[Freesurfer] problem with gyrification index extraction

[elisa veronese]

Dear FreeSurfers,

I'm facing a problem with the estimation of local gyrification index. I've
already performed the analysis with QDEC and the insertion of the MEASURE1
= pial_lgi line in the .Qdecrc file, but I'd like to see if it is possible
to use the *aparcstats2table *command in order to have more concise and
easy-to-read results.

>From the QDEC GUI I've drawn a label in the temporal pole, and applied it
to all my subjects (*mris_anatomical_stats -l rh.MR_TmpPole.label -t
rh.pial_lgi -b -f s1/stats/rh.MR_TmpPole.stats s1 rh*)

The problem is that when I call the
*aparcstats2table --hemi rh --subjects s1 s2 ... --parc MR_TmpPole -t
GI_MR_TmpPole.txt*

I get a .txt file like this:

rh.MR_TmpPole.area rh_rh.MR_TmpPole.label_area rh_WhiteSurfArea_area
s1  6623.0 96171.8
s2  6257.0 85247.3
...

but I'm not sure what those numbers stand for. I'm afraid they have nothing
to do with the gyrification index.

Thank you,

best

elisa


-- 
Elisa Veronese - PhD

*Research Unit on Brain Imaging and Neuropsychology (RUBIN)*


*Inter-University Center for Behavioral Neurosciences (ICBN)University of
Udine and University of Verona, ItalyICBN
Website: http://icbn.uniud.it/tiki-index.php
*
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Re: [Freesurfer] Talairach transformation

[Bruce Fischl]

Hi Roberta

we compute but do not apply the talairach transform, so all the volumes, 
surfaces, ROIs are in subject space, not talairach.


cheers
Bruce
On Mon, 13 Oct 2014, 
Roberta Santoro wrote:




Dear list,

 

I am new to Freesurfer and I have a doubt about the Talairach
transformation. As far I understand, the Talairach transformation is applied
to compute the surface representations. However, this seems to be a “hidden“
step, i.e. no volume is saved as Talairach transformed. Is this correct? Do
the final surfaces (and parcellations) show the brain before or after
Talairach transformation? I am asking this because I need to extract ROIs in
the original space, i.e. before Talairach transform.  

 

Thanks a lot for your help

 

Roberta


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[Freesurfer] Talairach transformation

[Roberta Santoro]

Dear list,

I am new to Freesurfer and I have a doubt about the Talairach transformation. 
As far I understand, the Talairach transformation is applied to compute the 
surface representations. However, this seems to be a “hidden“ step, i.e. no 
volume is saved as Talairach transformed. Is this correct? Do the final 
surfaces (and parcellations) show the brain before or after Talairach 
transformation? I am asking this because I need to extract ROIs in the original 
space, i.e. before Talairach transform.

Thanks a lot for your help

Roberta
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[Freesurfer] ICV for adolescent and young adult in longitudinal stream

[Knut J Bjuland]

Dear FreeSurfer export,

I have used the longitudinal stream in FreeSurfer. However, when I 
extracted the ICV for adolescents and young adult, I get the same number 
for those subjects that are present at two-time points.  Will 
registration to a common space cause the change in ICV? Can this change 
explain why the icv is equal at 15 and 19 years of age for all my 
subjects with two-time points?


Best regards,

Knut Jørgen Bjuland
PhD candidate
NTNU
Trondheim



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[Freesurfer] tracula failure

[Alena Piovar]

Dear freesurfer experts,
I am trying to run tracula but it fails on mri conversion of the data, it
creates the nifty files from dicoms, but fails to produce bvec file where
the problem could be?
The terminal info as well as configuration file used for preprocessing is
attached.
Looking forward to your answer
best regards
Alena


terminal_tracula_info.rtf
Description: RTF file


config_file
Description: Binary data
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Re: [Freesurfer] v5.1 control point mri_ca_normalize bug

[Marx, Gabe]

Thank you for your help!

So you are suggesting that after we insert the patch we run "-autorecon2 
-autorecon3 -clean-aseg" on all of the subjects who were previously run with 
the -nocanorm flag? How will this affect the edits previously made on them?

Thank you,
Gabe

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky, MGH
Sent: Sunday, October 12, 2014 12:14 PM
To: Bruce Fischl
Cc: Freesurfer support list
Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug

correct (the thing to do is comment-out the addition of the control points).

n.

On Wed, 2014-10-08 at 17:05 -0400, Bruce Fischl wrote:
> I don't think you want to run with -nocanorm. Just commenting out the 
> addition of the  -f $ControlPointsFile should be sufficient. Right Nick?
> On
> Wed, 8 Oct 2014, Marx, Gabe wrote:
> 
> > Hi Bruce,
> >
> > I appreciate the response!
> >
> > I am sorry, I am a bit confused. The release notes state:
> >
> > "An option is to disable the running of mri_ca_normalize when re-running 
> > the -autorecon2 or -autorecon2-cp stage after adding control points by 
> > adding the flag -nocanorm to the end of recon-all. We will continue to 
> > investigate a more automated solution to detection of this problem. The 
> > more permanent workaround for v5.1 users is to edit their recon-all script 
> > making the following change, which will disable usage of control points 
> > with ca_norm:
> >
> > # find these lines:
> > set cmd = (mri_ca_normalize)
> > if($UseControlPoints)  set cmd = ($cmd -f $ControlPointsFile)
> >
> > # and comment-out the second line like this:
> > set cmd = (mri_ca_normalize)
> > #if($UseControlPoints)  set cmd = ($cmd -f $ControlPointsFile)
> >
> > # then re-run your subjects with the flags: -autorecon2 -autorecon3 
> > -clean-aseg"
> >
> > Are you saying the -nocanorm flag will result in inaccurate data?
> >
> > Thanks!
> > Gabe
> >
> > -Original Message-
> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
> > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> > Fischl
> > Sent: Wednesday, October 08, 2014 8:12 AM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug
> >
> > Hi Gabe
> >
> > this wasn't really a bug per-se, just induced some behavior that people 
> > didn't like. You can't skip the mri_ca_normalize step or the aseg won't be 
> > accurate. The aseg patch I believe just starts autorecon2-cp after the aseg 
> > hs been created, but Nick or Zeke can correct me if I'm wrong.
> >
> > cheers
> > Bruce
> >
> >
> >
> > On Mon, 6 Oct 2014, Marx, Gabe wrote:
> >
> >>
> >> Hello Freesurfer experts,
> >>
> >>  
> >>
> >> I had a question regarding the v5.1 control point mri_ca_normalize 
> >> bug. I read the release notes and know that this bug can be worked 
> >> around by adding the –nocanorm flag to my recon-all however I have 
> >> become worried about the ramifications of skipping mri_ca_normalize in my 
> >> pipeline.
> >> Would someone be able to give me a better description as to what 
> >> mri_ca_normalize is doing and what I am sacrificing by taking it 
> >> out of my pipeline? Furthermore, in regards to the patch for the 
> >> recon-all script to fix this bug, what is the patch doing exactly?  
> >> If I had some data in which I used the –nocanorm flag and other 
> >> data in which I used the patch would I still be able to make valid 
> >> analysis if I merged them?
> >> Would there be significant inconsistencies?
> >>
> >>  
> >>
> >> Thanks!
> >>
> >>  
> >>
> >> Best,
> >>
> >> Gabe
> >>
> >>
> >>
> >
> > ___
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> >
> >
> >


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Re: [Freesurfer] Image normalization and pial/wm error

[Sneha Pandya]

Hi Bruce,

Sure, shall try to do that comparison and see if it works. Also would 
specifying image intensity in the expert option help in any case.

Thanks,
Sneha

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, October 10, 2014 3:01 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Image normalization and pial/wm error

I don't really know, sorry. You could to an inter- and intra-rater test
by editing some of the images twice
On Fri, 10 Oct 2014, Sneha Pandya wrote:

> Thanks again, yes that's what it looks like, but I just have one concern, if 
> I have to manually edit dura and wm in all the slices and in most of the 
> subjects, will it still give me reliable cortical thickness measure?
>
> Thanks,
> Sneha
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Friday, October 10, 2014 2:30 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Image normalization and pial/wm error
>
> Hi Sneha
>
> then I think manually editing is your best bet (sorry)
> Bruce
>
>
> On Fri, 10 Oct 2014, Sneha Pandya wrote:
>
>> Hi Bruce,
>>
>> Yes, there is a lot of dura. Unfortunately we do not have either flair or
>> T2 as a reference to remove dura. I tried running gcut to cut off dura,
>> it still won't help and I still had to manually edit whole volume to get
>> rid of it. If it helps I can send you orig.mgz, nu.mgz and brainmask.mgz
>> post graph cut to look at. However for other structures it is difficult
>> to tell about the accuracy because I feel contrast is a little poor.
>> Sequence of this subject is spgr with voxel size of
>> 1.01mm*1.35mm*1.5mm(sl. thk), with 26FOV. I even used cw256 flag to
>> restrict the field of view. So not really sure why is segmentation so
>> poor.
>>
>> Other subjects in this dataset has between 20 to 25FOV, and varying voxel
>> size from 0.93*1.25*1.5 to 1*1*2.
>>
>> Thanks,
>> Sneha
>> ___
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Friday, October 10, 2014 1:58 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Image normalization and pial/wm error
>>
>> Hi Sneha
>>
>> it looks like it is grabbing a bunch of dura. Do you happen to have a
>> hires T2 or flair image? If so, you can use that in recon-all
>> postprocessing to remove the dura. If not you can try using the graph
>> cuts skull stripping to get rid of some of it. I can't tell the accuracy
>> of the surfaces in other locations in the images. Other than dura is it
>> reasonably acurate?
>> cheers
>> Bruce
>>
>> On Fri, 10 Oct 2014, Sneha Pandya wrote:
>>
>>> Dear all,
>>>
>>> I am running recon-all on few SPGR T1s and few MPRAGE T1s. However most of
>>> my dataset, may it be SPGR or MPRAGE has some artifacts and poor wm/gm
>>> contrast. Have attached a screen shot of bad pial and wm error (going beyond
>>> dura). Even gcut did not do a good job of cutting of all the dura, and I had
>>> to manually edit voxels in all the slices. I feel even after that if I run
>>> recon-all, it will not give me any reliable cortical thickness measures.
>>>
>>> Can anyone please suggest me if I should still manually edit all other
>>> subjects for all the slices throughout the volume or exclude them from
>>> analysis?
>>>
>>> PS: attached image FOV is 260 and I used -cw256 flag to restrict FOV to 256.
>>> For other images FOV is within 256, but still there is lot of dura in the
>>> brainmask.
>>>
>>> Thanks,
>>> Sneha
>>>
>>>
>>>
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Re: [Freesurfer] Registering a parcellation from MNI_2mm space to subject native spac

[Zachary Greenberg]

Hi Bruce,

I'm chiming in because I've been having a similar issue with the method you
mention above. Though, my goal is just to move the surface rendering into
the subject's native space using tkregister2 and mri_surf2surf as suggested
here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

The problem I ran into is that the surface output from that procedure looks
fine overlaid on the subject's native T1 in freeview (even if the original
T1 was in LAS orientation). However, if I view the surface in any other
viewer (e.g., in matlab using surf() or tripatch()), the surface is flipped
left from right, and the frontal pole is facing down (what is usually
ventral). I'm assuming freeview applies some transformation to orient it
correctly, but I'm stumped there.

I was exchanging with Doug Greve about this and we couldn't figure it out.
Any advice you might have is much appreciated.

Thanks for your help!

-zack

On Sat, Oct 11, 2014 at 2:04 PM, Bruce Fischl 
wrote:

> Hi Marcelo
>
> you can use bbregister to register the surfaces to another volume, and
> mri_vol2surf to then map the volume onto the surface (or mri_vol2vol to
> apply the volume transform)
>
> cheers
> Bruce
> On Sat, 11 Oct 2014, Marcelo Mattar wrote:
>
> > Hello,
> > I'm new to Freesurfer, and I'm lost in something that I believe is very
> > basic. I have a parcellation of the brain in .nii format that is
> currently
> > in MNI space (2mm). I would like to move this parcellation to subject
> native
> > space, so that I can extract the BOLD timeseries from each region of the
> > parcellation.
> >
> > I understand that an option I have is to simply use FSL tools such as
> FLIRT
> > or FNIRT and move the parcellation file to subject space (using nearest
> > neighbor interpolation). However, given that I have reconstructed the
> > subject's anatomy to the surface space, I believe I can do a better job
> that
> > just an affine transformation.
> >
> > What should I do in this case?
> >
> > 1) Is there any freesurfer tool that would allow me to register a volume
> to
> > another volume, but aided by surface information?
> > 2) If so, what steps should I follow to extract BOLD timeseries for each
> > subject from the parcellation regions?
> >
> > Thank you very much,
> >
> > --
> > Marcelo Mattar
> > University of Pennsylvania
> >
> >
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Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis

[Emma Thompson]

Hi Anderson,
Thank you for your paper. I guess I am confused. I have analyzed my
structural data with qdec, specifically looking at a measure of cortical
thickness and volume. I'm considering looking at surface area as well but
was told it wasn't a very good measure using qdec, I have no other
information really. Could you speak to whether or not this measure is valid
in so far as one runs it using qdec?

Also, in your opinion, would it be redundant to look at surface area in
addition to measures of cortical thickness and cortical volume?

Thanks for your help and apologizes for my silly questions.

On Sun, Oct 12, 2014 at 3:00 PM, Anderson M. Winkler  wrote:

> Hi Donna,
>
> In that same paper we also comment on the differences between
> expansion/contraction and absolute areal measurements assessed at each face
> of the surface (i.e., facewise), which can, after interpolation, be
> converted to vertexwise to facilitate analysis using current tools (e.g.,
> mri_glmfit or qdec), without loss of areal quantities.
>
> All the best,
>
> Anderson
>
>
> On 11 October 2014 04:05, Donna Dierker  wrote:
>
>> Hi Emma,
>>
>> I might not be the only one who is unsure what you mean by a vertex-wise
>> cortical surface area measure.  Do you mean something like what is
>> illustrated in figures 2 and 3 here:
>>
>> http://www.pnas.org/content/107/29/13135.figures-only
>>
>> … which is similar, but not identical to the local gyrification index?
>>
>> If so, would you use this measure on surfaces before or after
>> registration to a target atlas?
>>
>> Donna
>>
>>
>> On Oct 10, 2014, at 4:19 PM, Emma Thompson  wrote:
>>
>> > Dear Freesurfers,
>> > I recently heard that there are several disadvantages to using a
>> measure of cortical surface area in Freesurfer, specifically due to
>> conducting a vertex-wise analysis. Can someone help me understand why a
>> measure of surface area using this approach might be flawed? Thanks!
>>
>>
>>
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[Freesurfer] Fwd: recon-all error

[Kate Riggall]

Hello,



I am using freesurfer for the first time, and I am having issues when I try
to run recon-all for my first subject.  My details are:



FREESURFER_HOME: /usr/local/freesurfer



Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0



Debian version: jessie/sid



Kernel info: Linux 3.13.0-37-generic i686



Subject name: Y03



Command line: fsuser@xubuntu-VirtualBox:~/host/Sprachlernen$ recon-all
 -all -subjid Y03



Error message: "recon-all exited with ERRORS at Fri Oct 10 02:42:23 EDT 2014
"



recon-all.log: attached.



I am running freesurfer within Virtual Box on a windows host, and my
subjects folder is in a shared folder



/home/fsuser/host



and is called



/home/fsuser/host/Sprachlernen/Subjects



I first mounted this shared folder by entering



sudo mount -t vboxsf Kate /home/fsuser/host



and then designated this as my subjects folder by entering



export  SUBJECTS_DIR=/home/fsuser/host/Sprachlernen/Subjects



I then created the subject data directory using



recon-all -i Y03_1 -i Y03_2 -subjid Y03



before running recon-all -all. Any assistance would be much appreciated.



Kind regards,



Kate Riggall


recon-all.log
Description: Binary data
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Re: [Freesurfer] Registering a parcellation from MNI_2mm space to subject native spac

[Bruce Fischl]

Hi Zack

there is a ras2vox transform in the surface file header that I believe 
freeview uses. I'll cc Ruopeng so he can confirm and give you details


cheers
Bruce
On 
Mon, 13 Oct 2014, Zachary Greenberg wrote:



Hi Bruce,
I'm chiming in because I've been having a similar issue with the method you 
mention above. Though, my goal is just to move the surface rendering into the 
subject's
native space using tkregister2 and mri_surf2surf as suggested here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

The problem I ran into is that the surface output from that procedure looks 
fine overlaid on the subject's native T1 in freeview (even if the original T1 
was in LAS
orientation). However, if I view the surface in any other viewer (e.g., in 
matlab using surf() or tripatch()), the surface is flipped left from right, and 
the frontal
pole is facing down (what is usually ventral). I'm assuming freeview applies 
some transformation to orient it correctly, but I'm stumped there. 

I was exchanging with Doug Greve about this and we couldn't figure it out. Any 
advice you might have is much appreciated.

Thanks for your help!

-zack

On Sat, Oct 11, 2014 at 2:04 PM, Bruce Fischl  
wrote:
  Hi Marcelo

  you can use bbregister to register the surfaces to another volume, and
  mri_vol2surf to then map the volume onto the surface (or mri_vol2vol to
  apply the volume transform)

  cheers
  Bruce
  On Sat, 11 Oct 2014, Marcelo Mattar wrote:

  > Hello,
  > I'm new to Freesurfer, and I'm lost in something that I believe is very
  > basic. I have a parcellation of the brain in .nii format that is 
currently
  > in MNI space (2mm). I would like to move this parcellation to subject 
native
  > space, so that I can extract the BOLD timeseries from each region of the
  > parcellation.
  >
  > I understand that an option I have is to simply use FSL tools such as 
FLIRT
  > or FNIRT and move the parcellation file to subject space (using nearest
  > neighbor interpolation). However, given that I have reconstructed the
  > subject's anatomy to the surface space, I believe I can do a better job 
that
  > just an affine transformation.
  >
  > What should I do in this case?
  >
  > 1) Is there any freesurfer tool that would allow me to register a 
volume to
  > another volume, but aided by surface information?
  > 2) If so, what steps should I follow to extract BOLD timeseries for each
  > subject from the parcellation regions?
  >
  > Thank you very much,
  >
  > --
  > Marcelo Mattar
  > University of Pennsylvania
  >
  >
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Re: [Freesurfer] Fwd: recon-all error

[Bruce Fischl]

Hi Kate

can you run:

cd /home/fsuser/host/Sprachlernen/Subjects/Y03/mri

mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz

and send us the full screen output?

thanks
Bruce



On Tue, 14 Oct 2014, Kate 
Riggall wrote:




Hello,

 

I am using freesurfer for the first time, and I am having issues when I try to 
run recon-all for my first subject.  My details are:

 

FREESURFER_HOME: /usr/local/freesurfer

 

Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0

 

Debian version: jessie/sid

 

Kernel info: Linux 3.13.0-37-generic i686

 

Subject name: Y03

 

Command line: fsuser@xubuntu-VirtualBox:~/host/Sprachlernen$ recon-all  -all 
-subjid Y03

 

Error message: "recon-all exited with ERRORS at Fri Oct 10 02:42:23 EDT 2014"

 

recon-all.log: attached.

 

I am running freesurfer within Virtual Box on a windows host, and my subjects 
folder is in a shared folder 

 

/home/fsuser/host 

 

and is called 

 

/home/fsuser/host/Sprachlernen/Subjects

 

I first mounted this shared folder by entering

 

sudo mount -t vboxsf Kate /home/fsuser/host

 

and then designated this as my subjects folder by entering

 

export  SUBJECTS_DIR=/home/fsuser/host/Sprachlernen/Subjects

 

I then created the subject data directory using 

 

recon-all -i Y03_1 -i Y03_2 -subjid Y03 

 

before running recon-all -all. Any assistance would be much appreciated.

 

Kind regards,

 

Kate Riggall



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Re: [Freesurfer] Fwd: recon-all error

[Kate Riggall]

Hi Bruce,

The output is as follows:

fsuser@xubuntu-VirtualBox:~$ cd
/home/fsuser/host/Sprachlernen/Subjects/Y03/mri
fsuser@xubuntu-VirtualBox:~/host/Sprachlernen/Subjects/Y03/mri$
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
orig.mgz --o orig_nu.mgz
/home/fsuser/host/Sprachlernen/Subjects/Y03/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o
orig_nu.mgz
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux xubuntu-VirtualBox 3.13.0-37-generic #64-Ubuntu SMP Mon Sep 22
21:30:01 UTC 2014 i686 i686 i686 GNU/Linux
Mon Oct 13 18:34:45 EDT 2014
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu)
on 2010-02-20 at 20:19:13
tmpdir is ./tmp.mri_nu_correct.mni.2131
/home/fsuser/host/Sprachlernen/Subjects/Y03/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2131/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2131/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 4.65661e-08, -5.82077e-08)
j_ras = (-1.40164e-07, -4.12911e-10, -1)
k_ras = (3.44589e-08, 1, 1.58252e-10)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.2131/nu0.mnc...


Iteration 1 Mon Oct 13 18:34:49 EDT 2014
nu_correct -clobber ./tmp.mri_nu_correct.mni.2131/nu0.mnc
./tmp.mri_nu_correct.mni.2131/nu1.mnc -tmpdir
./tmp.mri_nu_correct.mni.2131/0/ -iterations 1000 -distance 50
defined(@array) is deprecated at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639.
(Maybe you should just omit the defined()?)
[fsuser@xubuntu-VirtualBox:/home/fsuser/host/Sprachlernen/Subjects/Y03/mri/]
[2014-10-13 18:34:49] running:
  /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen
0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify
-b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir
./tmp.mri_nu_correct.mni.2131/0/ ./tmp.mri_nu_correct.mni.2131/nu0.mnc
./tmp.mri_nu_correct.mni.2131/nu1.imp

Assertion failed at line 827 in file templates/CachedArray.cc
nu_estimate_np_and_em: crashed while running volume_stats (termination
status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=256)
ERROR: nu_correct

Thanks for your help.

Kate

On Tue, Oct 14, 2014 at 8:29 AM, Bruce Fischl 
wrote:

> Hi Kate
>
> can you run:
>
> cd /home/fsuser/host/Sprachlernen/Subjects/Y03/mri
>
> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
> orig.mgz --o orig_nu.mgz
>
> and send us the full screen output?
>
> thanks
> Bruce
>
>
>
>
> On Tue, 14 Oct 2014, Kate Riggall wrote:
>
>
>> Hello,
>>
>>
>>
>> I am using freesurfer for the first time, and I am having issues when I
>> try to run recon-all for my first subject.  My details are:
>>
>>
>>
>> FREESURFER_HOME: /usr/local/freesurfer
>>
>>
>>
>> Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
>>
>>
>>
>> Debian version: jessie/sid
>>

[Freesurfer] Brainhack EDT - Boston Updates and Registration Details

[MCLAREN, Donald]

*October 18th and 19th, Boston*


*McGovern Institute for Brain Research @ MIT - *
*http://whereis.mit.edu/?go=46* 

*3rd floor Atrium *


*Doors will be locked, so we will have to let you in. If you are the door,
please call 4-3544 or (617-324-3544) or send a chat message here: *
*https://gitter.im/satra/brainhackEDT*




*BRAINHACK EDT - BOSTON NEWS/UPDATES:*

·  Siemens is providing funds to help host Brainhack EDT - Boston.

·  The Brainhack EDT - Boston organizing committee is excited to
announce that we will be providing lunch to attendees who register/confirm
their attendance and food choices by 6PM on October 15th (see instructions
below; http://goo.gl/tMfwa2).

·  The Brainhack EDT - Boston organizing committee is working on
organizing a group dinner (attendee pays) on Saturday night in Cambridge.

·  Amazon will provide credits for cloud computing ($100 per person)

·  NeuroElectrics will be bringing a couple of their wireless EEG
headsets for interested parties to hack on. Please check the column if you
are interested.

·  All attendees must confirm their registration by following the
registration instructions below.

*REGISTRATION DETAILS:*

With the generous support from Siemens, we will be providing lunch to
attendees of Brainhack Boston. In order to receive lunch, you must confirm
your registration (indicate YES/NO) and food choices by Noon on October 15th,
2014.


Please click here to register: http://goo.gl/tMfwa2


When you are registering please provide us with your lunch choices along
with whether or not you plan to attend the organized dinner on Saturday
Night (attendees pay for their own dinner). If you do not provide us with
your lunch choices, you will not get free lunch.

In addition, please indicate whether you are interested in working with/on
the Neuroelectrics headset.


*PROJECT PROPOSALS:*

We've heard rumors of several projects for Brainhack EDT - Boston. In order
to spread the word of these projects, we request that you add your
project(s) on the following page:

http://goo.gl/fSMgc3


Project proposal introductions will be 1 minute. If you want to use a slide
to introduce your project, please send the powerpoint slide to
mclaren.donal...@t-gmail.com


*BRAINHACK EDT - BOSTON SCEHDULE:*

*Saturday, October 18, 2014*

08:30   Attendee Arrival (with coffee)

09:00   Welcome reception

09:15   Ignite Talk with icebreaker

09:45   Project Pitch

10:00   Open Hacking

12:00  Onsite Lunch (Mexicali)

13:00  Crowd Annotation Projects (Dolphin Brain)

13:45   Unconference Session

15:00   Coffee Break

15:30  Open Hacking

18:30  Organized dinner (pay your own way)

20:30  Open Hacking



*Sunday, October 19, 2014*

08:30 Attendee Arrival

09:00   Ignite Session II

09:30   Unconference Session

10:30   Open Hacking

12:30   Onsite Lunch (Mexicali)

13:30   Open Hacking

15:00  Coffee Break

15:30   Open Hacking

17:00   Project Summaries and Wrap-up

18:30   Adjournment

19:00 Optional Dinner or Open Hacking

*The Boston Brainhack Committee*


Donald G McLaren, MGH/HMS

Satra Ghosh, MIT

Matt Hutchison, Harvard University
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