[Freesurfer] Freesurfer statement

[Juranek, Jenifer]

External Email - Use Caution

I pledge to do better. I pledge to pursue systemic change as passionately as I 
pursue research questions.

Thank you Freesurfer Team for speaking up so eloquently with your signed 
statement.


Jenifer Juranek
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] glibc error: newly formatted license file?

[Juranek, Jenifer]

External Email - Use Caution

Recently our cluster underwent a major upgrade...which broke my 
well-established Freesurfer v 6.0.0 recon-all pipeline.

1)  Error message from recon-all:
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 
/mri/rawavg.mgz...
--
GNU libc version: 2.22
ERROR: Systems running GNU glibc version greater than 2.15
  require a newly formatted license file (it's free). Please
  download a new one from the following page:
  http://surfer.nmr.mgh.harvard.edu/registration.html

2)  My attempt to download a "newly formatted" license file with this link 
results in what appears to be an identically-formatted license file (relative 
to my original one)

3)  Is there a different process for obtaining a "newly formatted" license 
file?

4)  Do I need to re-install Freesurfer v6.0.0?
Many Thanks,
JJ
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Jenifer Juranek, PhD
Director of the BRAIN Lab
Associate Professor
Department of Pediatrics
McGovern Medical School
UTHealth
Houston, TX 77030
713.500.8233

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Unusual hires T1 specs

[Juranek, Jenifer]

External Email - Use Caution

I offered to help a colleague with some Freesurfer analyses, but when I looked 
at the data they were processing, I found:
1) highly anisotropic voxdims
2) sub-mm in-plane resolution
Data were acquired on a 3T Siemens Tim Trio. I don't think they were trying to 
deviate from the recommended 1x1x1mm specs, but somehow it looks like they did 
since the 001.mgz file does not conform to the FS standard.
Output for mri_info on their 001.mgz file is listed below. They did not keep 
the file converted by mri_convert (nii or dicom) in their FS_sub directory, so 
I'm limited to the 001.mgz.
I'm running FSv6 in my lab, is the hires flag appropriate in this situation?
Any suggestions?
Many Thanks,
Jenifer

[orig]$ mri_info 001.mgz
Volume information for 001.mgz
  type: MGH
dimensions: 448 x 512 x 192
   voxel sizes: 0.478516, 0.478516, 1.00
  type: SHORT (4)
   fov: 245.000
   dof: 0
xstart: -107.2, xend: 107.2
ystart: -122.5, yend: 122.5
zstart: -96.0, zend: 96.0
___
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.

[Freesurfer] Matlab 2016b and localGI

[Juranek, Jenifer]

Hi,

Hope someone can identify my user error...I've listed below key bits of info 
(system info, cmdline and error message, echo $PATH, cat .bashrc, cat 
startup.m).

Really appreciate someone taking a look and walking me through a solution to my 
error?

Many Thanks!

Jenifer


1) Running Freesurfer_v6 on RHEL Centos7.3

and matlab 2016b (with imaging processing toolbox)

2) recon-all -s  -localGI

returns the following:

#@# Local Gyrification Index lh Thu Aug 10 15:39:03 CDT 2017

 mris_compute_lgi --i lh.pial

ERROR: Matlab is required to run mris_compute_lgi!
Linux localhost.localdomain 3.10.0-514.el7.x86_64 #1 SMP Wed Oct 19 11:24:13 
EDT 2016 x86_64 x86_64 x86_64 GNU/Linux


3) matlab is in my path

[jjuranek@localhost subjects]$ echo $PATH
/home/jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/fsfast/bin:/home/jjuranek/freesurfer/tktools:/home/jjuranek/fsl/bin:/home/jjuranek/freesurfer/mni/bin:/home/jjuranek/fsl/bin:/home/jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/fsfast/bin:/home/jjuranek/freesurfer/tktools:/home/jjuranek/freesurfer/mni/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/jjuranek/.local/bin:/home/jjuranek/bin:/home/jjuranek/matlab/R2016b/bin/matlab


4) my .bashrc file is as follows

# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi

# User specific aliases and functions

export FREESURFER_HOME=/home/jjuranek/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

matlab=/home/jjuranek/matlab/R2016b/bin/matlab
alias matlab=$matlab

export PATH=$PATH:/home/jjuranek/matlab/R2016b/bin/matlab

#/home/jjuranek/matlab/R2016b/bin/matlab
#MATLAB is selecting SOFTWARE OPENGL rendering.


5) my startup.m file is as follows

% FreeSurfer -%
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/matlab',fshome);
if (exist(fsmatlab) == 7)
addpath(genpath(fsmatlab));
end
clear fshome fsmatlab;
%-%

% FreeSurfer FAST %
fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
if (exist(fsfasttoolbox) == 7)
path(path,fsfasttoolbox);
end
clear fsfasthome fsfasttoolbox;
%-%

% FreeSurfer LGI %
FSH = getenv('FREESURFER_HOME');

fshmatlab = sprintf('%s/matlab',FSH);
path(path,fshmatlab);
clear fshmatlab FSH;

___
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.

Re: [Freesurfer] major lobes

[Juranek, Jenifer]

CentOs 6 running FS v 5.1.0. on the workstation where we have processed about 
300 datasets.

Many Thanks!
Jenifer

-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] 
Sent: Monday, March 24, 2014 2:44 PM
To: Juranek, Jenifer
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] major lobes

what version of FS do you have and what is your platform?
doug

On 03/24/2014 02:34 PM, Juranek, Jenifer wrote:
>
> Hi Doug,
>
> I recently saw your solution to a reported problem with grabbing StrictLobes 
> WM & GM (posted on the Freesurfer forum 12/04/2013; thread title= major 
> lobes).
> I have successfully grabbed the StrictLobes WM, but I am having trouble with 
> the GM.
> According to the forum (posted 12/04/2013), the solution that worked 
> was a link (you provided) to download a new binary for 
> mri_annotation2labelfrom the following 
> location:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve
> /mri_annotation2label However, this link appears to be broken now that 
> I am attempting to utilize your fix on my RHEL6 workstation. I checked the 
> download site , but there is no new version of Freesurfer since May 2013.
> Any chance you could provide a link to the new binary for 
> mri_annotation2label you had made available back in Dec 2013?
>
> Many Thanks,
>
> Jenifer Juranek
>

--
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: 
https://urldefense.proofpoint.com/v1/url?u=https://gate.nmr.mgh.harvard.edu/filedrop2&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=KYhu15jOA1qJABZpD6rPCt%2FRJ6SJVj3fv9ByC5Nb9Qc%3D%0A&m=CUnWEv7oihAUHfWFLVtFMYpQIfr3JxMsP2Fccfxo0Zc%3D%0A&s=194589fe62b38c03e70f3eeec66a184085c1f74d7f4877ebfce91a13303b5c08
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: 
https://urldefense.proofpoint.com/v1/url?u=ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=KYhu15jOA1qJABZpD6rPCt%2FRJ6SJVj3fv9ByC5Nb9Qc%3D%0A&m=CUnWEv7oihAUHfWFLVtFMYpQIfr3JxMsP2Fccfxo0Zc%3D%0A&s=a8c9f5a5d84271cf18c562de412081671dbc9e34c030de106f882dd648498488



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
https://urldefense.proofpoint.com/v1/url?u=http://www.partners.org/complianceline&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=KYhu15jOA1qJABZpD6rPCt%2FRJ6SJVj3fv9ByC5Nb9Qc%3D%0A&m=CUnWEv7oihAUHfWFLVtFMYpQIfr3JxMsP2Fccfxo0Zc%3D%0A&s=4f474ac54fc99701e6c4d0a28cbf9b4d4a82f69eb9ce12d2add1f2206ce23b62
 . 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.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] major lobes

[Juranek, Jenifer]

Hi Doug,

I recently saw your solution to a reported problem with grabbing StrictLobes WM 
& GM (posted on the Freesurfer forum 12/04/2013; thread title= major lobes).

I have successfully grabbed the StrictLobes WM, but I am having trouble with 
the GM.

According to the forum (posted 12/04/2013), the solution that worked was a link 
(you provided) to download a new binary for mri_annotation2label from the 
following 
location:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_annotation2label

However, this link appears to be broken now that I am attempting to utilize 
your fix on my RHEL6 workstation. I checked the download site , but there is no 
new version of Freesurfer since May 2013.

Any chance you could provide a link to the new binary for mri_annotation2label 
you had made available back in Dec 2013?

Many Thanks,
Jenifer Juranek

___
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.

[Freesurfer] wmparc 2 wmsurf

[Juranek, Jenifer]

I'm running FSv5.1.0 on RHEL6.

1)  My goal is to run a glm-fit on White Matter aparc regions for a 
"between group" surf-based analysis and evaluate spatial maps of significant 
differences.

2)  I noticed that fsaverage does not have a wmparc.mgz file, so I'm 
currently working with bert as my subject.

3)  I'd like to visualize each segid in the wmparc.mgz (volume-based) file 
on the white matter surface in the same subject (e.g. bert).

4)  I have been able to breakdown bert's wmparc.mgz file into separate 
masks (e.g. *.mgz) and labels (e.g. *.label) based on segid using mri_cor2label 
and mri_vol2surf. To get the vertices written into the label file, I have 
loaded each label and re-saved each label in tksurfer.
Q: Is there a better method for getting this (wmparc units moved from vol to 
surf) done (maybe using a matlab function?) Or is surf-based analysis of white 
matter not such a good idea.
Many Thanks for any assistance you can provide.
Cheers,
Jenifer
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Jenifer Juranek, PhD
University of Texas at Houston
___
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.

[Freesurfer] Now Hiring: Postdoc

[Juranek, Jenifer]

We have a current opening for a post-doctoral associate in the areas of *image 
analysis* (structural and functional) and *developmental neuroscience*. 
Available resources include a research-dedicated 3.0T MRI scanner and analysis 
platforms based in MATLAB/UNIX. The successful candidate will be expected to 
work independently (with some supervision) to analyze multimodal neuroimaging 
data (volumetrics, cortical thickness, DTI, resting state connectivity with 
fMRI and MEG/EEG, lesion identification and analysis) obtained from 
typically-developing and atypically developing pediatric study participants. 
The successful candidate should have a strong publication record and a 
continued interest preparing manuscripts for publication in the field of 
pediatric neuroimaging using multimodal imaging data.

The successful candidate should have a doctoral degree in a field related to 
developmental cognitive neuroscience (e.g., cognitive neuroscience, 
neuroscience, developmental psychology, medicine or psychology). Individuals 
with a background in electrical engineering, biomedical engineering or computer 
science will also be considered, as appropriate. The successful applicant must 
possess excellent English verbal and written communication skills. Applicants 
are expected to have a very strong research background in the design and 
statistical analysis of multimodal neuroimaging data. Experience with 
Freesurfer, FSL UNIX/LINUX/ and/or programming skills (MATLAB; Perl; bash) are 
highly desirable. For consideration please send a statement of interest, a CV 
and a list of three potential referees via email to Dr. Juranek at 
jenifer.jura...@uth.tmc.edu. This position 
is currently available; the search for a successful applicant will continue 
until the position is filled.
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Jenifer Juranek, PhD
Assistant Professor
UT Houston
Developmental Pediatrics
Children's Learning Institute
Voice: 713.500.3813
Fax: 713.500.3878

___
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.

[Freesurfer] mri_normalize

[Juranek, Jenifer]

I'm running a normal brain through FSv5.0.0 using the -cw256 flag and encounter 
a problem at the mri_normalize stage. The nu.mgz file looks fine...WM regions 
have intensity values >110; cortical GM regions have intensity values 70-106; 
csf intensity values are around 60. The output file (T1.mgz) is all black (no 
different when changing intensity/contrast display options). I tried a "kinder 
gentler" normalization to write out a T1_gentler.mgz file, but got the same 
result (all black output image). I see that the # of peaks is not >1 
(MRIsplineNormalize)...but not sure how to intervene at this stage.

Any ideas?
Many Thanks,
Jenifer

[jjuranek@localhost subjects]$ mri_normalize -gentle 
ATIS_0009_B_cw256/mri/nu.mgz ATIS_0009_B_cw256/mri/T1_gentle.mgz
performing kinder gentler normalization...
reading from ATIS_0009_B_cw256/mri/nu.mgz...
normalizing image...
talairach transform
 1.081  -0.071   0.112  -2.139;
 0.079   1.020   0.075  -20.692;
-0.117  -0.062   1.133  -11.092;
 0.000   0.000   0.000   1.000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRIsplineNormalize(): npeaks = 1
ERROR: number of peaks must be > 1 for spline
1d normalization failed - trying no1d...
building Voronoi diagram...
performing soap bubble smoothing...
3d normalization pass 1 of 2
building Voronoi diagram...
performing soap bubble smoothing...
3d normalization pass 2 of 2
building Voronoi diagram...
performing soap bubble smoothing...
writing output to ATIS_0009_B_cw256/mri/T1_gentle.mgz
3D bias adjustment took 0 minutes and 42 seconds.
___
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.

[Freesurfer] MCSRCH error

[Juranek, Jenifer]

While processing a normal brain through fsv5.0.0, an unfamiliar message popped 
up in the screen output (see below).
Any ideas what I should do about this message (anything in particular I should 
check)?

Many Thanks,
Jenifer

 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR 
RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE 
INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 1145193.0 
 tol 0.00
final transform:
 1.386  -0.067   0.094  -63.518;
 0.088   1.120  -0.108  -0.481;
-0.131   0.093   0.972  -2.704;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull.lta...
registration took 34 minutes and 38 seconds.

 mri_watershed -T1 -brain_atlas 
/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca 
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


Mode:  T1 normalized volume
Mode:  Use the information of atlas (default parms, --help for details)
 

___
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.

[Freesurfer] dura flag in fsv5.0.0

[Juranek, Jenifer]

Since the -dura flag is not recognized in FSv5.0.0, how should mempr data (4 
echoes) be passed to the latest version of FS?

Many Thanks,
Jenifer 
___
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.

Re: [Freesurfer] -legacy

[Juranek, Jenifer]

Great. Also, thanks so much for the Wiki entry on persistent edits. Looks like 
I could create an experts options file from the info contained in my 
recon-all.log to preserve any command line flags used in earlier versions of 
FS. Is the -notal-check flag required if used in an earlier FS version? From 
the wiki, it looks like an existing talairach.xfm file might keep the stream 
running (rather than stopping) at the tal check stage...but of course this 
depends on whether the tal check looks for that file before running the check...

Any clarification is greatly appreciated
Jenifer


-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] 
Sent: Wednesday, September 22, 2010 6:51 PM
To: Juranek, Jenifer
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] -legacy

yes, the -legacy flag was only necessary for the v3.0 to v4.0
transition.  v4.0 data should be fully compatible with reprocessing in
v5.

n.

On Wed, 2010-09-22 at 17:31 -0500, Juranek, Jenifer wrote:
> I'm hoping to push my legacy datasets (processed and edited in FSv4.0.5) 
> through FSv5.0.0. After installing FSv5.0.0, I received an error that it 
> didn't look like a legacy analysis (see below).  
> [jjura...@localhost subjects]$ recon-all -legacy -s SB_057_H21001
> ERROR: you have specified -legacy, but this does not look like 
>a legacy analysis. 
> 
> My recon-all.log file for this subjid reports the following build-stamp.txt: 
> freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5
> 
> How do I convince FSv5.0.0 that I am feeding it legacy data from FSv4.0.5? 
> Have I skipped too many versions to use this -legacy flag?
> 
> Many thanks,
> Jenifer
> 
> 
> ___
> 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.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] -legacy

[Juranek, Jenifer]

I'm hoping to push my legacy datasets (processed and edited in FSv4.0.5) 
through FSv5.0.0. After installing FSv5.0.0, I received an error that it didn't 
look like a legacy analysis (see below).  
[jjura...@localhost subjects]$ recon-all -legacy -s SB_057_H21001
ERROR: you have specified -legacy, but this does not look like 
   a legacy analysis. 

My recon-all.log file for this subjid reports the following build-stamp.txt: 
freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5

How do I convince FSv5.0.0 that I am feeding it legacy data from FSv4.0.5? Have 
I skipped too many versions to use this -legacy flag?

Many thanks,
Jenifer


___
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.

[Freesurfer] Gyrification index group differences

[Juranek, Jenifer]

Hi Nathan,
Check out this previous posting wrt using Qdec to visualize group maps (or 
group diff maps) based on pial_lgi data.

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09281.html

Cheers,
Jenifer
___
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.

Re: [Freesurfer] heterotopias

[Juranek, Jenifer]

Excellent.

Many Thanks!
Jenifer

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Monday, June 28, 2010 3:16 PM
To: Juranek, Jenifer
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] heterotopias

Hi Jenifer,

what does "handle" mean? You could label them  WM-hypointensities, and I 
think the new version should handle them in terms of not doing something 
strange in the surface deformation.

cheers
Bruce


On Mon, 28 Jun 2010, Juranek, Jenifer wrote:

> Any suggestions from anyone wrt handling heterotopias?
> Is it best to use a custom labelname to label them as such? Current 
labelname="WM-hypointensities". 
>
> Cheers,
> Jenifer
>


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.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] heterotopias

[Juranek, Jenifer]

Any suggestions from anyone wrt handling heterotopias?
Is it best to use a custom labelname to label them as such? Current 
labelname="WM-hypointensities".

Cheers,
Jenifer
___
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.

[Freesurfer] ICV for incomplete whole brain coverage

[Juranek, Jenifer]

A colleague asked me to look at some T1s for possible Freesurfer analyses. 
Unfortunately, several subjects do not have whole brain acquisitions (I know, 
quite unexpected and disappointing). Would it be possible to correct volumes of 
subcortical structures (which are covered by the acquisition) for ICV in the 
absence of whole brain coverage? The T1s were acquired in the coronal 
plane...so typically brain tissue is missing in either the anterior and/or 
posterior regions.

I reflexively think that whole brain coverage is required for accurate ICV 
calculated by Freesurfer...but I'm not positive.

Many Thanks for any thoughts you might have,
Jenifer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] POSTDOC POSITION OPEN

[Juranek, Jenifer]

Subject: POSTDOCTORAL POSITION - structure & function of fronto-cerebellar 
circuits in neurodevelopmental disorders



Applications are invited for an immediate postdoctoral opening in the 
Department of Psychology at the University of Houston, Houston TX. The position 
is full-time for 1 year, with the possibility of annual extensions up to 2 
years, depending on funding. The current opening entails analysis of already 
collected MRI datasets from children with and without a neurodevelopmental 
disorder and relating quantitative MRI findings to neuropsychological 
assessments. The successful candidate will be responsible for processing and 
analyzing structural data and writing up the results for publication in 
peer-reviewed journals. Essential skills include demonstrated knowledge of 
structural MRI analysis techniques, including Freesurfer and FSL. While this 
position requires some technical skill with image analysis, it is best suited 
for someone who is interested in understanding brain-behavior correlates of 
cognitive function in children with and without a developmental disorder rather 
than someone with a strict methods development orientation. Applications are 
welcomed from current Ph.D. students who will have submitted their 
dissertations in the near future. The position is available for a start date as 
soon as July 15th 2009.



Salary is expected to be $40,000, depending on knowledge and experience, and 
will come with full health and other benefits at the University of Houston, 
Houston TX.


Non US citizens are welcome to apply. Please send enquiries or applications 
(which must include a covering letter detailing professional objectives and 
interests, CV, and the names and email addresses of three references, all 
together in one pdf file) to Dr. Jack M Fletcher, 
jmfle...@central.uh.edu , with the subject line 
"Postdoctoral imaging position".


~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Jenifer Juranek, PhD
Assistant Professor
Developmental Pediatrics
University of Texas Health Science Center at Houston
713.500.3813 (voice)
jenifer.jura...@uth.tmc.edu
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] map label to subjects

[Juranek, Jenifer]

Hi,
I'm running fsv405 on a 64bit Linux centos5.
I have not had much success with using the File - Save Label - Filename within 
qdec (v1.1). The gui prompt has a default filename set to lh.untitled.label and 
I am unable to edit that name, but I can write the default filename to the 
default dir (e.g. /usr/local/fsaverage/label). Similarly, I am unable to use 
the File-MapLabeltoSubjects option within qdec. A default label name is not 
provided and I am unable to type something in the gui box field.

I have recursively changed permissions for the subjects dir from 
/usr/local/freesurfer such that I am the owner and chmod to be 770.

Is there a simple solution for my user error?


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] spherical template: CMA training set

[Juranek, Jenifer]

Ah...Excellent! Thanks so much for clearing things up for me.

Cheers,
Jenifer

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Wednesday, April 22, 2009 11:55 AM
To: Juranek, Jenifer
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] spherical template: CMA training set

Hi Jennifer,

the spherical stuff has nothing to do with the CMA. And in fact the 
spherical registration itself is not based on any manual labelings, just 
estimates of cortical geometry from a set of training subjects. The 
cortical parcellations do depend on manual labelings, but this is also 
not the CMA. Rather there are two sets - one done by Rahul Desikan (39 
subjects I think) and the other by Christophe Destrieux (12 or 14 
subjects). The current spherical template we use is from the same 39 that 
Rahul labeled.

cheers,
Bruce


On Wed, 22 Apr 2009, Juranek, Jenifer wrote:

> Is any information about the manually-parcellated (CMA) training set used to 
> create the spherical template used in fsv4.*? The information reported in 
> Cerebral Cortex (2004) 14(1):11-22 reports 36 MRI volumes from an ongoing 
> study.
>
> Does this sound about right?
> Or have there been any updates to the spherical template since then?
>
> Many Thanks for any info,
> Jenifer
>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] spherical template: CMA training set

[Juranek, Jenifer]

Is any information about the manually-parcellated (CMA) training set used to 
create the spherical template used in fsv4.*? The information reported in 
Cerebral Cortex (2004) 14(1):11-22 reports 36 MRI volumes from an ongoing study.

Does this sound about right?
Or have there been any updates to the spherical template since then?

Many Thanks for any info,
Jenifer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] scale axis range

[Juranek, Jenifer]

Hi,
Running fsv4.2.0 on RHEL4. Within qdec, the "graph average ROI" provides 
valuable information in scatterplot format. Is it possible for users to define 
the axis range (especially the Y-axis)? For some unknown reason, we have 
encountered several instances where data points are not displayed since the 
scale range of the automatic plot does not capture the entire range of 
individual subject data. Restarting qdec, re-running the design, and reloading 
the label does not alter the outcome.

Any thoughts or quick fixes?

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] graph average ROI

[Juranek, Jenifer]

Hi,
I'm running fsv420 on RHEL4. Within the qdec module (v1.2) menu options, View, 
Graph the ROI --> generates average +/- SD or SE?

Many Thanks,
Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] adding uncached variable to qdec

[Juranek, Jenifer]

Hi,
Running FSv4.2.0 on RHEL4.
I'd like to add a variable such as lgi to qdec analyses. I created a .Qdecrc 
and .fsgd file, ran the lgi files through mris_preproc  & mri_surf2surf 
(following instructions for Uncached Data posted under Group Analysis of the 
FsTutorial). While the output of mri_glmfit displays nicely in tksurfer, I'd 
like to look at the data within qdec (where scatter plots are easily viewed). 
The error I receive within qdec is as follows:
<1st subject in fsgd file>/surf/?h..fwhm.fsaverage.mgh does not exist

Is there an easy (e.g. scripted) way to generate the files within each 
subjects' /surf dir for a new variable not already recognized by the -qcache 
script for use by qdec?

Many Thanks for any suggestions/solutions,
Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] sulc & curv

[Juranek, Jenifer]

Rudolph, many thanks for the additional details.

Just a follow-up question (or two):

1.   Short stubby gyri might have the following morphometric
properties?

a)  Short feature: shallow sulcal depths would be expected to have
sulc values hovering around the mean surface (e.g. around 0) in negative
curvature areas

b)  Stubby feature: increased GM volume, increased surface area, and
perhaps increased cortical thickness depending on how the WM behaved

Thanks so much,

Jenifer

 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] qdec & ?h.sulc

[Juranek, Jenifer]

Thanks for the slide, Nick.

Just a follow-up question...

So does the info in ?h.sulc contain sulcal depth information wrt the
mean cortical surface? How does this differ from the positive values
contained in the ?h.curv file? 

 

Sorry for the confusion, but the wiki suggests that they are different
without going into how they differ. Any additional details are greatly
appreciated.

 

Thanks,

Jenifer

 

 

 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] qdec & ?h.sulc

[Juranek, Jenifer]

Hi,
Looking for a little clarification. 
Using qdec to look at group differences in the surface measure ?h.sulc.
Large positive values in ?h.sulc indicate greater sulcal depth, right?
Large negative values in ?h.sulc indicate something about gyri?
Small negative values in ?h.sulc indicate transition from gyral to sulcal or 
sulcal to gyral?

Many thanks for any additional info,
Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] template deformation error: global region empty

[Juranek, Jenifer]

Hi Bruce,
I forgot to ask that question! You're right on target with identifying the 
problem.

Many Thanks,
Jenifer

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Fri 1/16/2009 1:33 PM
To: Juranek, Jenifer 
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] template deformation error: global region empty
 
Hi Jenifer,

did you check the talairach visually to see if it is correct?

cheers,
Brue


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] template deformation error: global region empty

[Juranek, Jenifer]

Just wondering if there are any suggestions for finding a work-around when the 
"global region of the brain empty" error message appears after executing the 
following command: recon-all -autorecon1 -s CIP_H0519_ERR -notal-check. The T1 
image (001.mgz) looks fine. The -notal-check flag was added on the 2nd 
execution of recon-all due to failure at the talairach_avi stage. Same error 
occurs in 2/16 subjects we have recently attempted to process using freesurfer 
v405 on RHEL5.

Many Thanks for any suggestions,
Jenifer
 
#...@# Skull Stripping Fri Jan 16 12:06:43 CST 2009
/usr/local/freesurfer/subjects/CIP_H0519_ERR/mri

 mri_watershed -T1 -brain_atlas 
/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca 
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


Mode:  T1 normalized volume
Mode:  Use the information of atlas (default parms, --help for details)

*
The input file is T1.mgz
The output file is brainmask.auto.mgz
If this is incorrect, please exit with CTL-C

Weighting the input with atlas information before watershed

*WATERSHED**
Sorting...
  first estimation of the COG coord: x=140 y=158 z=147 r=70
  first estimation of the main basin volume: 1469917 voxels
  Looking for seedpoints 
2 found in the cerebellum 
6 found in the rest of the brain 
  global maximum in x=170, y=133, z=131, Imax=255
  CSF=20, WM_intensity=110, WM_VARIANCE=5
  WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
 preflooding height equal to 10 percent
done
Analyze

  main basin size=7426225090 voxels, voxel volume =1.000 
 = 7426225090 mmm3 = 7426225.152 cm3
done
PostAnalyze...Basin Prior
 533 basins merged thanks to atlas 
  * 0 basin(s) merged in 1 iteration(s)
  * 0 voxel(s) added to the main basin
done
Weighting the input with prior template 

TEMPLATE DEFORMATION

  second estimation of the COG coord: x=172,y=168, z=162, r=9871 iterations
   GLOBAL  CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 19890
  RIGHT_CERCSF_MIN=0, CSF_intensity=4, CSF_MAX=10 , nb = 1251
  LEFT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=9 , nb = 1089
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 7686
 LEFT_BRAINCSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 8289
OTHER  CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = 1575
mri_watershed Error: 
 GLOBAL region of the brain empty !
Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 
x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Fri Jan 16 12:07:31 CST 2009

[jjura...@localhost CIP_H0519_ERR]$ 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] MEMPR sequence for freesurfer analyses

[Juranek, Jenifer]

Has anyone attempted an MEMPR-like sequence as described by van der
Kouwe et al (2008 NeuroImage 40: 559-569) on a 3T Philips Intera? The
paper utilized a 3T Siemens TRIO.  Are the published sequence parameters
directly transferable to a 3T Philips Intera with an 8 channel head coil
and SENSE? Or is some "translation" between Siemens & Philips needed to
get it to work as well as published for the Siemens?

 

Many Thanks for any info,

Jenifer

 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] qdec X error of failed request

[Juranek, Jenifer]

Perfect fix!
Thanks so much...

Jenifer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] qdec X error of failed request

[Juranek, Jenifer]

Hi,
Running FSv405 on RHEL5. Recently obtained new error when qdec was
attempted. Have successfully run qdec before on this box using FSv405.
Only update made was to upgrade to FSLv412. Same error persists after
restarting X. Both tkmedit and tksurfer work fine.

Any ideas how to fix?

Many Thanks,
Jenifer

[jjura...@localhost subjects]$ qdec &
[1] 4306
[jjura...@localhost subjects]$ 
Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl

Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
X Error of failed request:  BadMatch (invalid parameter attributes)
  Major opcode of failed request:  66 (X_PolySegment)
  Serial number of failed request:  5529
  Current serial number in output stream:  5532

[1]Exit 1qdec

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Configure thresholds in overlay options

[Juranek, Jenifer]

Hi,
Running FSv405 on RHEL5. 
Is any descriptive information available for threshold options in the configure 
overlay display gui?
Specifically the bases for linear, linear opaque, and piecewise thresholds?
Visually, the three options appear dramatically different. Are there specific 
datatypes each overlay option is designed to handle?

Many thanks for any information you can provide,
Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] qdec patch

[Juranek, Jenifer]

Nick,

Just in case you're taking a head count, I would benefit from a patch
for qdec which reads ?h.pial_lgi files as mentioned in response to
Martin's posting yesterday.

 

Cheers,

Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] FreeSurferColorLUT & aparc

[Juranek, Jenifer]

yes, the correct Sgmtn label is displayed in the TkMedit Tools

-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED] 
Sent: Wednesday, October 22, 2008 4:30 PM
To: Juranek, Jenifer 
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] FreeSurferColorLUT & aparc

if you load it in tkmedit is it displayed properly?

On 
Wed, 22 Oct 2008, Juranek, Jenifer  wrote:

> I'm able to view the intensity values in FSL. Is there another
approach
> I can take to doublecheck?
>
> Jenifer
> -Original Message-
> From: Bruce Fischl [mailto:[EMAIL PROTECTED]
> Sent: Wednesday, October 22, 2008 4:15 PM
> To: Juranek, Jenifer
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] FreeSurferColorLUT & aparc
>
> Hi Jenifer,
>
> how are you getting those intensity values?
>
> Bruce
>
> On Wed, 22 Oct 2008, Juranek,
> Jenifer  wrote:
>
>> Hi,
>> Running fsv405 on RHEL5.
>> I've encountered some unexpected numerical values wrt
> FreeSurferColorLUT.txt. Are my expectations off?
>>
>> 1) In the aparc+aseg.mgz file, intensity values for the cortical
> labels range from -32768 to 654, with negative values falling in some
> regions in the left hemisphere.
>> 2) Identical results are obtained if mri_aparc2aseg is used to
> generate an output file:  mri_aparc2aseg --s mysubject --o
> ./aparc2aseg.mgz
>> 3) Values of aseg.mgz map perfectly well to FreeSurferColorLUT.txt
>>
>> Example values obtained from aparc+aseg.mgz are listed below:
>> lh.superiortemporal=484 (expecting 1030 from FreeSurferColorLUT.txt)
>> rh.superiortemporal=32767 (expecting 2030)
>>
>> Although these numerical values do not match the LUT, they are
> consistent across subjects.
>>
>> Many Thanks for any insights...
>> Jenifer
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] FreeSurferColorLUT & aparc

[Juranek, Jenifer]

I'm able to view the intensity values in FSL. Is there another approach
I can take to doublecheck?

Jenifer
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED] 
Sent: Wednesday, October 22, 2008 4:15 PM
To: Juranek, Jenifer 
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FreeSurferColorLUT & aparc

Hi Jenifer,

how are you getting those intensity values?

Bruce

On Wed, 22 Oct 2008, Juranek, 
Jenifer  wrote:

> Hi,
> Running fsv405 on RHEL5.
> I've encountered some unexpected numerical values wrt
FreeSurferColorLUT.txt. Are my expectations off?
>
> 1) In the aparc+aseg.mgz file, intensity values for the cortical
labels range from -32768 to 654, with negative values falling in some
regions in the left hemisphere.
> 2) Identical results are obtained if mri_aparc2aseg is used to
generate an output file:  mri_aparc2aseg --s mysubject --o
./aparc2aseg.mgz
> 3) Values of aseg.mgz map perfectly well to FreeSurferColorLUT.txt
>
> Example values obtained from aparc+aseg.mgz are listed below:
> lh.superiortemporal=484 (expecting 1030 from FreeSurferColorLUT.txt)
> rh.superiortemporal=32767 (expecting 2030)
>
> Although these numerical values do not match the LUT, they are
consistent across subjects.
>
> Many Thanks for any insights...
> Jenifer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] FreeSurferColorLUT & aparc

[Juranek, Jenifer]

Hi,
Running fsv405 on RHEL5.
I've encountered some unexpected numerical values wrt FreeSurferColorLUT.txt. 
Are my expectations off?

1) In the aparc+aseg.mgz file, intensity values for the cortical labels range 
from -32768 to 654, with negative values falling in some regions in the left 
hemisphere. 
2) Identical results are obtained if mri_aparc2aseg is used to generate an 
output file:  mri_aparc2aseg --s mysubject --o ./aparc2aseg.mgz
3) Values of aseg.mgz map perfectly well to FreeSurferColorLUT.txt

Example values obtained from aparc+aseg.mgz are listed below:
lh.superiortemporal=484 (expecting 1030 from FreeSurferColorLUT.txt)
rh.superiortemporal=32767 (expecting 2030)

Although these numerical values do not match the LUT, they are consistent 
across subjects.

Many Thanks for any insights...
Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] LGI error in make_outer_surface at 31

[Juranek, Jenifer]

Looks like my image processing toolbox from matlab was not properly
installed. Now that I have re-installed the image processing toolbox,
LGI appears to be working fine.

 

Cheers,

Jenifer

~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] LGI error in make_outer_surface at 31

[Juranek, Jenifer]

Hi,
Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB 
v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. 
Specific error is pasted below:

Any suggestions to correct my error?

Thanks,
Jenifer

>> reading filled volume...
closing volume...
??? Undefined function or method 'fspecial' for input arguments of type 'char'.

Error in ==> make_outer_surface at 31
Gaussian = fspecial('gaussian',[2 2],1);

>>
ERROR: make_outer_surface did not create output file 
'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!
Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 
x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008

[EMAIL PROTECTED] jjuranek_fsv405]$


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] WM intensity < CSF intensity?

[Juranek, Jenifer]

Thanks, Bruce.
The file upload to your server just finished.

-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED] 
Sent: Wednesday, September 03, 2008 12:34 PM
To: Juranek, Jenifer 
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] WM intensity < CSF intensity?

hmmm, do you want to send it to us and we'll take a look?
On Wed, 3 Sep 
2008, Juranek, Jenifer  wrote:

> Yes, in the T1.mgz, the WM is around 110 in the slices I sampled
across
> the ant-post extent of the brain.
>
> -Original Message-
> From: Bruce Fischl [mailto:[EMAIL PROTECTED]
> Sent: Wednesday, September 03, 2008 11:41 AM
> To: Juranek, Jenifer
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] WM intensity < CSF intensity?
>
> is the white  matter in the T1.mgz close to 110?
> On Wed, 3 Sep 2008,
> Juranek, Jenifer  wrote:
>
>> Hi,
>> I'm running fsv405 on RHEL5. I received the following message and
> reviewed the input images, but could not spot the problem. Any
> suggestions about where I should be looking in the T1.mgz?
>>
>> Many Thanks,
>> Jenifer
>>
>> White matter intensity 0 is lower than CSF intensity 14.
>> Please examine input images.  Will terminate ...
>> ***
>> ***
>> ***
>>
>> **
>> MRIstripSkull failed.
>> 
>>
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] WM intensity < CSF intensity?

[Juranek, Jenifer]

Yes, in the T1.mgz, the WM is around 110 in the slices I sampled across
the ant-post extent of the brain.

-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED] 
Sent: Wednesday, September 03, 2008 11:41 AM
To: Juranek, Jenifer 
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] WM intensity < CSF intensity?

is the white  matter in the T1.mgz close to 110?
On Wed, 3 Sep 2008, 
Juranek, Jenifer  wrote:

> Hi,
> I'm running fsv405 on RHEL5. I received the following message and
reviewed the input images, but could not spot the problem. Any
suggestions about where I should be looking in the T1.mgz?
>
> Many Thanks,
> Jenifer
>
> White matter intensity 0 is lower than CSF intensity 14.
> Please examine input images.  Will terminate ...
> ***
> ***
> ***
>
> **
> MRIstripSkull failed.
> 
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] WM intensity < CSF intensity?

[Juranek, Jenifer]

Hi,
I'm running fsv405 on RHEL5. I received the following message and reviewed the 
input images, but could not spot the problem. Any suggestions about where I 
should be looking in the T1.mgz?

Many Thanks,
Jenifer

White matter intensity 0 is lower than CSF intensity 14.
Please examine input images.  Will terminate ...
***
***
***

**
 MRIstripSkull failed.






___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] choroid plexus

[Juranek, Jenifer]

Hi,

Would like to sum all CSF compartments to get a global CSF volume for
each subject. 

Should Choroid plexus (L & R) be included in the summation? I have not
seen other "non-freesurfer" apps tease out the choroid plexus. 

 

So far, I have the following 8 compartments:

[Left-Lateral-Ventricle] + [Left-Inf-Lat-Vent] + [3rd-Ventricle] +
[4th-Ventricle] + [Right-Lateral-Ventricle] + [Right-Inf-Lat-Vent] +
[5th-Ventricle] + [CSF]

 

Many Thanks for any advice you can provide,

Jenifer

~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Floating exception (core dumped)

[Juranek, Jenifer]

Hi,
Running fsv405 on RHEL4 (64bit) and have encountered the following error after 
executing recon-all -all: Floating exception (core dumped). Did not encounter 
this error using fsv401 on the same box. See below for the standard output to 
screen.

Any ideas?

Many Thanks,
Jenifer

[EMAIL PROTECTED] subjects]$ recon-all -all -s PC_011_APO143_2mo
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rwxrwx---  1 jjuranek root 2271789 Jul 25 07:15 
/usr/local/freesurfer/subjects/ PC_011_APO143_2mo/scripts/recon-all.log
Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 
x86 _64 x86_64 x86_64 GNU/Linux
Floating exception (core dumped)
#
[EMAIL PROTECTED] MotionCor Tue Aug  5 11:38:42 CDT 2008
Found 1 runs
/usr/local/freesurfer/subjects/PC_011_APO143_2mo/mri/orig/001.mgz
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 /usr/local/freesurfer/subjects/PC_011_APO143_2mo/mri/orig/001.mgz 
/usr/local /freesurfer/subjects/PC_011_APO143_2mo/mri/rawavg.mgz

/usr/local/freesurfer/subjects/PC_011_APO143_2mo

 mri_convert /usr/local/freesurfer/subjects/PC_011_APO143_2mo/mri/rawavg.mgz 
/us r/local/freesurfer/subjects/PC_011_APO143_2mo/mri/orig.mgz --conform

mri_convert /usr/local/freesurfer/subjects/PC_011_APO143_2mo/mri/rawavg.mgz 
/usr /local/freesurfer/subjects/PC_011_APO143_2mo/mri/orig.mgz --conform






___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Hippo-Amyg defs

[Juranek, Jenifer]

Hi,

Is any documentation available for describing the anatomical landmarks
for demarcation of amygdala and hippocampus used by aseg?

 

Many Thanks,

Jenifer

 

 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow

[Juranek, Jenifer]

Nick,
I checked the /etc/X11/xorg.conf file. It already has a line uder Section 
"Module" listing Load "glx" (see below):

# nvidia-settings: X configuration file generated by nvidia-settings
# nvidia-settings:  version 1.0  ([EMAIL PROTECTED])  Fri Dec 15 10:40:57 P
ST 2006

Section "ServerLayout"
Identifier "Layout0"
Screen  0  "Screen0" 0 0
InputDevice"Keyboard0" "CoreKeyboard"
InputDevice"Mouse0" "CorePointer"
EndSection

Section "Files"
RgbPath "/usr/lib64/X11/rgb"
FontPath"unix/:7100"
EndSection

Section "Module"
Load   "dbe"
Load   "extmod"
Load   "type1"
Load   "freetype"
Load   "glx"
EndSection

Any other sections of the xorg.conf file I should check?
Is there a particular screen resolution I should check under Section "Screen" 
Options or Modes?

Thanks,
Jenifer

-Original Message-
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Wed 7/23/2008 4:04 PM
To: Juranek, Jenifer 
Cc: Freesurfer Mailing List
Subject: RE: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow
 
Jenifer,

In the file /etc/X11/xorg.conf, within the section titled Section
"Module", make sure this line exists:

  Load "glx"

You might need to have your administrator perform this change, as it
requires root access.  You will have to restart your X server after
making this change (Ctrl-Bksp).

Nick


On Wed, 2008-07-23 at 15:51 -0500, Juranek, Jenifer wrote:
> Hi Nick,
> This is the first time I have tried to use the qdec feature, so I am unable 
> to report whether new problem to v405 or not. 
> 
> I am running from the terminal window on the RHEL5 box (not across VPN or SSH 
> or VNC).
> 
> Thanks for any help you can provide,
> Jenifer
> 
> -Original Message-
> From: Nick Schmansky [mailto:[EMAIL PROTECTED]
> Sent: Wed 7/23/2008 3:47 PM
> To: Juranek, Jenifer 
> Cc: Freesurfer Mailing List
> Subject: Re: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow
>  
> Jenifer,
> 
> Is this new to v405, or have prior versions also had this problem?
> 
> Are you running directly from the terminal?  Or over an ssh or vnc
> connection?  If over vnc, from what kind of machine?
> 
> Nick
> 
> 
> On Wed, 2008-07-23 at 11:14 -0500, Juranek, Jenifer wrote:
> > Hi,
> > Running Freesurfer v405 on RHEL5. Tried to launch qdec from the command 
> > prompt. While the splash screen did appear with the inflated brain surface, 
> > the qdec interface did not appear (even after 10min). When I tried to 
> > CTRL-C the terminal window, the following error message appeared:
> > 
> > [EMAIL PROTECTED] subjects]$ qdec &
> > ERROR: In 
> > /usr/pubsw/packages/vtk/5.0.4/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, 
> > line 219
> > vtkXOpenGLRenderWindow (0x7e06290): Could not find a decent visual
> > 
> > [EMAIL PROTECTED] subjects]$ ps -ef | grep qdec
> > jjuranek 32682 32579  0 10:45 pts/11   00:00:00 /bin/tcsh -ef 
> > /usr/local/freesurfer/bin/qdec
> > jjuranek 32687 32682  0 10:45 pts/11   00:00:00 qdec.bin
> > jjuranek 32763  9505  0 11:13 pts/100:00:00 grep qdec
> > [EMAIL PROTECTED] subjects]$ kill -1 32687
> > 
> > Any ideas how to fix?
> > 
> > Thanks,
> > Jenifer
> > 
> > 
> > 
> > 
> > 
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > 
> 
> 
> 
> 



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow

[Juranek, Jenifer]

Hi Nick,
This is the first time I have tried to use the qdec feature, so I am unable to 
report whether new problem to v405 or not. 

I am running from the terminal window on the RHEL5 box (not across VPN or SSH 
or VNC).

Thanks for any help you can provide,
Jenifer

-Original Message-
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Wed 7/23/2008 3:47 PM
To: Juranek, Jenifer 
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow
 
Jenifer,

Is this new to v405, or have prior versions also had this problem?

Are you running directly from the terminal?  Or over an ssh or vnc
connection?  If over vnc, from what kind of machine?

Nick


On Wed, 2008-07-23 at 11:14 -0500, Juranek, Jenifer wrote:
> Hi,
> Running Freesurfer v405 on RHEL5. Tried to launch qdec from the command 
> prompt. While the splash screen did appear with the inflated brain surface, 
> the qdec interface did not appear (even after 10min). When I tried to CTRL-C 
> the terminal window, the following error message appeared:
> 
> [EMAIL PROTECTED] subjects]$ qdec &
> ERROR: In 
> /usr/pubsw/packages/vtk/5.0.4/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, 
> line 219
> vtkXOpenGLRenderWindow (0x7e06290): Could not find a decent visual
> 
> [EMAIL PROTECTED] subjects]$ ps -ef | grep qdec
> jjuranek 32682 32579  0 10:45 pts/11   00:00:00 /bin/tcsh -ef 
> /usr/local/freesurfer/bin/qdec
> jjuranek 32687 32682  0 10:45 pts/11   00:00:00 qdec.bin
> jjuranek 32763  9505  0 11:13 pts/100:00:00 grep qdec
> [EMAIL PROTECTED] subjects]$ kill -1 32687
> 
> Any ideas how to fix?
> 
> Thanks,
> Jenifer
> 
> 
> 
> 
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow

[Juranek, Jenifer]

Hi,
Running Freesurfer v405 on RHEL5. Tried to launch qdec from the command prompt. 
While the splash screen did appear with the inflated brain surface, the qdec 
interface did not appear (even after 10min). When I tried to CTRL-C the 
terminal window, the following error message appeared:

[EMAIL PROTECTED] subjects]$ qdec &
ERROR: In 
/usr/pubsw/packages/vtk/5.0.4/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, 
line 219
vtkXOpenGLRenderWindow (0x7e06290): Could not find a decent visual

[EMAIL PROTECTED] subjects]$ ps -ef | grep qdec
jjuranek 32682 32579  0 10:45 pts/11   00:00:00 /bin/tcsh -ef 
/usr/local/freesurfer/bin/qdec
jjuranek 32687 32682  0 10:45 pts/11   00:00:00 qdec.bin
jjuranek 32763  9505  0 11:13 pts/100:00:00 grep qdec
[EMAIL PROTECTED] subjects]$ kill -1 32687

Any ideas how to fix?

Thanks,
Jenifer






___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] major lobes of cerebellum

[Juranek, Jenifer]

Is there any interest in parcellation of the cerebellum into its major
regions: corpus medullare, anterior, superior-posterior,
inferior-posterior regions? Any easy approaches available for testing
out? Would a volume-based approach be sufficient, or would a
surface-based approach be necessary?

 

Anyone's input is greatly appreciated

Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] seg edits

[Juranek, Jenifer]

Running Freesurfer v4.0.5 on RHEL5 linux system.

 

General Question: after using the "Edit Segmentation" tool and saving
edits by overwriting the aseg.mgz file generated during $recon-all
-autorecon-all...which command should I pass to re-enter the analysis
pipeline at the most appropriate spot? I understand that after edits to
the wm.mgz file, it is fine to re-enter the pipeline with $recon-all
-autorecon2-wm -autorecon3. But unable to find much in the Wiki wrt
*aseg.mgz* edits and subsequent re-processing (other than "how to"
accomplish edits).

 

Specific info: Unusual case with enlarged lateral ventricles
(particularly posteriorly). Review of the aseg.mgz after completing
$recon-all -autorecon-all  indicated that the right lateral ventricle
(posterior portion) was partially incorrectly labeled in a range of
slices (COR: 86-48) with a "cocktail" of labels, including the
following: Right-Lateral-Ventricle; Right-Cerebral-White-Matter;
Right-Cerebral-Cortex; None; WM-hypointensities. 

 

After editing *wm.mgz* to fill-in missing voxels in the problem areas
and re-running $recon-all -autorecon2-wm -autorecon3, segmentation
labels of problem areas still required edits.  After using the "Edit
Segmentation" tool, I have now saved my edits by overwriting *aseg.mgz*.
So which command should I pass to re-enter the pipeline?

 

Many Thanks for any advice you can provide.

Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] atlas renormalization

[Juranek, Jenifer]

The atlas renormalization process described by Han & Fischl (2007)...which 
version of freesurfer was this introduced?
 
Many Thanks,
Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] SELinux AVC denial: Matlab

[Juranek, Jenifer]

While trying to check if -lgi will run on bert (on RHEL5,fsv404 and matlab 
r2008a), I received the following message from SELinux (please see summary 
below):

Sorry to be so cautious, but do I change to allow_execheap boolean? The 
system-wide impact statement makes me a little nervous...

Many thanks for any advice you can provide,
Jenifer

Summary:

SELinux is preventing MATLAB from changing the access protection of memory on
the heap.

Detailed Description:

[SELinux is in permissive mode, the operation would have been denied but was
permitted due to permissive mode.]

The MATLAB application attempted to change the access protection of memory on
the heap (e.g., allocated using malloc). This is a potential security problem.
Applications should not be doing this. Applications are sometimes coded
incorrectly and request this permission. The SELinux Memory Protection Tests
(http://people.redhat.com/drepper/selinux-mem.html) web page explains how to
remove this requirement. If MATLAB does not work and you need it to work, you
can configure SELinux temporarily to allow this access until the application is
fixed. Please file a bug report
(http://bugzilla.redhat.com/bugzilla/enter_bug.cgi) against this package.

Allowing Access:

If you want MATLAB to continue, you must turn on the allow_execheap boolean.
Note: This boolean will affect all applications on the system.

The following command will allow this access:

setsebool -P allow_execheap=1

Additional Information:

Source Contextroot:system_r:unconfined_t:SystemLow-SystemHigh
Target Contextroot:system_r:unconfined_t:SystemLow-SystemHigh
Target ObjectsNone [ process ]
SourceMATLAB
Source Path   /usr/local/MATLAB_R2008a/bin/glnxa64/MATLAB
Port  
Host  localhost.localdomain
Source RPM Packages   
Target RPM Packages   
Policy RPMselinux-policy-2.4.6-137.el5
Selinux Enabled   True
Policy Type   targeted
MLS Enabled   True
Enforcing ModePermissive
Plugin Name   allow_execheap
Host Name localhost.localdomain
Platform  Linux localhost.localdomain 2.6.18-92.el5 #1 SMP
  Tue Apr 29 13:16:15 EDT 2008 x86_64 x86_64
Alert Count   1
First SeenThu 29 May 2008 01:55:19 PM CDT
Last Seen Thu 29 May 2008 01:55:19 PM CDT
Local ID  547d8303-5b60-4883-adc1-5da588da0b2a
Line Numbers  

Raw Audit Messages

host=localhost.localdomain type=AVC msg=audit(1212087319.314:56): avc:  denied  
{ execheap } for  pid=9538 comm="MATLAB" 
scontext=root:system_r:unconfined_t:s0-s0:c0.c1023 
tcontext=root:system_r:unconfined_t:s0-s0:c0.c1023 tclass=process

host=localhost.localdomain type=SYSCALL msg=audit(1212087319.314:56): 
arch=c03e syscall=10 success=yes exit=0 a0=68d4000 a1=553 a2=7 a3=3 items=0 
ppid=9460 pid=9538 auid=0 uid=500 gid=500 euid=500 suid=500 fsuid=500 egid=500 
sgid=500 fsgid=500 tty=pts5 ses=1 comm="MATLAB" 
exe="/usr/local/MATLAB_R2008a/bin/glnxa64/MATLAB" 
subj=root:system_r:unconfined_t:s0-s0:c0.c1023 key=(null)



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] tksurfer display broken: fixed

[Juranek, Jenifer]

Not exactly sure how or what happened...but did manage to "fix" my tksurfer 
display problem.
Since others on the list had reported similar problems, I thought I'd post what 
I did to "fix" the problem. Since I'm not a Linux guru, my "fix" is probably 
just a "bandaid"...but it did work...and hopefully the info provides some 
assistance to others.

Just to note the following particulars of my system:
RHEL5 (DELL Precision 690n box went live April 16, 2008)
Linux_x86_64 architecture

2 kernels: 
drwxr-xr-x 18 root root 4096 May  9 13:50 2.6.18-53.1.19.el5-x86_64
drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64

NVIDIA Quadro Fx 3450/4000 SDI
Driver Version 1.0-9746

"Friendly" software also installed on the same box=fslv404
MATLAB r2008a is also installed (currently running -lgi on bert...I'll update 
on the outcome of this "friendliness" test)


As of yesterday, had several possible scenarios outlined:
1) rpm -e dell-nvidia-rhel5-169.12-1dkms.x86_64.rpm
   rpm -ivh dell-nvidia-9746-7dkms.x86_64.rpm
--> should return to a well-behaved (albeit "older") nvidia
driver...same as "out of the box"

2) restore original "out of the box" settings for entire system via
/usr/var/dell/reinstall.sh
--> should return ALL system settings to original "out of the box"...good for 
freesurfer and fsl apps but not so good for matlab...

3) boot into older kernel (I apparently have a total of 2 listed in
/usr/src/kernels)
[EMAIL PROTECTED] kernels]# ls -l
total 16
drwxr-xr-x 18 root root 4096 May  9 13:50 2.6.18-53.1.19.el5-x86_64
drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64

I attempted (1) first. However, the driver was not well-behaved for bert 
(tkmedit or tksurfer).
I attempted (3) second. However, no change in behavior.
While tarballing to prepare for (3)...since everything worked perfectly fine 
right out of the box -- before Matlab and before any package updates...I found 
my *original* /etc/X11/xorg.conf file (from April 16) and cp it into 
/etc/X11/xorg.conf & rebooted.

RESULTS:
Was *very* happy to see tksurfer & tkmedit behave properly for bert.
Proper behavior for tksurfer & tkmedit was observed in both kernels (after the 
xorg.conf file replacement).
Still waiting to see if matlab behaves for bert's -lgi.

I diff'd the "original" xorg.conf with the "broken" one and the following lines 
were returned:

Hope this helps others find their "bandaid" solution to get them up and running 
again.
Cheers,
Jenifer

[EMAIL PROTECTED] X11]# diff xorg.conf.backup.OLD xorg.conf.backup
1,4c1,2
< 
< # nvidia-xconfig: X configuration file generated by nvidia-xconfig
< # nvidia-xconfig:  version 1.0  ([EMAIL PROTECTED])  Fri Dec 15 10:40:27 PST 
2006
< # Xorg configuration created by system-config-display
---
> # nvidia-settings: X configuration file generated by nvidia-settings
> # nvidia-settings:  version 1.0  ([EMAIL PROTECTED])  Fri Dec 15 10:40:57 PST 
> 2006
7,10c5,8
<   Identifier "Default Layout"
<   Screen  0  "Screen0" 0 0
<   InputDevice"Mouse0" "CorePointer"
<   InputDevice"Keyboard0" "CoreKeyboard"
---
> Identifier "Layout0"
> Screen  0  "Screen0" 0 0
> InputDevice"Keyboard0" "CoreKeyboard"
> InputDevice"Mouse0" "CorePointer"
13a12,13
> RgbPath "/usr/lib64/X11/rgb"
> FontPath"unix/:7100"
17c17,21
<   Load  "glx"
---
> Load   "dbe"
> Load   "extmod"
> Load   "type1"
> Load   "freetype"
> Load   "glx"
21c25
<   Option  "AllowMouseOpenFail" "yes"
---
> Option "Xinerama" "0"
25d28
< 
27,32c30,35
<   Identifier  "Mouse0"
<   Driver  "mouse"
<   Option  "Protocol" "auto"
<   Option  "Device" "/dev/input/mice"
<   Option  "Emulate3Buttons" "no"
<   Option  "ZAxisMapping" "4 5"
---
> Identifier "Mouse0"
> Driver "mouse"
> Option "Protocol" "auto"
> Option "Device" "/dev/input/mice"
> Option "Emulate3Buttons" "no"
> Option "ZAxisMapping" "4 5"
36,39c39,43
<   Identifier  "Keyboard0"
<   Driver  "kbd"
<   Option  "XkbModel" "pc105"
<   Option  "XkbLayout" "us"
---
> # generated from data in "/etc/sysconfig/keyboard"
> Identifier "Keyboard0"
> Driver "kbd"
> Option "XkbLayout" "us"
> Option "XkbModel" "pc105"
43,49c47,53
<   Identifier   "Monitor0"
<   VendorName   "Unknown"
<   ModelName"Unknown"
<  ### Comment all HorizSync and VertSync values to use DDC:
<   HorizSync30.0 - 110.0
<   VertRefresh  50.0 - 150.0
<   Option  "DPMS"
---
> # HorizSync source: edid, VertRefresh source: edid
> Identifier "Monitor0"
> VendorName "Unknown"
> ModelName  "DELL 2007WFP"
> HorizSync   30.0 - 83.0
> VertRefresh 56.0 - 76.0
> Option "DPMS"
53,55c57,60
<   Identif

[Freesurfer] tksurfer display broken: post re-install nvidia 9746

[Juranek, Jenifer]

I re-installed the dell-nvidia driver (original with system). 
Some new behavior observed with bert:
tksurfer bert lh pial yields a complete "bert" window (entire pial surface is 
displayed). However, the lower window "TkSurfer Tools" is not visible.
Also, tkmedit bert norm.mgz fails to launch a display, simply returns a command 
prompt.

I've pasted the screen output for tksurfer below:

Any ideas are greatly appreciated.

[EMAIL PROTECTED] subjects]$ tksurfer bert lh pial
surfer: current subjects dir: /usr/local/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /usr/local/freesurfer/subjects
surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/T1.mgz
surfer: vertices=131168, faces=262332
Loading /usr/local/freesurfer/surface_labels.txt
surfer: ### redraw failed: no gl window open
surfer: single buffered window
surfer: tkoInitWindow(bert)
Tk_Init failed: this isn't a Tk applicationunknown color name "Black"
Tix_Init failed: this isn't a Tk applicationunknown color name "Black"
surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl
Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
Error sourcing /usr/local/freesurfer/lib/tcl/tksurfer.tcl:
this isn't a Tk applicationunknown color name "Black"
surfer: Error sending tcl command tkm_SetEnableGroupStatus 
mg_InflatedVSetLoaded 0:
can't read "glEnableGroups(mg_InflatedVSetLoaded)": no such variable
surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_PialVSetLoaded 0:
can't read "glEnableGroups(mg_PialVSetLoaded)": no such variable
surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_TimeCourseLoaded 
0:
can't read "glEnableGroups(mg_TimeCourseLoaded)": no such variable
surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_OverlayLoaded 0:
can't read "glEnableGroups(mg_OverlayLoaded)": no such variable
surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_CurvatureLoaded 0:
can't read "glEnableGroups(mg_CurvatureLoaded)": no such variable
surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_LabelLoaded 0:
can't read "glEnableGroups(mg_LabelLoaded)": no such variable
surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_FieldSignLoaded 0:
can't read "glEnableGroups(mg_FieldSignLoaded)": no such variable
surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_FieldMaskLoaded 0:
can't read "glEnableGroups(mg_FieldMaskLoaded)": no such variable
surfer: Error sending tcl command UpdateUndoItemLabel "Nothing to Undo":
invalid command name "UpdateUndoItemLabel"
surfer: Error sending tcl command tkm_SetEnableGroupStatus 
mg_OriginalVSetLoaded 1:
can't read "glEnableGroups(mg_OriginalVSetLoaded)": no such variable
surfer: Error sending tcl command LblLst_SetStructures { 0 Unknown 1 
G_cingularis 2 G_cuneus 3 G_frontalis_inf-pars_opercularis 4 
G_frontalis_inf-pars_orbitalis 5 G_frontalis_inf-pars_triangularis 6 
G_frontalis_medius 7 G_frontalis_sup-pars_lateralis 8 
G_frontalis_sup-pars_medialis 9 G_frontomarginalis 10 G_hippocampi 11 
G_insularis_breves 12 G_occipitalis_inf 13 G_occipitalis_medius-pars_inf 14 
G_occipitalis_medius-pars_sup 15 G_occipitalis_sup 16 G_lateralis 17 
G_lingualis 18 G_parahippocampi 19 G_orbitalis 20 G_paracentralis 21 
G_parietalis_inf-pars_angularis 22 G_parietalis_inf-pars_supramarginalis 23 
G_parietalis_sup 24 G_postcentralis 25 G_precentralis 26 G_precuneus 27 
G_rectus_and_S_orbitalis_medialis 28 G_rectus_and_S_orbitalis_medialis2 29 
G_subcentralis 30 G_supracingularis 31 G_temporalis_transversalis 32 
G_temporalis_inf 33 G_temporalis_medius 34 G_temporalis_sup-pars_lateralis 35 
G_temporalis_sup-planum_polare 36 G_temporalis_sup-planum_temporale 37 
Plica_falci!
 formis 38 Polus_occipitalis 39 Polus_temporalis 40 S_temporalis_transversalis 
42 S_angularis 43 S_calcarinus 44 S_centralis_insulae_&_G_insularis_longus 46 
S_centralis 47 S_cingularis 48 S_cingularis-pars_marginalis 49 
S_circularis_insulae_ant 50 S_circularis_insulae_inf 51 
S_circularis_insulae_sup 52 S_corpori_callosi 53 S_diagonalis 54 
S_frontalis_inf 55 S_frontalis_medialis 56 S_frontalis_medius 57 
S_frontalis_sup 58 S_frontomarginalis 59 S_intermedius_primus 60 
S_intermedius_secundus 61 S_intracingularis 62 S_intraoccipitalis_medius 63 
S_intraoccipitotemporalis_lateralis 64 S_intraparietalis 65 
S_lateralis-pars_ant-ramus_horizontalis 66 
S_lateralis-pars_ant-ramus_verticalis 67 S_lateralis-pars_horizontalis 68 
S_lateralis-pars_post 69 S_lunatus 70 S_occipitalis_ant 71 S_occipitalis_inf 72 
S_occipitalis_medius 73 S_occipitalis_sup 74 S_occipitalis_transversalis 75 
S_occipitopolaris 76 S_occipitotemporalis_lateralis 77 
S_occipitotemporalis_medialis 78 S_orbitales 79 S_orbi!
 talis_laterali

RE: [Freesurfer] tksurfer display broken: "smart" over-ride?

[Juranek, Jenifer]

Paul,
Actually, I did follow your suggestion *first* to add the 3 lines to 
X11/xorg.conf (see tailed file below). However, after reboot, the same problem 
persisted. So I followed Krish's advice to look at a previous thread which 
referenced the mesa-libGL-*.rpm files @ MGH. 

My mistake for not knowing which postings are system-dependent...I'm *very* 
glad the "smart" system prevented me from making things worse! 

Any follow-up advice to resolve my problem?

Many Thanks,
Jenifer


Section "Device"
Identifier "Videocard0"
Driver "nvidia"
VendorName "NVIDIA Corporation"
BoardName  "Quadro FX 3450/4000 SDI"
EndSection

Section "Screen"
Identifier "Screen0"
Device "Videocard0"
Monitor"Monitor0"
DefaultDepth16
Option "metamodes" "1600x1024 +0+0; 800x600 +0+0; 640x480 +0+0"
SubSection "Display"
Depth   16
Modes  "1600x1200" "1280x1024" "1024x768" "800x600" "640x480"
EndSubSection
EndSection

Section "Extensions"
Option "Composite" "Disable"
EndSection



-Original Message-
From: Paul Raines [mailto:[EMAIL PROTECTED]
Sent: Wed 5/28/2008 10:10 AM
To: Juranek, Jenifer 
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tksurfer display broken: "smart" over-ride?
 

I don't understand why you got a mesa-libGL rpm and are trying to
install it?  I think doing so could really mess up your system so it
is a good thing it is not letting you.

My email was about adding

Section "Extensions"
  Option "Composite" "Disable"
EndSection

to your /etc/X11/xorg.conf assuming you are using the propreitary
NVIDIA driver.  Which you should also upgrade to the latest one.

On Wed, 28 May 2008, Juranek, Jenifer  wrote:

> Krish & Paul,
> Many thanks for the quick advice. I have downloaded the 
> mesa-libGL-6.5.1-7.2.el5.x86_64.rpm from the RH network to my desktop. 
> However, a "smart" window pops up reporting that "a newer version than 
> /home/jjuranek/Desktop/mesa-libGL-6.5.1-7.2.el5.x86_64.rpm is already 
> installed". I select "OK" anyway, but a new window pops-up reporting that 
> "No packages were given for installation". How do I over-ride the "smart" 
> system to install the legacy driver I need to make sure that everything is 
> installed in the proper place(s) to make tksurfer happy again?
>
> Thanks so much,
> Jenifer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

-- 
---
Paul Rainesemail: raines at nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street Charlestown, MA 02129USA




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] tksurfer display broken: "smart" over-ride?

[Juranek, Jenifer]

Krish & Paul,
Many thanks for the quick advice. I have downloaded the 
mesa-libGL-6.5.1-7.2.el5.x86_64.rpm from the RH network to my desktop. However, 
a "smart" window pops up reporting that "a newer version than 
/home/jjuranek/Desktop/mesa-libGL-6.5.1-7.2.el5.x86_64.rpm is already 
installed". I select "OK" anyway, but a new window pops-up reporting that "No 
packages were given for installation". How do I over-ride the "smart" system to 
install the legacy driver I need to make sure that everything is installed in 
the proper place(s) to make tksurfer happy again?

Thanks so much,
Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] tksurfer display broken

[Juranek, Jenifer]

Hi,
I recently encountered a problem with tksurfer display (worked perfectly fine a 
couple of weeks ago). The only change I've made to my linux (centOs 5) system 
is the recent installation of MATLAB r2008a. Just a note: This was *not* a fun 
process since the MATLAB 2008a install required deprecated libs (e.g. libXp) 
which are no longer included with RHEL5. 

Bottom line: the beginning of my tksurfer display problem does coincide with 
this process of  attempting to install MATLAB r2008a. Although I finally 
succeeded in getting the MATLAB installed, is there a fix to restore tksurfer 
display to its proper functionality?

In descriptive terms, the tksurfer command launches a window containing a small 
sliver of the posterior region of the brain. Screen output is pasted below for 
calling up "bert". This morning I upgraded from freesurfer v403 to v404, but 
the problem still persists. I suspect I broke something in my RHEL5 while 
trying to fix the Matlab r2008a install failure.

BTW..."bert" looks fine in tkmedit (including aseg+aparc file)

Any ideas?
Jenifer

[EMAIL PROTECTED] freesurfer]$ tksurfer bert rh pial
surfer: current subjects dir: /usr/local/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /usr/local/freesurfer
surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/T1.mgz
surfer: vertices=131848, faces=263692
Loading /usr/local/freesurfer/surface_labels.txt
surfer: ### redraw failed: no gl window open
surfer: single buffered window
surfer: tkoInitWindow(bert)
surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl
Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] atlas renormalization

[Juranek, Jenifer]

Another curious question: The atlas renormalization process described by Han & 
Fischl (2007)...which version of freesurfer was this introduced?
 
Many Thanks,
Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] talairach_avi

[Juranek, Jenifer]

Just curious...
1) was talairach_avi (or more specifically, 4dfp suite) introduced with any 
particular version# of freesurfer? Or has it always been the default? 
2) Any comments on differences/similarities with mritotal as called by the 
-use-mritotal flag within freesurfer?
 
Many Thanks,
Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] lh.aparc.a2005s: S_subcentral_ant label

[Juranek, Jenifer]

We recently started playing with the ?h.aparc.a2005s annotation files (fsv401).
We noticed that in /freesurfer/subject/bert, the S_subcentral_ant label is not 
listed as a variable in the /stats/lh.aparc.a2005s output file. However, this 
variable name does *sometimes* appear in some of our study subjects. 
1) Is this normal behavior?
2) Is it possible to add a FieldName index (analagous to the aseg.stats file) 
to facilitate detailed accountings of "empty" variables in the ?h.aparc.a2005s 
files?

Many Thanks for any information you can provide,
Jenifer 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] LGI: EXITS with ERRORS

[Juranek, Jenifer]

Marie,
Thanks so much for your suggestion. You see it perfectly. I did not realize 
that matlab functionality was required to run lgi. Which essential components 
of matlab are suggested so that I may purchase the proper license(s)?
 
Jenifer


From: Marie Schaer [mailto:[EMAIL PROTECTED]
Sent: Sat 4/19/2008 7:44 AM
To: Juranek, Jenifer 
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] LGI: EXITS with ERRORS




Jenifer,

Have you installed Matlab on your computer? As far as I see it, either 
you don't have matlab, or the path to matlab is not set properly.

You can cd into the surf directory (cd SB_09_H20089/surf) and try directly:
mris_compute_lgi --debug --i lh.pial

If it finishes in a few seconds with "getmatlab", then you have to add 
the matlab directory to you $PATH environment variable.

Marie


Quoting "Juranek, Jenifer " <[EMAIL PROTECTED]>:

> I recently downloaded and installed fs4v03 (CentOS 4x86_64) on my  
> new 64bit linux box running RHEL 5 (Tikanga). I didn't see any  
> special notes on the download page for RHEL 5 (only RHEL 4 is noted).
>
> While test-driving my first dataset through the fsv403 pipeline, I  
> encountered some difficulties with my explorations of the new  
> feature of calculated local gyrification index.
> I tried the following cmd lines...each yielded the same standard out 
>  message pasted below
>
> Any ideas?
> Jenifer
>
> [EMAIL PROTECTED] subjects]$ recon-all -subjid SB_09_H20089 -localGI
> [EMAIL PROTECTED] subjects]$ recon-all -lgi -s SB_09_H20089
> [EMAIL PROTECTED] subjects]$ recon-all -lgi -sid SB_09_H20089
>
>
> [EMAIL PROTECTED] subjects]$ recon-all -lgi -s SB_09_H20089
> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> Actual FREESURFER_HOME /usr/local/freesurfer
> -rw-rw-r-- 1 jjuranek jjuranek 768975 Apr 18 17:30  
> /usr/local/freesurfer/subjects/SB_09_H20089/scripts/recon-all.log
> Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14  
> EST 2007 x86_64 x86_64 x86_64 GNU/Linux
> /usr/local/freesurfer/subjects/SB_09_H20089/surf
> #
> [EMAIL PROTECTED] Local Gyrification Index lh Fri Apr 18 17:45:32 CDT 2008
>
>  mris_compute_lgi --i lh.pial
>
> Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14  
> EST 2007 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all exited with ERRORS at Fri Apr 18 17:45:32 CDT 2008
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] LGI: EXITS with ERRORS

[Juranek, Jenifer]

I recently downloaded and installed fs4v03 (CentOS 4x86_64) on my new 64bit 
linux box running RHEL 5 (Tikanga). I didn't see any special notes on the 
download page for RHEL 5 (only RHEL 4 is noted).

While test-driving my first dataset through the fsv403 pipeline, I encountered 
some difficulties with my explorations of the new feature of calculated local 
gyrification index. 
I tried the following cmd lines...each yielded the same standard out message 
pasted below

Any ideas?
Jenifer

[EMAIL PROTECTED] subjects]$ recon-all -subjid SB_09_H20089 -localGI
[EMAIL PROTECTED] subjects]$ recon-all -lgi -s SB_09_H20089
[EMAIL PROTECTED] subjects]$ recon-all -lgi -sid SB_09_H20089


[EMAIL PROTECTED] subjects]$ recon-all -lgi -s SB_09_H20089
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-r-- 1 jjuranek jjuranek 768975 Apr 18 17:30 
/usr/local/freesurfer/subjects/SB_09_H20089/scripts/recon-all.log
Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 
x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/subjects/SB_09_H20089/surf
#
[EMAIL PROTECTED] Local Gyrification Index lh Fri Apr 18 17:45:32 CDT 2008

 mris_compute_lgi --i lh.pial 

Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 
x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Fri Apr 18 17:45:32 CDT 2008


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] CC q's

[Juranek, Jenifer]

Hi,
I'm running FSv4.0.1 on a 64bit linux platform and had a few questions about 
the new added feature wrt the corpus callosum segmentation added as early as 
v4.0.0...details were not readily returned in Wiki searches...so please point 
me in the correct direction?
 
1) The 5 separate regions of the CC...how are the boundaries determined? In 
equal subdivisions (20%) from the genu through the splenium? 
 
2) Although the LUT.txt contains entries for the CC subdivisions, I have been 
unsuccessful with attempts to display either the aseg.auto_CCseg.mgz or 
wmparc.mgz files in tkmedit  such that the boundaries between subdivisions are 
easy to visualize...do I need to modify the LUT.txt file with different entries 
in the last 4 columns than those already present to make it more obvious? 
EXAMPLE of current entries in LUT.txt...
251 CC_Posterior 0 0 64 0
252 CC_Mid_Posterior 0 0 112 0
253 CC_Central 0 0 160 0
254 CC_Mid_Anterior 0 0 208 0
255 CC_Anterior 0 0 255 0 
 
3) The aseg.stats file contains data for each subdivision...do the values 
represent area (mm2)? On the midsagittal slice?
 
Many Thanks for any info you can provide!
 
Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] xtra advice: /usr/local/freesurfer/fsl

[Juranek, Jenifer]

I'm considering downloading and installing fsl_v402 (centos4, 64 bit)

I currently have a stable freesurfer_v401 and MNE _v252 on the same
workstation.

 

Should the destination directory of the fsl package overwrite the
existing  directory: /usr/local/freesurfer/fsl 

Or should I maintain separate environments and install fsl in the
fmrib's recommended destination directory: /usr/local/fsl

 

Any advice is greatly appreciated...

 

Jenifer

 

~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] XYZ coordinates of vertices within aparc labels

[Juranek, Jenifer]

Thanks, Doug.
I have tried the following command:
[]
$ mri_annotation2label --subject EC
--hemi lh --outdir ./test_labels
--table ../../surface_labels.txt
--annotation aparc.a2005s

A total of 57 labels are returned
(expecting 94 after looking at the
surface_labels.txt file?)

Reading a single label file
[test_labels] $ more
lh.S_temporalis_transveralis.label

Returns the following structure
#!ascii label , from subject EC
394
64599-35.192-31.78411.805
0.00
64600-35.842-31.79911.554
0.00

The table specified in the wiki help pages
(Simple_surface_labels.txt)
does not appear to be located in my
$FREESURFER_HOME
directory...instead, the file
 appears in my
$FREESURFER_HOME dir.   

Have I missed something in the command line and/or specified table? 


Jenifer

-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED] 
Sent: Monday, October 01, 2007 1:20 PM
To: Juranek, Jenifer 
Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc
labels

use mri_annotation2label to create a text label file for each
annotation. These have the surface xyz in them.

doug

Juranek, Jenifer wrote: 

Thanks again for the info. However, I'm still not sure how to
get an
ascii file for each aparc label listing the vertex index, and
the RAS
coordinates (surface RAS is fine since I can use the
fscoordinates.pdf
and the wikipage on Coordinate systems to get back to vol
coordinates
and eventually scanner coordinates.)

Any suggestions how to access this information? From the help
pages, I
thought mri_annotation2label would do the trick...

Jenifer

-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED] 
Sent: Monday, October 01, 2007 1:05 PM
To: Bruce Fischl
    Cc: Juranek, Jenifer ; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] XYZ coordinates of vertices within
aparc
labels


I don't have code to do it, but you can look at this doc:


https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=Attac
hFile&do=get&target=fscoordinates.pdf

which explains how to get back to scanner coords

doug


Bruce Fischl wrote:

  

yes, I think Doug has documented how to do this on our
wiki. Doug: can



  

you point jenifer at the right place?

thanks,
Bruce

On Mon, 1 Oct 2007, Juranek, Jenifer  wrote:



Hi Bruce,
Many thanks for the information.
Yes, I'd like a table file for each aparc label
in each hemisphere.
Whether the annotation file is the
?h.aparc.a2005s.annot variety or
  

the
  

?h.aparc.annot variety is not crucial at this
point.

My goal is to map the XYZ vertex coordinates for
each aparc label
  

back
  

to the scanner XYZ coordinates. Is this
possible?

Jenifer

-Original Message-
From: Bruce Fischl
[mailto:[EMAIL PROTECTED]
Sent: Monday, October 01, 2007 10:25 AM
            To: Juranek, Jenifer
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] XYZ coordinates of
vertices within aparc
labels

Hi Jennifer,

do you need a table file? I thought not, since
the color table is
embedded in the .annot file. If you give it an
output directory it
should
extract a label for every different structure in
the .annot file. The
   

RE: [Freesurfer] XYZ coordinates of vertices within aparc labels

[Juranek, Jenifer]

Thanks again for the info. However, I'm still not sure how to get an
ascii file for each aparc label listing the vertex index, and the RAS
coordinates (surface RAS is fine since I can use the fscoordinates.pdf
and the wikipage on Coordinate systems to get back to vol coordinates
and eventually scanner coordinates.)

Any suggestions how to access this information? From the help pages, I
thought mri_annotation2label would do the trick...

Jenifer

-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED] 
Sent: Monday, October 01, 2007 1:05 PM
To: Bruce Fischl
Cc: Juranek, Jenifer ; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc
labels


I don't have code to do it, but you can look at this doc:

https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=Attac
hFile&do=get&target=fscoordinates.pdf

which explains how to get back to scanner coords

doug


Bruce Fischl wrote:

> yes, I think Doug has documented how to do this on our wiki. Doug: can

> you point jenifer at the right place?
>
> thanks,
> Bruce
>
> On Mon, 1 Oct 2007, Juranek, Jenifer  wrote:
>
>> Hi Bruce,
>> Many thanks for the information.
>> Yes, I'd like a table file for each aparc label in each hemisphere.
>> Whether the annotation file is the ?h.aparc.a2005s.annot variety or
the
>> ?h.aparc.annot variety is not crucial at this point.
>>
>> My goal is to map the XYZ vertex coordinates for each aparc label
back
>> to the scanner XYZ coordinates. Is this possible?
>>
>> Jenifer
>>
>> -Original Message-
>> From: Bruce Fischl [mailto:[EMAIL PROTECTED]
>> Sent: Monday, October 01, 2007 10:25 AM
>> To: Juranek, Jenifer
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc
>> labels
>>
>> Hi Jennifer,
>>
>> do you need a table file? I thought not, since the color table is
>> embedded in the .annot file. If you give it an output directory it
>> should
>> extract a label for every different structure in the .annot file. The
>> label file columns are:
>>
>> <1> vertex index
>> <2>-<5> surface RAS coordinates of the vertex, I believe from the
orig
>>     surface (could be white, I'm not positive)
>> <6> a slot to assocate a statistic with that vertex (e.g. fMRI
p-value)
>>
>> Does that answer your questions? I'm not sure...
>>
>> cheers,
>> Bruce
>>
>> On Mon, 1 Oct 2007, Juranek, Jenifer  wrote:
>>
>>> I'd like to retrieve information wrt XYZ coordinates of vertices
>>
>> within
>>
>>> aparc labels.
>>>
>>> I have tried the following command:
>>> []
>>> $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels
>>> --table ../../surface_labels.txt --annotation aparc.a2005s
>>>
>>> A total of 57 labels are returned (expecting 94 after looking at the
>>> surface_labels.txt file?)
>>>
>>> Reading a single label file
>>> [test_labels] $ more lh.S_temporalis_transveralis.label
>>>
>>> Returns the following structure
>>> #!ascii label , from subject EC
>>> 394
>>> 64599-35.192-31.78411.8050.00
>>> 64600-35.842-31.79911.5540.00
>>> etc
>>>
>>> 1) What is the name & location of the table file I should be
>>
>> specifying
>>
>>> to return all 94 labels? Or do I need to include additional flags in
>>
>> my
>>
>>> command line?
>>> 2) How are the columns ordered within each output file generated by
>>
>> the
>>
>>> mri_annotation2label command?
>>>
>>> I'm running FSv3.0.5 on linux (Centos 4).
>>> The table specified in the wiki help pages
(Simple_surface_labels.txt)
>>> does not appear to be located in my $FREESURFER_HOME
>>> directory...instead, the file  appears in my
>>> $FREESURFER_HOME dir.
>>>
>>> Many Thanks,
>>> Jenifer
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>
>>
>>
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] XYZ coordinates of vertices within aparc labels

[Juranek, Jenifer]

Hi Bruce,
Many thanks for the information. 
Yes, I'd like a table file for each aparc label in each hemisphere.
Whether the annotation file is the ?h.aparc.a2005s.annot variety or the
?h.aparc.annot variety is not crucial at this point. 

My goal is to map the XYZ vertex coordinates for each aparc label back
to the scanner XYZ coordinates. Is this possible?

Jenifer

-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED] 
Sent: Monday, October 01, 2007 10:25 AM
To: Juranek, Jenifer 
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc
labels

Hi Jennifer,

do you need a table file? I thought not, since the color table is 
embedded in the .annot file. If you give it an output directory it
should 
extract a label for every different structure in the .annot file. The 
label file columns are:

<1> vertex index
<2>-<5> surface RAS coordinates of the vertex, I believe from the orig
 surface (could be white, I'm not positive)
<6> a slot to assocate a statistic with that vertex (e.g. fMRI p-value)

Does that answer your questions? I'm not sure...

cheers,
Bruce

On Mon, 1 Oct 2007, Juranek, Jenifer  wrote:

> I'd like to retrieve information wrt XYZ coordinates of vertices
within
> aparc labels.
>
> I have tried the following command:
> []
> $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels
> --table ../../surface_labels.txt --annotation aparc.a2005s
>
> A total of 57 labels are returned (expecting 94 after looking at the
> surface_labels.txt file?)
>
> Reading a single label file
> [test_labels] $ more lh.S_temporalis_transveralis.label
>
> Returns the following structure
> #!ascii label , from subject EC
> 394
> 64599 -35.192 -31.784 11.805  0.00
> 64600 -35.842 -31.799 11.554  0.00
> etc
>
> 1) What is the name & location of the table file I should be
specifying
> to return all 94 labels? Or do I need to include additional flags in
my
> command line?
> 2) How are the columns ordered within each output file generated by
the
> mri_annotation2label command?
>
> I'm running FSv3.0.5 on linux (Centos 4).
> The table specified in the wiki help pages (Simple_surface_labels.txt)
> does not appear to be located in my $FREESURFER_HOME
> directory...instead, the file  appears in my
> $FREESURFER_HOME dir.
>
> Many Thanks,
> Jenifer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] XYZ coordinates of vertices within aparc labels

[Juranek, Jenifer]

I'd like to retrieve information wrt XYZ coordinates of vertices within
aparc labels. 

I have tried the following command:
[] 
$ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels
--table ../../surface_labels.txt --annotation aparc.a2005s

A total of 57 labels are returned (expecting 94 after looking at the
surface_labels.txt file?)

Reading a single label file
[test_labels] $ more lh.S_temporalis_transveralis.label

Returns the following structure
#!ascii label , from subject EC
394
64599   -35.192 -31.784 11.805  0.00
64600   -35.842 -31.799 11.554  0.00
etc

1) What is the name & location of the table file I should be specifying
to return all 94 labels? Or do I need to include additional flags in my
command line?
2) How are the columns ordered within each output file generated by the
mri_annotation2label command? 

I'm running FSv3.0.5 on linux (Centos 4).
The table specified in the wiki help pages (Simple_surface_labels.txt)
does not appear to be located in my $FREESURFER_HOME
directory...instead, the file  appears in my
$FREESURFER_HOME dir.

Many Thanks,
Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Simple_Surface_labels2005.txt

[Juranek, Jenifer]

I'd like to identify the voxel locations of each vertex within each
aparc label. I found the command "mri_annotation2label" and thought it
might do the trick. However, I noticed that the examples
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_5fannotation2label?action=h
ighlight&value=mri_annotation2label refer to a txt file which I do not
seem to have in my $FREESURFER_HOME dir. While the table specified in
the examples is  I only seem to have
 which appears to have 95 lines of text. Using the
surface_labels.txt file yields only 12 files rather than the expected
94. 

 

1)  Is strategy appropriate?

2)  Which file should be specified with the -table flag?

3)  Best guess as to where to find the proper file to be specified
with the -table flag?

 

Many Thanks for any assistance you can provide...

 

Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] binary masks: 1 output file per aseg label

[Juranek, Jenifer]

I'm interested in parsing aseg.mgz into separate binary mask files for
each aseg label. Is this possible? The closest topic I found was located
at the following URL:

 

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFu
nctionalSpace


2.0 Creating binary masks


The segmentation for a particular structure can be extracted to create a
binary mask (i.e., a volume where the voxel value is 1 if it is in the
structure and 0 otherwise). To make a binary mask of the left putamen,
which has been assigned label 12 (see
${FREESURFER_HOME}/FreeSurferColorLUT.txt), use the following command: 

avwmaths ./fbert.feat/reg/freesurfer/aparc+aseg.nii.gz \
-thr 12 -uthr 12 \
./fbert.feat/reg/freesurfer/lh.putamen.nii.gz

 

I checked the following for additional help...but still need some
help...

http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommands

 

Many Thanks,

Jenifer

 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] TBV fractions: aseg

[Juranek, Jenifer]

I'm using the aseg file located in /freesurfer/subjects//stats
folder to calculate Total Brain Volume Fractions of GM, WM, and CSF.

 

Within the aseg file, several csf compartments are listed, including:

Left-Lateral-Ventricle (segid 4)

Left-Inf-Lateral-Ventricle (segid 5)

3rd-Ventricle (segid 14)

4th-Ventricle (segid 15)

CSF (segid 24)

Right-Lateral-Ventricle (segid 43)

Right-Inf-Lateral-Ventricle (segid 44)

5th-Ventricle (segid 72)

 

Q: SegIds 24 and 72 are unfamiliar to me. Best place to find more info?
Should they be included in the SUM of CSF?

 

Many Thanks for any info you can provide...

 

Jenifer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] %GM, %WM, %CSF wrt ICV - including cerebellum

[Juranek, Jenifer]

I'd like to compute %GM, %WM, %CSF wrt ICV (eTIV)...including cerebellum 
gray/white.

Are the values returned by mris_wm_volume and mris_volume for cortical surfaces 
only (excluding cerebellum)?

So, in this case...
1) are the values in aseg.stats appropriate for both cerebral and cerebellar 
fractions? 
2) should a combination of cortical GM & WM from mris_volume be added to the 
cerebellar gm & wm values reported in aseg.stats to get TOTAL_GM and TOTAL_WM?
3) is it true that CSF= ICV - GM(cerebral and cerebellar) - WM(cerebral and 
cerebellar)

Any advice is greatly appreciated...

Many Thanks,
Jenifer Juranek
 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] 64bit centos utilities: mris_wm_volume & mris_volume

[Juranek, Jenifer]

Recently (7 Feb 2007) mris_wm_volume for 32bit centos was posted in
/pub/dist.

Is there any possibility of posting 64bit centos versions of
mris_wm_volume & mris_volume?

 

I'm running Freesurfer 3.0.4

 

Many Thanks,

Jenifer

 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Head Points data files

[Juranek, Jenifer]

Hi,

What are the file format requirements for the 2 files called
to load head points - *.hpts and *.trans into tkmedit or tksurfer?

 

We have a whole-head neuromagnetometer (4-D Neuroimaging 3600
Magnes MEG system) with 248 sensor channels.

I’d like to co-register my dipole locations with
FreeSurfer’s aseg+aparc.mgz to efficiently localize dipoles x ROIs. I
have already co-registered index points and headshape files to each subject’s
aMRI within 4D’s software. 

 

Any advice is greatly appreciated!

Jenifer

~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ 

Jenifer Juranek, PhD

Assistant Professor

University of Texas MEG Lab

1333 Moursund St,
  Ste H114

Houston, TX 77030

Phone: 713.797.7574

Fax: 713.797.7590

 






___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer