Re: [Freesurfer] Mindboggle official software release and publication!

[Arno Klein]

Great question!  You can certainly run Mindboggle on FreeSurfer output for
earlier versions of FreeSurfer.  In fact, we did this for part of the work
described in the PLoS Computational Biology article:

"For this study we used FreeSurfer v5.1-derived labels and meshes, but the
recently released FreeSurfer version 6 is recommended because it uses
Mindboggle’s DKT-100 surface-based atlas (with the DKT31 labeling protocol)
by default to generate labels on the cortical surfaces, and generates
corresponding labeled cortical and non-cortical volumes (wmparc.mgz) [75
<http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005350#pcbi.1005350.ref075>
]."

I am certain you can run a FreeSurfer command to update the cortical labels
to be in accord with the DKT-31 labeling protocol (
http://journal.frontiersin.org/article/10.3389/fnins.2012.00171/full) and
the new DKT-100 atlas used in FreeSurfer.  I will leave it to others on
this list who have greater FreeSurfer expertise than I to recommend the
appropriate command.

Cheers,
Arno

On Fri, Feb 24, 2017 at 6:55 AM Ritobrato Datta <rida...@mail.med.upenn.edu>
wrote:

> Hi Arno,
>
> This is fascinating stuff. In my research, I have come across instances
> when I felt that a hybrid of ANTS and freesurfer would be very useful. Is
> this pipeline possible for data processed with the earlier versions of
> freesurfer say 5.1 ? FS6 just got released in Jan 2017 and I am sure for
> most ongoing studies, the data have already been processed in earlier
> versions of freesurfer.
>
> If there is a patch or script to update the data processed using earlier
> versions of freesurfer, that will save a lot of time than running
> everything from scratch in FS6.
>
> Please let us know.
>
> Best
>
> Rito
>
> - Original Message -
> From: Arno Klein <binarybot...@gmail.com>
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Thu, 23 Feb 2017 20:37:44 -0500 (EST)
> Subject: [Freesurfer] Mindboggle official software release and publication!
>
> Announcing the official release of Mindboggle (http://mindboggle.info),
> open source software <http://mindboggle.info/software.html> and data
> <https://osf.io/ydyxu/> for analyzing the shapes of brain structures from
> human MRI data (processed through FreeSurfer and optionally through ANTs).
> The release coincides with a publication in PLoS Computational Biology that
> documents and evaluates the software:
>
> Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B,
> Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human
> brains. PLoS Computational Biology 13(3): e1005350.
> doi:10.1371/journal.pcbi.1005350
> <http://doi.org/10.1371/journal.pcbi.1005350>
>
> Cheers,
> @rno
>
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[Freesurfer] Mindboggle official software release and publication!

[Arno Klein]

Announcing the official release of Mindboggle (http://mindboggle.info),
open source software  and data
 for analyzing the shapes of brain structures from
human MRI data (processed through FreeSurfer and optionally through ANTs).
The release coincides with a publication in PLoS Computational Biology that
documents and evaluates the software:

Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B,
Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human
brains. PLoS Computational Biology 13(3): e1005350.
doi:10.1371/journal.pcbi.1005350


Cheers,
@rno
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[Freesurfer] New deadline for the Alzheimer's Disease Sage/DREAM Challenge!

[Arno Klein]

We have extended the Alzheimer's Disease Sage/DREAM Challenge #1 submission
period to October 17th -- Time to enter!

https://www.synapse.org/#!Synapse:syn2290704

Of particular interest to the members of this mailing list is subchallenge
3, which leverages brain imaging
​ (
FreeSurfer was used in the processing of the data
)​
, in addition to genetics, cognitive assessments, and demographic
information from cohorts ranging from cognitively normal to mild
cognitively impaired to individuals with AD.

Looking forward to your submissions to the leaderboard!:

https://www.synapse.org/#!Synapse:syn2290704/wiki/65302

​Cheers,
@rno
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[Freesurfer] Alzheimer's Disease Sage/DREAM Challenge

[Arno Klein]

The Alzheimer's Disease Sage/DREAM Challenge #1 (AD#1) launched earlier
this month!

The goal of the AD#1 is to apply an open science approach to rapidly
identify accurate predictive AD biomarkers that can be used by the
scientific, industrial and regulatory communities to improve AD diagnosis
and treatment. AD#1 will be the first in a series of AD Data Challenges to
leverage genetics and brain imaging in combination with cognitive
assessments, biomarkers and demographic information from cohorts ranging
from cognitively normal to mild cognitively impaired to individuals with AD.

FreeSurfer was instrumental in the processing of the image data.

For challenge details, please see:
https://www.synapse.org/#!Synapse:syn2290704

Cheers,
@rno
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[Freesurfer] Fwd: Alzheimer's Disease Sage/DREAM Challenge

[Arno Klein]

The Alzheimer's Disease Sage/DREAM Challenge #1 (AD#1) launched earlier
this month!

The goal of the AD#1 is to apply an open science approach to rapidly
identify accurate predictive AD biomarkers that can be used by the
scientific, industrial and regulatory communities to improve AD diagnosis
and treatment. AD#1 will be the first in a series of AD Data Challenges to
leverage genetics and brain imaging in combination with cognitive
assessments, biomarkers and demographic information from cohorts ranging
from cognitively normal to mild cognitively impaired to individuals with AD.

FreeSurfer was instrumental in the processing of the image data.

For challenge details, please see:
https://www.synapse.org/#!Synapse:syn2290704
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[Freesurfer] Fwd: calloc error

[Arno Klein]

please ignore the previous post -- the calloc errors i was getting were
restricted to only certain files that somehow got corrupted.

cheers,
@rno
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[Freesurfer] Fwd: calloc error

[Arno Klein]

i have tried running the centos 4  6 versions of freesurfer on ubuntu
12.04, and with either i am getting a memory error when i simply run
mri_info on an mgz file (this does not happen on my osx
machine
for the same file
, and the license file is fine):


znzTAGskip: tag=1667787808, failed to calloc 606085120 bytes!

Cannot allocate memory


any help would be appreciated.

cheers,
@rno
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[Freesurfer] Mindboggle-101 manually labeled brain data now available! {Disarmed} {Disarmed}

[Arno Klein]

We are happy to announce the release of the Mindboggle-101 dataset, the
largest and most complete set of free, publicly accessible, manually
labeled human brain images in the world:  http://mindboggle.info/data/

This has special relevance to the FreeSurfer community, since we made use
of FreeSurfer to extract and label surfaces, and to create surface
templates and classifier atlases. We also adapted the Desikan-Killiany
labeling protocol used by FreeSurfer.

An article describing the data and labeling protocol has just been
published:
http://www.frontiersin.org/brain_imaging_methods/10.3389/fnins.2012.00171/full

An excerpt of the abstract reads:
 To manually label the macroscopic anatomy in magnetic resonance images of
101 healthy participants, we created a new cortical labeling protocol that
relies on robust anatomical landmarks and minimal manual edits after
initialization with automated labels. The “Desikan–Killiany–Tourville”
(DKT) protocol is intended to improve the ease, consistency, and accuracy
of labeling human cortical areas. Given how difficult it is to label
brains, the Mindboggle-101 dataset is intended to serve as brain atlases
for use in labeling other brains, as a normative dataset to establish
morphometric variation in a healthy population for comparison against
clinical populations, and contribute to the development, training, testing,
and evaluation of automated registration and labeling algorithms...

Cheers,
@rno

 arno klein
a...@binarybottle.comhttps://mail.google.com/mail/?view=cmfs=1tf=1to=a...@binarybottle.com
http://www.binarybottle.com
--
research asst professor
psychiatry  behavioral science
stony brook university
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[Freesurfer] how to convert .vtk surface meshes with labels to .annot format?

[Arno Klein]

what is the best way to convert a .vtk surface mesh (with labels as
scalars) to freesurfer .annot format?  i am currently converting the vtk
file to freesurfer .label files, then using freesurfer to consolidate these
into an .annot file, which is slow, roundabout, and generates a lot of
files.

cheers,
@rno
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Re: [Freesurfer] mris_label2annot mislabeling

[Arno Klein]

thank you, doug!  i was hung up on the names of the .label files when all
that matters is the order of the labels in the lookup table.  i should have
figured that one out!

cheers,
@rno



On Sun, Jun 24, 2012 at 3:50 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 what was your command line? Can you send your color table? It will assign
 the first label to the first entry in the color table.


 On 06/24/2012 11:43 AM, Arno Klein wrote:


 yes, but i am confused as to how mris_label2annot uses the color table.
  according to http://surfer.nmr.mgh.harvard.**edu/fswiki/**
 LabelsClutsAnnotationFileshttp://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles,
 each .label file contains columns of vertex numbers, coordinate values, and
 a column of zeros.  i assume that mris_label2annot assigns the coordinates
 in the file to the anatomical name corresponding to the name of the file,
 but when i tried to set the color table region names to be the same as the
 names of the .label files, the output was the same as what i sent earlier:

 1 11829830 Left-Cerebral-Exterior
 2 16119285 Left-Cerebral-White-Matter
 ...

 even though my color table didn't have label numbers 1, 2, etc.!

 cheers,
 @rno

 On Sun, Jun 24, 2012 at 11:22 AM, Douglas Greve 
 gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
 wrote:

Weren't you concerned that the names in the annotation were
incorrect? You get to pick the names and the colors to be whatever
you want to be. By default, it uses FreeSurferColorLUT.txt.
doug


On 6/23/12 9:54 PM, Arno Klein wrote:


dear doug,

thank you for your response.  for the custom color table, what do
i assign for the different anatomical names and color values?
 why wouldn't the names and colors in FreeSurferColorLUT.txt work?

cheers,
@rno



 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: 
 surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: 
 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html




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Re: [Freesurfer] mris_label2annot mislabeling

[Arno Klein]

yes, but i am confused as to how mris_label2annot uses the color table.
 according to
http://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles, each
.label file contains columns of vertex numbers, coordinate values, and a
column of zeros.  i assume that mris_label2annot assigns the coordinates in
the file to the anatomical name corresponding to the name of the file, but
when i tried to set the color table region names to be the same as the
names of the .label files, the output was the same as what i sent earlier:

1 11829830 Left-Cerebral-Exterior
2 16119285 Left-Cerebral-White-Matter
...

even though my color table didn't have label numbers 1, 2, etc.!

cheers,
@rno

On Sun, Jun 24, 2012 at 11:22 AM, Douglas Greve
gr...@nmr.mgh.harvard.eduwrote:

  Weren't you concerned that the names in the annotation were incorrect?
 You get to pick the names and the colors to be whatever you want to be. By
 default, it uses FreeSurferColorLUT.txt.
 doug


 On 6/23/12 9:54 PM, Arno Klein wrote:


  dear doug,

  thank you for your response.  for the custom color table, what do i
 assign for the different anatomical names and color values?  why wouldn't
 the names and colors in FreeSurferColorLUT.txt work?

  cheers,
 @rno


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[Freesurfer] mris_label2annot mislabeling

[Arno Klein]

hello!

i have saved a couple of .label files and am trying to convert them to a
.annot file with:

mris_label2annot --h lh --s MMRR-21-1
--l  lh.superiorfrontal.label
--l  lh.superiorparietal.label
--ctab FreeSurferColorLUT.txt --a output

the stdout is:

ColorTable atlas_colortable.txt
AnnotName  output
nlables 2
LabelThresh 0 0.00
Loading /usr/local/freesurfer/subjects/MMRR-21-1/surf/lh.orig
 1 11829830 Left-Cerebral-Exterior
 2 16119285 Left-Cerebral-White-Matter
 Mapping unhit to unknown
...

clearly the anatomical names assigned are incorrect, and when i view the
output with tksurfer, the labeled patches are in the right places but are
assigned these same incorrect anatomical names.

i have tried renaming the .label files to no avail.  what am i doing wrong?

cheers,
@rno
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[Freesurfer] memory allocation error with mris_register for one subject

[Arno Klein]

hello!

i am able to run mris_register on all of the OASIS brain images that i have
tested except for one:  OAS1_0061_MR1:

mris_register -curv OASIS-0061_MR1/surf/rh.sphere
templates/freesurfer/rh.OASIS_template.tif
 OASIS-0061_MR1/surf/rh.sphere_to_OASIS_template.reg
using smoothwm curvature for final alignment
$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
reading surface from OASIS-0061_MR1/surf/rh.sphere...
TAGskip: tag=1717658469, failed to calloc 1868656640 bytes!
Cannot allocate memory

the .sphere files are the same size, but i get a memory error.  any idea
why this might be?

cheers,
@rno
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Re: [Freesurfer] memory allocation error with mris_register for one subject

[Arno Klein]

aha -- it seems that just the .sphere files, not the .pial or .white files,
are corrupted.  is there an easy way to generate just the .sphere files
again?

cheers,
@rno



On Mon, Jun 18, 2012 at 11:32 AM, Bruce Fischl
fis...@nmr.mgh.harvard.eduwrote:

 Hi Arno

 can you load that sphere file in tksurfer? And run mris_info or
 mris_euler_number on it? I'm wondering if it is corrupted.
 Bruce

 On Mon, 18 Jun 2012, Arno Klein wrote:


 hello!

 i am able to run mris_register on all of the OASIS brain images that i
 have
 tested except for one:  OAS1_0061_MR1:

 mris_register -curv OASIS-0061_MR1/surf/rh.sphere
 templates/freesurfer/rh.OASIS_**template.tif
  OASIS-0061_MR1/surf/rh.**sphere_to_OASIS_template.reg
 using smoothwm curvature for final alignment
 $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
   $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
 reading surface from OASIS-0061_MR1/surf/rh.sphere.**..
 TAGskip: tag=1717658469, failed to calloc 1868656640 bytes!
 Cannot allocate memory

 the .sphere files are the same size, but i get a memory error.  any idea
 why
 this might be?

 cheers,
 @rno





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[Freesurfer] mri_surf2surf source and target annot formats

[Arno Klein]

hello!

in mri_surf2surf, does anyone know how to specify the source and target
formats if --sval is annot without using --sval-annot, as in --sfmt or
--tfmt?

cheers,
@rno
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Re: [Freesurfer] memory allocation error with mris_register

[Arno Klein]

dear doug,

i am using FS v5.1 now but ran the 20 oasis subjects through FS v5.0.  i am
only having this trouble for one of the subjects.

after the mri_convert workaround i am still getting the same memory
allocation error.

cheers,
@rno



On Fri, Jan 20, 2012 at 4:23 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 This is a strange problem we've been having with some mgz files that were
 generated during a short period of time last summer when there was a bug in
 the mgz writing code. What version of FS are you using? In the current dev
 version, this should not be a problem. A work-around is to convert the
 orig.mgz to itself using mri_convert in the dev environment, ie,

 mri_convert orig.mgz orig.mgz

 doug

 Arno Klein wrote:


 i get the following memory allocation error for only one out of 20 oasis
 subjects that i processed with freesurfer 5.1 on an ubuntu 11.10 machine
 with 24gb memory:

 mris_register -curv subjects/OAS1_0061_MR1/surf/**lh.sphere
 templates_freesurfer/lh.KKI_2.**tif subjects/OAS1_0061_MR1/surf/**
 lh.sphere_to_KKItemplate.reg
 using smoothwm curvature for final alignment
 $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
 reading surface from subjects/OAS1_0061_MR1/surf/**lh.sphere...
 TAGskip: tag=1717658469, failed to calloc 1868656640 bytes!
 Cannot allocate memory

 system information:

 FREESURFER_HOME: /usr/local/freesurfer
 Build stamp: freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0
 Debian version: wheezy/sid
 Kernel info: Linux 3.0.0-14-generic x86_64

 cheers,
 @rno

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Re: [Freesurfer] memory allocation error with mris_register

[Arno Klein]

dear doug,

sadly, no dice.

cheers,
@rno



On Fri, Jan 20, 2012 at 4:45 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 Try doing it in matlab, so
 a = MRIread('orig.mgz');
 MRIwrite(a,'orig.mgz');

 doug

 Arno Klein wrote:


 dear doug,

 i am using FS v5.1 now but ran the 20 oasis subjects through FS v5.0.  i
 am only having this trouble for one of the subjects.

 after the mri_convert workaround i am still getting the same memory
 allocation error.
 cheers,
 @rno



 On Fri, Jan 20, 2012 at 4:23 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
 wrote:

This is a strange problem we've been having with some mgz files
that were generated during a short period of time last summer when
there was a bug in the mgz writing code. What version of FS are
you using? In the current dev version, this should not be a
problem. A work-around is to convert the orig.mgz to itself using
mri_convert in the dev environment, ie,

mri_convert orig.mgz orig.mgz

doug

Arno Klein wrote:


i get the following memory allocation error for only one out
of 20 oasis subjects that i processed with freesurfer 5.1 on
an ubuntu 11.10 machine with 24gb memory:

mris_register -curv subjects/OAS1_0061_MR1/surf/**lh.sphere
templates_freesurfer/lh.KKI_2.**tif
subjects/OAS1_0061_MR1/surf/**lh.sphere_to_KKItemplate.reg
using smoothwm curvature for final alignment
$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
 $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
reading surface from subjects/OAS1_0061_MR1/surf/**lh.sphere...
TAGskip: tag=1717658469, failed to calloc 1868656640 bytes!
Cannot allocate memory

system information:

FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0
Debian version: wheezy/sid
Kernel info: Linux 3.0.0-14-generic x86_64

cheers,
@rno

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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
 
Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422
tel:617-726-7422

Bugs: 
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 --
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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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] memory allocation error with mris_register

[Arno Klein]

dear bruce,

you're right -- i am able to view the pial surface, but when i try to view
the spherical surface with tksurfer i get the same memory error.

is there any way to fix the sphere without affecting anything else?
 neuromorphometrics has painstakingly manually edited the freesurfer labels
generated for this subject and i don't want to introduce any alterations to
the meshes that they labeled.

cheers,
@rno


On Fri, Jan 20, 2012 at 5:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 can you load the lh.sphere in tksurfer? I'm not sure it is the mgz file
 that is the problem. Maybe your partition filled up and the sphere file
 isn't complete?
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