Re: [Freesurfer] Building from source #2 -- dynamic binding

[R Edgar]

On 20 February 2016 at 17:28, Bruce Fischl  wrote:

> hmmm, the only thing that worries me about dynamic linking is that it
> will add variability to the outputs. Zeke has spent endless amounts of time
> tracking down e.g. mac vs. pc differences in math libs and such.

What sort of differences were found? Differences in transcendental
functions are to be expected (so long as they are small) and lots of
other things can cause slightly different results to be generated from
floating point calculations (for instance, when summing an array, the
result might vary with the number of OpenMP threads used). Were the
segmentations produced intolerably different?

Regards,

Richard
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Re: [Freesurfer] Building from source #2 -- dynamic binding

[Yaroslav Halchenko]

On Sat, 20 Feb 2016, Bruce Fischl wrote:

> hmmm, the only thing that worries me about dynamic linking is that it 
> will add variability to the outputs. Zeke has spent endless amounts of time 
> tracking down e.g. mac vs. pc differences in math libs and such. Won't 
> dynamic linking just make that a much more prevalent problem?

nope -- I am not talking about dynamically linking external libraries
ATM, but first about the internal ones, where the common code where
instead of absorbing the same .a or .o blobs into multiple binaries,
there would be a set of internal dynamic libraries which those
binaries would be linked against, so there will no copies of
binary code among different binaries.  I guess
https://www.gnu.org/software/automake/manual/html_node/Libtool-Convenience-Libraries.html
is a quick intro into those.

As for linking against external libraries -- those could be bundled
along with rpath pointing to their location or LD_LIBRARY_PATH
override assuring they are picked up (instead of possibly available
identically named system-wide ones). 

So overall it is possible to achieve absent variability while using
dynamic linking and allowing for possibility of the flexibility ;)

Cheers
-- 
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik
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Re: [Freesurfer] Building from source #2 -- dynamic binding

[Bruce Fischl]

hmmm, the only thing that worries me about dynamic linking is that it 
will add variability to the outputs. Zeke has spent endless amounts of time 
tracking down e.g. mac vs. pc differences in math libs and such. Won't 
dynamic linking just make that a much more prevalent problem?
Bruce



On Sat, 20 Feb 2016, Yaroslav Halchenko 
wrote:

> Hi again,
>
> While our "building from source" discussion is "hot" I wondered to ask
> if there was an attempt or may be plans for to switch to using dynamic
> linking (and collect functionality within a few internal
> libraries) instead of static duplication of binary code across
> binaries.
>
> At some point Michael Hanke and me have tried to achieve such a goal:
> http://anonscm.debian.org/cgit/pkg-exppsy/freesurfer.git/tree/debian/patches/internal_shared_libs
> (although a bit also mixing up with linking against system wide
> libraries) so overall it is possible and should shrink currently sized
> at almost 4GB bin (stripped of debug symbols) into probably (forgot the
> size we got then) 50-100MB.  I expect similar or may be even more
> drastic effect on debug symbols files (which are useful to provide as an
> option).  I hope I don't need to outline why 10-fold cut down in
> binaries size would be a good thing ;)
>
> So I wondered, if there are any plans, and if not (yet) -- may be we
> could proceed together to achieve that goal?  above experiment with
> creating and maintaining that huge patch ourselves obviously has failed,
> but taking incremental steps we might succeed eventually, IFF such
> changes would be accepted upstream (i.e. into your code).  Or do
> you see any possible reason why assembling few of internal dynamic
> libraries and linking against your libraries bundle would be a no go?
>
> With best regards,
>
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[Freesurfer] Building from source #2 -- dynamic binding

[Yaroslav Halchenko]

Hi again,

While our "building from source" discussion is "hot" I wondered to ask
if there was an attempt or may be plans for to switch to using dynamic
linking (and collect functionality within a few internal
libraries) instead of static duplication of binary code across
binaries.

At some point Michael Hanke and me have tried to achieve such a goal:
http://anonscm.debian.org/cgit/pkg-exppsy/freesurfer.git/tree/debian/patches/internal_shared_libs
(although a bit also mixing up with linking against system wide
libraries) so overall it is possible and should shrink currently sized
at almost 4GB bin (stripped of debug symbols) into probably (forgot the
size we got then) 50-100MB.  I expect similar or may be even more
drastic effect on debug symbols files (which are useful to provide as an
option).  I hope I don't need to outline why 10-fold cut down in
binaries size would be a good thing ;)

So I wondered, if there are any plans, and if not (yet) -- may be we
could proceed together to achieve that goal?  above experiment with
creating and maintaining that huge patch ourselves obviously has failed,
but taking incremental steps we might succeed eventually, IFF such
changes would be accepted upstream (i.e. into your code).  Or do
you see any possible reason why assembling few of internal dynamic
libraries and linking against your libraries bundle would be a no go?

With best regards,
-- 
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik
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Re: [Freesurfer] Reference about: MeanCurv, GausCurv, FoldInd, CurvInd?

[Bruce Fischl]

thanks Christophe

Bruce
On Sat, 20 Feb 2016, Christophe Destrieux wrote:


this was : 
Van Essen, D.C., Drury, H.A., 1997. Structural and functional analyses of
human cerebral cortex using a surface-based atlas. J Neurosci 17, 7079–102.
Cheers

— 
Christophe Destrieux, 
Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais
de Tours 
Service de Neurochirurgie 
Laboratoire d’Anatomie, Faculté de Médecine, 10 Bd Tonnellé - 37032 Tours -
France 
Bureau: +33 2 47 36 61 36 | Fax +33 2 47 36 62 07 | Mel Bureau:
christophe.destri...@univ-tours.fr
Web : http://www.u930.tours.inserm.fr/ 









  Le 20 févr. 2016 à 19:22, Bruce Fischl
   a écrit :

Hi Marta

A 2D surface (like the cortical white or pial models) has two
principal curvatures at each point - one in the direction of maximum
curvature and one in the direction of minimum curvature - typically
denoted k1 and k2. The mean curvature is the average of these
H=(k1+k2)/2 and the Gaussian curvature is the product of them K=(k1 *
k2).  So, MeanCurv is the integral of the absolute value of H and
GausCurv is the integral of the absolute value of K. FoldInd and
CurvInd are two indices proposed by David Van Essen in a paper from
years ago that we also compute. Sorry, I don't have the right
reference handy, perhaps someone else on the list does?

cheers
Bruce


On Tue, 16 Feb 2016, Karas, Marta wrote:

  H!
  I am working with data which is an output from
  the FreeSurfer processing. 
  I would like to kindly ask you to refer me to materials /
  precise
  "mathematical" definitions that could help to understand
  what are the
  following parameters:
  *  ​MeanCurv - Integrated Rectified Mean Curvature,
  *  GausCurv - Integrated Rectified Gaussian Curvature,
  *  FoldInd - Folding Index,
  *  CurvInd - Intrinsic Curvature Index.
  (I have been trying to google but not been successful,
  unfortunately.) 
  Kind regards,
  Marta Karas, M.S.
  Research Assistant, Department of Biostatistics
  Richard M. Fairbanks School of Public Health and School of
  Medicine
  Indiana University
  tel: 317-665-4551
  email: mka...@iu.edu

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Re: [Freesurfer] 1.5T GE dicom images into FreeSurfer

[Bruce Fischl]

Hi Peter

can you send us the command line you used and the entire screen output 
and recon-all.log file? Otherwise it's not possible for us to help you.

cheers
Bruce
On 
Sat, 20 Feb 2016, pda...@westol.com wrote:

> Hi,
>
> We would like to process 1.5 T GE dicom scans for over 200 individuals.  It
> is unclear how to import these into FreeSurfer and process in batch.
>
> Each subject folder consists of several subfolders.  Each subfolder
> consists of all the images of a single pulse sequence, e.g. sagittal spgr,
> axial T2, etc.
> The images in the subfolders are files labeled I.001.dcm, I.002.dcm, ... .
>
> Each image is a valid dicom image which can be individually opened in other
> dicom viewing programs. However, the entire series of images in the
> subfolder is not automatically recognized as a 3D set.
>
> Thank you,
>
> Peter Davis
>
> 
> mail2web.com ? What can On Demand Business Solutions do for you?
> http://link.mail2web.com/Business/SharePoint
>
>
>
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Re: [Freesurfer] Reference about: MeanCurv, GausCurv, FoldInd, CurvInd?

[Christophe Destrieux]

this was : 

Van Essen, D.C., Drury, H.A., 1997. Structural and functional analyses of human 
cerebral cortex using a surface-based atlas. J Neurosci 17, 7079–102.
Cheers

— 
Christophe Destrieux, 
Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de 
Tours 
Service de Neurochirurgie 
Laboratoire d’Anatomie, Faculté de Médecine, 10 Bd Tonnellé - 37032 Tours - 
France 
Bureau: +33 2 47 36 61 36 | Fax +33 2 47 36 62 07 | Mel Bureau: 
christophe.destri...@univ-tours.fr
Web : http://www.u930.tours.inserm.fr/  









> Le 20 févr. 2016 à 19:22, Bruce Fischl  a écrit :
> 
> Hi Marta
> 
> A 2D surface (like the cortical white or pial models) has two principal 
> curvatures at each point - one in the direction of maximum curvature and one 
> in the direction of minimum curvature - typically denoted k1 and k2. The mean 
> curvature is the average of these H=(k1+k2)/2 and the Gaussian curvature is 
> the product of them K=(k1 * k2).  So, MeanCurv is the integral of the 
> absolute value of H and GausCurv is the integral of the absolute value of K. 
> FoldInd and CurvInd are two indices proposed by David Van Essen in a paper 
> from years ago that we also compute. Sorry, I don't have the right reference 
> handy, perhaps someone else on the list does?
> 
> cheers
> Bruce
> 
> 
> On Tue, 16 Feb 2016, Karas, Marta wrote:
> 
>> H!
>> I am working with data which is an output from the FreeSurfer processing. 
>> I would like to kindly ask you to refer me to materials / precise
>> "mathematical" definitions that could help to understand what are the
>> following parameters:
>> *  ​MeanCurv - Integrated Rectified Mean Curvature,
>> *  GausCurv - Integrated Rectified Gaussian Curvature,
>> *  FoldInd - Folding Index,
>> *  CurvInd - Intrinsic Curvature Index.
>> (I have been trying to google but not been successful, unfortunately.) 
>> Kind regards,
>> Marta Karas, M.S.
>> Research Assistant, Department of Biostatistics
>> Richard M. Fairbanks School of Public Health and School of Medicine
>> Indiana University
>> tel: 317-665-4551
>> email: mka...@iu.edu
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> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
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Re: [Freesurfer] mris_make_surfaces dimensions error

[Bruce Fischl]

Hi Corinna

can you send us your full command line? Sounds like you are using a 
surface overlay as the cover_seg parameter instead of a volume one. Try 
running mri_info on it to make sure it is a volume (i.e. 256x256x256). If 
not, you will need to sample it into the volume with mri_surf2vol

thanks
Bruce

On Thu, 18 Feb 2016, Corinna Bauer 
wrote:

> Hello all,
> I am attempting to reshape the pial surfaces to fill the new boundaries in
> my edited ribbon.mgz file. I am using mris_make_surfaces with the -cover_seg
> flag but keep getting this error:
> ERROR: mris_make_surfaces-MRIcheckVolDims: volume1 height=256 != volume2
> height=1.
> 
> Any suggestions?
> 
> Thanks!
> Corinna
> 
> FYI: I am trying to reshape the pial boundary based off this previous
> thread.
> https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2014-November/04134
> 8.html
> 
>
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Re: [Freesurfer] eTIV question

[Bruce Fischl]

Hi Angel

the time1/time2 correlation of eTIV is pretty worrisome. Are you sure 
that there aren't outliers/failures in that set?

Bruce


On Sun, 14 Feb 2016, angela.fav...@unipd.it wrote:

> Dear Freesurfer experts,
> I have a question about eTIV (FS 5.3) which I use as a covariate where
> appropriate. Is it in some way influenced by the presence of brain
> atrophy?
> I have a new sample of subjects in a longitudinal study: at time 1 they
> have some atrophy (due to low body weight) that improves in time 2 (4
> months). I observed that eTIV-time1 is slightly correlated with weight
> (r=0.3) whereas no correlation is present at time 2. The correlation
> between eTIV-time1 and eTIV-time2 is somewhat lower than expected (r=0.53)
> and is lower than correlation between SegBrain_Vol_1 and SegBrain_Vol_2
> (0.65).
>
> Do you suggest in these cases to perform manual segmentation to obtain
> TIV? or is there any other method (in freesurfer) to obtain an estimate of
> TIV not influenced by brain atrophy? What about using BrainMask_to_TIV?
>
> Thank you for any suggestion
>
> Angela
>
>
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[Freesurfer] 1.5T GE dicom images into FreeSurfer

[pda...@westol.com]

Hi,

We would like to process 1.5 T GE dicom scans for over 200 individuals.  It
is unclear how to import these into FreeSurfer and process in batch. 

Each subject folder consists of several subfolders.  Each subfolder
consists of all the images of a single pulse sequence, e.g. sagittal spgr,
axial T2, etc. 
The images in the subfolders are files labeled I.001.dcm, I.002.dcm, ... .

Each image is a valid dicom image which can be individually opened in other
dicom viewing programs. However, the entire series of images in the
subfolder is not automatically recognized as a 3D set.

Thank you,

Peter Davis


mail2web.com ? What can On Demand Business Solutions do for you?
http://link.mail2web.com/Business/SharePoint



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Re: [Freesurfer] Error in surface-based interhemispheric registration

[Ilaria Mazzonetto]

Thank you for your prompt reply.

2016-02-18 18:58 GMT+01:00 Douglas N Greve :

> You should not be using 5.2. Use 5.3 instead, that will have fsaverage_sym
>
> On 02/18/2016 12:06 PM, Ilaria Mazzonetto wrote:
> > Hi Freesurfer experts,
> > I'm using freesurfer v5.2.0.
> > If I use surfreg --s $subject --t fsaverage_sym --lh, I have this
> > error: ERROR: cannot find /home/T1/fsaverage_sym/lh.reg.template.tif.
> > Does anyone know how can I fix this?
> > Thanks a lot.
> > Ilaria
> >
> >
> >
> > ___
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> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: 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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[Freesurfer] Fwd: Job Offer in Madrid

[José Ángel Pineda]

We are pleased to offer a 2-year post-doctoral position at the Reina Sofia
Foundation Alzheimer's Disease Centre in Madrid, Spain.

The successful applicant will be involved in neuroimaging analyses of a
5-year longitudinal study (currently in year 4) of 1200 healthy elderly
individuals (aged 70-85) to determine neuronal markers in the healthy state
which predict subsequent development of mild cognitive impairment and
dementia.

In addition, the Reina Sofia Alzheimer's Centre offers:

- A research-dedicated MRI facility attached to a 140-bed residence for
patients with Alzheimer’s disease.
- A brain-bank providing post-mortem histopathological confirmation of
dementia diagnosis for patients scanned pre-mortem.
- Ex-vivo MRI scanning.

A strong background in neuroimaging techniques is required. Applicants must
have a PhD in neuroscience, cognitive neuroscience, biomedical engineering,
neuropsychology or related field. Experience in dementia research is a
plus. Spanish language skills are NOT required.

Competitive annual salary depending on experience.

SUBMISSION
Interested candidates should send CV and a cover letter (including contact
details of 2 referees), to the following email address: bryan.stra...@upm.es


DEADLINE FOR SUBMISSION OF APPLICATIONS
March 4, 2016

Any questions, please feel free to contact me.
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