date:20121219

Re: [Freesurfer] recon-all: too many levels of symbolic links

2012-12-19 Thread Linda Zhang

Hi Bruce,

This is what I get:

FreeSurfer:~/freesurfer/lindadata> ls -l
drwxr-sr-x 42 virtualuser virtualuser 4096 2012-11-17 07:38 subjects
FreeSurfer:~/freesurfer/lindadata> ls /subjects/lh.EC_average/surf
ls: cannot access /subjects/lh.EC_average/surf: No such file or directory
FreeSurfer:~/freesurfer/lindadata> ls -l /subjects/lh.EC_average
lrwxrwxrwx 1 virtualuser virtualuser 51 2012-11-17 07:38
/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average ->
/home/virtualuser/freesurfer/subjects/lh.EC_average
FreeSurfer:~/freesurfer/lindadata> ls /home/virtualuser/freesurfer/subjects/
cvs_avg35  fsaverage  fsaverage3  fsaverage4  fsaverage5  fsaverage6
README  V1_average




On 19 December 2012 21:43, Bruce Fischl  wrote:

>  ls -1 $FREESURFER_HOME/subjects
> cvs_avg35/
> cvs_avg35_inMNI152/
> fsaverage/
> fsaverage3/
> fsaverage4/
> fsaverage5/
> fsaverage6/
> fsaverage_sym/
> lh.EC_average/
> README
> rh.EC_average/
> sample-001.mgz
> sample-002.mgz
> surfer.log
> V1_average/
>
> not sure why it thinks it doesn't exist. What are the permissions on
>
> /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average
>
> can you do an ls on
>
> /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average/surf
>
> and post the results? Also do:
>
> ls -l /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average
>
>
> On Wed, 19 Dec 2012, Linda Zhang wrote:
>
>  Dear all,
>>
>> I've run into the same error with recon-all -autorecon3.  It could be
>> that when I moved my data into the new SUBJECTS_DIR, I
>> missed something out.  What files should be in the
>> $FREESURFER_HOME/subjects directory?
>>
>> The error reads as follows:
>>
>> #@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012
>> INFO: lh.EC_average subject does not exist in SUBJECTS_DIR
>> INFO: Creating symlink to lh.EC_average subject...
>>
>>  cd /home/virtualuser/freesurfer/**lindadata/subjects; ln -s
>> /home/virtualuser/freesurfer/**subjects/lh.EC_average; cd -
>>
>> ln: creating symbolic link `./lh.EC_average': File exists
>>
>>  mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label
>> lh.entorhinal lh sphere.reg lh.EC_average
>> lh.entorhinal_exvivo.label
>>
>> painting output onto subject ncpoCCW.
>> processing subject lh.EC_average...
>> MRISread(/home/virtualuser/**freesurfer/lindadata/subjects/**
>> lh.EC_average/surf/lh.sphere.**reg): could not open file
>> eroding label 1 times before writing
>> thresholding label stat at 0.400 before writing
>> No such file or directory
>> mris_spherical_average: could not read surface file
>> /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**
>> average/surf/lh.sphere.reg
>> No such file or directory
>> Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC
>> 2011 i686 GNU/Linux
>>
>> recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012
>>
>> For more details, see the log file /home/virtualuser/freesurfer/**
>> lindadata/subjects/ncpoCCW/**scripts/recon-all.log
>> To report a problem, see http://surfer.nmr.mgh.harvard.**
>> edu/fswiki/BugReporting
>>
>>
>> Cheers,
>> Linda
>>
>>
>>
>> On 14 November 2012 22:29, Linda Zhang  wrote:
>>
>>   Thanks Bruce.  It has 6gb assigned to the virtualbox, I'm running
>> another process alongside it.  I'll stop the other
>>   one and try again.
>>
>>   On 14 Nov 2012 22:14, "Bruce Fischl" 
>> wrote:
>> sounds like you are running out of memory. How much ram is in
>> that machine? Are other processes running
>> at the same time?
>> On Wed, 14 Nov 2012, Linda Zhang wrote:
>>
>>   Dear all,
>>   After moving my data to a different folder, I've come
>> across a different error when running
>>   recon-all (autorecon2 and 3).  The
>>   last few lines are as follows:
>>
>>   0117: dt=32.368000, rms=0.713 (0.122%), neg=0,
>> invalid=766
>>   0118: dt=32.368000, rms=0.713 (0.033%), neg=0,
>> invalid=766
>>   0119: dt=32.368000, rms=0.712 (0.059%), neg=0,
>> invalid=766
>>   0120: dt=32.368000, rms=0.712 (0.081%), neg=0,
>> invalid=766
>>   0121: dt=16.184000, rms=0.712 (0.009%), neg=0,
>> invalid=766
>>   Killed
>>   ERROR: mri_ca_register with non-zero status 137
>>   but continuing despite the error
>>   #-**-
>>   #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012
>>   /home/virtualuser/freesurfer/**
>> lindadata/subjects/ncvoCYJ/mri
>>
>>mri_ca_register -invert-and-save
>> transforms/talairach.m3z
>>
>>   Loading, Inverting, Saving, Exiting ...
>>   Reading transforms/talairach.m3z
>>   ERROR: cannot find or read transforms/talairach.m3z
>>

Re: [Freesurfer] "nu_estimate_np_and_em" error during recon-all

2012-12-19 Thread Douglas Greve

Hi Tudor, I don't know how to solve this problem. Maybe Nick knows.
doug

On 12/19/12 6:59 AM, Tudor Popescu wrote:
Hi Doug, thanks for replying, here is the file attached. In case the 
attachment doesn't go through  please let me know if I should send it 
to a different address.

Tudor

On 18 December 2012 17:34, Douglas N Greve > wrote:

Can you send the recon-all.log file (located in the
subject/scripts folder).
doug

On 12/18/2012 11:41 AM, Tudor Popescu wrote:
> Hello,
>
> First of all, apologies for asking for help three times today!
THings
> will hopefully become clearer once I get used to FS a bit; I
really do
> appreciate the amazing support provided by the team behind
FreeSurfer!
>
> I ran the following command on one of my structurals:
>
> /recon-all -subject M01 -i M01.nii.gz -all/
>
> After a few minutes, recon-all ended with the following message:
>
> /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/
> /Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17
01:57:59
> UTC 2009 i686 GNU/Linux/
>
> I apologise for reporting an error that's already been reported
in the
> past, but unfortunately the solutions suggested in those past
threads
> did not work in my case. To address a few of them:
>
>   * my PATH (listed below) does not seem to include two MNI
installations
>

//home/virtualuser/freesurfer/bin:/home/virtualuser/freesurfer/fsfast/bin:/home/virtualuser/freesurfer/tktools:/home/virtualuser/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games/
>   * the version of FreeSurfer that I installed is the latest disk
> image available on the website
> (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full) - I did
> not see any dev version that would presumably include any
missing
> libraries presumably implied by the above error
>   * I tried updating the Xubuntu inside my VirtualBox, however it
> reports an insufficient space problem that from I can see
does not
> have a trivial fix
>
> Advance thanks for any help!
> Tudor
>
>
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--
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/BugReporting

FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] L-R Volume Flipping

2012-12-19 Thread Douglas Greve


Oh, right, that can be a problem. In 5.2, I've changed it to use nii by 
default. This breaks when spm2 is used, but then the user can spec to 
use img instead.
doug



On 12/19/12 5:38 PM, MCLAREN, Donald wrote:
> When we added the --spm-nii option, the problem disappears. The
> following thread is also relevant:
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017981.html
>
>
> On Tue, Dec 18, 2012 at 8:26 PM, MCLAREN, Donald
>  wrote:
>> Thanks, that's what I thought might be happening. I'll check a few
>> different programs to see if I can recover the correct orientation. If
>> we need to reverse the images, would you recommend doing it before or
>> after the bbregister step? Would it be sufficient just to change the
>> header of the image or do we need to physically change the data?
>>
>> 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
>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
>> intended only for the use of the individual or entity named above. If the
>> reader of the e-mail is not the intended recipient or the employee or agent
>> responsible for delivering it to the intended recipient, you are hereby
>> notified that you are in possession of confidential and privileged
>> information. Any unauthorized use, disclosure, copying or the taking of any
>> action in reliance on the contents of this information is strictly
>> prohibited and may be unlawful. If you have received this e-mail
>> unintentionally, please immediately notify the sender via telephone at (773)
>> 406-2464 or email.
>>
>>
>> On Tue, Dec 18, 2012 at 11:20 PM, Douglas Greve
>>  wrote:
>>> Hi Donald, it might be the case. If the fmri has an ordering such that the
>>> columns increase as you go from left to right, then they will have to be
>>> reversed when you map them to the orig.mgz. This is generally not a problem
>>> because we always keep track of which side is left and right. If you are
>>> using a visualization tool that does not read in and act on the geometry,
>>> then things can appear to flip around.
>>>
>>> doug
>>>
>>>
>>>
>>> On 12/18/12 8:47 PM, MCLAREN, Donald wrote:
>>>
>>> Dear All,
>>>
>>> I've noticed something strange with some data I'm helping to process:
>>>
>>> When looking at the L/R asymmetry in the brains (attached), the images
>>> seem to flip after bbregister/mri_vol2vol. The exact commands:
>>> bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2
>>> mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg
>>> register.dat --no-resample --o transformed_fMRI.nii
>>>
>>> I've attached a document that shows the flipping. You'll notice the
>>> highest point of the ventricle flips sides after
>>> bbregister/mri_vol2vol. Any thoughts on what is going on would be
>>> appreciated.
>>>
>>> The contents of register.dat are as follows:
>>> FS_D011
>>> 3.00
>>> 3.54
>>> 0.15
>>> -9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02
>>> 1.619825601577759e+00
>>> 6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01
>>> -1.230294322967529e+01
>>> 4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01
>>> -1.072110843658447e+01
>>> 0 0 0 1
>>> round
>>>
>>>
>>> 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
>>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
>>> intended only for the use of the individual or entity named above. If the
>>> reader of the e-mail is not the intended recipient or the employee or agent
>>> responsible for delivering it to the intended recipient, you are hereby
>>> notified that you are in possession of confidential and privileged
>>> information. Any unauthorized use, disclosure, copying or the taking of any
>>> action in reliance on the contents of this information is strictly
>>> prohibited and may be unlawful. If you have received this e-mail
>>> unintentionally, please immediately notify the sender via telephone at (773)
>>> 406-2464 or email.
>>>
>>>
>>>
>>> ___
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>>>
>>>
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>>> Frees

[Freesurfer] Diffusion Tensor Imaging

2012-12-19 Thread Yaniv Kaufman

Dear Freesurfers, 

I am not very experienced with Freesurfer and would like to construct a 
Diffusion Tensor Image. I have the .bvecs, .bvals and .img files which I 
believe should suffice. I am aware that the format is slightly old but I 
believe it should still be fine. I attempted to use dt_recon and freeview but 
could not quite get the results I anticipated. I would really appreciate any 
help.

Many thanks in advance, 
Yaniv
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Re: [Freesurfer] tracula - posterior density just one-dimensional curve

2012-12-19 Thread Anastasia Yendiki



Hi Andi - I managed to track this down by looking at the complete data set 
that you sent me. Your bvals file has no b=0, there's only b=2075 with 
some b=5 interspersed. The b=5 volumes must be your baseline volumes but 
unfortunately there's no way for the program to know this right now.


As a hack for now I'd just set the 5's to 0's in dmri/bvals and rerun the 
path reconstruction step, it should be a fine approximation for that step. 
I'll add support to this for the next version.


Sorry about that!
a.y

On Tue, 30 Oct 2012, Andi Heckel wrote:


Dear Tracula team,

I have noticed in a  multisubject tracula analysis, that the posterior density 
in many if not
all paths in the path.pd.nii.gz file is just a bright one-dimensional curve, 
rather than a
true distribution.
The path.map.nii.gz is empty. This is true for both flirt and bbreg registered 
versions in
many subjects.
Trac-all finished wiithout errors. So did Recon-all.

Could it actually be a memory (RAM) problem ? We are running tracula on a 
cluster with only
2.5 GB per core.

thx for any help and kind regards,
andi




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Re: [Freesurfer] L-R Volume Flipping

2012-12-19 Thread MCLAREN, Donald

When we added the --spm-nii option, the problem disappears. The
following thread is also relevant:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017981.html


On Tue, Dec 18, 2012 at 8:26 PM, MCLAREN, Donald
 wrote:
> Thanks, that's what I thought might be happening. I'll check a few
> different programs to see if I can recover the correct orientation. If
> we need to reverse the images, would you recommend doing it before or
> after the bbregister step? Would it be sufficient just to change the
> header of the image or do we need to physically change the data?
>
> 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
> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
> intended only for the use of the individual or entity named above. If the
> reader of the e-mail is not the intended recipient or the employee or agent
> responsible for delivering it to the intended recipient, you are hereby
> notified that you are in possession of confidential and privileged
> information. Any unauthorized use, disclosure, copying or the taking of any
> action in reliance on the contents of this information is strictly
> prohibited and may be unlawful. If you have received this e-mail
> unintentionally, please immediately notify the sender via telephone at (773)
> 406-2464 or email.
>
>
> On Tue, Dec 18, 2012 at 11:20 PM, Douglas Greve
>  wrote:
>> Hi Donald, it might be the case. If the fmri has an ordering such that the
>> columns increase as you go from left to right, then they will have to be
>> reversed when you map them to the orig.mgz. This is generally not a problem
>> because we always keep track of which side is left and right. If you are
>> using a visualization tool that does not read in and act on the geometry,
>> then things can appear to flip around.
>>
>> doug
>>
>>
>>
>> On 12/18/12 8:47 PM, MCLAREN, Donald wrote:
>>
>> Dear All,
>>
>> I've noticed something strange with some data I'm helping to process:
>>
>> When looking at the L/R asymmetry in the brains (attached), the images
>> seem to flip after bbregister/mri_vol2vol. The exact commands:
>> bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2
>> mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg
>> register.dat --no-resample --o transformed_fMRI.nii
>>
>> I've attached a document that shows the flipping. You'll notice the
>> highest point of the ventricle flips sides after
>> bbregister/mri_vol2vol. Any thoughts on what is going on would be
>> appreciated.
>>
>> The contents of register.dat are as follows:
>> FS_D011
>> 3.00
>> 3.54
>> 0.15
>> -9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02
>> 1.619825601577759e+00
>> 6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01
>> -1.230294322967529e+01
>> 4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01
>> -1.072110843658447e+01
>> 0 0 0 1
>> round
>>
>>
>> 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
>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
>> intended only for the use of the individual or entity named above. If the
>> reader of the e-mail is not the intended recipient or the employee or agent
>> responsible for delivering it to the intended recipient, you are hereby
>> notified that you are in possession of confidential and privileged
>> information. Any unauthorized use, disclosure, copying or the taking of any
>> action in reliance on the contents of this information is strictly
>> prohibited and may be unlawful. If you have received this e-mail
>> unintentionally, please immediately notify the sender via telephone at (773)
>> 406-2464 or email.
>>
>>
>>
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>>
>>
>>
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Re: [Freesurfer] space of T1.mgz

2012-12-19 Thread Mojdeh Zamyadi

Hi there,

Sorry, if my question is confusing. This is what I want to do, I have
two groups of controls and patients and I've already run recon-all on
them. I now want to know the head/body/tail volumes. What I did was:
1. used "mri_binarize" to get the right and left hippocampal masks from
the cortical segmentation (using label numbers 17, 53)
2. used "mri_convert" to convert left_hippo.mgz, right_hippo.mgz and
T1.mgz into .nii files.
3. use itk SNAP to manually segment the total hippocampus (the
freesurfer mask) into head, body and tail.

now, my questions is regarding the last step. If the individual
segmentations are in the native space, I can't be sure that the
landmarks I'm using for head/body/tail separation is always the same
(since some of the subjects might be in an oblique space). So would you
recommend that I first register the T1 and segmentations all into a
common space? Also, I was wondering if the segmentation is going to
effect the actual volume (since the brain is going to be stretched and
transformed while doing the registration). I hope I made my question
clear and I would greatly appreciate your advice.

Thanks,
-Mojdeh

On 12/18/2012 12:58 PM, Bruce Fischl wrote:
>  Hi Mojdeh
>
>  they are not in atlas space and the volumes are for that subject, so
>  you shouldn't have to do anything if I understand you correctly
>
>  cheers
>  Bruce
>
>  On Tue, 18 Dec 2012, Mojdeh Zamyadi wrote:
>
>>  Hi Doug,
>>
>>  Thanks for the quick reply. I actually saw this link before first
>>  posting my question but it doesn't quite answer my question. What I want
>>  to know is whether the T1.mgz&  aseg.mgz files are in an atlas space? if
>>  that's the case, it means the segmentation for all my subjects are in
>>  the same space and I don't need to convert anything if I want to compare
>>  their hippocampal volumes. I'm not quite sure if any sort of
>>  registration to an atlas is done in any steps of recon-all or not. I
>>  would appreciate if could clarify this for me.
>>
>>  Thanks,
>>  -Mojdeh
>>
>>  On 12/18/2012 12:18 PM, Douglas N Greve wrote:
>>>  Hi Mojdeh, try looking at this doc
>>>  http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
>>>  doug
>>>
>>>  On 12/18/2012 11:09 AM, Mojdeh Zamyadi wrote:
  Hi all,

  I want to segment the hippocampus into head/body/tail in itk SNAP
  using
  the hippocampus mask that I create from the result of recon-all
  segmentation. My question is, are the T1.mgz and aseg.mgz files in the
  native space of the image or in the atlas space? I know the voxel size
  is different (1x1x1 mm) from the original voxel size (0.49x0.49x0.45),
  but I want to know if the original images are registered to a common
  atlas space or just resampled to a different voxel size. The reason
  I'm
  asking this, is because I'm doing a group study and I want to make
  sure
  all my subjects are in the same space so that the segmentation I do is
  accurate for all.

  Thanks for your help,

  Mojdeh Zamyadi, MSc
  Clinical Research Project Assistant
  The Hospital for Sick Children
  555 University Avenue
  Toronto ON M5G 1X8

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>>
>>  ___
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>>
>>
>>
>
>
>  The information in this e-mail is intended only for the person to whom
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Re: [Freesurfer] recon-all: too many levels of symbolic links

2012-12-19 Thread Bruce Fischl


 ls -1 $FREESURFER_HOME/subjects
cvs_avg35/
cvs_avg35_inMNI152/
fsaverage/
fsaverage3/
fsaverage4/
fsaverage5/
fsaverage6/
fsaverage_sym/
lh.EC_average/
README
rh.EC_average/
sample-001.mgz
sample-002.mgz
surfer.log
V1_average/

not sure why it thinks it doesn't exist. What are the permissions on

/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average

can you do an ls on

/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf

and post the results? Also do:

ls -l /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average

On Wed, 19 Dec 2012, Linda Zhang wrote:


Dear all,

I've run into the same error with recon-all -autorecon3.  It could be that when 
I moved my data into the new SUBJECTS_DIR, I
missed something out.  What files should be in the $FREESURFER_HOME/subjects 
directory?

The error reads as follows:

#@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012
INFO: lh.EC_average subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to lh.EC_average subject...

 cd /home/virtualuser/freesurfer/lindadata/subjects; ln -s 
/home/virtualuser/freesurfer/subjects/lh.EC_average; cd -

ln: creating symbolic link `./lh.EC_average': File exists

 mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label 
lh.entorhinal lh sphere.reg lh.EC_average
lh.entorhinal_exvivo.label

painting output onto subject ncpoCCW.
processing subject lh.EC_average...
MRISread(/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg):
 could not open file
eroding label 1 times before writing
thresholding label stat at 0.400 before writing
No such file or directory
mris_spherical_average: could not read surface file
/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg
No such file or directory
Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 
i686 GNU/Linux

recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012

For more details, see the log file 
/home/virtualuser/freesurfer/lindadata/subjects/ncpoCCW/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Cheers,
Linda



On 14 November 2012 22:29, Linda Zhang  wrote:

  Thanks Bruce.  It has 6gb assigned to the virtualbox, I'm running another 
process alongside it.  I'll stop the other
  one and try again.

  On 14 Nov 2012 22:14, "Bruce Fischl"  wrote:
sounds like you are running out of memory. How much ram is in that 
machine? Are other processes running
at the same time?
On Wed, 14 Nov 2012, Linda Zhang wrote:

  Dear all,
  After moving my data to a different folder, I've come across 
a different error when running
  recon-all (autorecon2 and 3).  The
  last few lines are as follows:

  0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766
  0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766
  0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766
  0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766
  0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766
  Killed
  ERROR: mri_ca_register with non-zero status 137
  but continuing despite the error
  #--
  #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012
  /home/virtualuser/freesurfer/lindadata/subjects/ncvoCYJ/mri

   mri_ca_register -invert-and-save transforms/talairach.m3z 

  Loading, Inverting, Saving, Exiting ...
  Reading transforms/talairach.m3z 
  ERROR: cannot find or read transforms/talairach.m3z
  ERROR: mri_ca_register with non-zero status 0
  Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 
18:08:39 UTC 2011 i686
  GNU/Linux

  recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 14 
15:47:38 HKT 2012


  Another set is exiting simply with:

  #@# EM Registration Mon Nov 12 17:43:05 HKT 2012
  /home/virtualuser/freesurfer/lindadata/subjects/ncvoLML/mri

   mri_em_register -uns 3 -mask brainmask.mgz nu.mgz
  /home/virtualuser/freesurfer/average/RB_all_2008-03-26.gca
  transforms/talairach.lta 

  Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 
18:08:39 UTC 2011 i686
  GNU/Linux

  recon-all -s ncvoLML exited with ERRORS at Mon Nov 12 
17:43:06 HKT 2012

  To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



  What's the problem I should be addressing?

  Thanks!

  Cheers,

Re: [Freesurfer] mri_cc segfault

2012-12-19 Thread Pedro Paulo de Magalhães Oliveira Junior

Bruce found that the data had the direction cosine wrong.

I have fixed the direction and I'm running it again.

I've put the data in the ftp

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




On Tue, Dec 18, 2012 at 8:41 PM, Nick Schmansky
wrote:

> PPJ,
>
> Hi, if you want, you can send me the input files (the two aseg's and the
> lta) and i can try to replicate the segfault in a debugger.
>
> also, if you want, there is a beta of the upcoming v5.2 which is posted
> here:
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
> which you could try.  hopefully that mri_cc doesnt segfault.
>
> Nick
>
>
>
> On Tue, 2012-12-18 at 12:46 -0200, Pedro Paulo de Magalhães Oliveira
> Junior wrote:
> > I'm having a segfault with mri_cc it's happening sometimes using
> > FreeSurfer 5.1
> >
> >
> > Searching the mailing list I saw a similar problem in 2008 but with no
> > answers.
> >
> >
> > The relevant portion of recon-all.log:
> >
> >
> >  mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz
> > -lta
> /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta
> c70eb728-c505-46c2-a2a1-1ed409c36ea1
> >
> >
> > will read input aseg from aseg.auto_noCCseg.mgz
> > writing aseg with cc labels to aseg.auto.mgz
> > will write lta
> > as
> /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta
> > reading aseg
> > from
> /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/aseg.auto_noCCseg.mgz
> > reading norm
> > from
> /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/norm.mgz
> > 2358 voxels in left wm, 13846 in right wm, xrange [122, 136]
> > searching rotation angles z=[-10  4], y=[-31 -17]
> > ^Msearching scale 1 Z rot -9.8  ^Msearching scale 1 Z rot -9.5
> >  ^Msearching scale 1 Z rot -9.3  ^Msearching scale 1 Z rot -9.0
> >  ^Msearching scale 1 Z rot -8.8  ^Msearching scale 1 Z rot -8.5
> >  ^Msearching scale 1 Z rot -8.3  ^Msearching scale 1 Z rot -8.0
> >  ^Msearching scale 1 Z rot -7.8  ^Msearching scale 1 Z rot -7.5
> >  ^Msearching scale 1 Z rot -7.3  ^Msearching scale 1 Z rot -7.0
> >  ^Msearching scale 1 Z rot -6.8  ^Msearching scale 1 Z rot -6.5
> >  ^Msearching scale 1 Z rot -6.3  ^Msearching scale 1 Z rot -6.0
> >  ^Msearching scale 1 Z rot -5.8  ^Msearching scale 1 Z rot -5.5
> >  ^Msearching scale 1 Z rot -5.3  ^Msearching scale 1 Z rot -5.0
> >  ^Msearching scale 1 Z rot -4.8  ^Msearching scale 1 Z rot -4.5
> >  ^Msearching scale 1 Z rot -4.3  ^Msearching scale 1 Z rot -4.0
> >  ^Msearching scale 1 Z rot -3.8  ^Msearching scale 1 Z rot -3.5
> >  ^Msearching scale 1 Z rot -3.3  ^Msearching scale 1 Z rot -3.0
> >  ^Msearching scale 1 Z rot -2.8  ^Msearching scale 1 Z rot -2.5
> >  ^Msearching scale 1 Z rot -2.3  ^Msearching scale 1 Z rot -2.0
> >  ^Msearching scale 1 Z rot -1.8
> > ^Msearching scale 1 Z rot -1.5  ^Msearching scale 1 Z rot -1.3
> >  ^Msearching scale 1 Z rot -1.0  ^Msearching scale 1 Z rot -0.8
> >  ^Msearching scale 1 Z rot -0.5  ^Msearching scale 1 Z rot -0.3
> >  ^Msearching scale 1 Z rot -0.0  ^Msearching scale 1 Z rot 0.2
> >  ^Msearching scale 1 Z rot 0.5  ^Msearching scale 1 Z rot 0.7
> >  ^Msearching scale 1 Z rot 1.0  ^Msearching scale 1 Z rot 1.2
> >  ^Msearching scale 1 Z rot 1.5  ^Msearching scale 1 Z rot 1.7
> >  ^Msearching scale 1 Z rot 2.0  ^Msearching scale 1 Z rot 2.2
> >  ^Msearching scale 1 Z rot 2.5  ^Msearching scale 1 Z rot 2.7
> >  ^Msearching scale 1 Z rot 3.0  ^Msearching scale 1 Z rot 3.2
> >  ^Msearching scale 1 Z rot 3.5  ^Msearching scale 1 Z rot 3.7  global
> > minimum found at slice 129.0, rotations (-2.52, -3.27)
> > final transformation (x=129.0, yr=-2.521, zr=-3.273):
> >  0.997   0.057  -0.044  -2.975;
> > -0.057   0.998   0.003  -6.742;
> >  0.044  -0.000   0.999  -9.547;
> >  0.000   0.000   0.000   1.000;
> > Segmentation fault
> >
> >
> > Thanks
> >
> >
> > PPJ
> > -
> > Pedro Paulo de Magalhães Oliveira Junior
> > Netfilter & SpeedComm Telecom
> > -- www.netfilter.com.br
> > -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the

[Freesurfer] new atlas

2012-12-19 Thread Gabriel Gonzalez Escamilla

Dear Freesurfers,Sorry for so many and basic questions lately.I'm working with my set of subjects (T1), and I'm looking for a different WM parcellation than the aseg.mgz, I have an atlas (JHU atlas in MNI space, Mori et al 1999, and some other in Colin27 space).I'm guessing I will have to use the FSaverage subject as target space. Since FS has many algorithms to make registrations, and the mris_ca_train requieres the predefined labels into an anootation file. I'm wondering about the best way to translate all the WM labeling from this atlas into FS space. Many thanks in advanced,Gabriel
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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
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.

Re: [Freesurfer] recon-all: too many levels of symbolic links

2012-12-19 Thread Linda Zhang

Dear all,

I've run into the same error with recon-all -autorecon3.  It could be that
when I moved my data into the new SUBJECTS_DIR, I missed something out.
What files should be in the $FREESURFER_HOME/subjects directory?

The error reads as follows:

#@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012
INFO: lh.EC_average subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to lh.EC_average subject...

 cd /home/virtualuser/freesurfer/lindadata/subjects; ln -s
/home/virtualuser/freesurfer/subjects/lh.EC_average; cd -

ln: creating symbolic link `./lh.EC_average': File exists

 mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label
lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label

painting output onto subject ncpoCCW.
processing subject lh.EC_average...
MRISread(/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg):
could not open file
eroding label 1 times before writing
thresholding label stat at 0.400 before writing
No such file or directory
mris_spherical_average: could not read surface file
/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg
No such file or directory
Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC
2011 i686 GNU/Linux

recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012

For more details, see the log file
/home/virtualuser/freesurfer/lindadata/subjects/ncpoCCW/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Cheers,
Linda



On 14 November 2012 22:29, Linda Zhang  wrote:

> Thanks Bruce.  It has 6gb assigned to the virtualbox, I'm running another
> process alongside it.  I'll stop the other one and try again.
>
>  On 14 Nov 2012 22:14, "Bruce Fischl"  wrote:
>
>> sounds like you are running out of memory. How much ram is in that
>> machine? Are other processes running at the same time?
>> On Wed, 14 Nov 2012, Linda Zhang wrote:
>>
>>  Dear all,
>>> After moving my data to a different folder, I've come across a different
>>> error when running recon-all (autorecon2 and 3).  The
>>> last few lines are as follows:
>>>
>>> 0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766
>>> 0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766
>>> 0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766
>>> 0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766
>>> 0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766
>>> Killed
>>> ERROR: mri_ca_register with non-zero status 137
>>> but continuing despite the error
>>> #-**-
>>> #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012
>>> /home/virtualuser/freesurfer/**lindadata/subjects/ncvoCYJ/mri
>>>
>>>  mri_ca_register -invert-and-save transforms/talairach.m3z
>>>
>>> Loading, Inverting, Saving, Exiting ...
>>> Reading transforms/talairach.m3z
>>> ERROR: cannot find or read transforms/talairach.m3z
>>> ERROR: mri_ca_register with non-zero status 0
>>> Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39
>>> UTC 2011 i686 GNU/Linux
>>>
>>> recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 14 15:47:38 HKT 2012
>>>
>>>
>>> Another set is exiting simply with:
>>>
>>> #@# EM Registration Mon Nov 12 17:43:05 HKT 2012
>>> /home/virtualuser/freesurfer/**lindadata/subjects/ncvoLML/mri
>>>
>>>  mri_em_register -uns 3 -mask brainmask.mgz nu.mgz
>>> /home/virtualuser/freesurfer/**average/RB_all_2008-03-26.gca
>>> transforms/talairach.lta
>>>
>>> Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39
>>> UTC 2011 i686 GNU/Linux
>>>
>>> recon-all -s ncvoLML exited with ERRORS at Mon Nov 12 17:43:06 HKT 2012
>>>
>>> To report a problem, see http://surfer.nmr.mgh.harvard.**
>>> edu/fswiki/BugReporting
>>>
>>>
>>>
>>> What's the problem I should be addressing?
>>>
>>> Thanks!
>>>
>>> Cheers,
>>> Linda
>>>
>>>
>>>
>>> On 2 November 2012 21:40, Bruce Fischl 
>>> wrote:
>>>   Hi Linda
>>>
>>>   it sounds like you put your own subjects into the directory
>>> $FREESURFER_HOME/subjects, which is where we store our
>>>   average data and symlink within your SUBJECTS_DIR. Try putting
>>> them somewhere else
>>>
>>>   cheers
>>>   Bruce
>>>
>>>
>>>   On Fri, 2 Nov 2012, Linda Zhang wrote:
>>>
>>> Dear all,
>>> I've been running recon-all on my dataset, but all of them
>>> are exiting with
>>> the same error.
>>>
>>> The command line is:
>>> recon-all -subjid ncpoCCW -autorecon2 -autorecon3
>>>
>>> The error reads:
>>> #@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33
>>> HKT 2012
>>> INFO: lh.EC_average subject does not exist in SUBJECTS_DIR
>>> INFO: Creating symlink to lh.EC_average subject...
>>>
>>>  cd /home/virtualuser/freesurfer/**subjects; ln -s
>>> /home/virt

Re: [Freesurfer] recon-all: too many levels of symbolic links

Re: [Freesurfer] "nu_estimate_np_and_em" error during recon-all

Re: [Freesurfer] L-R Volume Flipping

[Freesurfer] Diffusion Tensor Imaging

Re: [Freesurfer] tracula - posterior density just one-dimensional curve

Re: [Freesurfer] L-R Volume Flipping

Re: [Freesurfer] space of T1.mgz

Re: [Freesurfer] recon-all: too many levels of symbolic links

Re: [Freesurfer] mri_cc segfault

[Freesurfer] new atlas

Re: [Freesurfer] recon-all: too many levels of symbolic links

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