91a1358c/attachment-0001.html
------------------------------
Message: 4
Date: Wed, 23 Aug 2017 22:44:34 +0000
From: "Mehta, Chintan" <chintan.mehta@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:
<BN6PR08MB27232E7C14230287DC7A51419D850@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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170823/ce79b473/attachment-0001.html
------------------------------
Message: 5
Date: Wed, 23 Aug 2017 18:49:59 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_coreg
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <534b8894-1b63-a5f1-6373-7d03275a194f@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
greve@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" <LLEATHEM@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-D032DACA1183@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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170824/1757a633/attachment-0001.html
------------------------------
Message: 7
Date: Thu, 24 Aug 2017 17:04:34 +0900
From: ??? <dryicepa@naver.com>
Subject: [Freesurfer] Qdec keyboard input error
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <bcaf88847233f755bb8e93fcca52a07@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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170824/0acfd873/attachment-0001.html
------------------------------
Message: 8
Date: Thu, 24 Aug 2017 08:59:45 +0000
From: fengmei fan <fanfengmei@live.com>
Subject: [Freesurfer] Xlib: extension "GLX" missing on display "0.0"
when
running freeview
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<DM5PR17MB11305535C2A1EAF01143C022A19A0@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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170824/a7f029e2/attachment-0001.html
------------------------------
Message: 9
Date: Thu, 24 Aug 2017 09:59:23 +0000
From: <Markus.Mertens@evkb.de>
Subject: [Freesurfer] cudadetect fails: wrong amount of memory and
number of
cores detected
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<387E7487CD0F4B4F9588C783CCC2CE6505A4B537@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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170824/2addb769/attachment-0001.html
------------------------------
Message: 10
Date: Thu, 24 Aug 2017 06:24:24 -0400
From: "Joudy.carter" <joudy.carter@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: greve@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
greve@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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170824/f3a545f1/attachment-0001.html
------------------------------
Message: 11
Date: Thu, 24 Aug 2017 14:41:45 +0200
From: Antonietta Pepe <antonietta.pepe@u-bordeaux.fr>
Subject: Re: [Freesurfer] QA tools for FS vs 6.0
To: Falk L?sebrink <falk.luesebrink@ovgu.de>
Cc: "yongli86@gmail.com" <yongli86@gmail.com>,
Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Message-ID: <18EF28ED-6645-4EB6-AA8C-2AF0810AAA7A@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.luesebrink@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170824/5900c961/attachment-0001.html
------------------------------
Message: 12
Date: Thu, 24 Aug 2017 10:29:37 -0400
From: John Anderson <John.anderso@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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170824/cfe440d1/attachment-0001.html
------------------------------
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 162, Issue 52
*******************************************