[Freesurfer] -cw256 and -hires

[Chris Adamson]

In the git version I'm trying to use the -hires option on an image. It 
initially says that I need the cw256 option to restrict the FOV to 256. I tried 
this but initially it did nothing and then when I edited recon-all it add 
-cw256 to the mri_convert command to create orig.mgz but the same error about 
the FOV came up. Any thoughts?

Chris.

Dr Chris Adamson
Senior Research Officer
Developmental Imaging, Clinical Sciences

Murdoch Childrens Research Institute
The Royal Children's Hospital
Flemington Road, Parkville, VIC 3052 Australia
E chris.adam...@mcri.edu.au
www.mcri.edu.au


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[Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error

[Derek A Pisner]

Hi Anastasia,

I am getting the following error when running trac-all –paths on all of my
diffusion images using the newly updated TRACULA:

*vlogin03.ls5(97)$*
/work/04171/dpisner/stampede/Applications/freesurfer/bin/trac-all
-no-isrunning -path -c
/work/04171/dpisner/data/ABM/TRACULA/tractography_output/s002/trac_config.txt

niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm

WARNING: niiRead(): unknown time units 0 in
/work/04171/dpisner/data/ABM/TRACULA/tractography_output/s002/dmri/dwi.nii.gz



Any idea what’s going on here?



Thanks as always,



Derek Pisner

Doctoral Student

CLA 4.600

Mood Disorders Laboratory (MDL)

Department of Psychology | The University of Texas at Austin



P.S. Here is the header information on my dwi.nii.gz file:

*vlogin03.ls5(105)$* fslhd dwi.nii.gz

filename   dwi.nii.gz

sizeof_hdr 348

data_type  FLOAT32

dim0   4

dim1   115

dim2   115

dim3   56

dim4   55

dim5   1

dim6   1

dim7   1

vox_units  Unknown

time_units Unknown

datatype   16

nbyper 4

bitpix 32

pixdim00.00

pixdim12.00

pixdim22.00

pixdim32.00

pixdim41.00

pixdim51.00

pixdim61.00

pixdim71.00

vox_offset 352

cal_max0.

cal_min0.

scl_slope  1.00

scl_inter  0.00

phase_dim  0

freq_dim   0

slice_dim  0

slice_name Unknown

slice_code 0

slice_start0

slice_end  0

slice_duration 0.00

time_offset0.00

intent Unknown

intent_code0

intent_name

intent_p1  0.00

intent_p2  0.00

intent_p3  0.00

qform_name Unknown

qform_code 0

qto_xyz:1  2.00  0.00  0.00  0.00

qto_xyz:2  0.00  2.00  0.00  0.00

qto_xyz:3  0.00  0.00  2.00  0.00

qto_xyz:4  0.00  0.00  0.00  1.00

qform_xorient  Left-to-Right

qform_yorient  Posterior-to-Anterior

qform_zorient  Inferior-to-Superior

sform_name Aligned Anat

sform_code 2

sto_xyz:1  -2.00  0.00  0.00  114.551003

sto_xyz:2  0.00  2.00  0.00  -74.456001

sto_xyz:3  0.00  0.00  2.00  -0.960182

sto_xyz:4  0.00  0.00  0.00  1.00

sform_xorient  Right-to-Left

sform_yorient  Posterior-to-Anterior

sform_zorient  Inferior-to-Superior

file_type  NIFTI-1+

file_code  1

descrip

aux_file

-- 
Derek Pisner
#!/bin/tcsh
set workingDIR = "/work/04171/dpisner/data/ABM/TRACULA"
set SUBJECTS_DIR = $workingDIR/diffusion_recons
setenv SUBJECTS_DIR $workingDIR/diffusion_recons
set dtroot =  $workingDIR/tractography_output
set subjlist = ( s002 )
set dcmroot = 
/work/04171/dpisner/data/ABM//work/04171/dpisner/data/ABM/dti_preproc
set dcmlist = ( $dcmroot/s002/dmri/dwi.nii.gz )
set bvecfile = ( 
/work/04171/dpisner/data/ABM/TRACULA/tractography_output/s002/dmri/bvecs )
set bvalfile = 
/work/04171/dpisner/data/ABM/TRACULA/tractography_output/s002/dmri/bvals
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)
source $FREESURFER_HOME/SetUpFreeSurfer.csh
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Re: [Freesurfer] Reviewer questions...

[Antonin Skoch]

Dear Jerome,

I think I could chime in with my opinion: The Schoemaker et al paper results 
are based on hippocampus/amygdala segmentations in FreeSurfer 4.4. 

Hippocampal subfields segmentation module from development version you used 
should be more precise than 4.4. version and also the anatomical landmarks are 
well specified in paper Iglesias et al, 2015:

https://www.ncbi.nlm.nih.gov/pubmed/25936807
I think this paper can be used as a good basis for arguments to your reviewer.

Concerning the reliability of estimation of particular hippocampal subfields, I 
think it also depend on what resolution was your input images, and whether you 
used additional high-resolution T2. The effect of various image resolution on 
the reliability of results is also well discussed in above-mentioned paper I 
think.

Regards,

Antonin Skoch

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Re: [Freesurfer] surface based analysis (projfrac)

[John Anderson]

Thank you very much Doug and thank you for briniging the issue of "partial volume effect " to my attention. Kindly, I have one last question.

 

I found in wiki that the default values for projfrc value are between 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1, 2 ", In other words, less than zero means the surface based analysis is running at a lower level of the white matter. Can the issue of the partial volume effect be avoided by using larger numbers for "projfrac" ?

 

Bests,
John 

 
 

Sent: Thursday, January 12, 2017 at 5:08 PM
From: "Douglas N Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis (projfrac)

yes, that is correct. However, understand that there might only be a
difference of 1mm between those two locations, so it could easily be a
partial volume effect


On 01/11/2017 08:50 AM, John Anderson wrote:
> Thank you Doug,
> Exactly! I meant GM near the CC.
> When I used "projfrac=0.5 " there was no differnce between the groups
> at "cwp 0.05", and when I changed the "projfrac to 0" I got
> significant differnce between the groups in specific areas at "cwp
> 0.01". Kindly, how can this be explained? I highly appreciate if you
> help me to understand this point:
> For "projfrac =0" I expect the surface based analysis to
> be running close to white matter. Right? and when I used
> "projfrac=0.5" the analysis is running in the middle area between pial
> and white. When the analysis is not showing any differne between the
> groups for "projfrac 0.5" and showing differnce for "projfrac 0" that
> means the differnce between the groups is deeper and closer to white
> matter. Is this correct?
> Thank you for any input and clarification!
> Bests,
> John
> *Sent:* Tuesday, January 10, 2017 at 10:51 AM
> *From:* "Douglas Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
>
> When you say in the corpus callosum, do you mean in WM? The
> surface-based analysis is only for cortical GM. If you mean in GM near
> the CC, then the analysis is appropriate. The projfrac parameter sets
> the sampling location between the white and pial surfaces where 0.5
> means half way.
>
> On 1/10/17 8:07 AM, John Anderson wrote:
>
> Dear FS experts,
> I am working on surface based analysis using freesurfer. I want to
> inquire about the flag "projfrac" in the command "mris_preproc"
> I ran voxel wise analysis including the same subjects. I found
> differnce between the groups in areas close to the corpus
> callosum. I want to get the same results using surface based
> analysis. If I use the projfrac=0.5 is this able to show the same
> results that I got in voxel wise analysis at the level of the
> corpus callosum. Do I need to use differnt number for projfrac ?
> Thank you for any advice.
>
> Best,
> John
>
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>
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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/BugReporting
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Re: [Freesurfer] Binary Mask Overlay

[Douglas N Greve]

Use mri_surf2surf to transfer the mask from one subject to another. 
Because this is a binary mask, you should include --mapmethod  nnf on 
the command line


On 01/11/2017 03:43 PM, Dincer, Aylin wrote:
>
> Hi FreeSurfer Team,
>
>
> I used QDEC to do a group analysis and from that I generated a 
> surface-based mask using the command "mri_binarize --i sig.mgh --min 3 
> --o mask.mgz" Ultimately, I would like to overlay this mask on an 
> individual subject (other than the fsaverage "lh.inflated" surface). 
>  Using freeview, I uploaded the lh.inflated surface of an individual 
> subject and tried to overlay the "mask.mgz" file, but it doesn't seem 
> to work.  There are no error messages and it is visible in the 
> "overlay" drop down menu.  However, nothing appears on the surface. 
> The chosen subject was in the QDEC group analysis and all 
> subjects were run with FreeSurfer v5.3. I did try this on the 
> fsaverage surface and the mask is visible.  What are your suggestions 
> for this overlay issue?
>
>
> Let me know if you need any more information!
>
>
> Best,
>
> Aylin
>
> 
>
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If 
> you are not the intended recipient, be advised that any unauthorized 
> use, disclosure, copying or the taking of any action in reliance on 
> the contents of this information is strictly prohibited. If you have 
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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
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Re: [Freesurfer] error: mean: DIM must be an integer and a valid dimension / selxavg3-sess with octave

[Douglas N Greve]

Thanks Michael. This will be in the next version


On 01/11/2017 07:47 AM, Michael Schirner wrote:
> Dear FreeSurfers,
>
> I just wanted to share a solution for an issue that can arise when running
> selxavg3-sess with octave instead of Matlab.
>
> In fast_selxavg3.m (which is called by selxavg3) there is a line (579 in
> my version) that computes the mean of an array by calling the mean
> function with the DIM argument, which specifies the dimension over which
> the average should be computed (4th dimension in this case):
>
> rho1mn.vol = mean(rho1.vol,4);
>
> This line will throw an error under octave if the number of dimensions of
> the array rho1.vol is smaller than 4. In Matlab it will simply return the
> array.
>
> To solve this issue for octave users one can use a simple if-else
> statement to check for the number of dimensions and return the unchanged
> volume if the number of dimensions is smaller than four or if the fourth
> dimension is a singleton, like this:
>
> if 4 > ndims(rho1.vol) || size(rho1.vol,4) == 1
> rho1mn.vol = rho1.vol;
> else
> rho1mn.vol = mean(rho1.vol,4);
> end
>
> Best,
> Michael
>
>
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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
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Re: [Freesurfer] surface based analysis (projfrac)

[Douglas N Greve]

yes, that is correct. However, understand that there might only be a 
difference of 1mm between those two locations, so it could easily be a 
partial volume effect


On 01/11/2017 08:50 AM, John Anderson wrote:
> Thank you Doug,
> Exactly! I meant GM near the CC.
> When I used "projfrac=0.5 " there was no differnce between the groups 
> at "cwp 0.05", and when I changed the "projfrac to 0" I got 
> significant differnce between the groups in specific areas at "cwp 
> 0.01". Kindly, how can this be explained? I highly appreciate if you 
> help me to understand this point:
> For "projfrac =0" I expect the surface based analysis to 
> be running close to white matter. Right? and when I used 
> "projfrac=0.5" the analysis is running in the middle area between pial 
> and white. When the analysis is not showing any differne between the 
> groups for "projfrac 0.5" and showing differnce for "projfrac 0" that 
> means the differnce between the groups is deeper and closer to white 
> matter. Is this correct?
> Thank you for any input and clarification!
> Bests,
> John
> *Sent:* Tuesday, January 10, 2017 at 10:51 AM
> *From:* "Douglas Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
>
> When you say in the corpus callosum, do you mean in WM? The 
> surface-based analysis is only for cortical GM. If you mean in GM near 
> the CC, then the analysis is appropriate. The projfrac parameter sets 
> the sampling location between the white and pial surfaces where 0.5 
> means half way.
>
> On 1/10/17 8:07 AM, John Anderson wrote:
>
> Dear FS experts,
> I am working on surface based analysis using freesurfer. I want to
> inquire about the flag "projfrac" in the command "mris_preproc"
> I ran voxel wise analysis including the same subjects. I found
> differnce between the groups in areas close to the corpus
> callosum. I want to get the same results using surface based
> analysis. If I use the projfrac=0.5 is this able to show the same
> results that I got in voxel wise analysis at the level of the
> corpus callosum. Do I need to use differnt number for projfrac ?
> Thank you for any advice.
>
> Best,
> John
>
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> Freesurfer@nmr.mgh.harvard.edu
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>
>
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> information in this e-mail is intended only for the person to whom it 
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>
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MGH-NMR Center
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Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] bbregister surfaces

[Douglas N Greve]

the pial surface is not currently used. It is possible in the current 
version to use pial surface if you want to


On 01/12/2017 04:35 PM, Christopher Markiewicz wrote:
> Hi all,
>
> According to 
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25476.html, 
> bbregister uses the white matter surface and cortical thickness 
> measures to perform its registrations, though there was some 
> possibility of using the pial surface in further releases. I just want 
> to verify that this is still the case, and the pial surface is not 
> currently being used.
>
> Thanks,
> Chris Markiewicz
>
>
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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
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[Freesurfer] bbregister surfaces

[Christopher Markiewicz]

Hi all,

According to
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25476.html,
bbregister uses the white matter surface and cortical thickness measures to
perform its registrations, though there was some possibility of using the
pial surface in further releases. I just want to verify that this is still
the case, and the pial surface is not currently being used.

Thanks,
Chris Markiewicz
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[Freesurfer] Fwd: OHBM 2017 Call For Council Nominations

[Douglas N Greve]

fyi



 Forwarded Message 
Subject:OHBM 2017 Call For Council Nominations
Date:   Thu, 12 Jan 2017 12:42:40 -0600
From:   i...@humanbrainmapping.org
Reply-To:   i...@humanbrainmapping.org
To: gr...@nmr.mgh.harvard.edu



Dear Douglas,

The OHBM Nominating Committee is extending the deadline for members to 
submit Council nominations until *January 19, 2017. *Open positions 
include Chair-Elect, Secretary-Elect, Treasurer-Elect, Program 
Chair-Elect and Education Chair-Elect and the term of service begins in 
June 2017, and each term is for three years.

Make**your nominations by completing the *Call for Nominations* 
 form no 
later than *Thursday, January 19^th at* *11:59 PM US CST*. 
Self-nominations are welcome and encouraged.

The OHBM By-Laws 
, 
Article 5 provides the framework and process for the election of new 
Council members.

*OHBM Nominating Committee:*
Tor Wager, Secretary
Christian Grefkes, Secretary-Elect
Tonya White, Past Secretary
Alan Evans, Chair
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Re: [Freesurfer] pial surface vs. aparc segmentation inconsistency

[Douglas N Greve]

This is due to an inconsistency between the volume labeling and the 
surface placement. The volume labeling thinks those voxels are 
cerebellum. In the lh.aparc.stats, those voxels would be counted as 
parahippo. If the problem is with the volume labeling, then there is 
nothing you need to do as the aparc.stats is correct. If the problem is 
with the surface placement, I'm not sure what you can do. Maybe edit 
those voxels out of the brain.finalsurfs.mgz and re-run -autorecon2-wm 
and autorecon3


On 01/12/2017 02:37 AM, Gabor Perlaki wrote:
>
> Dear all,
>
> In some of our subjects the border of ctx_lh_parahippocampal (green 
> color) is inconsistent with the border of pial surface (red color) in 
> the sense that some small region within the pial surface is segmented 
> as cerebellum (orange) coming from the subcortical segmentation 
> stream. This problem is present in all three planes. It is hard to 
> decide whether the colored border of ctx_lh_parahippocampal or the 
> pial surface is more realistic, but it would be nice to know which one 
> is used for the parahippocampal statistics in lh.aparc.stats file. Do 
> I need to correct for this inaccuracy? How should I correct this type 
> of missegmentation?
>
> Best Regards,
> Gabor
>
>
>
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Re: [Freesurfer] autorecon1 crash (with nu_correct).

[Jamie Hanson]

OK, I just uploaded it via the FileDrop (and sent it to Zeke)...

On Thu, Jan 12, 2017 at 4:02 AM, Z K  wrote:

> Could you please upload the a copy of the subject data and I'll take a
> look early next week when I get back. Also, what Linux distribution are you
> on?
>
> On Jan 12, 2017, at 1:55 AM, Jamie Hanson  wrote:
>
> Hello Zeke,
>
> I included the terminal output error for the stable version of Freesurfer,
> but get the same error with the dev version. Here's an example, pasted
> below:
>
> Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
> Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
> INFO: SUBJECTS_DIR is /home/jamielh/Volumes/Hanson/
> Pardini_Projects/K_award
> Actual FREESURFER_HOME /usr/local/pkg/freesurfer-dev
> Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016
> x86_64 x86_64 x86_64 GNU/Linux
> '/usr/local/pkg/freesurfer-dev/bin/recon-all' ->
> '/home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/
> 10107/scripts/recon-all.local-copy'
> #
> #@# MotionCor Wed Jan 11 20:49:48 EST 2017
> Found 1 runs
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/
> 10107/mri/orig/001.mgz
> Checking for (invalid) multi-frame inputs...
> WARNING: only one run found. This is OK, but motion
> correction cannot be performed on one run, so I'll
> copy the run to rawavg and continue.
>  cp 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig/001.mgz
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/rawavg.mgz
>
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107
>  mri_convert 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/rawavg.mgz
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz
> --conform
> mri_convert.bin 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/rawavg.mgz
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz
> --conform
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/
> 10107/mri/rawavg.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (0, -0.971961, -0.235142)
> j_ras = (0, -0.235142, 0.971961)
> k_ras = (1, -1.11022e-16, -1.66533e-16)
> changing data type from float to uchar (noscale = 0)...
> MRIchangeType: Building histogram
> Reslicing using trilinear interpolation
> writing to /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/
> 10107/mri/orig.mgz...
>  mri_add_xform_to_header -c /home/jamielh/Volumes/Hanson/
> Pardini_Projects/K_award/10107/mri/transforms/talairach.xfm
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz
> INFO: extension is mgz
> #
> #@# Talairach Wed Jan 11 20:50:00 EST 2017
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri
>  mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1
> --proto-iters 1000 --distance 50
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri
> /usr/local/pkg/freesurfer-dev//bin/mri_nu_correct.mni
> --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000
> --distance 50
> nIters 1
> $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
> Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016
> x86_64 x86_64 x86_64 GNU/Linux
> Wed Jan 11 20:50:00 EST 2017
> Program nu_correct, built from:
> Package MNI N3, version 1.10, compiled by nicks@minerva
> (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
> /usr/bin/bc
> tmpdir is ./tmp.mri_nu_correct.mni.130158
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri
> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.130158/nu0.mnc -odt float
> mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.130158/nu0.mnc -odt
> float
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from orig.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> changing data type from uchar to float (noscale = 0)...
> writing to ./tmp.mri_nu_correct.mni.130158/nu0.mnc...
>
> 
> Iteration 1 Wed Jan 11 20:50:03 EST 2017
> nu_correct -clobber ./tmp.mri_nu_correct.mni.130158/nu0.mnc
> ./tmp.mri_nu_correct.mni.130158/nu1.mnc -tmpdir 
> ./tmp.mri_nu_correct.mni.130158/0/
> -iterations 1000 -distance 50
>
> Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at
> /usr/local/pkg/freesurfer//mni/bin/nu_estimate_np_and_em line 165.
>
> nu_correct: crashed while running nu_estimate_np_and_em (termination
> status=65280)
> ERROR: nu_correct
> Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016
> x86_64 x86_64 x86_64 GNU/Linux
> recon-all -s 10107 exited with ERRORS at Wed Jan 11 20:50:03 EST 2017
> For more de

Re: [Freesurfer] Editing annot files

[Bruce Fischl]

Hi Martin

I guess you could do it in tksurfer. This functionality hasn't been 
addded to freeview yet


cheers
Bruce
On Tue, 10 Jan 2017, Martin Juneja wrote:


Hi,
I was wondering if there is any way to edit annot file e.g. I would like to
edit lh.Yeo2011_7Networks_N1000.annot file in such a way when I overlay this
file in freeview, I just display limbic network from Yeo 7 network atlas and
hide other 6 networks.

I would prefer to use MATLAB for this but would really appreciate any other
simple way to do that.

Thanks.

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Re: [Freesurfer] Viewing Atlas for Cortical Parcellations

[Bruce Fischl]

Hi Tamara

sorry, not easily - we have no visualization tools for the cortical 
atlases (*.gcs files)

cheers
Bruce
On Thu, 12 Jan 2017, Tamara Tavares wrote:

> Hello,
> 
> I was wondering whether it is possible to view the atlases that are used to
> construct the cortical surface ROIs in a visualization program?
> 
> Thank you in advance for your help.
> 
> Best,
> Tamara
> 
>
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[Freesurfer] Viewing Atlas for Cortical Parcellations

[Tamara Tavares]

Hello,

I was wondering whether it is possible to view the atlases that are used to
construct the cortical surface ROIs in a visualization program?

Thank you in advance for your help.

Best,
Tamara
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[Freesurfer] Fwd: Editing annot files

[Martin Juneja]

-- Forwarded message --
From: Martin Juneja 
Date: Tue, Jan 10, 2017 at 5:32 PM
Subject: Editing annot files
To: Freesurfer support list 


Hi,

I was wondering if there is any way to edit annot file e.g. I would like to
edit *lh.Yeo2011_7Networks_N1000.annot* file in such a way when I overlay
this file in freeview, I just display limbic network from Yeo 7 network
atlas and hide other 6 networks.

I would prefer to use MATLAB for this but would really appreciate any other
simple way to do that.

Thanks.
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Re: [Freesurfer] Cannot allocate memory error

[Bruce Fischl]

Hi Aziz

freeview is the tool for visualizing the data, so use it to examine the 
outputs of recon-all and figure out what is causing the big defect


cheers
Bruce
On Thu, 
12 Jan 2017, Aziz Nanthaamornphong wrote:



Hi Bruce,
So, I  should run the freeview after got those error messages. I will try. 

Thank you,
Aziz.

On Thu, Jan 12, 2017 at 10:32 PM, Bruce Fischl 
wrote:
  Hi Aziz

  it will be in the subject's surf dir. You can visualize it via:

  freeview -f $SUBJECTS_DIR//surf/lh.inflated.nofix


  cheers
  Bruce


  On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote:

Hi Bruce,
How can I look at inflated.nofix as you mentioned? I
think I ran recon-all
for the 001.mgz without other files. 

Best Regards,
Aziz.

On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl

wrote:
      Hi Aziz

      yes, you ran out of RAM. That said, a defect
with 66K vertices
      is pretty big - more than 1/3 of a typical
surface. You should
      check to make sure nothing big is wrong (hemis
attached, skull
      left around, etc). Look at the
inflated.nofix surface and it
      should be obvious what the defect is

      cheers
      Bruce
      On Thu, 12 Jan 2017, Aziz Nanthaamornphong
wrote:

            Hi experts,

            I ran the command

            $recon-all -all  -subjid 0696 

            I have got these error messages

            CORRECTING DEFECT 46 (vertices=66623,
convex
            hull=8931)
            Excessive topologic defect encountered:
could not
            allocate 322592700 edges
            for retessellation
            Cannot allocate memory

            Linux xubuntu-VirtualBox
3.2.0-23-generic #36-Ubuntu
            SMP Tue Apr 10 20:41:14
            UTC 2012 i686 i686 i386 GNU/Linux

            I am not sure if this problem came from
the
             insufficient memory on my
            computer. Otherwise, please let me
suggestions for
            solving this problem.

            Thank you,
            Aziz.



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--

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information
Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz



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--

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz


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Re: [Freesurfer] Cannot allocate memory error

[Aziz Nanthaamornphong]

Hi Bruce,

So, I  should run the freeview after got those error messages. I will try.

Thank you,
Aziz.

On Thu, Jan 12, 2017 at 10:32 PM, Bruce Fischl 
wrote:

> Hi Aziz
>
> it will be in the subject's surf dir. You can visualize it via:
>
> freeview -f $SUBJECTS_DIR//surf/lh.inflated.nofix
>
>
>
> cheers
> Bruce
>
>
> On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote:
>
> Hi Bruce,
>> How can I look at inflated.nofix as you mentioned? I think I ran recon-all
>> for the 001.mgz without other files.
>>
>> Best Regards,
>> Aziz.
>>
>> On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl > >
>> wrote:
>>   Hi Aziz
>>
>>   yes, you ran out of RAM. That said, a defect with 66K vertices
>>   is pretty big - more than 1/3 of a typical surface. You should
>>   check to make sure nothing big is wrong (hemis attached, skull
>>   left around, etc). Look at the inflated.nofix surface and it
>>   should be obvious what the defect is
>>
>>   cheers
>>   Bruce
>>   On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote:
>>
>> Hi experts,
>>
>> I ran the command
>>
>> $recon-all -all  -subjid 0696
>>
>> I have got these error messages
>>
>> CORRECTING DEFECT 46 (vertices=66623, convex
>> hull=8931)
>> Excessive topologic defect encountered: could not
>> allocate 322592700 edges
>> for retessellation
>> Cannot allocate memory
>>
>> Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu
>> SMP Tue Apr 10 20:41:14
>> UTC 2012 i686 i686 i386 GNU/Linux
>>
>> I am not sure if this problem came from the
>>  insufficient memory on my
>> computer. Otherwise, please let me suggestions for
>> solving this problem.
>>
>> Thank you,
>> Aziz.
>>
>>
>>
>> ___
>> 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 e-mail.
>>
>>
>>
>>
>> --
>>
>> Aziz Nanthaamornphong, Ph.D.,
>> Chair of Master of Science Program in Information Technology
>> Department of ICT
>> Faculty of Technology and Environment
>> Prince of Songkla University, Phuket Campus
>> +66 7627 6716 (v)
>> http://research.te.psu.ac.th/aziz
>>
>>
>>
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>
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> dispose of the e-mail.
>
>


-- 

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz
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Re: [Freesurfer] Cannot allocate memory error

[Bruce Fischl]

Hi Aziz

it will be in the subject's surf dir. You can visualize it via:

freeview -f $SUBJECTS_DIR//surf/lh.inflated.nofix


cheers
Bruce


On Thu, 12 
Jan 2017, Aziz Nanthaamornphong wrote:



Hi Bruce,
How can I look at inflated.nofix as you mentioned? I think I ran recon-all
for the 001.mgz without other files. 

Best Regards,
Aziz.

On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl 
wrote:
  Hi Aziz

  yes, you ran out of RAM. That said, a defect with 66K vertices
  is pretty big - more than 1/3 of a typical surface. You should
  check to make sure nothing big is wrong (hemis attached, skull
  left around, etc). Look at the inflated.nofix surface and it
  should be obvious what the defect is

  cheers
  Bruce
  On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote:

Hi experts,

I ran the command

$recon-all -all  -subjid 0696 

I have got these error messages

CORRECTING DEFECT 46 (vertices=66623, convex
hull=8931)
Excessive topologic defect encountered: could not
allocate 322592700 edges
for retessellation
Cannot allocate memory

Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu
SMP Tue Apr 10 20:41:14
UTC 2012 i686 i686 i386 GNU/Linux

I am not sure if this problem came from the
 insufficient memory on my
computer. Otherwise, please let me suggestions for
solving this problem.

Thank you,
Aziz.



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--

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz


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[Freesurfer] Fwd: Error of fsaverage unknown during mri_glmfit

[Xiuyi Wang]

Hello FreeSurfer Developers,

I am attempting to repeat the group analysis with the tutorial data on
FreeSurfer website, as described on the FsTutorial/GroupAnalysis (
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). But I
received an error message when running the mri_glmfit command lines.

At first, the command lines that I types:

mri_glmfit --y xiuyi_lh_thickness.10.mgh  --fsgd gender_age.fsgd dods --C
lh-Avg-thickness-age-Cor.mtx \ —-surf fsaverage lh \—-cortex —glmdir
xiuyi_lh.gender_age.glmdir
Errors:
MRISread(/Users/xiuyi/Documents/tutorial_data/buckner_data/tutorial_subjs/
group_analysis_tutorial/glm/fsaverage/surf/lh. —-cortex): could not open
file
No such file or directory
mri_glmfit: could not read surface /Users/xiuyi/Documents/tutorial_data/
buckner_data/tutorial_subjs/group_analysis_tutorial/glm/fsaverage/surf/lh.
—-cortex
No such file or directory

Then I changed the command lines, replacing "surf fsaverage lh.white" with
"surf fsaverage lh".

The exact command lines are:

mri_glmfit --y xiuyi_lh_thickness.10.mgh  --fsgd gender_age.fsgd dods --C
lh-Avg-thickness-age-Cor.mtx \ —-surf fsaverage lh.white \—-cortex —glmdir
xiuyi_lh.gender_age.glmdir


The error message is:

gdfReadHeader: reading gender_age.fsgd

INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

Continuous Variable Means (all subjects)

0 age 57.175 26.6006

Class Means of each Continuous Variable

1 genderFemale  59.1429

2 genderMale  55.

INFO: gd2mtx_method is dods

*ERROR: Option fsaverage unknown.*

I have searched the list and found this type of error has been reported by
another person but no reply was found.(https://mail.nmr.mgh.
harvard.edu/pipermail//freesurfer/2010-May/014401.html)


1) FreeSurfer Version: freesurfer-Darwin-lion-stable-pub-v5.3.0

2) Flatform: macOS Sierra version 10:12


Thank you for your reply.


Xiuyi
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Re: [Freesurfer] Cannot allocate memory error

[Aziz Nanthaamornphong]

Hi Bruce,

How can I look at inflated.nofix as you mentioned? I think I ran recon-all
for the 001.mgz without other files.

Best Regards,
Aziz.

On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl 
wrote:

> Hi Aziz
>
> yes, you ran out of RAM. That said, a defect with 66K vertices is pretty
> big - more than 1/3 of a typical surface. You should check to make sure
> nothing big is wrong (hemis attached, skull left around, etc). Look at
> the inflated.nofix surface and it should be obvious what the defect is
>
> cheers
> Bruce
>
> On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote:
>
> Hi experts,
>>
>> I ran the command
>>
>> $recon-all -all  -subjid 0696
>>
>> I have got these error messages
>>
>> CORRECTING DEFECT 46 (vertices=66623, convex hull=8931)
>> Excessive topologic defect encountered: could not allocate 322592700 edges
>> for retessellation
>> Cannot allocate memory
>>
>> Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
>> 20:41:14
>> UTC 2012 i686 i686 i386 GNU/Linux
>>
>> I am not sure if this problem came from the  insufficient memory on my
>> computer. Otherwise, please let me suggestions for solving this problem.
>>
>> Thank you,
>> Aziz.
>>
>>
>>
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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.
>
>


-- 

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz
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Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream

[Martin Reuter]

Hi Tamara, 

that information is in the screen output:


 Determinant : 1.03358


also 
Scale = diag([  1.0109774487584  1.0113715685396  1.0108915357302  ])

so it finds some scaling (approx 1% in each axis direction, so a total of 3%). 
This can happen in individual cases, but if it is consistent I would be worried.

Best, Martin


> On 11 Jan 2017, at 21:21, Tamara Tavares  wrote:
> 
> Hi Dr. Reuter.
> 
> Thank you again for your help.  
> 
> I ran the following command: "mri_robust_register --mov rawavg_1.mgz --dst 
> rawavg_2.mgz --lta v1to2.lta --affine --satit" on the two rawavg.mgz images; 
> one from each time point from the cross-sectional outputs. I have attached 
> the information from the terminal and the output. Are these outputs 
> appropriate to find the scaling information? If so, where can I find it? I am 
> not very familiar with transformations, thus any information or directions to 
> resources I can use would be very much appreciated.
> 
> Thank you in advance for you help.
> 
> Best,
> Tamara
> 
> 
> Message: 6
> Date: Tue, 10 Jan 2017 21:18:34 +0100
> From: Martin Reuter  >
> Subject: Re: [Freesurfer] Brighter image at baseline vs. follow up
> using   longitudinal processing stream
> To: Freesurfer support list  >
> Message-ID: <9bcb373d-d368-4b36-b607-69e6a14af...@nmr.mgh.harvard.edu 
> >
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi Tamara,
> 
> mvoing in and popping out sounds like a scaling problem. We do only rigid 
> transforms, so the scaling would already be in your original inputs. If that 
> is the case, it could mean that there was a scanner calibration or something 
> that caused scaled images and that would not be good. It should however 
> appear in all images that have the calibration in between time points.
> 
> You can try to use mri_robust_register with the affine flag to see if any 
> scaling is present in the rawavg.mgz images between the two time points (it 
> should report scaling separately on the screen output), else use lta_diff 
> with the appropriate flags. You can also look at the affininely registered 
> images and see if it looks better.
> 
> Anyway if there is global scaling in the images, I would try to investigate a 
> where this comes from and also drop that image from the study.
> 
> Best, Martin
> 
> 
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Re: [Freesurfer] Cannot allocate memory error

[Bruce Fischl]

Hi Aziz

yes, you ran out of RAM. That said, a defect with 66K vertices is pretty 
big - more than 1/3 of a typical surface. You should check to make sure 
nothing big is wrong (hemis attached, skull left around, etc). Look 
at the inflated.nofix surface and it should be obvious what the defect is


cheers
Bruce
On 
Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote:



Hi experts,

I ran the command

$recon-all -all  -subjid 0696 

I have got these error messages

CORRECTING DEFECT 46 (vertices=66623, convex hull=8931)
Excessive topologic defect encountered: could not allocate 322592700 edges
for retessellation
Cannot allocate memory

Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14
UTC 2012 i686 i686 i386 GNU/Linux

I am not sure if this problem came from the  insufficient memory on my
computer. Otherwise, please let me suggestions for solving this problem.

Thank you,
Aziz.


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Re: [Freesurfer] autorecon1 crash (with nu_correct).

[Z K]

Could you please upload the a copy of the subject data and I'll take a look 
early next week when I get back. Also, what Linux distribution are you on?

> On Jan 12, 2017, at 1:55 AM, Jamie Hanson  wrote:
> 
> Hello Zeke,
> 
> I included the terminal output error for the stable version of Freesurfer, 
> but get the same error with the dev version. Here's an example, pasted below:
> 
> Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
> Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
> INFO: SUBJECTS_DIR is /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award
> Actual FREESURFER_HOME /usr/local/pkg/freesurfer-dev
> Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 
> x86_64 x86_64 GNU/Linux
> '/usr/local/pkg/freesurfer-dev/bin/recon-all' -> 
> '/home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/scripts/recon-all.local-copy'
> #
> #@# MotionCor Wed Jan 11 20:49:48 EST 2017
> Found 1 runs
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig/001.mgz
> Checking for (invalid) multi-frame inputs...
> WARNING: only one run found. This is OK, but motion
> correction cannot be performed on one run, so I'll
> copy the run to rawavg and continue.
>  cp 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig/001.mgz 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/rawavg.mgz 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107
>  mri_convert 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/rawavg.mgz 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz 
> --conform 
> mri_convert.bin 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/rawavg.mgz 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz 
> --conform 
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/rawavg.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (0, -0.971961, -0.235142)
> j_ras = (0, -0.235142, 0.971961)
> k_ras = (1, -1.11022e-16, -1.66533e-16)
> changing data type from float to uchar (noscale = 0)...
> MRIchangeType: Building histogram 
> Reslicing using trilinear interpolation 
> writing to 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz...
>  mri_add_xform_to_header -c 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/transforms/talairach.xfm
>  /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz 
> INFO: extension is mgz
> #
> #@# Talairach Wed Jan 11 20:50:00 EST 2017
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri
>  mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 
> --proto-iters 1000 --distance 50 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri
> /usr/local/pkg/freesurfer-dev//bin/mri_nu_correct.mni
> --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 
> 50
> nIters 1
> $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
> Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 
> x86_64 x86_64 GNU/Linux
> Wed Jan 11 20:50:00 EST 2017
> Program nu_correct, built from:
> Package MNI N3, version 1.10, compiled by nicks@minerva 
> (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
> /usr/bin/bc
> tmpdir is ./tmp.mri_nu_correct.mni.130158
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri
> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.130158/nu0.mnc -odt float
> mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.130158/nu0.mnc -odt float 
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from orig.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> changing data type from uchar to float (noscale = 0)...
> writing to ./tmp.mri_nu_correct.mni.130158/nu0.mnc...
> 
> 
> Iteration 1 Wed Jan 11 20:50:03 EST 2017
> nu_correct -clobber ./tmp.mri_nu_correct.mni.130158/nu0.mnc 
> ./tmp.mri_nu_correct.mni.130158/nu1.mnc -tmpdir 
> ./tmp.mri_nu_correct.mni.130158/0/ -iterations 1000 -distance 50
> 
> Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at 
> /usr/local/pkg/freesurfer//mni/bin/nu_estimate_np_and_em line 165.
> 
> nu_correct: crashed while running nu_estimate_np_and_em (termination 
> status=65280)
> ERROR: nu_correct
> Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 
> x86_64 x86_64 GNU/Linux
> recon-all -s 10107 exited with ERRORS at Wed Jan 11 20:50:03 EST 2017
> For more details, see the log file 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/scripts/recon-al

[Freesurfer] pial surface vs. aparc segmentation inconsistency

[Gabor Perlaki]

Somehow, my earlier post is unvisible on the maillist, therefore I send it
again without the attached image.


Dear all,

In some of our subjects the border of ctx_lh_parahippocampal (green color)
is inconsistent with the border of pial surface (red color) in the sense
that some small region within the pial surface is segmented as cerebellum
(orange) coming from the subcortical segmentation stream. This problem is
present in all three planes. It is hard to decide whether the colored
border of ctx_lh_parahippocampal or the pial surface is more realistic, but
it would be nice to know which one is used for the parahippocampal
statistics in lh.aparc.stats file. Do I need to correct for this
inaccuracy? How should I correct this type of missegmentation?

Best Regards,
Gabor

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[Freesurfer] Cannot allocate memory error

[Aziz Nanthaamornphong]

Hi experts,

I ran the command

$recon-all -all  -subjid 0696

I have got these error messages

*CORRECTING DEFECT 46 (vertices=66623, convex hull=8931)*
*Excessive topologic defect encountered: could not allocate 322592700 edges
for retessellation*
*Cannot allocate memory*

*Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux*

I am not sure if this problem came from the  insufficient memory on my
computer. Otherwise, please let me suggestions for solving this problem.

Thank you,
Aziz.
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