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Today's Topics:
1. Re: Coordinate transformation to average surface space
(ISAAC PEDISICH)
2. Re: using multiple cores (Z K)
3. Fwd: Fwd: Optseq2: ntp (Conchy PF)
4. Help with subject's functional overlay (Cesar Echavarria)
5. Re: Help with subject's functional overlay (Bruce Fischl)
6. Re: Help with subject's functional overlay (Cesar Echavarria)
7. Re: problems about extracting specific vertex thickness value
and getting a average thickness for a specific mask (Douglas N Greve)
8. Re: Fwd: Fwd: Optseq2: ntp (Douglas N Greve)
9. Re: When/What to edit? (Douglas N Greve)
10. Re: qdec question (Douglas N Greve)
11. Re: Help with subject's functional overlay (Douglas N Greve)
12. Re: Brain Seg Volumes (Douglas N Greve)
13. Re: using multiple cores (Lukas.Scheef@ukb.uni-bonn.de)
14. Re: comparing two conditions with disproportionate number of
trials (Eryilmaz, Huseyin Hamdi)
15. Re: Help with subject's functional overlay (Cesar Echavarria)
16. Re: using multiple cores (Z K)
17. Re: Help with subject's functional overlay (Douglas N Greve)
18. Re: using multiple cores (Bruce Fischl)
19. Registering functional data to inflated brain (Sherryse Corrow)
20. Viewing functional data on the inflated brain (Sherryse Corrow)
21. vertex-wise cortical thickness and whole brain labeling (Caka)
22. Re: Registering functional data to inflated brain (Douglas Greve)
23. Re: LOOK FOR HELP (???)
24. LOOK FOR HELP (???)
25. Re: vertex-wise cortical thickness and whole brain labeling
(Douglas Greve)
26. Re: Viewing functional data on the inflated brain (Douglas Greve)
27. Two positions are available @ Queensland Brain Institute
(Yong Liu)
28. Re: qdec question (Anna Jonsson)
29. aseg.stats volume mismatch (Gabor Perlaki)
30. Re: aseg.stats volume mismatch (Bruce Fischl)
31. -3T and -mprage flags (Jason Tourville)
32. Re: LOOK FOR HELP (Douglas Greve)
33. Re: qdec question (Douglas Greve)
34. Re: -3T and -mprage flags (Bruce Fischl)
35. freeview fails to open (JacobML@nmr.mgh.harvard.edu)
36. mri_glmfit restricted to a label (Garikoitz Lerma-Usabiaga)
37. Re: freeview fails to open (Ruopeng Wang)
38. Re: freeview fails to open (JacobML@nmr.mgh.harvard.edu)
39. Re: freeview fails to open (Ruopeng Wang)
40. Re: freeview fails to open (JacobML@nmr.mgh.harvard.edu)
----------------------------------------------------------------------
Message: 1
Date: Mon, 5 May 2014 12:19:29 -0400
From: ISAAC PEDISICH <iped@sas.upenn.edu>
Subject: Re: [Freesurfer] Coordinate transformation to average surface
space
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAPUS5aqNf_zYu185Sf723Ad9wpp59b02hC3e-K0KZ2nLjQJMdQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Any other thoughts as to what might be going wrong with our coordinate
transformations / any other transformations that we might not be taking
into account?
Thanks,
Isaac
On Tue, Apr 29, 2014 at 4:52 PM, ISAAC PEDISICH <iped@sas.upenn.edu> wrote:
> The purpose of what I'm trying to do is getting specific points from the
> CT onto the average surface.
> These points lie on the surface of the brain.
>
> Originally, we were using flirt to register the CT to the MRI, then
> registering the MRI to the talairach brain, to get the CT into the same
> space as the surface. This method worked okay, but we were hoping to
> improve on it.
>
> The new method, using robust register and tkregsiter2, produces
> coordinates that are on the surface of the brain in freeview, but not in
> matlab (for some subjects).
>
> Here is the info for one problem subject:
>
> mri_info --vox2ras-tkr [subj]_CT_combined.img
> INFO: using NIfTI-1 qform
> -0.47461 0.00000 0.00000 121.50000
> 0.00000 0.00000 0.62634 -69.83636
> 0.00000 -0.47461 0.00000 121.50000
> 0.00000 0.00000 0.00000 1.00000
>
>
> # transform file reg_avg.lta
> # created by ---- on Thu Mar 27 15:55:39 2014
> type = 1
> nxforms = 1
> mean = 256.0000 228.0000 111.0000
> sigma = 10000.0000
> 1 4 4
> 9.349995851516724e-01 -2.874486744403839e-01 -2.077235281467438e-01
> -3.043334960937500e+01
> 3.062604963779449e-01 9.497789144515991e-01 6.422379612922668e-02
> 1.133301696777344e+02
> 1.788303703069687e-01 -1.236666887998581e-01 9.760769009590149e-01
> -1.039845886230469e+02
> 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
> 1.000000000000000e+00
> src volume info
> valid = 1 # volume info valid
> filename = [subj]_CT_combined.img
> volume = 512 512 223
> voxelsize = 4.746093750000000e-01 4.746093750000000e-01
> 6.263351440429688e-01
> xras = -9.999999403953552e-01 0.000000000000000e+00 0.000000000000000e+00
> yras = 0.000000000000000e+00 9.703245759010315e-01 2.418061196804047e-01
> zras = -0.000000000000000e+00 -2.418061196804047e-01
> 9.703245759010315e-01
> cras = 7.629394531250000e-06 -1.615307769775391e+02 1.476517486572266e+02
> dst volume info
> valid = 1 # volume info valid
> filename = /data/eeg/freesurfer/subjects/average/mri/orig.mgz
> volume = 256 256 256
> voxelsize = 1.000000000000000e+00 1.000000000000000e+00
> 1.000000000000000e+00
> xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
> yras = -2.220446049250313e-16 -1.490116119384766e-08
> -1.000000000000000e+00
> zras = 4.440892098500626e-16 1.000000000000000e+00 8.443226899772703e-18
> cras = 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
>
>
> Here are a set of eight coordinates, all of which are on the surface in
> CRS space on the CT:
> 242 267 47
> 241 283 36
> 234 298 28
> 221 313 23
> 203 321 19
> 183 323 24
> 172 312 33
> 164 297 42
>
> After applying the transform, these coordinates come out as:
> 5.2486 -168.8798 78.8261
> 2.2243 -174.6209 70.8729
> 2.5230 -179.4546 62.9121
> 6.0596 -183.3221 54.4805
> 12.6010 -187.6878 48.8390
> 22.2656 -187.3245 46.1419
> 29.8070 -184.1168 50.5152
> 36.3566 -180.7347 57.0374
>
> Those middle coordinates are all off the brain - the coordinates are far
> too negative.
>
> When run through the first method, they come out to:
> 20.6235 -15.8172 -23.1366
> 19.041 -5.94338 -28.5567
> 20.8091 3.8041 -32.346
> 25.8047 13.9764 -34.4435
> 34.3347 20.7722 -36.4294
> 44.7823 23.7184 -33.5718
> 52.1009 18.1343 -29.1088
> 58.3186 10.0044 -24.8649
>
> Which are (approximately) on the surface of the brain.
>
> However, when I load up the average surface in freeview, and apply
> reg_avg.lta to the CT, the two overlay exactly.
>
> I'm mostly trying to figure out why the coordinates that I get in MATLAB
> do not agree with the coordinates that I see in freeview.
>
> Thanks again for your help,
> Isaac
>
> On Tue, Apr 29, 2014 at 1:43 PM, Douglas N Greve <
> greve@nmr.mgh.harvard.edu> wrote:
>
>>
>> It sounds like you are doing the right thing with the right equation.
>> Can you elaborate on what is going wrong?
>>
>>
>> On 04/28/2014 05:10 PM, ISAAC PEDISICH wrote:
>> > Sorry - I meant just the matrix.
>> >
>> > I'm trying to map from CRS in the CT to tkrRAS in the anatomical, I
>> > believe. I'm a little unclear as to what exactly anat space means, but
>> > I know that I'm trying to get it from CRS in the CT to the space in
>> > which the surface is plotted in MATLAB, which I believe is tkrRAS,
>> > anatomical. I'm certain it's no longer CRS space, as the x-coordinates
>> > must contain some negative indices.
>> >
>> >
>> >
>> > On Mon, Apr 28, 2014 at 5:02 PM, Douglas N Greve
>> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>> >
>> >
>> > When you say the content is the same, do you mean exactly the same
>> or
>> > just the matrix? Also, what coordinate system are you trying to go
>> to?
>> > The equation you have below takes CRS in the CT and maps it to
>> > tkrRAS in
>> > the anatomical. If you want to map the CRS in the anat then use
>> >
>> > inv(Tanat) * inv(Reg_avg) * Tmov * CT_coords
>> >
>> >
>> > On 04/28/2014 03:58 PM, ISAAC PEDISICH wrote:
>> > > Hi Doug,
>> > > Thanks for the response.
>> > > I'm not seeing lta_convert as an executable that I can run. I have
>> > > freesurfer v5.3.0 installed - is there another version that I
>> should
>> > > be using?
>> > >
>> > > For using tkregister2, I'm a bit confused as to what I should be
>> > > doing. I had assumed (erroneously, it seems) that the .lta and
>> .dat
>> > > files contained the same information.
>> > > I just tried re-running tkregister2 with the command:
>> > > tkregsiter2 --mov [sub_CT].img --reg reg_avg.dat --surf pial --s
>> > > average --lta reg_avg.lta
>> > > Such that I can pass in the reg_avg.lta file created from robust
>> > > register, and have it output a reg_avg.dat file. The contents of
>> > these
>> > > two files, however, seem to be exactly the same.
>> > >
>> > > I also running tkregister2 with the --fslregout and --freeview
>> > flags,
>> > > but neither of those produced a correct transformation either.
>> > >
>> > > Martin:
>> > > We are indeed registering the CT to an average MRI, and for the
>> > moment
>> > > we are correcting inaccuracies manually with tkregister2.
>> > > I just tried bbregister with one of our problem subjects, and it
>> > still
>> > > produced a matrix that had to be significantly adjusted in
>> > > tkregister2. Furthermore, the matrix that it produced still did
>> not
>> > > transform the coordinates correctly in MATLAB.
>> > >
>> > > -Isaac
>> > >
>> > >
>> > > On Mon, Apr 28, 2014 at 2:32 PM, Douglas N Greve
>> > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>> > <mailto:greve@nmr.mgh.harvard.edu
>> > <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
>> > >
>> > >
>> > > The matrix in the lta is probably not the right one. Try using
>> > > lta_convert or tkregister2 to change it to a register.dat file
>> > > (which is
>> > > what is expected in your formula)
>> > > doug
>> > >
>> > > On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote:
>> > > > Hi All,
>> > > >
>> > > > I am attempting to transform sets of coordinates from
>> > subject CRS
>> > > > space into the surfaceRAS space of an average subject,
>> > made with
>> > > > make_average_subject.
>> > > >
>> > > > By our current method, we register the individual CT to
>> > the average
>> > > > surface using mri_robust_register with the command:
>> > > > mri_robust_register --mov [subj_CT].img --dst
>> > average_orig.mgz
>> > > --lta
>> > > > reg_avg.lta --iscale --satit
>> > > > and then check and adjust the registration with:
>> > > > tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf
>> pial
>> > > --s average
>> > > >
>> > > > These steps work fine, and when I load the average brain in
>> > > freeview,
>> > > > then load the subject CT with with the registration file
>> > reg_avg.lta
>> > > > applied, the two overlap just as they should.
>> > > >
>> > > > However, when I attempt to do the same thing in matlab,
>> > some (though
>> > > > not all) of the subjects present a problem.
>> > > > I do the coordinate transformation (as suggested on
>> > > > http://freesurfer.net/fswiki/CoordinateSystems) by
>> applying:
>> > > >
>> > > > inv(Reg_avg) * Tmov * CT_coords
>> > > >
>> > > > with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as
>> > > > reg_avg.lta, and CT_coords as the relevant coordinates in
>> > CRS space
>> > > > from the CT (with a vector of ones appended).
>> > > >
>> > > > As I said, some of the scans come out fine, with the
>> > coordinates in
>> > > > the correct place on the average surface, while others are
>> > very far
>> > > > removed from their correct location. How can I fix this?
>> > > >
>> > > > Thanks,
>> > > > Isaac
>> > > >
>> > > >
>> > > > _______________________________________________
>> > > > Freesurfer mailing list
>> > > > Freesurfer@nmr.mgh.harvard.edu
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
>> > <mailto: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 <mailto:greve@nmr.mgh.harvard.edu>
>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu
>> >>
>> > > Phone Number: 617-724-2358 <tel:617-724-2358>
>> > <tel:617-724-2358 <tel:617-724-2358>>
>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
>> > <tel:617-726-7422>>
>> > >
>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> > > <http://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
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>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>> > <mailto: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.
>> > >
>> > >
>> > >
>> > >
>> > > _______________________________________________
>> > > Freesurfer mailing list
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>> >
>> > --
>> > Douglas N. Greve, Ph.D.
>> > MGH-NMR Center
>> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>> > Phone Number: 617-724-2358 <tel:617-724-2358>
>> > Fax: 617-726-7422 <tel:617-726-7422>
>> >
>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> > <http://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 <mailto:
>> Freesurfer@nmr.mgh.harvard.edu>
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> 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/
>>
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Message: 2
Date: Mon, 05 May 2014 12:46:38 -0400
From: Z K <zkaufman@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] using multiple cores
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>,
Lukas.Scheef@ukb.uni-bonn.de
Message-ID: <5367C06E.4050501@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Lukas,
The Mac build does not support openmp. This is because the initial
version of gcc we were using for the Mac build did not support it. We
are now using a version of gcc for the Mac build which does support
oppenmp so the current plan is that any subsequent releases of
freesurfer will support openmp on both Linux and Mac builds.
Sorry for the late response.
-Zeke
On 05/02/2014 03:16 PM, Matt Glasser wrote:
> If you are compiling with clang openmp might not work.
>
> Peace,
>
> Matt.
>
> On 5/2/14, 2:13 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote:
>
>> Hi Lukas
>>
>> sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going
>> on?
>> Does OpenMP have to be enabled somehow?
>>
>> Bruce
>>
>>
>> On Fri, 2 May 2014,
>> Lukas.Scheef@ukb.uni-bonn.de wrote:
>>
>>> Hi Bruce!
>>>
>>> I just run: recon-all -s ernie2 -autorecon2 -openmp 4
>>>
>>> mri_ca_register uses 100.9% CPU at most ...
>>>
>>> Any idea? Should I try to recompile FS for the current MacOS release?
>>> If
>>> so, do I have to take care on special librariwa in order to enable the
>>> openmp option?
>>>
>>> Best wishes,
>>>
>>> Lukas
>>>
>>>> Hi Bruce!
>>>>
>>>> Thanks for the fast response. I used the current stable version 5.3.0.1
>>>> (freesurfer-Darwin-lion-stable-pub-v5.3.0.1).
>>>> So I will try as you have suggested ...
>>>>
>>>> Best wishes,
>>>>
>>>> Lukas
>>>
>>>>> Bruce Fischl Fri, 02 May 2014 05:47:26 -0700
>>>>>
>>>>> Hi Luke
>>>>>
>>>>> what version of FS are you running? We see significant speedups. Try
>>>>> running top in a unix terminal and seeing if the cpu usage of
>>>>> mri_ca_register (during autorecon2, the longest single step) is
>>> morethan
>>>>> 100%
>>>>>
>>>>> cheers
>>>>> Bruce
>>>>>
>>>>> On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote:
>>>>>
>>>>>
>>>>>> Hi folks!
>>>>>>
>>>>>> I try to use -openmp option on an iMAC with 4 cores.
>>> Unfortunately, I
>>>>>> do not
>>>>>> see any accelartion when processing a single data set with or
>>> without
>>>>>> the
>>>>>> flag -openmp flag set.
>>>>>>
>>>>>> recon-all -s ernie_1 -all
>>>>>>
>>>>>> leads to ~6,4h processing time.
>>>>>>
>>>>>> Unfortunately
>>>>>> recon-all -s ernie_2 -all -openmp 4
>>>>>>
>>>>>> did not change anything. Do I miss anything? Do I have to prepare
>>> my
>>>>>> system
>>>>>> in a special way? Or run any scripts in advance?
>>>>>>
>>>>>> (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS
>>>>>> version)
>>>>>>
>>>>>> Best wishes,
>>>>>>
>>>>>> Luke
>>>
>>>
>>>
>>>
>>> _______________________________________________
>> 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
>> 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.
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
------------------------------
Message: 3
Date: Mon, 5 May 2014 18:53:58 +0200
From: Conchy PF <conchipafran@gmail.com>
Subject: [Freesurfer] Fwd: Fwd: Optseq2: ntp
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CABEhXgC=6r9cpSa+DOhiAr=zJ-99viPmAgfxs9kznufAFHPFCA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi everybody,
I have a question about optseq2.
In order to calculate ntp, I need to know the total time that my run lasts.
Thus, I do not know whether I have to include in the total trial time the
fixation cross time (500 ms) + event (1000 ms) + variable ISI average (1 s,
ranging from 500 to 4000 ms), or not to include the variable ISI,
increasing the total run time by 50% at the end.
On the other hand, I have the same dilema about the event command (ev) and
the duration of the stimulus that I should set. Also, if I use the fixation
cross plus event duration, they would add together 1.5 ms, while the tr is
2. According to the program's instructions, the stimulus duration must be a
multiple of tr. Then, I guess that I should use to calculate the whole
thing the fixation cross (500 ms) + the event (1000) + the variable ISI
average (1 s). Am I right?
Thank you very much and kind regards,
C
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Message: 4
Date: Mon, 5 May 2014 14:10:07 -0400
From: Cesar Echavarria <cechavarria60@gmail.com>
Subject: [Freesurfer] Help with subject's functional overlay
To: freesurfer@nmr.mgh.harvard.edu
Cc: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Message-ID:
<CADBoJQjj05kiMG2jpTp6B4y9SbJG4iuMExsRuKb+DvXgMTJ8PA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hello freesurfer experts,
The functional overlay for one of our subjects looks like the image
attached. You'll notice the "holes" on the overlay that have a value of 0.
I'm trying to get ride of these as I expect (as with other subjects) to
have values for these vertices that are not 0. Myself and a colleague have
tried improving the registration as much as we see possible, but the
problem remains. Any tips on how to correct this issue would be greatly
appreciated.
Thanks in advance for your help!
Cesar Echavarria
Research Assistant
Martinos Center for Biomedical Imaging, Harvard-MGH
Brain & Cognitive Sciences | MIT 2012
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Message: 5
Date: Mon, 5 May 2014 14:57:38 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Help with subject's functional overlay
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Message-ID: <alpine.LRH.2.03.1405051457001.11306@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Cesar
what command lines did you run to register and sample?
Bruce
On Mon, 5 May 2014,
Cesar Echavarria wrote:
> Hello freesurfer experts,
> The functional overlay for one of our subjects looks like the image attached. You'll notice
> the "holes" on the overlay that have a value of 0. I'm trying to get ride of these as I
> expect (as with other subjects) to have values for these vertices that are not 0. Myself and
> a colleague have tried improving the registration as much as we see possible, but the problem
> remains. Any tips on how to correct this issue would be greatly appreciated.
>
> Thanks in advance for your help!
> [cleardot.gif]
> Cesar Echavarria
> Research AssistantMartinos Center for Biomedical Imaging, Harvard-MGH
> Brain & Cognitive Sciences |?MIT 2012
>
>
------------------------------
Message: 6
Date: Mon, 5 May 2014 15:17:25 -0400
From: Cesar Echavarria <cechavarria60@gmail.com>
Subject: Re: [Freesurfer] Help with subject's functional overlay
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Message-ID:
<CADBoJQgtYvZC_84FCbqdkqmVLj7M+teCe-tbWEWHY8NW5-XWzw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Bruce,
After unpacking the data, I simply run the selxavg command below and allow
it to do the automatic pre-processing.
selxavg3-sess -s Subjects/myla -a LOC_fsaverage_5p3.rh
The analysis was generated with the following command:
mkanalysis-sess -analysis LOC_fsaverage_5p3.rh -surface fsaverage rh -fwhm
5 -paradigm LOC.par -event-related -polyfit 1 -gammafit 2.25 1.25 -mcextreg
-TR 2.000 -nconditions 2 -refeventdur 16 -per-run -force -fsd bold
After fixing up the registration I saved the registration file under
:Subjects/myla/bold/014/register.dof6.dat" and ran bbregister for all the
runs within the subject folder as below.
bbregister --mov Subjects/myla/bold/015/f.nii --reg
Subjects/myla/bold/015/register.dof6.dat --init-reg
Subjects/myla/bold/014/register.dof6.dat --bold
I then ran the selxavg3-sess again.
Let me know if you need any more information to help.
Thanks!
Cesar
On Mon, May 5, 2014 at 2:57 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>wrote:
> Hi Cesar
>
> what command lines did you run to register and sample?
>
> Bruce
>
> On Mon, 5 May 2014, Cesar Echavarria wrote:
>
> Hello freesurfer experts,
>> The functional overlay for one of our subjects looks like the image
>> attached. You'll notice
>> the "holes" on the overlay that have a value of 0. I'm trying to get ride
>> of these as I
>> expect (as with other subjects) to have values for these vertices that
>> are not 0. Myself and
>> a colleague have tried improving the registration as much as we see
>> possible, but the problem
>> remains. Any tips on how to correct this issue would be greatly
>> appreciated.
>>
>> Thanks in advance for your help!
>> [cleardot.gif]
>> Cesar Echavarria
>> Research AssistantMartinos Center for Biomedical Imaging, Harvard-MGH
>>
>> Brain & Cognitive Sciences | MIT 2012
>>
>>
> _______________________________________________
> 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
> 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.
>
>
--
Cesar Echavarria
Research Assistant
Martinos Center for Biomedical Imaging, Harvard-MGH
Brain & Cognitive Sciences | MIT 2012
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------------------------------
Message: 7
Date: Mon, 05 May 2014 15:27:50 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] problems about extracting specific vertex
thickness value and getting a average thickness for a specific mask
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5367E636.1010001@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 04/30/2014 11:38 PM, charujing123 wrote:
> Hi FS experts and users
> I have done the each subjects' surface regestration on fsaverage
> surface, and merge all of them into a *.mgh. Group analysis is also
> completed.
> Now I have two questions:
> 1,I want to extract the VtxMax vertex number thickness for all
> subjects. The VtxMax vertex number can be got in the
> *.sig.cluster.summary file. And it represents the most significant
> vertex in that cluster. I search my question in google and find these
> scripts which maybe helpful:
> for i in `seq 1 $numsubject`
> do
> mri_convert --frame $i y.mgh
> $SUBJECTS_DIR/fsaverage/surf/lh.$i.mgh
> mris_convert -c $i.mgh
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated lh.$i.asc
> done
> I got the lh.*.asc file and open it. there are five columes in this
> file: I guess that: first colume is vertex number, the 2nd-4th columes
> represent MNI coordinates in surface, and the 5th colume is thickness
> of this vertex. If I want to deal with my 1st question, all I need to
> get the lh.*.asc file and search the specific vertex number in this
> file. All of above, is there anything wrong?
I don't think so although I've never done it myself. I would probably
use something like
mri_segstats --i y.mgh --vox vertexno 0 0 --avgwf file.dat
This will save all of the subjects' data from vertex vertexno in file.dat
> 2, I created a surface mask, and want to extract the average thickness
> value in this mask for every subject. How can I complete it?
mri_segstats --i lh.thickness --seg mask.mgh --id 1 --sum
averagethickness.summary
doug
> Any reply will be highly appreaciated.
> Thanks
> All the best.
> Rujing Zha
> 2014-05-01
> ------------------------------------------------------------------------
> charujing123
>
>
> _______________________________________________
> 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: 8
Date: Mon, 05 May 2014 15:34:13 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Fwd: Fwd: Optseq2: ntp
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5367E7B5.40907@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
The total time is the time from when you start the scanner until the
scanner turns off. The duration of the stimulus should be the just that
of the stimulus. If you want to have a minimum amount of fixation
between events, then use --tnullmin.
doug
On 05/05/2014 12:53 PM, Conchy PF wrote:
>
> Hi everybody,
>
> I have a question about optseq2.
>
> In order to calculate ntp, I need to know the total time that my run
> lasts. Thus, I do not know whether I have to include in the total
> trial time the fixation cross time (500 ms) + event (1000 ms) +
> variable ISI average (1 s, ranging from 500 to 4000 ms), or not to
> include the variable ISI, increasing the total run time by 50% at the end.
>
> On the other hand, I have the same dilema about the event command (ev)
> and the duration of the stimulus that I should set. Also, if I use the
> fixation cross plus event duration, they would add together 1.5 ms,
> while the tr is 2. According to the program's instructions, the
> stimulus duration must be a multiple of tr. Then, I guess that I
> should use to calculate the whole thing the fixation cross (500 ms) +
> the event (1000) + the variable ISI average (1 s). Am I right?
>
> Thank you very much and kind regards,
>
> C
>
>
> _______________________________________________
> 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: 9
Date: Mon, 05 May 2014 15:38:00 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] When/What to edit?
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5367E898.60605@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
I've looked at the actual editing of voxels (ie, erasing and deleting)
vs putting control points in terms of their effect on a group analysis
of aging. CPs have an appreciable effect. I could not find much of an
effect of editing, probably because the edits rarely lined up across
subject. I think the jury is still out. I think it is a hard t thing to
evaluate because it can be population specific.
doug
On 05/04/2014 05:26 PM, Bruce Fischl wrote:
> Hi Andrew
>
> I'm not sure I have any useful advise for you. When/what to edit
> depends in part of your hypotheses, in part on how significant the
> error is, and in part on how easily fixed it is. You also have to be
> careful that you don't edit too much and significantly lower
> inter-rater (or intra-rater) reliability. Maybe Doug can comment as he
> has looked at the effects of editing vs. not editing in some large
> scale datasets and I believe hasn't found much of an effect. We've
> also done a number of inter-rater studies and not found any effect or
> rater (all unpublished).
>
> Sorry, as I said, I'm not sure how useful any of this is
>
> cheers
> Bruce
>
>
> On Fri, 2 May 2014, O'Shea,Andrew wrote:
>
>> Hello FS experts, I have had a continuing curiosity regarding
>> when/what to
>> edit in FS cortical reconstructions. The wiki does a good job at
>> showing how
>> to deal with large scale problems, (i.e. invalid tal transformation,
>> white
>> matter not being recognized, large portions of the skull included in the
>> surface) however I have yet to come across much that guides edits
>> besides a
>> "trained eye". How do we know when a problem is "big enough" that it
>> needs
>> attention?
>>
>> Are there any tool boxes/ quantitative guidelines that may help someone
>> determine which scans need edits? I know QA tools outputs info on
>> SNR/white
>> matter intensity and I have looked for outliers here. However, I was
>> wondering how else to automate/guide the decision process. Much of the
>> discussion I have seen on this topic in manuscripts is either vague or
>> nonexistent.
>>
>> Does anyone know of any manuscripts that have compared "raw" FS
>> datasets to
>> "selectively edited" datasets? What sort of effects do edits make in the
>> grand scheme of a study? One could imagine problems with someone
>> editing the
>> data when they are knowledgable of the study's hypotheses and groups.
>>
>> Any additional info or guidance on this topic would be much appreciated.
>>
>> -Andrew
>>
>>
>
>
> _______________________________________________
> 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: 10
Date: Mon, 05 May 2014 15:39:26 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] qdec question
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5367E8EE.30703@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
DOSS is not working in QDEC. It should be disabled in 5.3
doug
On 05/05/2014 09:39 AM, Anna Jonsson wrote:
> Dear group,
>
> when using the qdec gui interface, I was wondering where the "button"
> or the likes is to change the estimation from its standard doss to
> dods (different osnet, different slope). I believe I can do this
> somewhere on the qdec gui without changing to mri_glmfit?
>
>
> _______________________________________________
> 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: 11
Date: Mon, 05 May 2014 15:43:42 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Help with subject's functional overlay
To: Cesar Echavarria <cechavarria60@gmail.com>, Freesurfer support
list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <5367E9EE.7070406@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
It could be that the brain mask is too aggressive. Try looking at
Subjects/myla/bold/RRR/masks/brain.nii.gz
doug
On 05/05/2014 03:17 PM, Cesar Echavarria wrote:
> Hi Bruce,
>
> After unpacking the data, I simply run the selxavg command below and
> allow it to do the automatic pre-processing.
>
> selxavg3-sess -s Subjects/myla -a LOC_fsaverage_5p3.rh
>
> The analysis was generated with the following command:
>
> mkanalysis-sess -analysis LOC_fsaverage_5p3.rh -surface fsaverage rh
> -fwhm 5 -paradigm LOC.par -event-related -polyfit 1 -gammafit 2.25
> 1.25 -mcextreg -TR 2.000 -nconditions 2 -refeventdur 16 -per-run
> -force -fsd bold
>
> After fixing up the registration I saved the registration file under
> :Subjects/myla/bold/014/register.dof6.dat" and ran bbregister for all
> the runs within the subject folder as below.
>
> bbregister --mov Subjects/myla/bold/015/f.nii --reg
> Subjects/myla/bold/015/register.dof6.dat --init-reg
> Subjects/myla/bold/014/register.dof6.dat --bold
>
> I then ran the selxavg3-sess again.
>
> Let me know if you need any more information to help.
>
> Thanks!
> Cesar
>
>
> On Mon, May 5, 2014 at 2:57 PM, Bruce Fischl
> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
>
> Hi Cesar
>
> what command lines did you run to register and sample?
>
> Bruce
>
> On Mon, 5 May 2014, Cesar Echavarria wrote:
>
> Hello freesurfer experts,
> The functional overlay for one of our subjects looks like the
> image attached. You'll notice
> the "holes" on the overlay that have a value of 0. I'm trying
> to get ride of these as I
> expect (as with other subjects) to have values for these
> vertices that are not 0. Myself and
> a colleague have tried improving the registration as much as
> we see possible, but the problem
> remains. Any tips on how to correct this issue would be
> greatly appreciated.
>
> Thanks in advance for your help!
> [cleardot.gif]
> Cesar Echavarria
> Research AssistantMartinos Center for Biomedical Imaging,
> Harvard-MGH
>
> Brain & Cognitive Sciences | MIT 2012
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto: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.
>
>
>
>
> --
> Cesar Echavarria
> Research Assistant
> Martinos Center for Biomedical Imaging, Harvard-MGH
> Brain & Cognitive Sciences | MIT 2012
--
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: 12
Date: Mon, 05 May 2014 15:51:32 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Brain Seg Volumes
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5367EBC4.2080600@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
They are not computed in exactly the same way, but the results are still
a little surprising. What is the value of BrainSegVolNotVent? That
should always be less than BrainSegVol.
On 05/05/2014 08:22 AM, Bruce Fischl wrote:
> Hi Kristina
>
> do the results look accurate. 2 is pretty close to (or past) the limit of
> where we generate reliable results.
>
> Not sure about your other question - I don't remember how they are
> calculated. Someone else should know, although note that we are putting on
> a class this week so response times will be slower than usual
>
> cheers
> Bruce
>
>
> On Mon, 5 May 2014, Mayer Kristina
> wrote:
>
>> Hi there,
>> I am using freesurfer for datas of two year olds.
>> - Is there a special command to run freesurfer on children's data?
>> - When I checked the seg.stats for volumes, I got a higher value for BrainSegVolNotVentSurf (value: 845377 mm3), than for the BrainSegVol (value: 839497) in one patient. The recon-all -all finished without error. How is this possible?
>>
>> Thanks in advance,
>> Kristina
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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: 13
Date: Mon, 5 May 2014 21:59:39 +0200
From: Lukas.Scheef@ukb.uni-bonn.de
Subject: Re: [Freesurfer] using multiple cores
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<OFF25D00A6.F76180E1-ONC1257CCF.006DD507-C1257CCF.006DD50E@ukb.uni-bonn.de>
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Message: 14
Date: Mon, 5 May 2014 20:04:23 +0000
From: "Eryilmaz, Huseyin Hamdi" <HERYILMAZ@partners.org>
Subject: Re: [Freesurfer] comparing two conditions with
disproportionate number of trials
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<174E343C2712C341AE1B77A15DE30FA77195E6@PHSX10MB3.partners.org>
Content-Type: text/plain; charset="iso-8859-1"
Thanks Donald for the clarification. In our design, for the condition A (errors in a memory task), number of trials depends on subjects' performances and therefore we've got some between subject variability there. If the number of trials is not considered and as long as it is sufficient to produce a stable estimate for the mean response, I guess we don't need to worry about this issue. Nevertheless, we probably need to exclude subjects with very few errors from the group analysis...
Best,
Hamdi
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of MCLAREN, Donald [mclaren.donald@gmail.com]
Sent: Monday, May 05, 2014 11:20 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] comparing two conditions with disproportionate number of trials
For the contrast A>B, the number of trials is not considered. When you contrast A and B, you are assessing the mean response to trials of condition A to the mean response to trials of condition B. You wouldn't want to weight this by the number of trials as then the contrast would not make sense.
The number of trials can effect the accuracy of the estimate of the mean response to a condition. In this way, A could be stronger or weaker than it actually is in each subject. Because of the decreased accuracy, you could also have increased variability between subjects.
As a result of the increased variability, the mean response needed for A to be different from 0, will be greater than that in B. However, this not imply that A will be greater than B as the significance of A doesn't tell you anything about A>B. In fact, you could construct a case where B>A and where A>0 is significant, but B>0 is not significant. In A vs B, you are using the within-subject variance and fro A or B vs 0, you are using the variance between subjects.
Generally, you need 30-40 trials to get a stable estimate of the mean response of each condition.
Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=====================
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
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intended only for the use of the individual or entity named above. If the
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unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.
On Mon, May 5, 2014 at 10:57 AM, Eryilmaz, Huseyin Hamdi <HERYILMAZ@partners.org<mailto:HERYILMAZ@partners.org>> wrote:
Dear FS experts,
I have a question about the way contrasts work in an event-related design. I am wondering if freesurfer is doing some sort of weighing when it compares two different conditions with incomparable number of trials. For example condition A is represented by 10 trials in the paradigm file, whereas condition B consists of 80 trials. In that case, for the contrast A>B does freesurfer compensate for the small number of trials in condition A? If so, could it lead to inflated activations? We suspected this as in our results, the condition with fewer trials depicted strong activations.
Thanks very much for the tips!
Best,
Hamdi
--
Hamdi Eryilmaz, PhD
Massachusetts General Hospital
A.A. Martinos Center for Biomedical Imaging
Brain Genomics Laboratory
149 13th St, Charlestown, MA 02129
Phone: +1 617 643 7462<tel:%2B1%20617%20643%207462>
_______________________________________________
Freesurfer mailing list
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
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Message: 15
Date: Mon, 5 May 2014 16:08:38 -0400
From: Cesar Echavarria <cechavarria60@gmail.com>
Subject: Re: [Freesurfer] Help with subject's functional overlay
To: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CADBoJQgFLb-PDVFJtpof+sikk1bhuZ7UZ4Q7Y4hHnsFS-efODQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
I used the command below to check the brain mask relative to the subject's
anatomy:
tkmedit myla_anat orig.mgz -over Subjects/myla/bold/masks/brain.nii.gz
The mask looked fine in that no portion of the brain appeared to lie
outside the mask.
Cesar
On Mon, May 5, 2014 at 3:43 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu>wrote:
> It could be that the brain mask is too aggressive. Try looking at
> Subjects/myla/bold/RRR/masks/brain.nii.gz
>
> doug
>
>
>
> On 05/05/2014 03:17 PM, Cesar Echavarria wrote:
>
>> Hi Bruce,
>>
>> After unpacking the data, I simply run the selxavg command below and
>> allow it to do the automatic pre-processing.
>>
>> selxavg3-sess -s Subjects/myla -a LOC_fsaverage_5p3.rh
>>
>> The analysis was generated with the following command:
>>
>> mkanalysis-sess -analysis LOC_fsaverage_5p3.rh -surface fsaverage rh
>> -fwhm 5 -paradigm LOC.par -event-related -polyfit 1 -gammafit 2.25 1.25
>> -mcextreg -TR 2.000 -nconditions 2 -refeventdur 16 -per-run -force -fsd bold
>>
>> After fixing up the registration I saved the registration file under
>> :Subjects/myla/bold/014/register.dof6.dat" and ran bbregister for all
>> the runs within the subject folder as below.
>>
>> bbregister --mov Subjects/myla/bold/015/f.nii --reg
>> Subjects/myla/bold/015/register.dof6.dat --init-reg
>> Subjects/myla/bold/014/register.dof6.dat --bold
>>
>> I then ran the selxavg3-sess again.
>>
>> Let me know if you need any more information to help.
>>
>> Thanks!
>> Cesar
>>
>>
>> On Mon, May 5, 2014 at 2:57 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu<mailto:
>> fischl@nmr.mgh.harvard.edu>> wrote:
>>
>> Hi Cesar
>>
>> what command lines did you run to register and sample?
>>
>> Bruce
>>
>> On Mon, 5 May 2014, Cesar Echavarria wrote:
>>
>> Hello freesurfer experts,
>> The functional overlay for one of our subjects looks like the
>> image attached. You'll notice
>> the "holes" on the overlay that have a value of 0. I'm trying
>> to get ride of these as I
>> expect (as with other subjects) to have values for these
>> vertices that are not 0. Myself and
>> a colleague have tried improving the registration as much as
>> we see possible, but the problem
>> remains. Any tips on how to correct this issue would be
>> greatly appreciated.
>>
>> Thanks in advance for your help!
>> [cleardot.gif]
>> Cesar Echavarria
>> Research AssistantMartinos Center for Biomedical Imaging,
>> Harvard-MGH
>>
>> Brain & Cognitive Sciences | MIT 2012
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu <mailto: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.
>>
>>
>>
>>
>> --
>> Cesar Echavarria
>> Research Assistant
>> Martinos Center for Biomedical Imaging, Harvard-MGH
>> Brain & Cognitive Sciences | MIT 2012
>>
>
> --
> 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/
>
>
--
Cesar Echavarria
Research Assistant
Martinos Center for Biomedical Imaging, Harvard-MGH
Brain & Cognitive Sciences | MIT 2012
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Message: 16
Date: Mon, 05 May 2014 17:48:56 -0400
From: Z K <zkaufman@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] using multiple cores
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>,
Lukas.Scheef@ukb.uni-bonn.de
Message-ID: <53680748.2040409@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
I do not have any information to give in regards to when a new release
would be available. Compiling freesurfer from source is not exactly
something I would call "fun". That said, I have been working on a brief
"how-to-guide" on how to build freesurfer on Mac OSX and I have already
packaged the 3rd party libraries into a single bundle.
I plan on releasing this guide next week and I will email it to you.
Once you have it, compiling should be fairly straight forward.
If you dont hear from me by next week feel free to ping me.
-Zeke
On 05/05/2014 03:59 PM, Lukas.Scheef@ukb.uni-bonn.de wrote:
> Hi Zeke!
>
> Thanks a lot for the response. Better a late response than none :o)!
> Do you have any vague estimate when a new release will be available?
> So far I did not try to compile it from the sources, because it is not my
> daily business and for an inexperienced it most likely ends up with pure
> frustration.
> If a new release would be close, I would definitely keep my fingers from
> compiling ...
> Or are any "how to's" available for compiling FS from the sources...?
>
> Best wishes,
>
> Luke
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
------------------------------
Message: 17
Date: Mon, 05 May 2014 18:04:40 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Help with subject's functional overlay
To: Cesar Echavarria <cechavarria60@gmail.com>
Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <53680AF8.1010909@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
Have you checked the registration? If so, are you sure that the
activation is exactly 0? Also, look at cortex.label to check whether
somehow those vertices were not labeled.
On 05/05/2014 04:08 PM, Cesar Echavarria wrote:
> I used the command below to check the brain mask relative to the
> subject's anatomy:
>
> tkmedit myla_anat orig.mgz -over Subjects/myla/bold/masks/brain.nii.gz
>
> The mask looked fine in that no portion of the brain appeared to lie
> outside the mask.
>
> Cesar
>
>
> On Mon, May 5, 2014 at 3:43 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> It could be that the brain mask is too aggressive. Try looking at
> Subjects/myla/bold/RRR/masks/brain.nii.gz
>
> doug
>
>
>
> On 05/05/2014 03:17 PM, Cesar Echavarria wrote:
>
> Hi Bruce,
>
> After unpacking the data, I simply run the selxavg command
> below and allow it to do the automatic pre-processing.
>
> selxavg3-sess -s Subjects/myla -a LOC_fsaverage_5p3.rh
>
> The analysis was generated with the following command:
>
> mkanalysis-sess -analysis LOC_fsaverage_5p3.rh -surface
> fsaverage rh -fwhm 5 -paradigm LOC.par -event-related -polyfit
> 1 -gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 2
> -refeventdur 16 -per-run -force -fsd bold
>
> After fixing up the registration I saved the registration file
> under :Subjects/myla/bold/014/register.dof6.dat" and ran
> bbregister for all the runs within the subject folder as below.
>
> bbregister --mov Subjects/myla/bold/015/f.nii --reg
> Subjects/myla/bold/015/register.dof6.dat --init-reg
> Subjects/myla/bold/014/register.dof6.dat --bold
>
> I then ran the selxavg3-sess again.
>
> Let me know if you need any more information to help.
>
> Thanks!
> Cesar
>
>
> On Mon, May 5, 2014 at 2:57 PM, Bruce Fischl
> <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>
> <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>>> wrote:
>
> Hi Cesar
>
> what command lines did you run to register and sample?
>
> Bruce
>
> On Mon, 5 May 2014, Cesar Echavarria wrote:
>
> Hello freesurfer experts,
> The functional overlay for one of our subjects looks
> like the
> image attached. You'll notice
> the "holes" on the overlay that have a value of 0. I'm
> trying
> to get ride of these as I
> expect (as with other subjects) to have values for these
> vertices that are not 0. Myself and
> a colleague have tried improving the registration as
> much as
> we see possible, but the problem
> remains. Any tips on how to correct this issue would be
> greatly appreciated.
>
> Thanks in advance for your help!
> [cleardot.gif]
> Cesar Echavarria
> Research AssistantMartinos Center for Biomedical Imaging,
> Harvard-MGH
>
> Brain & Cognitive Sciences | MIT 2012
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto: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.
>
>
>
>
> --
> Cesar Echavarria
> Research Assistant
> Martinos Center for Biomedical Imaging, Harvard-MGH
> Brain & Cognitive Sciences | MIT 2012
>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
>
> --
> Cesar Echavarria
> Research Assistant
> Martinos Center for Biomedical Imaging, Harvard-MGH
> Brain & Cognitive Sciences | MIT 2012
--
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: 18
Date: Mon, 5 May 2014 18:08:39 -0400
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] using multiple cores
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <F3F0DBBD-C703-44E9-8C44-4852AE6A5B44@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=us-ascii
And fun, right?
> On May 5, 2014, at 5:48 PM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:
>
> I do not have any information to give in regards to when a new release
> would be available. Compiling freesurfer from source is not exactly
> something I would call "fun". That said, I have been working on a brief
> "how-to-guide" on how to build freesurfer on Mac OSX and I have already
> packaged the 3rd party libraries into a single bundle.
>
> I plan on releasing this guide next week and I will email it to you.
> Once you have it, compiling should be fairly straight forward.
>
> If you dont hear from me by next week feel free to ping me.
>
> -Zeke
>
>
>
>
>> On 05/05/2014 03:59 PM, Lukas.Scheef@ukb.uni-bonn.de wrote:
>> Hi Zeke!
>>
>> Thanks a lot for the response. Better a late response than none :o)!
>> Do you have any vague estimate when a new release will be available?
>> So far I did not try to compile it from the sources, because it is not my
>> daily business and for an inexperienced it most likely ends up with pure
>> frustration.
>> If a new release would be close, I would definitely keep my fingers from
>> compiling ...
>> Or are any "how to's" available for compiling FS from the sources...?
>>
>> Best wishes,
>>
>> Luke
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
------------------------------
Message: 19
Date: Mon, 5 May 2014 15:57:33 -0700
From: Sherryse Corrow <sherryse.corrow@eyecarecentre.org>
Subject: [Freesurfer] Registering functional data to inflated brain
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <CF8D656D.ADBE%sherryse.corrow@eyecarecentre.org>
Content-Type: text/plain; charset="us-ascii"
Dear FreeSurfer community,
We are having some issues registering our functional data (or masks) from FSL to an inflated brain in FreeSurfer. Some of our masks, when registered to the inflated brain and viewed in FreeSurfer, are not showing up on the cortical surface. We have followed web-tutorials for registration but are still having the issue. Any suggestions?
Sherryse, University of British Columbia
--
Sherryse Corrow, Ph.D. / Postdoctoral Fellow
Human Vision and Eye Movement Lab
Department of Ophthalmology & Visual Sciences
UBC/VGH Eye Care Centre
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Message: 20
Date: Mon, 5 May 2014 16:55:42 -0700
From: Sherryse Corrow <sherryse.corrow@eyecarecentre.org>
Subject: [Freesurfer] Viewing functional data on the inflated brain
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <CF8D730E.ADD4%sherryse.corrow@eyecarecentre.org>
Content-Type: text/plain; charset="us-ascii"
Hi all,
Earlier today, I posted the message listed below. However, we discovered part of our issue. When we run reg-feat2anat, there is no anat2exf.register.dat file created. Therefore, we have no registration matrix to use. Before, we were inadvertently using the anat2std file instead. Any suggestions on how to get the anat2exf.register.dat file created?
Thanks,
Sherryse
--
Sherryse Corrow, Ph.D. / Postdoctoral Fellow
Human Vision and Eye Movement Lab
Department of Ophthalmology & Visual Sciences
UBC/VGH Eye Care Centre
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Message: 21
Date: Tue, 6 May 2014 10:41:21 +0800
From: Caka <qiongmin.ma@gmail.com>
Subject: [Freesurfer] vertex-wise cortical thickness and whole brain
labeling
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <C777E0D9-18B4-4B97-9B0B-9A5261ACCE41@gmail.com>
Content-Type: text/plain; charset=GB2312
Hi Douglas and all,
I have used the ?recon-all? command to segment the gray matter of 140 subjects. I have three questions:
(1) as the segmentation is done in the individual space, how can I register the results into the template brain? The results includes the surface and the vertex. Is it ?mri_surf2surf??
(2) If the gray matter is registered into the template brain, then same number of vertex in every region would be obtained. Then what information does the value of each vertex stands? Is it the cortical thickness changes?
(3) We know that Freesurfer provides two kinds of brain region labeling, 68 regions and 77 regions in the cerebral cortex respectively. I am wondering whether I can use my own labeling, like 1000 regions? How can I do this?
Thank you very much!
Qiongmin Ma
------------------------------
Message: 22
Date: Mon, 05 May 2014 22:49:35 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Registering functional data to inflated
brain
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <53684DBF.3090307@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
Can you tell us specifically what you have done? I mean command lines ...
doug
On 5/5/14 6:57 PM, Sherryse Corrow wrote:
> Dear FreeSurfer community,
>
> We are having some issues registering our functional data (or masks)
> from FSL to an inflated brain in FreeSurfer. Some of our masks, when
> registered to the inflated brain and viewed in FreeSurfer, are not
> showing up on the cortical surface. We have followed web-tutorials
> for registration but are still having the issue. Any suggestions?
>
> Sherryse, University of British Columbia
> --
> Sherryse Corrow, Ph.D. / Postdoctoral Fellow
> Human Vision and Eye Movement Lab
> Department of Ophthalmology & Visual Sciences
> UBC/VGH Eye Care Centre
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 23
Date: Tue, 6 May 2014 10:52:47 +0800
From: ??? <lldbuestc@gmail.com>
Subject: Re: [Freesurfer] LOOK FOR HELP
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAFS0b_0VbArd-Ps+UEF3K3Wraw4cjwb4jwTfNL1koe1YjXE-ZQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear Freesurfer:
I have some problems with using mri_surf2vol .I'd like to ask if you
could help me with this.--volreg Contains the matrix that maps XYZ in the
reference anatomical to XYZ in the functional volume. And to get this reg I
use bbregister. But the result of bbregister is functional to anatomial
volume,so I need to inverse the matrix.When I use convert_xfm in fsl I
found the register.dat(which is the reslut of bbregister)is not a 4*4
matrix ,it just like
dsub1
1.000000
1.000000
0.150000
9.999998807907104e-01 3.475215926300734e-04 3.422866575419903e-04
1.634627580642700e-02
-3.475832345429808e-04 9.999999403953552e-01 1.798802986741066e-04
-4.015868902206421e-02
-3.422244917601347e-04 -1.799785532057285e-04 1.000000000000000e+00
-2.181045338511467e-02
0 0 0 1
round
Is there a command I can use to inverse the register.dat?Or if I use
convert_xfm which part of the register.dat should I use?
Thank you !
Yours
Dongbo Liu
2014-05-06 10:22 GMT+08:00 ??? <lldbuestc@gmail.com>:
> Dear Freesurfer:
> I have some problems with using mri_surf2vol .I'd like to ask if you
> could help me with this.--volreg Contains the matrix that maps XYZ in the
> reference anatomical to XYZ in the functional volume. And to get this reg
> I use bbregister. But the result of bbregister is functional to anatomial
> volume,so I need to inverse the matrix.When I use convert_xfm in fsl I
> found the register.dat(which is the reslut of bbregister)is not a 4*4
> matrix ,it just like
> dsub1
> 1.000000
> 1.000000
> 0.150000
> 9.999998807907104e-01 3.475215926300734e-04 3.422866575419903e-04
> 1.634627580642700e-02
> -3.475832345429808e-04 9.999999403953552e-01 1.798802986741066e-04
> -4.015868902206421e-02
> -3.422244917601347e-04 -1.799785532057285e-04 1.000000000000000e+00
> -2.181045338511467e-02
> 0 0 0 1
> round
> Is there a command I can use to inverse the register.dat?Or if I use
> convert_xfm which part of the register.dat should I use?
> Thank you !
>
> Yours
> Dongbo Liu
>
>
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Message: 24
Date: Tue, 6 May 2014 10:54:41 +0800
From: ??? <lldbuestc@gmail.com>
Subject: [Freesurfer] LOOK FOR HELP
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAFS0b_1r5ujxB8nvnaQkoPsp4nrvrbxrrV5ExNxtsX8w6p8mHQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear Freesurfer:
I have some problems with using mri_surf2vol .I'd like to ask if you
could help me with this.--volreg Contains the matrix that maps XYZ in the
reference anatomical to XYZ in the functional volume. And to get this reg I
use bbregister. But the result of bbregister is functional to anatomial
volume,so I need to inverse the matrix.When I use convert_xfm in fsl I
found the register.dat(which is the reslut of bbregister)is not a 4*4
matrix ,it just like
dsub1
1.000000
1.000000
0.150000
9.999998807907104e-01 3.475215926300734e-04 3.422866575419903e-04
1.634627580642700e-02
-3.475832345429808e-04 9.999999403953552e-01 1.798802986741066e-04
-4.015868902206421e-02
-3.422244917601347e-04 -1.799785532057285e-04 1.000000000000000e+00
-2.181045338511467e-02
0 0 0 1
round
Is there a command I can use to inverse the register.dat?Or if I use
convert_xfm which part of the register.dat should I use?
Thank you !
Yours
Dongbo Liu
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Message: 25
Date: Mon, 05 May 2014 22:55:13 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] vertex-wise cortical thickness and whole
brain labeling
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <53684F11.2080409@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=GB2312
On 5/5/14 10:41 PM, Caka wrote:
> Hi Douglas and all,
>
> I have used the ?recon-all? command to segment the gray matter of 140 subjects. I have three questions:
>
> (1) as the segmentation is done in the individual space, how can I register the results into the template brain? The results includes the surface and the vertex. Is it ?mri_surf2surf??
mri_surf2surf is used when mapping surface data to the surface of an
average subject such as fsaverage. Is that what you want?
>
> (2) If the gray matter is registered into the template brain, then same number of vertex in every region would be obtained. Then what information does the value of each vertex stands? Is it the cortical thickness changes?
I don't understand what you mean.
>
> (3) We know that Freesurfer provides two kinds of brain region labeling, 68 regions and 77 regions in the cerebral cortex respectively. I am wondering whether I can use my own labeling, like 1000 regions? How can I do this?
Do you mean you've labeled 1000 regions on a brain? You would have to do
that for a number of subjects (eg, 40), you can then build an atlas. The
problem is that such small regions will not be very reliable
doug
>
> Thank you very much!
>
> Qiongmin Ma
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
------------------------------
Message: 26
Date: Mon, 05 May 2014 22:56:41 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Viewing functional data on the inflated
brain
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <53684F69.8030805@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
Run reg-feat2anat. If that does not work, then send the command line and
terminal output. Just saying that something does not work will not get
you closer to a solution. We need to know what you did and what happened
doug
On 5/5/14 7:55 PM, Sherryse Corrow wrote:
> Hi all,
>
> Earlier today, I posted the message listed below. However, we
> discovered part of our issue. When we run reg-feat2anat, there is no
> anat2exf.register.dat file created. Therefore, we have no
> registration matrix to use. Before, we were inadvertently using the
> anat2std file instead. Any suggestions on how to get the
> anat2exf.register.dat file created?
>
> Thanks,
> Sherryse
> --
> Sherryse Corrow, Ph.D. / Postdoctoral Fellow
> Human Vision and Eye Movement Lab
> Department of Ophthalmology & Visual Sciences
> UBC/VGH Eye Care Centre
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 27
Date: Tue, 6 May 2014 12:07:33 +0800
From: Yong Liu <liuyong.ccm@gmail.com>
Subject: [Freesurfer] Two positions are available @ Queensland Brain
Institute
To: SPM@jiscmail.ac.uk, "FSL - FMRIB's Software Library"
<FSL@jiscmail.ac.uk>, freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAND3CV1s_iQ6JMh-VT=aj++4ktd-OhCpCEqEotsFno066rAhqg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear all,
Two positions are available @ Queensland Brain Institute.
*POSITION 1:*
Postdoctoral Fellow Position in Neuroimaging and Brain Network Analysis at
Queensland Brain Institute
The Neuroimaging and Brainnetome Laboratory of Queensland Brain Institute
(QBI) and Centre for Advanced Imaging (CAI) at the University of
Queensland, Australia, solicits applications for postdoctoral fellow
positions in neuroimaging and brain network analysis in healthy and
neuropsychiatric diseases. We are looking for an excellent and highly
motivated candidate with a PhD degree in neuroimaging, physics,
mathematics, computer science, neurobiology, experimental psychology or
comparable background. Interest and/or previous experience in/with
neuroscience, MRI methods, design and image analysis are a plus. Experience
with the LINUX/UNIX operating system is a positive add on. The successful
candidate will participate in the multidisciplinary project involves
developing algorithms of neuroimage processing and brain network analysis
and software and applying them to neurosychiatric diseases. The main focus
of this project is twofold: (1) developing new algorithms for structural
MRI, functional MRI, DTI, and resting state MRI; (2) the assessment of
differences between psychiatric patients and healthy controls in brain
functioning, anatomy, default mode and functional connectivity. The
postdoctoral fellows will be jointly supervised by Professor Tianzi Jiang
and other Professors (QBI) who are experts in neuroscience. As at 30 June
2014, an applicant must not have had more than five years full-time
equivalent professional research experience since the award of a PhD. The
current salary range for the award is on a four-level scale from
A$71,528.60 ? A$79,708.50 per annum. Commencing salaries are based strictly
on the number of full years? experience since receiving a doctorate. Salary
scales are reviewed from time to time.
Please contact Professor Tianzi Jiang on tianzi.jiang@uq.edu.au for
research plan.
To submit an application for these positions, please refer to
http://www.uq.edu.au/research/research-management/uq-postdoctoral-research-fellowships
.
The application deadline is *19 May 2014.*
*POSITION 2: *
Postdoctoral Position in Imaging Genetics at Queensland Brain Institute
The Neuroimaging and Brainnetome Laboratory of Queensland Brain Institute
(QBI) and Centre for Advanced Imaging (CAI) at the University of
Queensland, Australia, solicits applications for postdoctoral fellow
positions in imaging genetics of the human and mice. We are looking for an
excellent and highly motivated candidate with a PhD degree in neurobiology,
genetics, experimental psychology, and neuroimaging or comparable
background. Interest and/or previous experience in/with neuroscience,
animal MRI, design and image analysis as well as wet lab experience are a
plus. The successful candidate will participate in the multidisciplinary
project involves developing transgenic mice model of psychiatric and
neurological diseases. The main focus of this project is to address how
risky genes of schizophrenia and Alzheimer?s disease affect brain networks
in the human and mice. The postdoctoral fellows will be jointly supervised
by Professor Tianzi Jiang and other Professors (QBI) who are experts in
neuroscience. As at 30 June 2014, an applicant must not have had more than
five years full-time equivalent professional research experience since the
award of a PhD. The current salary range for the award is on a four-level
scale from A$71,528.60 ? A$79,708.50 per annum. Commencing salaries are
based strictly on the number of full years? experience since receiving a
doctorate. Salary scales are reviewed from time to time.
Please contact Professor Tianzi Jiang on tianzi.jiang@uq.edu.au for
research plan.
To submit an application for these positions, please refer to
http://www.uq.edu.au/research/research-management/uq-postdoctoral-research-fellowships.
The application deadline is *19 May 2014.*
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Message: 28
Date: Tue, 6 May 2014 08:55:11 +0100
From: Anna Jonsson <ajonsson09@gmail.com>
Subject: Re: [Freesurfer] qdec question
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CADzVL0e7768VL-jDcL+LydiNMCeNnDWvuXc-y-SYD2Z2Hy0oeA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
thank you. I have another question; I am getting several significant
clusters for group, when correcting for multiple comparisons and total
brain size and age, but when I enter sex in, msot of these disappear, but i
do not understand whether this is a power issue (as qdec automatically
incorporates the interaction effect) or whether this is actually a gender
effect? Because the group*gender interaction is non-significant, and the
main effect of gender does not have a significant effect of any of the
cortical measures either? Please, any help would be greatly appreciated.
Kind Wishes,
Anna
On Mon, May 5, 2014 at 8:39 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu>wrote:
>
> DOSS is not working in QDEC. It should be disabled in 5.3
> doug
>
> On 05/05/2014 09:39 AM, Anna Jonsson wrote:
> > Dear group,
> >
> > when using the qdec gui interface, I was wondering where the "button"
> > or the likes is to change the estimation from its standard doss to
> > dods (different osnet, different slope). I believe I can do this
> > somewhere on the qdec gui without changing to mri_glmfit?
> >
> >
> > _______________________________________________
> > 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
> 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: 29
Date: Tue, 6 May 2014 14:11:36 +0200
From: Gabor Perlaki <petzinger.gabor@gmail.com>
Subject: [Freesurfer] aseg.stats volume mismatch
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CA+f2votdFynZU1++Q7gf3FXYDyOFzBKy+Mf1gRAvZG7_pVChyQ@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear all,
I've loaded the mri/aseg.mgz in slicer3D and done a label statistics
on the image. The left caudate was reported to be 4005 mm^3 and the
right caudate to be 4011 mm^3 by Slicer3D. However, these numbers are
somewhat different from the values reported in aseg.stats: 3757 mm^3
and 3901 mm^3. Could anyone help me how to resolve these findings?
Thanks,
Gabor
------------------------------
Message: 30
Date: Tue, 6 May 2014 08:48:21 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] aseg.stats volume mismatch
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <alpine.LRH.2.03.1405060848050.19669@nmr.mgh.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Hi Gabor
we do partial volume correction when we compute the aseg.stats
cheers
Bruce
On Tue, 6 May
2014, Gabor Perlaki wrote:
> Dear all,
>
> I've loaded the mri/aseg.mgz in slicer3D and done a label statistics
> on the image. The left caudate was reported to be 4005 mm^3 and the
> right caudate to be 4011 mm^3 by Slicer3D. However, these numbers are
> somewhat different from the values reported in aseg.stats: 3757 mm^3
> and 3901 mm^3. Could anyone help me how to resolve these findings?
>
> Thanks,
> Gabor
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
------------------------------
Message: 31
Date: Tue, 6 May 2014 09:58:22 -0400
From: Jason Tourville <jaytour@gmail.com>
Subject: [Freesurfer] -3T and -mprage flags
To: freesurfer@nmr.mgh.harvard.edu
Cc: "Chang, Soo-Eun" <sooeunc@med.umich.edu>
Message-ID:
<CAJc-rQga17Qst_frOtRHu=KdYEHc=1U7tEyJ-1mQN8=A6_N71Q@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi there,
I am working on a project that involves pediatric data, ages 3-12. We are
using Freesurfer to generate cortical surfaces. Information regarding the
T1 acquisition is listed below. Is it appropriate to use the -3T and
mprage flags for such data? Is there an alternative, pediatric atlas, that
can be used for the Talariach and/or normalization steps that would be an
improvement over the standard (or Schwartz) atlases?
Any input that you can provide would be greatly appreciated.
Cheers,
Jason
Below please see some details on the MPRAGE that is being collected for my
study.
GE 3T Signa? HDx MR scanner (GE Healthcare, Waukesha, WI) with an 8-channel
head coil. During each session, 180 T1-weighted 1-mm3 isotropic volumetric
inversion recovery fast spoiled gradient-recalled images (10 minute scan
time), with cerebrospinal fluid (CSF) suppressed, were obtained to cover
the whole brain with the following parameters: time of echo (TE) = 3.8 ms,
time of repetition (TR) of acquisition = 8.6 ms, time of inversion (TI) =
831 ms, TR of inversion = 2332 ms, flip angle = 8?, field of view (FOV) =
25.6 cm ? 25.6 cm, matrix size = 256 ? 256, slice thickness = 1 mm, and
receiver bandwidth = ? 20.8 kHz.
--
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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Message: 32
Date: Tue, 06 May 2014 10:03:24 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] LOOK FOR HELP
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5368EBAC.9020304@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
What command lines are you using? You don't need to invert the BBR
registration matrix with surf2vol
doug
On 5/5/14 10:54 PM, ??? wrote:
> Dear Freesurfer:
> I have some problems with using mri_surf2vol .I'd like to ask if
> you could help me with this.--volreg Contains the matrix that maps XYZ
> in the reference anatomical to XYZ in the functional volume. And to
> get this reg I use bbregister. But the result of bbregister is
> functional to anatomial volume,so I need to inverse the matrix.When I
> use convert_xfm in fsl I found the register.dat(which is the reslut of
> bbregister)is not a 4*4 matrix ,it just like
> dsub1
> 1.000000
> 1.000000
> 0.150000
> 9.999998807907104e-01 3.475215926300734e-04 3.422866575419903e-04
> 1.634627580642700e-02
> -3.475832345429808e-04 9.999999403953552e-01 1.798802986741066e-04
> -4.015868902206421e-02
> -3.422244917601347e-04 -1.799785532057285e-04 1.000000000000000e+00
> -2.181045338511467e-02
> 0 0 0 1
> round
> Is there a command I can use to inverse the register.dat?Or if I use
> convert_xfm which part of the register.dat should I use?
> Thank you !
>
> Yours
> Dongbo Liu
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 33
Date: Tue, 06 May 2014 10:04:50 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] qdec question
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5368EC02.8060302@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
If you don't see an effect of gender, then it is ok to leave it out of
the model. I could be affecting the power as you suspect.
doug
On 5/6/14 3:55 AM, Anna Jonsson wrote:
> thank you. I have another question; I am getting several significant
> clusters for group, when correcting for multiple comparisons and total
> brain size and age, but when I enter sex in, msot of these disappear,
> but i do not understand whether this is a power issue (as qdec
> automatically incorporates the interaction effect) or whether this is
> actually a gender effect? Because the group*gender interaction is
> non-significant, and the main effect of gender does not have a
> significant effect of any of the cortical measures either? Please, any
> help would be greatly appreciated.
>
> Kind Wishes,
>
> Anna
>
>
> On Mon, May 5, 2014 at 8:39 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
> DOSS is not working in QDEC. It should be disabled in 5.3
> doug
>
> On 05/05/2014 09:39 AM, Anna Jonsson wrote:
> > Dear group,
> >
> > when using the qdec gui interface, I was wondering where the
> "button"
> > or the likes is to change the estimation from its standard doss to
> > dods (different osnet, different slope). I believe I can do this
> > somewhere on the qdec gui without changing to mri_glmfit?
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto: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 <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://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 <mailto: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.
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 34
Date: Tue, 6 May 2014 10:15:05 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] -3T and -mprage flags
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Avi Snyder <avi@npg.wustl.edu>, "Chang, Soo-Eun"
<sooeunc@med.umich.edu>
Message-ID: <alpine.LRH.2.03.1405061014100.6320@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Jason
it's hard to say a priori, particularly since this probably isn't even
really an mp-rage (given that it's a GE scanner) and that you are using
an 8 channel array. I guess I would say try it out and see.
As far as a pedi atlas, I'm not sure, perhaps Avi can comment?
Bruce
On Tue, 6 May
2014, Jason Tourville wrote:
> Hi there,
> I am working on a project that involves pediatric data, ages 3-12. We are
> using Freesurfer to generate cortical surfaces. Information regarding the T1
> acquisition is? listed below. Is it appropriate to use the -3T and mprage
> flags for such data? Is there an alternative, pediatric atlas, that can be
> used for the Talariach and/or normalization steps that would be an
> improvement over the standard (or Schwartz) atlases?
>
> Any input that you can provide would be greatly appreciated.
>
> Cheers,
> Jason
>
>
> Below please see some details on the MPRAGE that is being collected for my
> study.
>
> GE 3T Signa? HDx MR scanner (GE Healthcare, Waukesha, WI) with an 8-channel
> head coil. During each session, 180 T1-weighted 1-mm3 isotropic volumetric
> inversion recovery fast spoiled gradient-recalled images (10 minute scan
> time), with cerebrospinal fluid (CSF) suppressed, were obtained to cover the
> whole brain with the following parameters: time of echo (TE) = 3.8 ms, time
> of repetition (TR) of acquisition = 8.6 ms, time of inversion (TI) = 831 ms,
> TR of inversion = 2332 ms, flip angle = 8?, field of view (FOV) = 25.6 cm ?
> 25.6 cm, matrix size = 256 ? 256, slice thickness = 1 mm, and receiver
> bandwidth = ? 20.8 kHz.
>
> --
> Jason A. Tourville, Ph.D.
> Research Assistant Professor
> Department of Speech, Language,
> and Hearing Sciences
> Boston University
> 677 Beacon St.
> Boston, MA 02215
> Phone: (617)353-9484
> Fax: (617)353-7755
>
>
------------------------------
Message: 35
Date: Tue, 6 May 2014 10:15:34 -0400 (EDT)
From: "JacobML@nmr.mgh.harvard.edu" <jacobml@nmr.mgh.harvard.edu>
Subject: [Freesurfer] freeview fails to open
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<50990.172.20.147.36.1399385734.squirrel@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1
Hello All,
Any idea why freeview fails to open? Below I have included the terminal
output.
I have checked my quota and I have plenty of available memory. I also
tried running the 2 options (-start_in_debugger and
-on_error_attach_debugger), but these were not recognized. I was next
going to attempt to configure, but I fear I may do more damage if I start
messing around with cmds that I do not understand.
Thank you for the assistance!
Jacob
[purkinje:mri] (nmr-stable53-env) freeview
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Signal received!
[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: Unknown Name on a linux-gnu named
purkinje.nmr.mgh.harvard.edu by jacobml Tue May 6 10:07:13 2014
[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: User provided function() line 0 in unknown directory
unknown file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
------------------------------
Message: 36
Date: Tue, 6 May 2014 16:22:48 +0200
From: Garikoitz Lerma-Usabiaga <garikoitz@gmail.com>
Subject: [Freesurfer] mri_glmfit restricted to a label
To: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAMrepeYVagcaeZ7LdfXu70Q9sh-ZqrL9xep2twGA5oCLnxze9A@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi,
we are trying to run glmfit restricted to a label, with the following
commands:
mri_glmfit --y lh.p.thickness.10.mgh --label lh.l.label --fsgd f.fsgd
--C C.mtx --surf fsaverage lh --cortex --glmdir
lh.p.thickness.10.glmdir
mri_glmfit-sim --glmdir lh.p.thickness.10.glmdir --sim mc-z 10000 1.3
mc-z.abs --sim-sign abs --cache-label lh.l.label --cwpvalthresh .999
--overwrite
but if we check mc-z.abs.sig.masked.mgh and mc-z.abs.sig.cluster.mgh, we
found clusters outside the label (see image below).
Are we doing it properly? How can we be sure that both the analysis and the
correction are done inside the label?
thanks!
Gari
[image: Inline image 1]
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------------------------------
Message: 37
Date: Tue, 6 May 2014 10:30:28 -0400
From: Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freeview fails to open
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <FFA773D6-DD11-4981-A3E3-826AA3516146@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=us-ascii
Have you tried dev version?
On May 6, 2014, at 10:15 AM, "JacobML@nmr.mgh.harvard.edu" <jacobml@nmr.mgh.harvard.edu> wrote:
> Hello All,
>
> Any idea why freeview fails to open? Below I have included the terminal
> output.
>
> I have checked my quota and I have plenty of available memory. I also
> tried running the 2 options (-start_in_debugger and
> -on_error_attach_debugger), but these were not recognized. I was next
> going to attempt to configure, but I fear I may do more damage if I start
> messing around with cmds that I do not understand.
>
> Thank you for the assistance!
>
> Jacob
>
>
> [purkinje:mri] (nmr-stable53-env) freeview
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
> find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [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: Unknown Name on a linux-gnu named
> purkinje.nmr.mgh.harvard.edu by jacobml Tue May 6 10:07:13 2014
> [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: User provided function() line 0 in unknown directory
> unknown file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
------------------------------
Message: 38
Date: Tue, 6 May 2014 10:34:22 -0400 (EDT)
From: "JacobML@nmr.mgh.harvard.edu" <jacobml@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freeview fails to open
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<51144.172.20.147.36.1399386862.squirrel@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1
I have not tried dev version. Can you please let me know how I can load that?
> Have you tried dev version?
>
> On May 6, 2014, at 10:15 AM, "JacobML@nmr.mgh.harvard.edu"
> <jacobml@nmr.mgh.harvard.edu> wrote:
>
>> Hello All,
>>
>> Any idea why freeview fails to open? Below I have included the terminal
>> output.
>>
>> I have checked my quota and I have plenty of available memory. I also
>> tried running the 2 options (-start_in_debugger and
>> -on_error_attach_debugger), but these were not recognized. I was next
>> going to attempt to configure, but I fear I may do more damage if I
>> start
>> messing around with cmds that I do not understand.
>>
>> Thank you for the assistance!
>>
>> Jacob
>>
>>
>> [purkinje:mri] (nmr-stable53-env) freeview
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>> [0]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> [0]PETSC ERROR: or see
>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
>> find memory corruption errors
>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and
>> run
>> [0]PETSC ERROR: to get more information on the crash.
>> [0]PETSC ERROR: --------------------- Error Message
>> ------------------------------------
>> [0]PETSC ERROR: Signal received!
>> [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: Unknown Name on a linux-gnu named
>> purkinje.nmr.mgh.harvard.edu by jacobml Tue May 6 10:07:13 2014
>> [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: User provided function() line 0 in unknown directory
>> unknown file
>> [unset]: aborting job:
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
------------------------------
Message: 39
Date: Tue, 6 May 2014 11:15:36 -0400
From: Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freeview fails to open
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <E93C239E-3ED9-4E6B-B08A-14641E1D181F@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=us-ascii
Just run:
source /usr/local/freesurfer/nmr-dev-env
> On May 6, 2014, at 10:34 AM, "JacobML@nmr.mgh.harvard.edu" <jacobml@nmr.mgh.harvard.edu> wrote:
>
> I have not tried dev version. Can you please let me know how I can load that?
>
>> Have you tried dev version?
>>
>> On May 6, 2014, at 10:15 AM, "JacobML@nmr.mgh.harvard.edu"
>> <jacobml@nmr.mgh.harvard.edu> wrote:
>>
>>> Hello All,
>>>
>>> Any idea why freeview fails to open? Below I have included the terminal
>>> output.
>>>
>>> I have checked my quota and I have plenty of available memory. I also
>>> tried running the 2 options (-start_in_debugger and
>>> -on_error_attach_debugger), but these were not recognized. I was next
>>> going to attempt to configure, but I fear I may do more damage if I
>>> start
>>> messing around with cmds that I do not understand.
>>>
>>> Thank you for the assistance!
>>>
>>> Jacob
>>>
>>>
>>> [purkinje:mri] (nmr-stable53-env) freeview
>>> [0]PETSC ERROR:
>>> ------------------------------------------------------------------------
>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>>> probably memory access out of range
>>> [0]PETSC ERROR: Try option -start_in_debugger or
>>> -on_error_attach_debugger
>>> [0]PETSC ERROR: or see
>>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>>> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
>>> find memory corruption errors
>>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>>> and
>>> run
>>> [0]PETSC ERROR: to get more information on the crash.
>>> [0]PETSC ERROR: --------------------- Error Message
>>> ------------------------------------
>>> [0]PETSC ERROR: Signal received!
>>> [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: Unknown Name on a linux-gnu named
>>> purkinje.nmr.mgh.harvard.edu by jacobml Tue May 6 10:07:13 2014
>>> [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: User provided function() line 0 in unknown directory
>>> unknown file
>>> [unset]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
------------------------------
Message: 40
Date: Tue, 6 May 2014 11:18:23 -0400 (EDT)
From: "JacobML@nmr.mgh.harvard.edu" <jacobml@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freeview fails to open
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<51327.172.20.147.36.1399389503.squirrel@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1
Thank you for the source details for dev. I just tried running freeview
under the dev environment and I still received the same error message.
Any other ideas on what may be going on?
Thank you!
> Just run:
> source /usr/local/freesurfer/nmr-dev-env
>
>> On May 6, 2014, at 10:34 AM, "JacobML@nmr.mgh.harvard.edu"
>> <jacobml@nmr.mgh.harvard.edu> wrote:
>>
>> I have not tried dev version. Can you please let me know how I can load
>> that?
>>
>>> Have you tried dev version?
>>>
>>> On May 6, 2014, at 10:15 AM, "JacobML@nmr.mgh.harvard.edu"
>>> <jacobml@nmr.mgh.harvard.edu> wrote:
>>>
>>>> Hello All,
>>>>
>>>> Any idea why freeview fails to open? Below I have included the
>>>> terminal
>>>> output.
>>>>
>>>> I have checked my quota and I have plenty of available memory. I also
>>>> tried running the 2 options (-start_in_debugger and
>>>> -on_error_attach_debugger), but these were not recognized. I was next
>>>> going to attempt to configure, but I fear I may do more damage if I
>>>> start
>>>> messing around with cmds that I do not understand.
>>>>
>>>> Thank you for the assistance!
>>>>
>>>> Jacob
>>>>
>>>>
>>>> [purkinje:mri] (nmr-stable53-env) freeview
>>>> [0]PETSC ERROR:
>>>> ------------------------------------------------------------------------
>>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>>>> probably memory access out of range
>>>> [0]PETSC ERROR: Try option -start_in_debugger or
>>>> -on_error_attach_debugger
>>>> [0]PETSC ERROR: or see
>>>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>>>> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple
>>>> to
>>>> find memory corruption errors
>>>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>>>> and
>>>> run
>>>> [0]PETSC ERROR: to get more information on the crash.
>>>> [0]PETSC ERROR: --------------------- Error Message
>>>> ------------------------------------
>>>> [0]PETSC ERROR: Signal received!
>>>> [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: Unknown Name on a linux-gnu named
>>>> purkinje.nmr.mgh.harvard.edu by jacobml Tue May 6 10:07:13 2014
>>>> [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: User provided function() line 0 in unknown directory
>>>> unknown file
>>>> [unset]: aborting job:
>>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
------------------------------
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