[Freesurfer] Freeview scripting reference

[Inge Kasbohm Amlien]

Hi list, 
I am looking for a complete reference to scriptable commands for Freeview, 
comparable to what exists for tksurfer (e.g. 
http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferScripting/TkSurferScriptingReference)

Does this exist? 

Thanks!

___
Inge Kasbohm Amlien
E-mail: inge.aml...@psykologi.uio.no
Phone: +47 97106525
Psychologist // Ph.D candidate
Centre for the Study of Human Cognition
Department of Psychology, University of Oslo

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[Freesurfer] Flipping an overlay

[Inge Kasbohm Amlien]

Hi list, 
I have a rh overlay (from caret) registered to fsaverage rh. I need it on 
fsaverage left hemi. Is there an easy way to flip an overlay? 

Cheers
Inge 



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contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] Tutorial data

[Inge Kasbohm Amlien]

I read a while back the tutorial data had been reprocessed with version 3.0,
but not uploaded yet. Is the new data uploaded now?
If so, is this the correct dataset for the morphometry and reconstruction
tutorial?
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-tutorial_subjs.tar.gz

(The datestamps on the ftp says January-something.)

Thanks
Inge Amlien

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RE: [Freesurfer] Tutorial data

[Inge Kasbohm Amlien]

That's great Nick, thanks.

/Inge

-Original Message-
From: Nick Schmansky [mailto:[EMAIL PROTECTED] 
Sent: 23. mai 2006 00:44
To: Inge Kasbohm Amlien
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] Tutorial data

Inge,

Funny you should ask.  We are busily updating this data right now in
preparation for an upcoming Freesurfer course.  The data should be
posted for download by the end of the week (along with an updated
tutorial wiki).  

We'll post to this mailing list when it is ready.

However, the existing dataset and wiki tutorial is entirely compatible
with version 3.0.  The updates just account for the fact that freesurfer
v3.0 fixes more defects than prior freesurfer versions, so some defects
will no longer exist in the updated dataset.

Nick

On Tue, 2006-05-23 at 00:24 +0200, Inge Kasbohm Amlien wrote:
> I read a while back the tutorial data had been reprocessed with version
3.0,
> but not uploaded yet. Is the new data uploaded now?
> If so, is this the correct dataset for the morphometry and reconstruction
> tutorial?
>
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-tutorial_subjs.tar.gz
> 
> (The datestamps on the ftp says January-something.)
> 
> Thanks
> Inge Amlien
> 
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 


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[Freesurfer] Gradient unwarp problem

[Inge Kasbohm Amlien]

Hello list,
we are looking into the possibility of adding the gradient unwarp tool 
(http://www.nbirn.net/tools/gradient_non_linearity/index.shtm) to our

Freesurfer processing stream, but we are experiencing some problems with
the output.

Our physicist sent me what he believed was the sympathetic harmonics
expansion for the Siemens Avanto, "coeff.grad". We are using
mprages from said scanner.

Following the readme:
1) set all environment vars,
(ADDED not in readme: # setenv MATLAB_DIR $GRAD_UNWARP_DIR/matlab)

2) cd $GRAD_UNWARP_DIR

3) perl scripts/gradient_unwarp_converter.pl avanto/coeff.grad

4) create_displacement_table siemens avanto

5) grad_unwarp -i mpr1.mgh -o mpr1_uw.mgh -unwarp avanto

The scripts run fine, and generate output, see attached screenshot and 
log. The output opens in tkmedit, but has intensity values ranging from 
about 28-30. Am I missing a step here?


Any and all tips appreciated.

Thank you, and kind regards,
Inge Amlien
Dept. of psychology
University of Oslo
Norway


Attached:
coeff.grad
grad_unwarp_logfile.txt
mpr1_uw.mgh.jpg

<>grad_unwarp log file
version: Version for distribution, 1.0, author: SC
id: id
pwd: pwd
executable:
/usit/psi-brain/u1/Felles/labdata/lab-data/lab_tools/grad_unwarp/scripts/grad_unwarp
uname: uname -a
date: date
Warning: Unable to open display iconic, MATLAB is starting without a display.
  You will not be able to display graphics on the screen.
Warning:
  MATLAB is starting without a display, using internal event queue.
  You will not be able to display graphics on the screen.


  < M A T L A B >
  Copyright 1984-2005 The MathWorks, Inc.
   Version 7.1.0.183 (R14) Service Pack 3
  August 02, 2005

Warning: Name is nonexistent or not a directory:
/psyklab/local/eeglab/eeglab.
Warning: Name is nonexistent or not a directory:
/psyklab/local/eeglab/eeglab.

  To get started, type one of these: helpwin, helpdesk, or demo.
  For product information, visit www.mathworks.com.

 >> >>

GRADWARPPATH=/usit/psi-brain/u1/Felles/labdata/lab-data/lab_tools/grad_unwarp/grad_unwarp_tables
TABLE=/usit/psi-brain/u1/Felles/labdata/lab-data/lab_tools/grad_unwarp/grad_unwarp_tables/table.mat
QuitOnError=1
Interp method is cubic
INFO: loading mgh (mgz) format infile mpr1.mgh
INFO: loading mgh (mgz) volume mpr1.mgh
Beginning unwarping and/or resampling
Full 3D unwarping...
gradfilename is
/usit/psi-brain/u1/Felles/labdata/lab-data/lab_tools/grad_unwarp/grad_unwarp_tables/avanto.gwv.
 Loading...
Unwarp data loaded.
slice   1/256  5.1e-05
slice   2/256  1.12689
slice   3/256  2.10518
slice   4/256  3.05796
slice   5/256  4.00608
slice   6/256  4.95446
slice   7/256  5.91948
slice   8/256  6.86984
slice   9/256  7.8175
slice  10/256  8.76374
slice  11/256  9.71455
slice  12/256  10.6598
slice  13/256  11.597
slice  14/256  12.5634
slice  15/256  13.5075
slice  16/256  14.4586
slice  17/256  15.4105
slice  18/256  16.3562
slice  19/256  17.3188
slice  20/256  18.2675
slice  21/256  19.2181
slice  22/256  20.164
slice  23/256  21.1119
slice  24/256  22.0761
slice  25/256  23.0236
slice  26/256  23.972
slice  27/256  24.9196
slice  28/256  25.8645
slice  29/256  26.8296
slice  30/256  27.7808
slice  31/256  28.7291
slice  32/256  29.6701
slice  33/256  30.6195
slice  34/256  31.5611
slice  35/256  32.5032
slice  36/256  33.4483
slice  37/256  34.395
slice  38/256  35.329
slice  39/256  36.2756
slice  40/256  37.2212
slice  41/256  38.1632
slice  42/256  39.111
slice  43/256  40.0735
slice  44/256  41.0182
slice  45/256  41.9631
slice  46/256  42.9138
slice  47/256  43.86
slice  48/256  44.806
slice  49/256  45.7543
slice  50/256  46.6898
slice  51/256  47.6285
slice  52/256  48.5789
slice  53/256  49.5268
slice  54/256  50.4915
slice  55/256  51.4393
slice  56/256  52.386
slice  57/256  53.3357
slice  58/256  54.2901
slice  59/256  55.2521
slice  60/256  56.1993
slice  61/256  57.1479
slice  62/256  58.0982
slice  63/256  59.0494
slice  64/256  60.0154
slice  65/256  60.9627
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slice  70/256  65.7184
slice  71/256  66.6661
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slice  73/256  68.5513
slice  74/256  69.5043
slice  75/256  70.4383
slice  76/256  71.38
slice  77/256  72.3238
slice  78/256  73.2688
slice  79/256  74.2183
slice  80/256  75.1645
slice  81/256  76.1128
slice  82/256  77.0769
slice  83/256  78.0238
slice  84/256  78.974
slice  85/256  79.9211
slice  86/256  80.8692
slice  87/256  81.8363
slice  88/256  82.7843
slice  89/256  83.735
slice  90/256  84.6873
slice  91/256  85.6363
slice  92/256  86.5989
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slice  95/256  89.4413
slice  96/256  90.3891
slice  97/256  91.3517
slice  98/256  92.2982
slice  99/256  93.247
slice 100/256  94.1918
slice 101/256  95.1394
slice 102/256  96.08
slice 103/256  97.0161
slice 104/256  97.9512
slice 105/256  98.8936
slice 106/256  99