[caret-users] Re: Script to streamline import of Freesurfer surfaces -- revised

2006-03-03 Thread Donna Dierker

Hi caret-users,

Three things:

1. *h.white -- not *h.smoothwm:  The initial version of this script 
averaged the Freesurfer smoothwm and pial to generate a mid-thickness 
fiducial.  On Feb 23, 2006, Bruce Fischl wrote to David Van Essen:


I also kept meaning to mention to you that the ?h.smoothwm surface  is 
not the one we use for the gray/white boundary. It's an initial  
estimate that gets refined to create the ?h.white surface.


So I have changed the script to use the white surface.  Users of this 
script should do the same.


2. Origin setting:  The settings in this script produce a segmentation 
volume whose AFNI .HEAD produces this 3dinfo output (AFNI command line 
utility):


R-to-L extent: -128.000 [R] -to- 127.000 [L] -step- 1.000 mm [256 voxels]
A-to-P extent: -127.000 [A] -to- 128.000 [P] -step- 1.000 mm [256 voxels]
I-to-S extent: -127.000 [I] -to- 128.000 [S] -step- 1.000 mm [256 voxels]

This was based on my interpretation of 
http://www.wideman-one.com/gw/brain/fs/coords/fscoords.htm.  Per Ziad 
Saad, 2/14/2006 
(http://afni.nimh.nih.gov/afni/community/board/read.php?f=1i=9147t=9128), 
What you have posted is correct to our knowledge.  This doesn't 
eliminate the disclaimer, but at least two of us will be wrong if it 
it's not accurate.;-)


3. This has nothing to do with Freesurfer, but I have changed my name.

Stay tuned for a forthcoming announcement of Caret 5.33...

Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)


On 02/16/2006 08:46 AM, Donna Hanlon wrote:


Hi caret-users,

This script may be helpful to those who import Freesurfer surfaces 
into Caret for various purposes.
http://brainmap.wustl.edu/pub/donna/SCRIPTS/FREESURFER/freesurfer2caret.sh 


login pub
password download

It does the following:

* calls mris_convert to convert the Freesurfer binary surfaces to ASCII
* converts the Freesurfer ASCII surfaces to Caret coord/topo files
* averages the pial and smoothwm surfaces to generate a midthickness 
coord

* creates a spec file with the hem_flag as left or right
* generates the sulcal depth and geography paint file from the 
midthickness surface


Run this script in a 'subjects' directory where there is a 
subdirectory for each case/subject.  This script assumes there is a 
surf subdirectory under each case subdirectory, e.g.:


./ED/surf
./EF/surf
./EG/surf
./FH/surf
./FK/surf
./FL/surf
./FM/surf
./FN/surf

Then, change this line in the script to reflect your actual 
case/subject subdirectory names:


CASES=ED EF EG FH FK FL FM FN

If you have additional layers between the case subdirectory and your 
Freesurfer surf subdirectory, then you'll need to tweak these lines 
accordingly:


 cd $CASE/surf
 ...
 cd ../..

Disclaimers:

1. The origin setting in the caret_command -volume-create step 
reflects my best current understanding of where the Freesurfer origin 
actually is.  Help in clarifying this issue is most welcome.  The 
bottom line is that the depth measures will be accurate regardless of 
the actual origin input here, because the segmentation and derivative 
hull volume will be generated from the same origin, so the resulting 
distance between the fiducial and hull surfaces will not be affected 
by the actual origin setting; however, someone might try to align 
these derivative volumes with an actual anatomical generated from the 
COR-* slices and midthickness fiducial surface.  There may be slight 
offset issues, although the alignment looks good to me.  More 
importantly, it would be nice to add a Freesurfer atlas space for the 
-volume-create and paint/metric-to-volume features.


2. I confess I haven't tested it as thoroughly as I'd like to.

Apologies: Sorry I didn't get this up sooner; my daughter was sick 
yesterday.


Donna




Re: [caret-users] caret list posting query

2006-03-29 Thread Donna Dierker

Hi Jason,

Which part of the five page Methods section didn't you understand? ;-)  
Seriously, though, was there a step or two that seemed particularly 
opaque?  Here is my readers' digest condensed version:


* Register each structural volume to wustl.edu's 711-2C space via affine 
transform (711-2C is based on the ICBM template, something about 
Lancaster, I think).
* Segment structural volume using SureFit (now part of Caret); 
tessellate segmentation - midthickness 3D surface.
* Generate cerebral hull volume: Dilate segmentation volume six times 
and erode by six times to fill sulci, but keep overall brain size same; 
tessellate hull.
* Generate depth (midthickness node-scalar mapping): Find distance from 
fiducial surface node to closest cerebral hull node.
* Flatten and register midthickness surface: Use Core6 landmarks to 
constrain spherical deformation.  (Flattening provides an easy way to 
draw registration landmarks.)
* Apply deformation map to depth - one depth column/file for each 
subject all on PALS_B12 standard mesh.

* Average resulting depth columns/files.

Segmentation is by far the most difficult, time-intensive step; it's 
downhill from there.


Since the PALS_B12 paper, we have been using t-maps to look for 
anatomical differences across populations.  We hope you will soon be 
reading about this in the Journal of Neuroscience, if I can ever 
complete some important enhancements to the depth generation algorithm 
-- important enough for us to rework all the figures (but not change the 
ROIs much).


One important consideration for you is your choice of landmarks.  Using 
the Core 6 landmarks will normalize away any differences in the central 
sulci, because the central sulcus is one of the landmarks.  If you want 
to align the central sulci, this is good; if you're looking for 
cross-group differences there, this is bad.  You can delete that 
landmark, but keep the others (and perhaps add another elsewhere), but 
this is something to think about.  Importantly, you can run the 
registration both ways, using different deformation prefices (e.g., 
defCore6_ and defNoCeS_), and create average depth and/or t-maps using 
the respective results.  Each result will be valid in context, but will 
tell you something different.


Hope this helps.

On 03/28/2006 06:08 PM, Jason D Connolly wrote:


Dear Caret-users,

Could someone please instruct me as to how the spherical and flattened
maps were averaged in the van essen 05 paper?  We hope to create an avg
struct image with the pixel intesity reflecting the degree of
overlap/similarity across anatomical datasets (see figs 2 and 6).  The
goal is to see how the central sulci line up across subjects.  


Many thanks, Jason.




Jason D. Connolly, PhD  
Center for Neural Science, New York University

6 Washington Place Room 875, New York, NY 10003
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html



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(Formerly Donna Hanlon; no change in marital status -- see 
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Re: [caret-users] caret list posting query

2006-03-29 Thread Donna Dierker

I need to qualify something I said below:

On 03/29/2006 08:12 AM, Donna Dierker wrote:


Hi Jason,

Which part of the five page Methods section didn't you understand? 
;-)  Seriously, though, was there a step or two that seemed 
particularly opaque?  Here is my readers' digest condensed version:


* Register each structural volume to wustl.edu's 711-2C space via 
affine transform (711-2C is based on the ICBM template, something 
about Lancaster, I think).
* Segment structural volume using SureFit (now part of Caret); 
tessellate segmentation - midthickness 3D surface.
* Generate cerebral hull volume: Dilate segmentation volume six times 
and erode by six times to fill sulci, but keep overall brain size 
same; tessellate hull.
* Generate depth (midthickness node-scalar mapping): Find distance 
from fiducial surface node to closest cerebral hull node.
* Flatten and register midthickness surface: Use Core6 landmarks to 
constrain spherical deformation.  (Flattening provides an easy way to 
draw registration landmarks.)
* Apply deformation map to depth - one depth column/file for each 
subject all on PALS_B12 standard mesh.

* Average resulting depth columns/files.

Segmentation is by far the most difficult, time-intensive step; it's 
downhill from there.


Since the PALS_B12 paper, we have been using t-maps to look for 
anatomical differences across populations.  We hope you will soon be 
reading about this in the Journal of Neuroscience, if I can ever 
complete some important enhancements to the depth generation algorithm 
-- important enough for us to rework all the figures (but not change 
the ROIs much).


One important consideration for you is your choice of landmarks.  
Using the Core 6 landmarks will normalize away any differences in the 
central sulci


Actually, it won't normalize true depth differences in the CeS.  If the 
CeS is truly deeper in group A than in group B, the Core6 landmarks will 
detect that difference.  What it won't detect is a shift (e.g., anterior 
or posterior) across groups, because it will align their respective CeS 
locations on the sphere.


, because the central sulcus is one of the landmarks.  If you want to 
align the central sulci, this is good; if you're looking for 
cross-group differences there, this is bad.  You can delete that 
landmark, but keep the others (and perhaps add another elsewhere), but 
this is something to think about.  Importantly, you can run the 
registration both ways, using different deformation prefices (e.g., 
defCore6_ and defNoCeS_), and create average depth and/or t-maps using 
the respective results.  Each result will be valid in context, but 
will tell you something different.


Hope this helps.

On 03/28/2006 06:08 PM, Jason D Connolly wrote:


Dear Caret-users,

Could someone please instruct me as to how the spherical and flattened
maps were averaged in the van essen 05 paper?  We hope to create an avg
struct image with the pixel intesity reflecting the degree of
overlap/similarity across anatomical datasets (see figs 2 and 6).  The
goal is to see how the central sulci line up across subjects. 
Many thanks, Jason.





Jason D. Connolly, PhD  Center for Neural Science, New York University
6 Washington Place Room 875, New York, NY 10003
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html



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(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] Macaque Segmentation

2006-03-29 Thread Donna Dierker
The only difference that comes to mind is the voxdims.  Resampling your 
macaque structural to cubic 0.5mm rather than cubic 1.0mm tends to work 
best (although I've seen 0.75mm work well).  You definitely do NOT want 
to resample to cubic 1.0mm for monkeys.


On 03/29/2006 09:53 AM, Faden, Eric (NIH/NIMH) [F] wrote:


Hey All,

Are there any special steps required outside of the standard tutorial for 
segmenting a Macaque brain?  Or would the normal tutorial work correctly if 
followed?

-Eric Faden

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Re: [caret-users] Macaque Segmentation + AC/PC Align

2006-03-29 Thread Donna Dierker
I have tried doing this in AFNI before realizing that AFNI automatically 
resamples to cubic 1.0mm voxels.  But you can probably get away with 
this if you lie to to3d (or edit your .HEAD) to make AFNI think your 
voxdims are cubic 1.0mm, when they really are something else.  Then, you 
can fix the .HEAD later.


You can also so this using trial and error affine rotations/translations 
with the Window: Transformation Matrix feature.  It's not terribly fun, 
but I've done it on several non-primates.


On 03/29/2006 02:14 PM, John Harwell wrote:


Eric,

The AC/PC align in volume attributes is something I recently added  
but has received only limited testing (I tried it on two volumes).  I  
believe AFNI (afni.nimh.nih.gov) can AC-PC align a volume so you  
might try AFNI or another volume type program.


Good luck.

--
John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.Box 8108
St. Louis, MO 63110   USA

On Mar 29, 2006, at 10:57 AM, Faden, Eric ((NIH/NIMH)) [F] wrote:

I actually resampled them at .5mm already.  The other problem I am  
having is that the way our monkeys are scanned they need to be  
rotated to the correct orientation (45 degrees or so).  I tried to  
use the AC/PC align in Volume Attributes Editor.  I selected the AC  
and PC then clicked align.  After about 10 minutes I got a white  
cube where my volume used to be.  Any thoughts on what this is? or  
what is a good way to AC/PC align my volume?


-Eric


-Original Message-
From: Donna Dierker [mailto:[EMAIL PROTECTED]
Sent: Wed 3/29/2006 10:58 AM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] Macaque Segmentation

The only difference that comes to mind is the voxdims.  Resampling  your
macaque structural to cubic 0.5mm rather than cubic 1.0mm tends to  work
best (although I've seen 0.75mm work well).  You definitely do NOT  want
to resample to cubic 1.0mm for monkeys.

On 03/29/2006 09:53 AM, Faden, Eric (NIH/NIMH) [F] wrote:


Hey All,

Are there any special steps required outside of the standard  
tutorial for segmenting a Macaque brain?  Or would the normal  
tutorial work correctly if followed?


-Eric Faden

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(Formerly Donna Hanlon; no change in marital status -- see http:// 
home.att.net/~donna.hanlon for details.)


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Re: [caret-users] posting

2006-03-29 Thread Donna Dierker

Hi Jason,

Sounds like some catastrophic problem.  First, are you using the atlas 
target dataset cited here:


http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html

Second, check your landmark border polarity.

Third, while handles are unlikely to cause holes in the cusrface, 
they'll cause other trouble (i.e., inaccurate results), so you should 
fix them.


If you toggle on the Show first link in red option in the Borders menu 
and generate some captures of you landmark borders on the inflated 
surface, it will help us figure out what is going wrong.  Views like the 
ones shown in the web site above are what we're looking for.


On 03/29/2006 02:27 PM, Jason D Connolly wrote:


Dear Caret-users,

I have successfully warped a set of individual subject right
hemispheres to the PALS sphere.  Problem?  There is a huge whole in each
of the deformed images around the central sulcus.  In the inflated
brains, the image looks scrambled in a portion of the central sulcus.
Is this a handles issue?  I do not recall having any existing handles
in this region.  Second, when the deform process was running, it said
that I had roughly 200 cross-overs.  What is a cross-over and is that
related to the above problem?  Thank you.  Jason.


Jason D. Connolly, PhD  
Center for Neural Science, New York University

6 Washington Place Room 875, New York, NY 10003
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html



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(Formerly Donna Hanlon; no change in marital status -- see 
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Re: [caret-users] Macaque Segmentation

2006-03-31 Thread Donna Dierker

Hi Eric,

Based on what you describe, you probably have some non-uniformity in 
your volume that bias correction may help.  I use FSL's fast for this 
purpose (which uses BET as preprocessing), but there are many other 
options (e.g., MNI's nu_correct and AFNI's 3dUniformize).  You can 
upload your volume here and I can either confirm or rule out this issue:


http://pulvinar.wustl.edu/cgi-bin/upload.cgi

Peak tweaking makes a huge difference in segmentation quality.  This 
page might be helpful:


http://brainvis.wustl.edu/help/peak_tweaking/

If you're getting good results out of Freesurfer, then you can use the 
resulting surface in Caret (e.g., for registration, visualization, or 
other purposes).  Except in cases where the quality of the structural 
MRI is exceptionally poor (e.g., acquisition resolution way to low; 
non-uniformity beyond hope -- like the surface coil scans I used to 
see), then bias correction and peak tweaking usually give good results 
in Caret.


On 03/31/2006 11:03 AM, Faden, Eric (NIH/NIMH) [F] wrote:


I have tried two different approaches thus far and neither seems to yield 
reasonable results.  I first tried to feed in the full scan in ACPC coords.  
The image was rotated in brains, converted to AFNI, and then imported to caret. 
 It is correctly oriented and looks ok although the contrast seems a bit off 
(some of the image seems to white).  After cutting the brain into just the left 
hemi I ran it through the segmentation process which yielded a pretty bad 
surface that still included about 90% of the eyes and a very large chunk of the 
skull.  I then decided to try it with just a brain image (as I already had a 
brain mask in brains).  Following the same steps as the first attempt with the 
brain only image also yielded a fairly bad initial surface as well as leaving a 
large block of the hindbrain.  Are there any other tricks people could provide? 
 Is there a trick to picking the gray/white matter peaks?  For reference I have 
run the same image through a modified freesurfer surface generation which works 
fairly well, but was curious to see if caret could top it.

-Eric
 




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Re: [caret-users] posting

2006-04-07 Thread Donna Dierker

Hi Jason,

Dr. Van Essen and I just discussed your question, and we'd like more 
information about what you're trying to do.  Often, there are easier 
ways to accomplish goals than posters envision.


But to answer your question directly, no -- there are no published 
materials for adapting the core6 landmarks.  (We typically use more 
landmarks for nonhuman primates, for whom variability is much less of an 
issue.  I often refer users to the old Caret 4.6 Tutorial Part II, 
tutorial 8, Register Flat Maps, because I think it's a useful reference 
-- even though we don't use the flat map registration as a method anymore.)


In principle, it's possible to add landmarks.  In general, you would 
need to do this for each of the 24 PALS_B12 hemispheres (12 left, 12 right):


1.  Identify the landmark on the fiducial surface.
2.  Draw the border (probably easiest on the PALS flat surface, using 
the deformed folding as a shape underlay; we don't believe a composite 
folding file is available in sumsdb, but we have them).

3.  Project the border.
4.  Load the PALS_B12 spherical surface, and save the border relative to 
that surface.
5. Average the resulting borders to create an average PreCes target 
border for each hemisphere; add this border to the Core6 landmarks to 
generate a new landmark set -- let's call it Connolly7.


Before going down this path, we think you would benefit from a warm-up 
exercise that might help you understand why the PreCes is not a core 
seventh landmark; we believe its variability makes it difficult to 
establish correspondence across subjects.  Even where you can establish 
clear guidelines that can be applied consistently, we think this 
landmark will add more variance -- not reduce it.


To see this personally, download the PALS tutorial here:

http://sumsdb.wustl.edu/sums/directory.do?id=6332260

Go to scene 6A, Case1.R sulcal depth, four configurations.
Switch the D/C menu from Scene to Surface Shape.
Looking just at the very inflated and flat maps, toggle among the 
deformed depth columns for each of the 12 PALS_B12 right hemispheres.
On each depth map, locate the PreCes on both the flat and very inflated 
maps.


Note that the fiducial for Case 1 is shown in Window 3; since there 
aren't preset scenes for each subject, you'll need to use File: Open 
Data File: Coord file and navigate to your 
CARET_HOME/data_files/fmri_mapping_files directory to load fiducial 
coord files for the other PALS_B12 subjects.  (For each hemisphere, 
there is a coord file for each of the six atlas spaces we support; for 
the purposes of this exercise, it doesn't matter which you choose, as 
long as you get the right case number and make sure it's a right 
hemisphere -- named like *.R.*.)


Case 1 has a nicely defined PreCes, so it won't be a problem.  But 
several of the other cases illustrate the nature of the correspondence 
problem with this landmark.  For registration purposes, we believe this 
problem creates more problems than it solves.


But if you decide to go ahead and add additional landmarks, then we 
recommend you register your data both ways:  Using the Core6 and the 
Connolly7.  Once you get your data segmented and flattened, running 
registration multiple ways is easy; just make sure you use a different 
deformation prefix (fourth tab on the registration menu) and/or atlas 
target directory.  (I'd recommend separate atlas target spec files, if 
not separate directories.)  This way, you can compare the two and see 
which results you prefer.  You may find they both are helpful, but tell 
you different things.  Having the Core6 results will give you a way to 
compare your results with those of other labs who have used the Core6 
landmarks.


Happy morphing!

On 04/06/2006 01:02 PM, Jason D Connolly wrote:


Dear Caret-users,

Is there any information in the tutorials, manuals etc. that can
instruct us as to how to go about adapting the core6 landmarks to use
our own landmarks (in addition to the core6) for morphing to the PALS
atlas?  We hope to use the precentral sulcus as an additional
registration landmark ...

Many thanks, Jason.


Jason D. Connolly, PhD  
Center for Neural Science, New York University

6 Washington Place Room 875, New York, NY 10003
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html



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Re: [caret-users] help needed

2006-04-11 Thread Donna Dierker

Hi Shantanu,

From your registration, I see you are using Windows XP.  You will need 
Winzip or some other software that can extract zip archives.  We 
typically extract the file caret_distribution.v5.33.windows.zip to the 
C: drive.  When it extracts, it will create a caret folder under your C: 
drive.  Then, you can create a shortcut to C:\caret\bin\caret5.exe on 
your desktop, or associate the extension .spec with the 
C:\caret\bin\caret5.exe executable, so that when you double-click on a 
spec file, Caret is launched.


After you get Caret installed, a good place to start is by taking the 
PALS tutorial:


http://sumsdb.wustl.edu/sums/directory.do?id=6332260

Click on the diskette-shaped icon to the left of these names:

PALS_ATLAS_CARET_5.3_TUTORIAL_June_05.pdf
PALS_TUTORIAL_DATA_JUNE_05.zip

Use Adobe Acrobat to view the PDF document, and use Winzip or other zip 
file extractor to unpack the .zip file dataset.  The PDF document will 
walk you through the tutorial dataset.


On 04/10/2006 11:19 PM, shantanu ghosh wrote:

i have downloaded the caret software from the site but i cannot 
install it. how can i start?

Shantanu


Shantanu Ghosh, PhD
Department of Humanities and Social Sciences
Indian Institute of Technology, Delhi
Hauz Khas
New Delhi 110016
INDIA
Tel.: +91-11-2659 6589
Fax: +91-11-2659 6509


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Re: [caret-users] help needed

2006-04-19 Thread Donna Dierker

Hi Binyam,

See inline responses below.

On 04/18/2006 06:28 PM, Binyam Nardos wrote:



Dear Caret support,
Just started using Caret and I have what might be some elementary 
questions for you. I have been trying to make the central sulcus 
landmark appear in my fiducial and inflated surfaces that I've mapped 
regions of interest on. However, I can't seem to be able to get it to 
show, I tried loading all the border data files that I could find in 
the PALS folder but the only thing I can get to show up are the lobe 
markers(the border files for the central sulcus marker do show up in 
the display control window so I'm thinking they are loaded); I also 
tried playing with the border colors(specifically those for the 
central sulcus marker) but still couldn't get it.


Which spec file are you using?  If you got it from sumsdb.wustl.edu, do 
you know the directory or archive ID, so I can find it quickly?  If not, 
then perhaps just the name of the spec file will help.  I assume you're 
using a publicly available PALS_B12 dataset, rather than a surface you 
reconstructed and registered of your own.




One more question: I have a volume anatomy file that I've loaded 
regions of interest as functional volume files. They show up fine but 
I was wondering if there was a way to make each individual region 
appear in a different color. Now i've been able to do this while 
mapping regions on a fiducial surface by defining a different area 
color for each region, is the same thing possible in the volume 
anatomy view.?


There is a way to do this -- at least if your paint/ROI 
intensities/indices are ordered sequentially (i.e., 1, 2, 3, ...).  If 
not, then I'm not sure how to do this.  Back on 9/2005, a user wanted to 
map the AAL ROIs to PALS, but it's intensity-to-parcel scheme looked 
like this (116 labels):


FAGPrecentral_L2001
FADPrecentral_R2002
F1GFrontal_Sup_L2101
...
VER8Vermis_89150
VER9Vermis_99160
VER10Vermis_109170

The trouble is that the paint index to paint name mapping is stored in 
the AFNI .HEAD file like this:


type  = string-attribute
name  = LUT_NAMES
count  = 423
'???~???_not_used~GYRAL~SUL.STS~SUL.AS~SUL.SF~SUL.ITS~SUL.PoCeS~SUL.PoSubCeS~SUL.CeS~SUL.IPrCeS~SUL.pITS~SUL~SUL.IFS~SUL.IPS~SUL.AOS~SUL.OTS~CENTRAL~SUL.intFS~SUL.SPrCeS~SUL.FOS~SUL.MFS~SUL.TOrbS~SUL.LOS~SUL.FMS~SUL.SFS~SUL.CoS~SUL.TOS~SUL.SupPS~SUL.RhS~CALCARINE~MEDIAL.WALL~SUL.CaSd~SUL.OrbS~SUL.HF~SUL.CaSv~SUL.POS~SUL.CiSmr~SUL.CiS~SUL.SSS~SUL.SubPS~SUL.OlfS~SUL.ILS~SUL.SRS~SUL.ISS~SUL.MPrCeS~SUL.PaCeS~SUL.IRS~SUL.LuS~

The ordinal position of the name corresponds to the intensity (first is 
intensity=1; second is intensity=2, and so on).  But for the AAL volume, 
we'd need 2000 bogus names just to get to the first real AAL label, 
whose intensity is 2001.


I'm not sure how you get this info into Caret using the GUI; in the 
past, I've simply edited the .HEAD file with a text editor (I know, 
naughty Donna, but the AFNI police probably already have warrants out 
for us for using a non-standard attribute such as LUT_NAMES;-).




Much appreciated,
Binyam Nardos



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(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] posting

2006-04-19 Thread Donna Dierker

Jason,

I'm getting ready to walk out the door (I get in around 7am), and a file 
named fordonna.tar.gz was just uploaded -- presumably from you.  I 
looked at it, and with sane file selections, I don't see the black hole 
you described.  Make sure you're using the topo that doesn't begin with 
deformed, but use the inflated and fiducial coords that are named like 
deformed*.  I do see something funky with the topology, though, at the 
location indicated on the attached capture.  I suspect it stems from 
your original surface, and has nothing to do with registration.  Could 
you upload your original surface directory (using the same copy spec 
file, archive, upload approach), so I can be sure?


It occurred to me:  By black, you're not referring to the sulcal depth 
underlay, which makes deeper nodes appear darker, are you?  You can turn 
this off, but we find it informative.


On 04/19/2006 08:01 AM, Donna Dierker wrote:


On 04/18/2006 03:50 PM, Jason D Connolly wrote:


Dear David and Donna,

I re-ran the left hemisphere deformation and I noticed that the deformed
flat maps look alright.  It is only the fiducial, inflated and spheres
that are black.
 

Make a fordonna subdirectory and use Copy Spec file to copy the spec 
file you are viewing to that subdirectory.  Then, create a zip or 
tar.gz archive of that subdirectory and upload it here:


http://pulvinar.wustl.edu/cgi-bin/upload.cgi

I need to know exactly which CLOSED topo and fiducial, inflated, and 
spherical coord files you have loaded.  Make sure only one CLOSED topo 
file is loaded.



I also noticed that when the spherical deformation is run, the central
sulcus appears on the right side and the medial wall on the left during
warping. 


This is normal.  During registration, left hemispheres are flipped and 
treated as if they were right hemispheres.  This is normal behavior 
and causes no problems.



Following deformation there are 2 sets of borders that appear
on the spheres the left set and also concurrently a right (or
perhaps target) set.  The two sets are overlaid on the spheres.
 

Sounds to me like you have the target border file 
Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.SPHERE.border selected.


I'm still in the dark as to what your goal is -- the type of data 
you're trying to register to PALS (e.g., sulcal depth? functional data?).



Jason.


Jason D. Connolly, PhD  Center for Neural Science, New York University
6 Washington Place Room 875, New York, NY 10003
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html



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inline: funky_topo.jpginline: funky_topo_on_sphere.jpg

Re: [caret-users] posting reply for Donna

2006-04-20 Thread Donna Dierker

Jason:  See inline replies below.

On 04/19/2006 04:40 PM, Jason D Connolly wrote:


Dear Donna,

I have uploaded the .spec file containing the black inflated, fiducial
and spherical left hemisphere datasets.  The file is a tar.gz format
labelled fordonna.  Thank you again for your help.  We are trying to
deform the sulcal depth maps of subjects left hemispheres to the PALS
atlas.  Again, following spherical deformation, the left - but not right
- fiducial, inflated and spherical hemispheres appear black, as shown
in the screen captures that are appended in jpg format.
 

A picture is worth a thousand words.  Try this when viewing these same 
surfaces:  Surface: Normals: Flip Normals.  I'll bet the problem 
disappears.  How your normals got flipped is another question; I don't 
know the answer, but it happens now and then.  These were 
Caret-generated surfaces, right?


I can't replicate the problem on my end; when I select only these files, 
the surface looks fine, other than the topology issue (see green ID node 
in attached capture):


deformed_Human.6.L.Fiducial.2006-02-13.64283.coord
Human.sphere_6.73730.topo
deformed_Human.6.L.surface_shape_file_24.2006-02-13.64283.surface_shape


One important point is that when you click on the deformed lateral view,
you get a medial view, so something is wrong here.  

Solve this problem by entering this command in the directory where the 
spec is located:


echo hem_flag left  deformed_Human.6.L.spec

It would be nice if Caret inserted the hem_flag into the deformed spec 
file, but to be honest, we don't use these deformed spec files much.  
Instead, we create composite files of the deformed*shape and 
deformed*metric, and then use an analysis/visualization spec.



There is a dorsal
view of the deformed depth fiducial map; a dorsal view of the deformed
sphere, and the medial view of the deformed inflated surface.  As you
will see, the appended and deformed flat maps look fine.  


Indeed, only one CLOSED topo file is loaded.  The CLOSED topo file is:

CLOSED Human.sphere_6.73730.topo

The fiducial, inflated and spherical coord files are:

deformed_Human.6.L.Fiducial.2006-02-13.64283.coord
deformed_Human.6.L.Inflated.2006-02-13.64283.coord
deformed_Human.6.L.SPHERE_ALIGN.2006-02-13.64283.coord

We have tried troubleshooting this by performing this deform on other
subjects left hemispheres, and the results are the same (so it cannot be
due to a bad subjects dataset.  We have also tried this on the right
hemisphere using the same target atlas, so the atlas files are not
corrupted.  Finally, we have tried this on both the Linux and Mac
platforms and we get the same results, i.e. bad left - but not right -
hemisphere images.
 

It is almost certainly a case of flipped normals, and my guess is that 
the impact is 0, other than the visualization anomaly that is easily 
corrected. If you are using the atlas target dataset linked here, then 
you're using what we're using, and your deformed shape files are fine:


http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html

What I need to add, though, are links to the visualization and analysis 
specs (e.g., including the latest/greatest average fiducials and the 
distortion metric files needed to run processes like Attributes: Surface 
Shape: Find Significant Cluster).



Best, Jason.


Jason D. Connolly, PhD  
Center for Neural Science, New York University

6 Washington Place Room 875, New York, NY 10003
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html



 













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inline: fiducial.jpg

Re: [caret-users] help needed

2006-04-26 Thread Donna Dierker

Hi Shantanu,

There are a couple of ways to do this.  If you're lucky enough to have 
access to either a ROI or functional volume (e.g., AFNI +tlrc or FSL/SPM 
avg152 space group statistical output maps), then you can map them onto 
the PALS atlas using the procedure outlined in the PALS_B12 tutorial


http://sumsdb.wustl.edu:8081/sums/directory.do?dir_id=6332260

If you just have a stereotaxic coordinate, then you can use the Layers: 
Foci: Map Stereotaxic Focus feature.  See page 43 of this tutorial:


Caret 5.2 Tutorial - Introduction, Installation, Visualization, and 
Registration

http://brainmap.wustl.edu/caret/pdf/Caret_5_12_Tutorial_Intro.pdf

When doing metanalyses, one thing to keep in mind is that people use the 
term Talairach loosely.  They may call coordinates talairach, when 
they're really in another stereotaxic space (e.g., icbm 152 or Wash U's 
711-2B).  The PALS atlas contains several different average fiducial 
surfaces (in the Caret data_files/fmri_mapping_fils directory) to 
support various grids.  See this link for more details:


http://brainvis.wustl.edu/help/pals_volume_normalization/

When mapping foci or functional data, make sure you use the average 
fiducial surface that most closely resembles the space of your 
coordinates/volume.  If they're different, then your results are garbage.


On 04/26/2006 04:35 AM, shantanu ghosh wrote:


Dear Caret support
How can I paint  Talairach coordinates for different tasks with 
different colors onto a single cortical surface for illustration in 
metaanalysis?

thanks in advance,
shantanu


Shantanu Ghosh, PhD
Department of Humanities and Social Sciences
Indian Institute of Technology, Delhi
Hauz Khas
New Delhi 110016
INDIA
Tel.: +91-11-2659 6589
Fax: +91-11-2659 6509


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Re: [caret-users] 2D Cell Coordinates

2006-04-27 Thread Donna Dierker

Hi Ed -- see inline replies below.

On 04/27/2006 02:28 PM, Edward Craft wrote:


Hi,

I would like to extract the 2D flat-map coordinates of cells that were
projected onto a 3D reference surface. Is there a way to save the 2D
coordinates directly from within Caret, or will I need to compute them using
the values in the cell projection file?
 

If your Caret version is, say, six to 12 months old, then yes:  On the 
File: Save Data File: Foci file menu (and I assume Cell as well, since 
they're near identical), there is a drop-down menu at the bottom:  Foci 
Associated with Surface Type.  You can select the flat surface from this 
list, and write the cells/foci out relative to the flat surface.  (Of 
course, you must have projected them first.)


My April 2006 version of Caret can't seem to read my existing foci 
files, and even when I map a new focus, it disappears when I project it, 
so there may be something squirrelly with cell/foci handling in more 
recent versions.  We've had a few reports about this, and I think John 
either fixed it or it's on his list.



If I need to use the projection file, I found the file format listing in the
documentation (included below), but could you please explain what each entry
means (e.g. does cdistance(3) refer to a set of barycentric coordinates as
discussed in Drury et al. 1996; why are there three closest-tile-area values
for the inside projection; etc.)? Thanks,
 

I don't know the answer, but I hope the File: Save Data File: Cell 
option makes it moot.



   -- Ed Craft


From Caret Help File
INSIDE PROJECTION
cell-number section name class-name INSIDE comment# hemisphere
dist-to-surface
closest-tile-vertices(3)  closest-tile-areas(3) cdistance(3) (9 items
total)

OUTSIDE PROJECTION
cell-number section name class-name OUTSIDE comment# hemisphere
dist-to-surface
fracRI  fracRJ  dR  thetaR  phiR
triangles-fiducial-coordinates (2 triangles, 3 vertices, xyz)(18 items
total)
triangles-vertices  (2 triangles, 3 vertices)  (6 items total)
vertices-fiducial-coordinates (2 vertices, xyz)  (6 items total)
vertex-1  vertex-2  cell-fiducial-X  cell-fiducial-Y  cell-fiducial-Z

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Re: [caret-users] Re: MNI, Talairach, and other coordinate systems

2006-05-05 Thread Donna Dierker

On 05/04/2006 03:30 PM, Terry Sewards wrote:


Hi Donna,

I'm a little confused about coordinates of foci reported in the literature.
 


You're in excellent company.


In a study by Mechelli et al. (2005)  [NeuroImage 30: 992-1002] the authors
state that the functional images were spatially normalized to a standard
MNI-305 template using nonlinear-basis functions, but in the tables in
which the coordinates are listed it says Co-ordinates [x, y, z] are
reported in Talairach space.  There is no mention of a coordinate
transformation from MNI to TT space.  I had assumed that reported in
Talairach space meant exactly that, but now I am unsure.  I would
appreciate it if you could clarify this for me.  Thanks.
 

You'll need to ask the authors, I'm afraid.  Like you, I believe MNI-305 
does not equal Talairach, and if converting one to another, it's good 
form to specify how in the methods.  But you probably also know that 
many people use the term Talairach loosely, as a synonym for 
stereotaxic.  My guess is that they used the standard SPM2 templates, 
which means MNI-305 is more accurate than Talairach.


So I wish I could clarify, but I'm as much in the dark as you are.  Sorry.


Terry Sewards





- Original Message -
From: [EMAIL PROTECTED]
To: caret-users@brainvis.wustl.edu
Sent: Wednesday, April 26, 2006 11:00 AM
Subject: caret-users Digest, Vol 31, Issue 17


 


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Today's Topics:

  1. Re: help needed (shantanu ghosh)
  2. Re: help needed (Donna Dierker)


--

Message: 1
Date: Wed, 26 Apr 2006 10:35:58 +0100 (BST)
From: shantanu ghosh [EMAIL PROTECTED]
Subject: Re: [caret-users] help needed
To: Caret, SureFit, and SuMS software users
caret-users@brainvis.wustl.edu
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=iso-8859-1

Dear Caret support
 How can I paint  Talairach coordinates for different tasks with
   


different colors onto a single cortical surface for illustration in
metaanalysis?
 


 thanks in advance,
 shantanu


 Shantanu Ghosh, PhD
 Department of Humanities and Social Sciences
 Indian Institute of Technology, Delhi
 Hauz Khas
 New Delhi 110016
 INDIA
 Tel.: +91-11-2659 6589
 Fax: +91-11-2659 6509





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Message: 2
Date: Wed, 26 Apr 2006 08:37:09 -0500
From: Donna Dierker [EMAIL PROTECTED]
Subject: Re: [caret-users] help needed
To: Caret, SureFit, and SuMS software users
caret-users@brainvis.wustl.edu
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Shantanu,

There are a couple of ways to do this.  If you're lucky enough to have
access to either a ROI or functional volume (e.g., AFNI +tlrc or FSL/SPM
avg152 space group statistical output maps), then you can map them onto
the PALS atlas using the procedure outlined in the PALS_B12 tutorial

http://sumsdb.wustl.edu:8081/sums/directory.do?dir_id=6332260

If you just have a stereotaxic coordinate, then you can use the Layers:
Foci: Map Stereotaxic Focus feature.  See page 43 of this tutorial:

Caret 5.2 Tutorial - Introduction, Installation, Visualization, and
Registration
http://brainmap.wustl.edu/caret/pdf/Caret_5_12_Tutorial_Intro.pdf

When doing metanalyses, one thing to keep in mind is that people use the
term Talairach loosely.  They may call coordinates talairach, when
they're really in another stereotaxic space (e.g., icbm 152 or Wash U's
711-2B).  The PALS atlas contains several different average fiducial
surfaces (in the Caret data_files/fmri_mapping_fils directory) to
support various grids.  See this link for more details:

http://brainvis.wustl.edu/help/pals_volume_normalization/

When mapping foci or functional data, make sure you use the average
fiducial surface that most closely resembles the space of your
coordinates/volume.  If they're different, then your results are garbage.

On 04/26/2006 04:35 AM, shantanu ghosh wrote:

   


Dear Caret support
How can I paint  Talairach coordinates for different tasks with
different colors onto a single cortical surface for illustration in
metaanalysis?
thanks in advance,
shantanu


Shantanu Ghosh, PhD
Department of Humanities and Social Sciences
Indian

Re: Rif: Re: [caret-users] Re: MNI, Talairach, and other coordinate systems

2006-05-05 Thread Donna Dierker

Hi Dr. Carducci,

Thanks for pointing out Matthew Brett's excellent page; I've cited that 
link many times myself.


But in addition to the two approaches for converting coordinates listed 
on that page, there are still other methods, and papers should specify 
which one(s) was(were) used.


On 05/05/2006 09:06 AM, [EMAIL PROTECTED] wrote:


Hi,

you can visit the site 
http://www.mrc-cbu.cam.ac.uk/Imaging/Common/mnispace.shtml.


 

At this site there is also a Matlab script to convert MNI coordinates 
into Talairach space.


 


Filippo Carducci

 


__

Dr. Filippo Carducci PhD

University of Rome La Sapienza

Dept. Human Physiology and Pharmacology

 

 




*Donna Dierker [EMAIL PROTECTED]*
Inviato da: [EMAIL PROTECTED]
05/05/2006 08:21 EST
Per favore, rispondere a Caret, SureFit, and SuMS software users

Per: Caret, SureFit, and SuMS software users 
caret-users@brainvis.wustl.edu

Cc:
Ccr: Filippo 
Carducci/Dip-Fisio_Um/Dipartimenti/Didattica/Ateneo/Uniroma1/it
Oggetto: Re: [caret-users] Re: MNI, Talairach, and other coordinate 
systems
 


On 05/04/2006 03:30 PM, Terry Sewards wrote:

Hi Donna,

I'm a little confused about coordinates of foci reported in the 
literature.



You're in excellent company.

In a study by Mechelli et al. (2005)  [NeuroImage 30: 992-1002] the 
authors

state that the functional images were spatially normalized to a standard
MNI-305 template using nonlinear-basis functions, but in the tables in
which the coordinates are listed it says Co-ordinates [x, y, z] are
reported in Talairach space.  There is no mention of a coordinate
transformation from MNI to TT space.  I had assumed that reported in
Talairach space meant exactly that, but now I am unsure.  I would
appreciate it if you could clarify this for me.  Thanks.


You'll need to ask the authors, I'm afraid.  Like you, I believe MNI-305
does not equal Talairach, and if converting one to another, it's good
form to specify how in the methods.  But you probably also know that
many people use the term Talairach loosely, as a synonym for
stereotaxic.  My guess is that they used the standard SPM2 templates,
which means MNI-305 is more accurate than Talairach.

So I wish I could clarify, but I'm as much in the dark as you are.  Sorry.

Terry Sewards





- Original Message -
From: [EMAIL PROTECTED]
To: caret-users@brainvis.wustl.edu
Sent: Wednesday, April 26, 2006 11:00 AM
Subject: caret-users Digest, Vol 31, Issue 17




Send caret-users mailing list submissions to
caret-users@brainvis.wustl.edu

To subscribe or unsubscribe via the World Wide Web, visit
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You can reach the person managing the list at
[EMAIL PROTECTED]

When replying, please edit your Subject line so it is more specific
than Re: Contents of caret-users digest...


Today's Topics:

   1. Re: help needed (shantanu ghosh)
   2. Re: help needed (Donna Dierker)


--

Message: 1
Date: Wed, 26 Apr 2006 10:35:58 +0100 (BST)
From: shantanu ghosh [EMAIL PROTECTED]
Subject: Re: [caret-users] help needed
To: Caret, SureFit, and SuMS software users
caret-users@brainvis.wustl.edu
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=iso-8859-1

Dear Caret support
  How can I paint  Talairach coordinates for different tasks with


different colors onto a single cortical surface for illustration in
metaanalysis?


  thanks in advance,
  shantanu


  Shantanu Ghosh, PhD
  Department of Humanities and Social Sciences
  Indian Institute of Technology, Delhi
  Hauz Khas
  New Delhi 110016
  INDIA
  Tel.: +91-11-2659 6589
  Fax: +91-11-2659 6509





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Message: 2
Date: Wed, 26 Apr 2006 08:37:09 -0500
From: Donna Dierker [EMAIL PROTECTED]
Subject: Re: [caret-users] help needed
To: Caret, SureFit, and SuMS software users
caret-users@brainvis.wustl.edu
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Shantanu,

There are a couple of ways to do this.  If you're lucky enough to have
access to either a ROI or functional volume (e.g., AFNI +tlrc or FSL/SPM
avg152 space group statistical output maps), then you can map them onto
the PALS atlas using the procedure outlined in the PALS_B12 tutorial

http://sumsdb.wustl.edu:8081/sums/directory.do?dir_id=6332260

If you just have a stereotaxic coordinate, then you can use the Layers:
Foci: Map Stereotaxic Focus feature.  See page 43 of this tutorial:

Caret 5.2 Tutorial - Introduction, Installation, Visualization

Re: [caret-users] Re: Deforming borderprojection files

2006-05-12 Thread Donna Dierker

Hi Terry,

You're in territory I fear to tread.  I've never done a cross-species 
registration myself, but in theory it's doable. Like you, I'm guessing 
the route from PALS_B12 to F99UA1 will be through Colin.  If you search 
http://sumsdb.wustl.edu/sums/index.jsp for filename F99UA1 and file type 
deform_map, the most recent entries are from 2004 (probably the Denys 
and Orban papers), which used colin for the human target.


There are Colin - PALS_B12 deform_maps in sumsdb, so you could deform 
a file in two steps:  Once from PALS to colin, then from colin to 
F99UA1.  Once you get the deformation maps, then you can use Surface: 
Deformation: Apply Deformation Map on your borderproj file.  You'll have 
to change the source and target directories, since they won't match your 
file system pathnames.


Flat registration shouldn't be required; in fact, registration shouldn't 
be required.  It's just a matter of hunting down the right deform_map 
files in sumsdb; making sure you have all the F99UA1, Colin, and 
PALS_B12 files those deform_map files need; and applying them in the 
right polarity/sequence.


Give it a go on your own, and if you get stuck, let us know.  David's 
the real cross-species expert (hope that doesn't come off wrong), but 
he's in Seattle and heads to Japan next week.


On 05/12/2006 10:48 AM, Terry Sewards wrote:


Hi,

I've been trying to deform *.borderproj files from the PALS Atlas to the
Macaque Atlas (and vice versa), but I'm having trouble figuring out the
procedures involved.  Do I have to deform to the Colin atlas first, and how
is this done?  Does it require flat surface deformation, and if so is there
a goaround for the Windows version?  Thanks in advance.

Terry Sewards

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Re: [caret-users] Mapping foci

2006-05-22 Thread Donna Dierker

Hi Alex,

Just a few things to add to John's replies:

* Why are you using Colin instead of PALS?  Unless you have a very 
specific reason to use Colin, I would use the PALS_B12 atlas for this 
purpose.  In this case, you would use the average fiducial corresponding 
to the stereotaxic space.  You will find several of them in your 
$CARET_HOME/data_files/fmri_mapping_files subdirectory.  This page 
describes the methods used for normalizing the 12 Buckner brains to the 
various spaces:


http://brainvis.wustl.edu/help/pals_volume_normalization/

* The above link also explains how FLIRT, SPM2, and SPM99 use the same 
template/target, but the methods produce subtle differences 
(http://brainvis.wustl.edu/help/mni305_diffs/arch_diffs_mni305.html) -- 
enough so that David felt it was worth having separate surfaces.  I 
tried to talk him out of it, mostly because I'm lazy.;-)  (Notice there 
is no SPM5 version yet.;-)


* The AFNI coords are the only ones we have in true Talairach space, 
so yes -- these are the ones to use for mni2tal'd coordinates.


* I know nothing about SPM96, but the spm_templates.man file in my SPM2 
distribution contains this helpful excerpt:


% In SPM96, we released  a  single  subject  brain  for  use  as  a
% template.   Although  the  MNI  gave  us  this  data,  they never
% recommended that this brain  should  be  used  as  a  stereotaxic
% standard.   This   is  something  that we at the FIL chose to do.
% The official standard  for  the   ICBM   stereotactic  space   is
% the   MNI305  brain  -  which  this was not.  This brain has many
% merits for simulation but it  suffers   from   all   the   single
% brain  criticisms  that apply to Talairach.  In this release, the
% single subject T1 has been replaced by a 152 subject average.  We
% (in  the  SPM  group)  chose  to  use the 152 subject T1-weighted
% average rather than the 305 brain average because there are  also
% T2-,  and  PD-weighted  images of the same subjects.  This should
% allow  much  more  flexibility  in  the  range  of  different  MR
% contrasts   that   can   be  spatially  normalized  to  the  same
% stereotaxic space (by registering  to  a  linear  combination  of
% template images).

On 05/22/2006 08:55 AM, John Harwell wrote:


Alex,

When mapping foci using the Map Stereotaxic Focus Dialog, the focus  
entered is projected using the fiducial surface displayed in the main  
window.  So, the main window surface must be in the same stereotaxic  
space as the focus that is being mapped.  The stereotaxic space entry  
on the Map Stereotaxic Focus dialog is a meta-data entry for now.


Map foci as follows:

1) As needed, change the fiducial surface in the main window so that  
it is in the appropriate stereotaxic space for the focus currently  
being mapped.  It is okay to load multiple fiducial surfaces in Caret.

2) Save the foci projection file.
3) Exit Caret.
4) Start Caret.
5) Reopen the spec file and choose the foci projection file just  
saved and choose only one of the fiducial surfaces.


Since the foci projection file stores the foci relative to a triangle  
in the surface, the foci will be approximately transformed from the  
other stereotaxic spaces.


Good Luck.

--
John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.Box 8108
St. Louis, MO 63110   USA

On May 22, 2006, at 12:36 AM, Fornito, Alexander wrote:


Hi,
I'd like to map some foci from past studies onto the Colin surface.  
I've noticed that there seems to be 2 options for selecting co- 
ordinate type during this process;


1 -  when loading the Colin spec file, there is the option of  
choosing the SPM99, SPM2, etc fidcucial surface.
2 - in the 'studies' tab of the 'map stereotaxic focus' dialog, it  
is possible to choose the stereotaxic space used in the study.


Just want to check that I've got this right:

If I chose the Colin fiducial to be SPM2, then that means the  
surface has been registered to SPM2 template space. If I want to  map 
the focus of a study that  used SPM99 space, will choosing  SPM99 in 
the 'map stereotaxic focus' dialog automatically convert  the coords 
so the focus appears in the (roughly) correct spot on  the SPM2-space 
surface?


If so,if a study has reported coords that have been transformed  from 
MNI to talairach (e.g., using Matthew Brett's method), would  
choosing 'AFNI' in the 'map stereotaxic focus' dialog be the most  
appropriate?


Finally, there are some studies that used SPM96. Does anyone know  if 
there are large differences between SPM96 and SPM99 spaces, or  
indeed, between SPM99 and SPM2 spaces?


Thanks for your help,
Alex




Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
National Neuroscience Facility
The University of Melbourne
Levels 2  3, Alan Gilbert Building
161 

Re: [caret-users] Mapping foci

2006-05-25 Thread Donna Dierker

On 05/25/2006 03:27 AM, Fornito, Alexander wrote:


Never mind again!
I found the surface_shape files in the tutorial, but there only seems to be the right hemisphere ones. I'm particularly interested in the 3D variability maps for the PALS atlas (left and right). 
 

3D variability -- not depth variability, right?  This shape file has 
both left and right hem 3D variability:


Human.PALS_B12.LR.B_1-12.BOTH-DEPTHnr_LoContrastAVG_StdDev_3D-Variability.73730.surface_shape
http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6486399

It has these columns:

LoContrast AVERAGE B1-12 RIGHT DEPTH
3D VARIABILITY - RIGHT_HEM Human.PALS_B12
LoContrast AVG DEPTH B1-12 LEFT (Women + Men)
3D VARIABILITY - LEFT_HEM Human.PALS_B12


If you don't have the left hemispher map handy, is there anyway that I'd be 
able to generate one myself?
 

The 3D variability is generated using Surface: Create Average Coordinate 
File, and checking the Create Sample Standard Deviation.  Just make sure 
you choose the right coord files (e.g., don't mix left and right hems).  
If you're averaging native coordinates, then expect much higher 
deviation than if you're averaging AC-PC aligned, or better yet some 
scale-controlled space (Talairach, icbm*, or 711-2*).



Also, does it matter what space the PALS atlas is in when viewing the 
variability map? There seems to be only one surface_shape file in the tutorial.
 

We only generated these measures on the 711-2C surfaces (the ones we 
originally segmented).  I wouldn't expect significant differences using 
the other spaces, although the SPM ones use nonlinear volume 
registration methods, so those differences might be vary.  Try it and 
let us know whether you think the differences are worth worrying about.



Sorry about all the emails anhd thanks again,
Alex


Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
National Neuroscience Facility
The University of Melbourne
Levels 2  3, Alan Gilbert Building
161 Barry St
Carlton South Vic 3053 Australia
Ph:+61 3 8344 1624
Fax:   +61 3 9348 0469
email: [EMAIL PROTECTED]



-Original Message-
From: Fornito, Alexander
Sent: Thu 5/25/2006 1:10 PM
To: Caret, SureFit, and SuMS software users; Caret, SureFit, and SuMS software 
users
Subject: RE: [caret-users] Mapping foci

Never mind, I found it. Its a separate coord file - right?
Are there any surface-shape files for depth hidden anywhere, or do I generate 
that myself?
Thanks again,
Alex

Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
National Neuroscience Facility
The University of Melbourne
Levels 2  3, Alan Gilbert Building
161 Barry St
Carlton South Vic 3053 Australia
Ph:+61 3 8344 1624
Fax:   +61 3 9348 0469
email: [EMAIL PROTECTED]



-Original Message-
From: [EMAIL PROTECTED] on behalf of Donna Dierker
Sent: Tue 5/23/2006 12:45 AM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] Mapping foci

Hi Alex,

Just a few things to add to John's replies:

* Why are you using Colin instead of PALS?  Unless you have a very 
specific reason to use Colin, I would use the PALS_B12 atlas for this 
purpose.  In this case, you would use the average fiducial corresponding 
to the stereotaxic space.  You will find several of them in your 
$CARET_HOME/data_files/fmri_mapping_files subdirectory.  This page 
describes the methods used for normalizing the 12 Buckner brains to the 
various spaces:


http://brainvis.wustl.edu/help/pals_volume_normalization/

* The above link also explains how FLIRT, SPM2, and SPM99 use the same 
template/target, but the methods produce subtle differences 
(http://brainvis.wustl.edu/help/mni305_diffs/arch_diffs_mni305.html) -- 
enough so that David felt it was worth having separate surfaces.  I 
tried to talk him out of it, mostly because I'm lazy.;-)  (Notice there 
is no SPM5 version yet.;-)


* The AFNI coords are the only ones we have in true Talairach space, 
so yes -- these are the ones to use for mni2tal'd coordinates.


* I know nothing about SPM96, but the spm_templates.man file in my SPM2 
distribution contains this helpful excerpt:


% In SPM96, we released  a  single  subject  brain  for  use  as  a
% template.   Although  the  MNI  gave  us  this  data,  they never
% recommended that this brain  should  be  used  as  a  stereotaxic
% standard.   This   is  something  that we at the FIL chose to do.
% The official standard  for  the   ICBM   stereotactic  space   is
% the   MNI305  brain  -  which  this was not.  This brain has many
% merits for simulation but it  suffers   from   all   the   single
% brain  criticisms  that apply to Talairach.  In this release, the
% single subject T1 has been replaced by a 152 subject average.  We
% (in  the  SPM  group)  chose  to  use the 152 subject T1-weighted
% average rather than the 305 brain average because there are  also
% T2-,  and  PD-weighted

Re: [caret-users] [SPAM] posting

2006-05-31 Thread Donna Dierker

Hi Jason,

Not everyone knows about these handy command line utilities:

/146Gb/caret_distribution/caret/bin/caret_copy_spec
/146Gb/caret_distribution/caret/bin/caret_map_fmri
/146Gb/caret_distribution/caret/bin/mpeg_encode
/146Gb/caret_distribution/caret/bin/mpeg_play
/146Gb/caret_distribution/caret/bin/caret_metric
/146Gb/caret_distribution/caret/bin/caret_command
/146Gb/caret_distribution/caret/bin/caret_edit
/146Gb/caret_distribution/caret/bin/caret_zip_spec
/146Gb/caret_distribution/caret/bin/caret_file_convert

Enter caret_map_fmri -help to get the full usage.  When you do the 
same for caret_command, redirect the output to a text file; it's 954 
lines, but it's one handy utility.


On 05/31/2006 04:06 PM, Jason D Connolly wrote:


Dear David or Donna,

We hope to import a large number of externally generated beta maps into
caret and then generate surface statistics.  Is there any way to execute
map volume(s) to surface(s) at the command line (Linux platform),
instead of having to open up each of the files in caret?  Moreover, is
there documentation for different caret operations processed via command
lines? 

Many thanks, Jason. 



Jason D. Connolly, PhD  
Center for Neural Science, New York University

6 Washington Place Room 875, New York, NY 10003
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html




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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] [SPAM] posting

2006-06-05 Thread Donna Dierker
Thank John Harwell for the handy dandy feature:  caret_command 
-surface-deformation-apply


The attached script calls this command on a bunch of files.

You may need to get an updated version of caret_command, if your version 
doesn't have it.  It's roughly April vintage (i.e., when we were 
regenerating a BUNCH of depth files).


On 06/05/2006 05:39 PM, Jason D Connolly wrote:


Dear Donna,

Thank you for your assistance regarding the caret command line
utilities.  The 'caret_map_fmri' utility works like a charm.

We now have many, many statistical maps (.metric files).  Therefore, a
slow down is caused by having to enter and execute the 'apply
deformation map' utility for each metric file, to warp the individual
metric file to the PALS atlas space.  Can this function also be executed
at the command line?  I didn't see anything in the list you provided. 
This would allow us to automate this step and thus would speed things up ...


Thank you,

Jason.


Jason D. Connolly, PhD  
Center for Neural Science, New York University

6 Washington Place Room 875, New York, NY 10003
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562 
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html




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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)

#!/bin/sh
set -x

ATLAS_TGT_DIR=/backup/erin/HUMAN_PALS_B12/PALS_B12.LR/BUCKNER
MAP_LIST=/tmp/map_list.$$.txt
ls $ATLAS_TGT_DIR/*map |sort  $MAP_LIST
DIR_LIST=/tmp/dir_list.$$.txt

cat  $DIR_LIST  EOF
BATCH1_FEMALE_SUMS/Human_Buckner_Case01/BUCKNER_Case01.L
BATCH1_FEMALE_SUMS/Human_Buckner_Case01/BUCKNER_Case01.R
BATCH1_FEMALE_SUMS/Human_Buckner_Case02/BUCKNER_Case02.L
BATCH1_FEMALE_SUMS/Human_Buckner_Case02/BUCKNER_Case02.R
BATCH1_FEMALE_SUMS/Human_Buckner_Case03/BUCKNER_Case03.L
BATCH1_FEMALE_SUMS/Human_Buckner_Case03/BUCKNER_Case03.R
BATCH1_FEMALE_SUMS/Human_Buckner_Case04/BUCKNER_Case04.L
BATCH1_FEMALE_SUMS/Human_Buckner_Case04/BUCKNER_Case04.R
BATCH1_FEMALE_SUMS/Human_Buckner_Case05/BUCKNER_Case05.L
BATCH1_FEMALE_SUMS/Human_Buckner_Case05/BUCKNER_Case05.R
BATCH1_FEMALE_SUMS/Human_Buckner_Case06/BUCKNER_Case06.L
BATCH1_FEMALE_SUMS/Human_Buckner_Case06/BUCKNER_Case06.R
BATCH2_MALE_SUMS/Human_Buckner_Case07/BUCKNER_Case07.L
BATCH2_MALE_SUMS/Human_Buckner_Case07/BUCKNER_Case07.R
BATCH2_MALE_SUMS/Human_Buckner_Case08/BUCKNER_Case08.L
BATCH2_MALE_SUMS/Human_Buckner_Case08/BUCKNER_Case08.R
BATCH2_MALE_SUMS/Human_Buckner_Case09/BUCKNER_Case09.L
BATCH2_MALE_SUMS/Human_Buckner_Case09/BUCKNER_Case09.R
BATCH2_MALE_SUMS/Human_Buckner_Case10/BUCKNER_Case10.L
BATCH2_MALE_SUMS/Human_Buckner_Case10/BUCKNER_Case10.R
BATCH2_MALE_SUMS/Human_Buckner_Case11/BUCKNER_Case11.L
BATCH2_MALE_SUMS/Human_Buckner_Case11/BUCKNER_Case11.R
BATCH2_MALE_SUMS/Human_Buckner_Case12/BUCKNER_Case12.L
BATCH2_MALE_SUMS/Human_Buckner_Case12/BUCKNER_Case12.R
BATCH3_FEMALE_SUMS/Human_Buckner_Case13/BUCKNER_Case13.L
BATCH3_FEMALE_SUMS/Human_Buckner_Case13/BUCKNER_Case13.R
BATCH3_FEMALE_SUMS/Human_Buckner_Case14/BUCKNER_Case14.L
BATCH3_FEMALE_SUMS/Human_Buckner_Case14/BUCKNER_Case14.R
BATCH3_FEMALE_SUMS/Human_Buckner_Case15/BUCKNER_Case15.L
BATCH3_FEMALE_SUMS/Human_Buckner_Case15/BUCKNER_Case15.R
BATCH3_FEMALE_SUMS/Human_Buckner_Case16/BUCKNER_Case16.L
BATCH3_FEMALE_SUMS/Human_Buckner_Case16/BUCKNER_Case16.R
BATCH3_FEMALE_SUMS/Human_Buckner_Case17/BUCKNER_Case17.L
BATCH3_FEMALE_SUMS/Human_Buckner_Case17/BUCKNER_Case17.R
BATCH3_FEMALE_SUMS/Human_Buckner_Case18/BUCKNER_Case18.L
BATCH3_FEMALE_SUMS/Human_Buckner_Case18/BUCKNER_Case18.R
BATCH4_MALE_SUMS/Human_Buckner_Case19/BUCKNER_Case19.L
BATCH4_MALE_SUMS/Human_Buckner_Case19/BUCKNER_Case19.R
BATCH4_MALE_SUMS/Human_Buckner_Case20/BUCKNER_Case20.L
BATCH4_MALE_SUMS/Human_Buckner_Case20/BUCKNER_Case20.R
BATCH4_MALE_SUMS/Human_Buckner_Case21/BUCKNER_Case21.L
BATCH4_MALE_SUMS/Human_Buckner_Case21/BUCKNER_Case21.R
BATCH4_MALE_SUMS/Human_Buckner_Case22/BUCKNER_Case22.L
BATCH4_MALE_SUMS/Human_Buckner_Case22/BUCKNER_Case22.R
BATCH4_MALE_SUMS/Human_Buckner_Case23/BUCKNER_Case23.L
BATCH4_MALE_SUMS/Human_Buckner_Case23/BUCKNER_Case23.R
BATCH4_MALE_SUMS/Human_Buckner_Case24/BUCKNER_Case24.L
BATCH4_MALE_SUMS/Human_Buckner_Case24/BUCKNER_Case24.R
EOF

for DIR in `cat $DIR_LIST`
do
  cd $DIR
  COMMAND=caret_command -surface-deformation-apply 
  CASE_HEM=`echo $DIR |sed 's#.*/BUCKNER_##g'| sed 's/Case0/Case/g'`
  DEFORM_MAP=`grep $CASE_HEM $MAP_LIST`
  COMMAND=$COMMAND $DEFORM_MAP SURFACE_SHAPE
  SHAPE_IN=`ls *DEPTH_FIXED_SHN.surface_shape`
  COMMAND=$COMMAND $SHAPE_IN
  SHAPE_OUT=$ATLAS_TGT_DIR/def_$SHAPE_IN
  COMMAND=$COMMAND $SHAPE_OUT
  echo $COMMAND
  $COMMAND
  cd ../../..
done


Re: [caret-users] Cortical Thickness Measurement

2006-06-13 Thread Donna Dierker

Hi Darren,

Sorry to be the bearer of bad news, but no:  Caret/SureFit doesn't 
compute cortical thickness.  For a while, a student was working on it, 
but it never went anywhere.  Occasionally, people mistake our sulcal 
depth measure for cortical thickness, but the two are completely 
different measures.  (See David's PALS paper 
(http://www.sciencedirect.com/science?_ob=MImg_imagekey=B6WNP-4H4T34K-1-3_cdi=6968_user=4275_orig=browse_coverDate=11%2F15%2F2005_sk=999719996view=cwchp=dGLbVzb-zSkzkmd5=0920fddff1134928d23f0a23d746935fie=/sdarticle.pdf), 
figure 1, for a description of sulcal depth.)


The only good news I can give those who are interested in cortical 
thickness is that you can import your freesurfer surfaces and thickness 
maps into Caret in a mostly automated way, and generate sulcal depth on 
them, if desired.  You can then register them to the PALS_B12 atlas, 
although this requires drawing our Core6 landmark borders:


http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html

Due to algorithmic differences between Freesurfer's and Caret's 
registration algorithms, seeking a second opinion can be useful, 
depending on the nature of your study.  For example, the algorithm that 
best aligns intrasubject anatomy across multiple timepoints may not be 
ideal for finding group anatomical differences.


On 06/12/2006 09:09 PM, Darren Weber wrote:


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1


Hi,

I have been using FreeSurfer for a while, to obtain cortical thickness
measures.  Is it now possible to obtain thickness measures with caret?

There is a previous thread from 2003 indicating this feature was on a
wish-list:

http://brainvis.wustl.edu/pipermail/caret-users/2003-September/76.html


Thanks, Darren


- --

Darren L. Weber, Ph.D.
Postdoctoral Scholar

Dynamic Neuroimaging Laboratory,
UCSF Department of Radiology,
185 Berry Street, Suite 350, Box 0946,
San Francisco, CA 94107, USA.

Tel: +1 415 353-9444
Fax: +1 415 353-9421
www: http://dnl.ucsf.edu/users/dweber

To explicate the uses of the brain seems as difficult
a task as to paint the soul, of which it is commonly
said, that it understands all things but itself.
 Thomas Willis (The Anatomy of the Brain and Nerves, 1664)
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.3 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFEjh5kxaCYN7qs0v4RAh7lAJ93FoghevMObd2n4idytpsuYLxoJQCeOdKY
/817YAHiHOSBRPgzJbB1IJI=
=/WHa
-END PGP SIGNATURE-

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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] Cortical Thickness Measurement

2006-06-13 Thread Donna Dierker

Hi Eric,

We haven't updated the old Freesurfer-to-Caret tutorial, but you might 
find these caret-users posts helpful:


http://brainvis.wustl.edu/pipermail/caret-users/2006-February/000686.html
http://brainvis.wustl.edu/pipermail/caret-users/2006-February/000687.html

Entering caret_command -help at the command line will spew 954 lines of 
helpful text, as well.


If these don't cover what you want to do, post back here and we'll see 
if we can help.


On 06/13/2006 08:31 AM, Faden, Eric (NIH/NIMH) [F] wrote:


Are there instructions somewhere for importing from FreeSurfer to Caret 5.4 
somewhere?  The only instructions seem to be fairly old and it looks like 
things have changed a bit since then.

-Eric

-Original Message-
From: Donna Dierker [mailto:[EMAIL PROTECTED]
Sent: Tue 6/13/2006 8:36 AM
To: [EMAIL PROTECTED]; Caret, SureFit,and SuMS software users
Subject: Re: [caret-users] Cortical Thickness Measurement

Hi Darren,

Sorry to be the bearer of bad news, but no:  Caret/SureFit doesn't 
compute cortical thickness.  For a while, a student was working on it, 
but it never went anywhere.  Occasionally, people mistake our sulcal 
depth measure for cortical thickness, but the two are completely 
different measures.  (See David's PALS paper 
(http://www.sciencedirect.com/science?_ob=MImg_imagekey=B6WNP-4H4T34K-1-3_cdi=6968_user=4275_orig=browse_coverDate=11%2F15%2F2005_sk=999719996view=cwchp=dGLbVzb-zSkzkmd5=0920fddff1134928d23f0a23d746935fie=/sdarticle.pdf), 
figure 1, for a description of sulcal depth.)


The only good news I can give those who are interested in cortical 
thickness is that you can import your freesurfer surfaces and thickness 
maps into Caret in a mostly automated way, and generate sulcal depth on 
them, if desired.  You can then register them to the PALS_B12 atlas, 
although this requires drawing our Core6 landmark borders:


http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html

Due to algorithmic differences between Freesurfer's and Caret's 
registration algorithms, seeking a second opinion can be useful, 
depending on the nature of your study.  For example, the algorithm that 
best aligns intrasubject anatomy across multiple timepoints may not be 
ideal for finding group anatomical differences.


On 06/12/2006 09:09 PM, Darren Weber wrote:

 


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1


Hi,

I have been using FreeSurfer for a while, to obtain cortical thickness
measures.  Is it now possible to obtain thickness measures with caret?

There is a previous thread from 2003 indicating this feature was on a
wish-list:

http://brainvis.wustl.edu/pipermail/caret-users/2003-September/76.html


Thanks, Darren


- --

Darren L. Weber, Ph.D.
Postdoctoral Scholar

Dynamic Neuroimaging Laboratory,
UCSF Department of Radiology,
185 Berry Street, Suite 350, Box 0946,
San Francisco, CA 94107, USA.

Tel: +1 415 353-9444
Fax: +1 415 353-9421
www: http://dnl.ucsf.edu/users/dweber

To explicate the uses of the brain seems as difficult
a task as to paint the soul, of which it is commonly
said, that it understands all things but itself.
Thomas Willis (The Anatomy of the Brain and Nerves, 1664)
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.3 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFEjh5kxaCYN7qs0v4RAh7lAJ93FoghevMObd2n4idytpsuYLxoJQCeOdKY
/817YAHiHOSBRPgzJbB1IJI=
=/WHa
-END PGP SIGNATURE-

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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] Cortical Thickness Measurement

2006-06-14 Thread Donna Dierker

Hi Eric,

I think I remember talking to you at NIH in February.  First, let me 
clarify:  Do you already have Freesurfer surfaces for these macaques?  
Or do you want to segment using Caret?


If you already have Freesurfer surfaces, then the import script should 
still work for macaques.  (The only iffy thing there might be the 
caret_command -volume-create parameters in the generate_depth part.)


The general flattening and registration *procedures* are similar, but 
there are some important differences:


1.  Registration target:  There is no PALS for macaques -- at least not 
yet.  (Some folks at Wash U are working on a multi-subject macaque 
atlas.)  Meanwhile, we use our F99UA1 single subject macaque atlas as a 
registration target:


Left: http://sumsdb.wustl.edu/sums/directory.do?dir_id=681250
Right: http://sumsdb.wustl.edu/sums/directory.do?dir_id=681256

2.  Landmark set:  Because macaques are so much less variable than 
humans in their folding patterns, you can count on more landmarks.  The 
goals of your study dictate which landmarks are optimal.  Do you want to 
optimize alignment of sulci/gyri across subjects, or look for anatomical 
differences across groups?


On 06/13/2006 02:09 PM, Faden, Eric (NIH/NIMH) [F] wrote:


I suppose I should have been more specific.  Is there any Macaque specific 
information?

-Eric


-Original Message-
From: Donna Dierker [mailto:[EMAIL PROTECTED]
Sent: Tue 6/13/2006 2:48 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] Cortical Thickness Measurement

Hi Eric,

We haven't updated the old Freesurfer-to-Caret tutorial, but you might 
find these caret-users posts helpful:


http://brainvis.wustl.edu/pipermail/caret-users/2006-February/000686.html
http://brainvis.wustl.edu/pipermail/caret-users/2006-February/000687.html

Entering caret_command -help at the command line will spew 954 lines of 
helpful text, as well.


If these don't cover what you want to do, post back here and we'll see 
if we can help.


On 06/13/2006 08:31 AM, Faden, Eric (NIH/NIMH) [F] wrote:

 


Are there instructions somewhere for importing from FreeSurfer to Caret 5.4 
somewhere?  The only instructions seem to be fairly old and it looks like 
things have changed a bit since then.

-Eric

-Original Message-
From: Donna Dierker [mailto:[EMAIL PROTECTED]
Sent: Tue 6/13/2006 8:36 AM
To: [EMAIL PROTECTED]; Caret, SureFit,and SuMS software users
Subject: Re: [caret-users] Cortical Thickness Measurement

Hi Darren,

Sorry to be the bearer of bad news, but no:  Caret/SureFit doesn't 
compute cortical thickness.  For a while, a student was working on it, 
but it never went anywhere.  Occasionally, people mistake our sulcal 
depth measure for cortical thickness, but the two are completely 
different measures.  (See David's PALS paper 
(http://www.sciencedirect.com/science?_ob=MImg_imagekey=B6WNP-4H4T34K-1-3_cdi=6968_user=4275_orig=browse_coverDate=11%2F15%2F2005_sk=999719996view=cwchp=dGLbVzb-zSkzkmd5=0920fddff1134928d23f0a23d746935fie=/sdarticle.pdf), 
figure 1, for a description of sulcal depth.)


The only good news I can give those who are interested in cortical 
thickness is that you can import your freesurfer surfaces and thickness 
maps into Caret in a mostly automated way, and generate sulcal depth on 
them, if desired.  You can then register them to the PALS_B12 atlas, 
although this requires drawing our Core6 landmark borders:


http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html

Due to algorithmic differences between Freesurfer's and Caret's 
registration algorithms, seeking a second opinion can be useful, 
depending on the nature of your study.  For example, the algorithm that 
best aligns intrasubject anatomy across multiple timepoints may not be 
ideal for finding group anatomical differences.


On 06/12/2006 09:09 PM, Darren Weber wrote:



   


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1


Hi,

I have been using FreeSurfer for a while, to obtain cortical thickness
measures.  Is it now possible to obtain thickness measures with caret?

There is a previous thread from 2003 indicating this feature was on a
wish-list:

http://brainvis.wustl.edu/pipermail/caret-users/2003-September/76.html


Thanks, Darren


- --

Darren L. Weber, Ph.D.
Postdoctoral Scholar

Dynamic Neuroimaging Laboratory,
UCSF Department of Radiology,
185 Berry Street, Suite 350, Box 0946,
San Francisco, CA 94107, USA.

Tel: +1 415 353-9444
Fax: +1 415 353-9421
www: http://dnl.ucsf.edu/users/dweber

To explicate the uses of the brain seems as difficult
a task as to paint the soul, of which it is commonly
said, that it understands all things but itself.
Thomas Willis (The Anatomy of the Brain and Nerves, 1664)
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.3 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFEjh5kxaCYN7qs0v4RAh7lAJ93FoghevMObd2n4idytpsuYLxoJQCeOdKY
/817YAHiHOSBRPgzJbB1IJI=
=/WHa
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Re: [caret-users] Questions regarding foci assignment in Caret5

2006-07-05 Thread Donna Dierker

On 07/05/2006 01:58 PM, [EMAIL PROTECTED] wrote:

Hi, my name is David Kiamanesh and I am a second year medical student 
at WashU.  I am beginning to learn Caret so that I could map fMRI data 
which I have collected from published papers.  I have been working on 
learning how to use the stereotaxix foci feature which Caret has and 
it is great.  I have come across a couple of things however that I was 
hoping you could help me out with.


1)  For some reason every once in a while, in the D/C under Foci, in 
the colors tab the new foci I entered will be awkwardly placed, not 
indented like the rest of the list.  Any subsequent foci that I define 
would then be listed directly on top of the last one, i.e. the words 
will be on top of each other, therefore unreadable.  I really have no 
idea why it does that, I've tried saving the data file and restarting 
it and it appears that the problem goes away, so I really dont know 
what the deal is with it.


I have never seen this myself.  Like you, I have no idea what the deal 
is with it.




2) I'm unclear what the foci projections are.  I saved the foci 
projections and then loaded it the next time and some of the foci were 
duplicated in the foci report, off by about 0.02.  I'm not sure if 
I need these projections or what exactly they are.


Projecting foci allows you to to view them on a surface other than the 
fiducial surface.  I think of foci as free points out in space; 
projecting them attaches them to the closest tile in the active 
fiducial.  If you load both the foci and fociproj files concurrently, 
you will see duplicates.  You shouldn't see dups when viewing one or the 
other.




I appreciate any help that you can give me and would like to thank you 
for offering such a powerful and well designed program for free use.


Sincerely,
David Kiamanesh



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(Formerly Donna Hanlon; no change in marital status -- see 
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Re: [caret-users] Script to streamline import of Freesurfer surfaces

2006-08-01 Thread Donna Dierker

Hi Svetlana,

Depending on which version of Caret you're running, you may need to 
download a more recent version of this script:


http://brainmap.wustl.edu/pub/donna/SCRIPTS/FREESURFER/freesurfer2caret.sh
login pub
password download

This version replaces the  -hem flag in the caret_file_convert steps 
with  -struct (not sure exactly when this change took effect in 
caret_file_convert).  Thanks to Johannes Klein for pointing this out.  
Note that I haven't tested this script.


In an attempt to be more clear, I also replaced these lines:

   CASES=ED EF EG FH FK FL FM FN
   CASES=FH

... with this one:

   CASES=MYSUBJECT_01 MYSUBJECT_02 MYSUBJECT_03

Earlier this year, the gracious folks in Bob Cox's AFNI group at NIH 
provided us some Freesurfer cases from an old Mike Beauchamp study, for 
the purposes of importing them into Caret, so this is what the ED EF EG 
... cases are.  The second line (CASES=FH) is just overriding the 
previous line, having the effect of running the script solely on case FH 
(e.g., probably to troubleshoot something).


In your case, you would replace this line:

   CASES=MYSUBJECT_01 MYSUBJECT_02 MYSUBJECT_03

... with this one:

   CASES=sub01

Then, cd to the directory containing sub01 and run the script.

If you don't care about sulcal depth, then comment out the 
generate_depth lines near the end of the script to greatly reduce 
run-time.  (Even if you're doing an anatomical study, you might use 
Freesurfer's convexity metric, rather than sulcal depth.  In this case, 
you'll need to add a few more lines to convert the curvature-like 
convexity file to Freesurfer ASCII, and then into a Caret surface_shape 
file.  I believe this is the *h.sulc file; please correct me if I'm wrong.)


On 08/01/2006 06:42 AM, Svetlana Georgieva wrote:

Hi Donna,

Since I am a new caret user and trying to convert some freesurfer flat 
maps your script 'freesurfer2caret.sh.rev' sound grate to me.  Could 
you please explain me haw exactly to run this script.  Is it working 
under freesurfer?


If I would like to run it for one subject (for example ‘sub01’) what 
should I write in the following rows?


CASES=ED EF EG FH FK FL FM FN
CASES=FH

Thanks,
Svetlana

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(Formerly Donna Hanlon; no change in marital status -- see 
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Re: [caret-users] SPM2 Caret

2006-08-01 Thread Donna Dierker

Hi Dr. Schlund,

I interpret simple overlays of functional data as mapping functional 
data onto the PALS atlas.  In that case, step 1 is to take the PALS 
tutorial, if you haven't already done so:


PDF: http://sumsdb.wustl.edu/sums/download.do?id=6363278
dataset: http://sumsdb.wustl.edu/sums/download.do?archive_id=6362705

Next step is to create a SPM2-oriented visualization spec.  This could 
be one of the four spec files in the PALS atlas tutorial, or it could be 
something more streamlined, such as the following specs:


Human.PALS_B12.B1-12.DEPTH_ANALYSES_LEFT.73730.spec
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6486316
Human.PALS_B12.B1-12.DEPTH_ANALYSES_RIGHT.73730.spec
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6486393

Or it could be something in between (e.g., the streamlined + the 
composite paint/borders).


Next, in those starter spec files, replace the existing PALS average 
fiducial coord files (711-2C atlas space) with these SPM2 versions in 
your CARET_HOME/data_files/fmri_mapping_files directory/folder:


Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord
Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord

Replace them not only on the file system, but also in the spec file 
(using a text editor, or by using File: Open Data File: Coord file to 
open them the first time, which should add them to the spec file by 
default).


Now open that spec file and make sure the SPM2 average fiducial surface 
is loaded.


While a MeanBuckner12 version for SPM2 does exist, you might instead 
consider using the actual atlas target used (e.g., avg152T1) as the 
volume anatomy file underlay for slice views.  Use File: Open Data file: 
Volume Anatomy file and navigate to your SPM2 templates directory to 
open the appropriate volume.  Make sure left appears on left.


Use File: Open Data File: Volume Functional file to open your functional 
volume; select the volume is SPM2 volume with right on left if your 
spm_defaults.m has analyze.flip=1.


Press Toolbar: D/C and select Overlay/Underlay Volume and select the 
avg152T1 as underlay; your functional volume as primary overlay.  They 
should align well.  Switch to the Settings tab and toggle on the surface 
outline, if desired, to make sure the alignment between the PALS average 
fiducial surface and the anatomical volume is good.


Now map the functional data onto the PALS surface:

Select Attributes: Map functional volumes to surfaces: Metric
Add loaded volumes; next
Map to spec file with atlas; select the currently loaded spec file; 
Space SPM2; PALS (left or right); ok; next

Data file: change to a more meaningful output name
Mapping algorithm: Enclosing and interpolated voxel are both popular; 
next; finish

Toolbar: spec: metric: open the output filename you specified
D/C Overlay Underlay/Surface: primary overlay metric; select column of 
choice

Toggle between fiducial and alternative views (inflated, flat).

Over a year ago, creating space-specific visualization specs was on my 
to-do list, but I'm afraid this item has been buried well below many 
other priorities.  If you have trouble with this step, let me know.


Good luck.

On 08/01/2006 08:46 AM, Michael Schlund wrote:

Hi folks,

Caret newbie, who is very, very impressed with this software. My
question
is whether anyone has a SPM+caret for dummies guide available that we
might have---just a simple Word doc would be extremely helpful. We are
using SPM2 and have been having quite a bit of trouble with just the
basics of implementing caret for doing simple overlays of functional
data.
We are using the most updated version of caret and have cruised the
website and email archives but we are still, well, floundering badly.
Any
comments for 'how to' help would be truly spectacular.

Mike Schlund, Ph.D.
Assistant Professor, Department of Psychiatry, Johns Hopkins University
School of Medicine
Research Scientist, Department of Behavior Analysis, University of North
Texas
Faculty  Director, Neurobehavioral Imaging Laboratory, Kennedy Krieger
Institute
Adjunct Assistant Professor, Department of Psychology  Department of
Psychiatry, University of Pittsburgh
412-624-5018: [EMAIL PROTECTED], [EMAIL PROTECTED]



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[caret-users] mapping SPM5 functional results onto PALS atlas

2006-08-17 Thread Donna Dierker

Hi Nicola,

Your .hdr file is missing this origin information:

SPM originator decodes to 40 57 26

Try writing the volume out in NIfTI format and mapping it in Caret; 
you'll have better luck (I hope).  There are other work-arounds if this 
fails, but this is a classic example of why NIfTI was invented.


I confess two things:

1.  I haven't personally switched over to NIfTI yet.  I really, really 
should.  I'm just mid-project in so many projects now.


2.  I haven't yet created SPM5 versions of the PALS surfaces.  I'm 
hoping they don't differ much from SPM2.


This page illustrates how results from mapping to SPM99 differ from SPM2:

http://brainvis.wustl.edu/help/mni305_diffs/arch_diffs_mni305.html

 Original Message 

Subject: mapping SPM5 functional results onto PALS atlas
From: Nicola Canessa [EMAIL PROTECTED]
Date: Thu, 17 Aug 2006 11:35:55 +0200 (CEST)
To: caret-users@brainvis.wustl.edu

Dear experts,
I am trying to map functional data obtained with SPM5 (the attached *.img
+ *.hdr) onto a flattened image of the left hemisphere (the PALS B.12),
using Caret 5.4 (attributes: map  volumes(s) to surface(s)). I remember I
could do it easily on SPM2-data using Caret 5.3, but now I get the
following error message (and no mapping  of the functional data):

You have selected a .hdr file. If this .hdr file does not contain an
SPM generator, it is unlikely that it will get mapped to the surface
correctly.

I searched through the tutorials but I could not find a solution to this
problem. Any suggestions would be greatly appreciated..

Many thanks in advance,
  nicola

***
Nicola Canessa, Ph.d
Cognitive Neuroscience Sector
SISSA
Trieste, Italy
***



Re: [caret-users] [SPAM] caret on AMD64

2006-08-29 Thread Donna Dierker

Try making sure /usr/lib64 is in your LD_LIBRARY_PATH variable, e.g.:

setenv LD_LIBRARY_PATH /usr/lib64:$LD_LIBRARY_PATH

... or if your shell is bash:

export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH

Thanks for reporting the issue with the mailing list. It sounds like I 
need to check the spam settings for [EMAIL PROTECTED]


On 08/29/2006 03:01 AM, Marco Tettamanti wrote:

Dear Donna and John,
first of all I would like to express my congratulations for the
improvements you made in Caret! I haven't been using the software for
some times, but now that I have some new data to work on and I have
started to use the latest release (5.4), I find that many options have
been made more intuitive and easy to use, especially for the manual
correction of segmentation errors.

I am trying to install caret on an an AMD64 linux architecture (CentOS
4.3, kernel 2.6.9, 2 x AMD Opteron dual-core).
I have tried installing from the linux binaries, but I receive an error
message that some libraries cannot be opened (error while loading
shared libraries: libpng12.so.0: cannot open shared object file: No such
file or directory), even if I create symbolic links to e.g.
/usr/lib64/libpng12.so.0.
Is there any way I can get the caret binaries to work on AMD64, without
having to build from the source files?

Thank you a lot for your help,
Marco

P.S.: I am using this alternative email address because but I have 
tried several times to send an email to caret-users@brainvis.wustl.edu 
from my address [EMAIL PROTECTED], but for some reasons my 
emails are rejected with the following error message:


The Symantec Mail Security program

caret-users@brainvis.wustl.edu: host 
acuda.wustl.edu[128.252.248.242] said:

550 [EMAIL PROTECTED]: Sender address rejected: Blocked (in reply
to RCPT TO command)

--
Marco Tettamanti, Ph.D.
San Raffaele Scientific Institute
Facoltà di Psicologia
Via Olgettina 58
I-20132 Milano, Italy
Tel. ++39-02-26434888
Fax ++39-02-26434892
Email: [EMAIL PROTECTED]


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Re: [caret-users] [windows problem] RadialPositionMap+orig.HEAD not found

2006-08-30 Thread Donna Dierker

H Leonardo,

A while back, there was a bug in the Windows version of Caret that 
caused some files to get written to the $CARET_HOME/bin directory 
instead of the current working directory.  This bug has been fixed for a 
while, so I suggest trying the snapshot caret5.exe:


http://brainmap.wustl.edu/pub/caret/caret5_exe_windows.zip
login pub
password download

Move your old caret5.exe file (perhaps in c:\caret\bin or the bin 
subdirectory under the folder in which you installed caret) to 
caret5_old.exe; unzip the downloaded zip file; and move the caret5.exe 
to the caret bin subdirectory.


Good luck!

On 08/30/2006 02:44 AM, leonardo cerliani wrote:

hello everyone,
I had to install caret under windows in my pc at work. I have the
following problem: when I start the volume--segmentation, it goes on,
but soon after the first fiducial reconstruction, it pops out that it
cannot find RadialPositionMap+orig.HEAD. I obviously checked in the
directory I was working in and it is there. I also tried to restart
the segmentation process from the automatic error correction, but it
suddenly stops telling me that the segmentation was successfully
performed. The result that I can see from now is that it does not
perform automatic error correction. Can you help me in some way?

thanks a lot for your attention

leonardo cerliani
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Re: [SPAM] Re: Re: [caret-users] [SPAM] caret on AMD64

2006-08-30 Thread Donna Dierker

Hi Marco,

It doesn't seem like this should be necessary, but let's see how your 
ldd caret5 output is affected by this:


export LD_LIBRARY_PATH=/usr/lib64:/usr/lib:/usr/X11R6/lib64/lib

Add any other library directories to the path above (delimited by :) 
that you think might help.


On 08/30/2006 08:14 AM, Marco Tettamanti wrote:

Hi Donna!
Upon a fresh login, the output of 'echo $LD_LIBRARY_PATH' is usually 
empty.
After giving the command 'export 
LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH', the output is:


echo $LD_LIBRARY_PATH
/usr/lib64:

The output of the 'find' command is:
find / -name libX11.so.6
/usr/X11R6/lib64/libX11.so.6

Thank you again,
Marco


*/Donna Dierker [EMAIL PROTECTED]/* wrote:

Hi Marco,

John may have more concrete suggestions, but I want to see the
output of
two commands:

echo $LD_LIBRARY_PATH

and the other is:

find / -name libX11.so.6

Based on the output below, I still suspect an issue with your
LD_LIBRARY_PATH. It could also be that there are too many shared
library
differences between our Linux build platform and your runtime
platform.
But let's clarify before reaching that conclusion.

On 08/30/2006 07:06 AM, Marco Tettamanti wrote:
 Hi Donna and John,
 thank you for your answers! Unfortunately I couldn't solve the
problem.

 I have tried exporting /usr/lib64 to LD_LIBRARY_PATH, but I
still get
 the same error message:
 error while loading shared libraries: libpng12.so.0: cannot open
 shared object file: No such file or directory

 The output of ldd caret5 is:

 [EMAIL PROTECTED] bin]# ldd caret5
 linux-gate.so.1 = (0xe000)
 libpng12.so.0 = not found
 libSM.so.6 = not found
 libICE.so.6 = not found
 libXi.so.6 = not found
 libXrender.so.1 = not found
 libXrandr.so.2 = not found
 libXcursor.so.1 = not found
 libfreetype.so.6 = not found
 libfontconfig.so.1 = not found
 libXext.so.6 = not found
 libX11.so.6 = not found
 libz.so.1 = not found
 libpthread.so.0 = /lib/tls/libpthread.so.0 (0xf7fdb000)
 libdl.so.2 = /lib/libdl.so.2 (0xf7fd7000)
 libGLU.so.1 = not found
 libGL.so.1 = /usr/lib/libGL.so.1 (0xf7f51000)
 libm.so.6 = /lib/tls/libm.so.6 (0xf7f2e000)
 libc.so.6 = /lib/tls/libc.so.6 (0x00669000)
 /lib/ld-linux.so.2 (0x0065)
 libGLcore.so.1 = /usr/lib/libGLcore.so.1 (0xf776c000)
 libnvidia-tls.so.1 = /usr/lib/tls/libnvidia-tls.so.1 (0xf776a000)
 libXext.so.6 = not found
 libX11.so.6 = not found

 I have tried creating a symolic link to the existing
 /usr/lib64/libpng12.so.0 both in the /lib and /usr/lib directories,
 but I still get the same error message.
 Permissions and file integrity should all be ok.

 Do you have any other suggestions?
 Thank you a lot!
 Marco



 Marco Tettamanti wrote:


 */Donna Dierker /* wrote:

 Date: Tue, 29 Aug 2006 08:47:13 -0500
 From: Donna Dierker
 To: Caret, SureFit, and SuMS software users

 Subject: Re: [caret-users] [SPAM] caret on AMD64

 Try making sure /usr/lib64 is in your LD_LIBRARY_PATH variable,
e.g.:

 setenv LD_LIBRARY_PATH /usr/lib64:$LD_LIBRARY_PATH

 ... or if your shell is bash:

 export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH

 Thanks for reporting the issue with the mailing list. It sounds
like I
 need to check the spam settings for [EMAIL PROTECTED]

 On 08/29/2006 03:01 AM, Marco Tettamanti wrote:
  Dear Donna and John,
  first of all I would like to express my congratulations for the
  improvements you made in Caret! I haven't been using the
software for
  some times, but now that I have some new data to work on and
I have
  started to use the latest release (5.4), I find that many options
 have
  been made more intuitive and easy to use, especially for the
manual
  correction of segmentation errors.
 
  I am trying to install caret on an an AMD64 linux architecture
 (CentOS
  4.3, kernel 2.6.9, 2 x AMD Opteron dual-core).
  I have tried installing from the linux binaries, but I receive an
 error
  message that some libraries cannot be opened (error while
loading
  shared libraries: libpng12.so.0: cannot open shared object file:
 No such
  file or directory), even if I create symbolic links to e.g.
  /usr/lib64/libpng12.so.0.
  Is there any way I can get the caret binaries to work on AMD64,
 without
  having to build from the source files?
 
  Thank you a lot for your help,
  Marco
 
  P.S.: I am using this alternative email address because but I
have
  tried several times to send an email to
 caret-users@brainvis.wustl.edu
  from my address [EMAIL PROTECTED], but for some reasons my
  emails are rejected

Re: [caret-users] [SPAM] CARET-memory problem

2006-09-01 Thread Donna Dierker

Just a couple of things to add to John's reply:

* Most users who segment using Caret, 1Gb of memory is enough, but if 
your volume is very high resolution or otherwise is very large (e.g., 
dimensions of 300x300x300 are above those of a typical Caret user; most 
volumes are something like 150x200x150 or smaller in size). During 
processing, Caret has multiple volumes in memory concurrently.


* Once at least a year ago, I saw this error when the user's real 
trouble was disk space. He was working on a network drive that wasn't 
big enough for the intermediate files. Try running it in a local drive 
with gigabytes of free space (several times your volume size).


On 09/01/2006 02:55 PM, John Harwell wrote:

Hi Elena,

How old is your version of Caret? The date is listed in the main 
window titlebar.


There was fix related to crashing during error correction made on 24 
Jan 2006.


In any case, an updated snapshot of caret (which contains just the 
executable) is available at 
http://pub:[EMAIL PROTECTED]/pub/caret/. I would suggest 
that you try the update, and, if the problem still occurs, let me know.


--
John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA

On Sep 1, 2006, at 1:47 PM, Elena Spieker wrote:

While working with CARET on my desktop computer, during the manual 
error correction, I received a message stating Out of memory: Caret 
is unable to get memory that it needs either because the computer 
lacks sufficient RAM memory or too many files are loaded. If Caret is 
continued it may crash. This is the second time I have received this 
message, the first time was on my laptop following the initial 
segmentation and I had assumed it was perhaps because the laptop was 
not capable of running the program. Is there a specific amount of 
memory required for running CARET? Do I simply need a computer with 
more memory or is there another way I can remedy this problem because 
the desktop I was working on does not contain much other 
information/programs? Thank you and I look forward to hearing from 
you regarding this problem.


Elena Spieker


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Re: [caret-users] CARET file

2006-09-13 Thread Donna Dierker

Yes, this is almost certainly Elena's issue.

The AFNI file format is such that you can have multiple sub-bricks 
within the same file (e.g., multiple types of summary group 
statistics).  These show up as separate columns or menu picks in the 
drop-down menus.  But when doing segmentation, you typically want Label 
= Filename, so you have to enter the change in both places.


On 09/13/2006 08:41 AM, Erin Reid wrote:

Elena,

I believe that all you have to do to fix this issue is to change the 
'Volume Label'  which is located at the bottom of the Save Data File 
pop-up.  You'll can change it to whatever you want but changing it to 
the File Name usually makes thing less confusing.  The Label name is 
what appears in the drop down menu from the D/C.


Let us know if that is not the fix you needed.

Thanks,
Erin

At 08:32 AM 9/13/2006, Elena Spieker wrote:
Well Caret is not having any more problems with memory or crashing, 
however, I do notice after I remove handles and save the file 
(renaming it as instructed to segment_errorcorrected_fix1 from 
segment_errorcorrected) I am not prompted to select that recently 
saved file (...fix1) as the volume file to use for my next 
segmentation. My choices only include the previously saved volume 
files but not the most recently saved file, though I can locate it in 
my working directory. I simply cannot access it as an item in the 
drop down menu for the second segmentation as is shown in the 
tutorial. Please direct me as to how to remedy this as I am certain 
the difference in which file is selected isl affecting the result of 
the segmentation. Thank you and have a great day.


Elena

 [EMAIL PROTECTED] 9/1/2006 5:18 PM 
Just a couple of things to add to John's reply:

* Most users who segment using Caret, 1Gb of memory is enough, but if
your volume is very high resolution or otherwise is very large (e.g.,
dimensions of 300x300x300 are above those of a typical Caret user; most
volumes are something like 150x200x150 or smaller in size). During
processing, Caret has multiple volumes in memory concurrently.

* Once at least a year ago, I saw this error when the user's real
trouble was disk space. He was working on a network drive that wasn't
big enough for the intermediate files. Try running it in a local drive
with gigabytes of free space (several times your volume size).

On 09/01/2006 02:55 PM, John Harwell wrote:
 Hi Elena,

 How old is your version of Caret? The date is listed in the main
 window titlebar.

 There was fix related to crashing during error correction made on 24
 Jan 2006.

 In any case, an updated snapshot of caret (which contains just the
 executable) is available at
 http://pub:[EMAIL PROTECTED]/pub/caret/. I would suggest
 that you try the update, and, if the problem still occurs, let me 
know.


 --
 John Harwell
 [EMAIL PROTECTED]
 314-362-3467

 Department of Anatomy and Neurobiology
 Washington University School of Medicine
 660 S. Euclid Ave. Box 8108
 St. Louis, MO 63110 USA

 On Sep 1, 2006, at 1:47 PM, Elena Spieker wrote:

 While working with CARET on my desktop computer, during the manual
 error correction, I received a message stating Out of memory: Caret
 is unable to get memory that it needs either because the computer
 lacks sufficient RAM memory or too many files are loaded. If Caret is
 continued it may crash. This is the second time I have received this
 message, the first time was on my laptop following the initial
 segmentation and I had assumed it was perhaps because the laptop was
 not capable of running the program. Is there a specific amount of
 memory required for running CARET? Do I simply need a computer with
 more memory or is there another way I can remedy this problem because
 the desktop I was working on does not contain much other
 information/programs? Thank you and I look forward to hearing from
 you regarding this problem.

 Elena Spieker


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Re: [caret-users] ROIs

2006-09-20 Thread Donna Dierker

Hi Jason,

On 09/20/2006 12:17 PM, Jason D Connolly wrote:
Dear Donna, 
 
Thank you for your help in the past. 
 
We are currently trying to draw an ROI (or a mask) around activated 
regions on the flat map (and hopefully save these ROIs in *.cub format) 
to then select region-specific event-related timecourses via a matlab 
function. 
 
Can you give me any assistance regarding exactly how to go about drawing 
and saving such an ROI (and saving these as enclosed 'masks' in a *.cub 
format or something very similar)? 
 
Any help would be greatly appreciated. 
 
Best regards, Jason. 
 
 
Jason D. Connolly, PhD   
Center for Neural Science, New York University 
6 Washington Place Room 875, New York, NY 10003 
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562  
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html 
  

... and later on 09/20/2006 12:32 PM, Jason D Connolly wrote:
Also, a related question is how does one reverse project these saved 
flattened map ROIs back onto the 3D functional MRI datasets, i.e. in .cub 
format? 
  
Sorry, but I've never heard of *.cub format before.  But maybe you can 
get to *.cub from one of our other output file formats.


Maybe try something like this:

1.  Use Layers: Draw Borders, type Closed, Assign Voxels to Within 
Closed Border to draw the ROI region.


2.  Project the borders and save as a borderproj file, even if your main 
interest is in the paint file.


3.  If desired, save the border as a border file -- relative to the 
fiducial surface, to get an ASCII list of border point coordinates.


4.  Attributes: Paint: Convert Paint Column to Paint Volume.

5.  File: Save Data File: Volume Files: AFNI, NIFTI, or SPM and MEDx 
(really Analyze).  Change volume type to Paint.  I vaguely recall that 
the paint type may only be available for AFNI and WUNIL 4dfp output 
types, but give it a shot.


The AFNI .BRIK file is just like an Analyze .img (i.e., the raw data 
with no header), so perhaps you can import it into *.cub.


--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] Radiological LPI conversion bug?

2006-09-21 Thread Donna Dierker
I was just thinking FSL's command line utilities also could get the job 
done, but again -- don't think there's a Windows version.  (Morgan would 
certainly know.;-)  My guess is John will need to go the Cygwin route, 
unless he gets MacOSX or Linux access soon.


To make John feel a bit worse, note the Unix tag way at the bottom of 
the MRIcro page (http://www.sph.sc.edu/comd/rorden/mricro.html):


FormatConvert  [Unix] Pittsburgh 1.0, Afni, GE (I*.nnn files, E*.MR 
files), BrainVoyager (VMR, VTC, STC, VMP)


Keep hounding Brain Innovation for real NIfTI support.

On 09/21/2006 04:03 AM, Morgan G. Hough wrote:

John,

I don't know if someone has already suggested this but I have used
Format Convert from the Fiswidget tools to convert BrainVoyager data to
NIfTI but I think you will still need some form of UNIX environment (or
Cygwin) to get this working. Here's a link to check out. 


http://grommit.lrdc.pitt.edu/

Hope this helps. 


Cheers,

-Morgan

On Thu, 2006-09-21 at 09:09 +0100, John Taylor wrote:
  
Donna - Thanks for the ideas. You confirmed exactly what I saw in terms 
of the memory stick up. The BVQX user guide does imply the existence of 
a plugin to provide a NIfTI export option but I have so far been unable 
to trace the actual plugin and as yet have had no reply from other BV 
users regarding this option. If there is anyone on this list who has 
sucessfully exported tal-space .vmr files into CARET as NIfTI, I'd be 
very interested to hear from you! I currently only have access to a 
Windows PC in the lab (although this is likely to change) which rules 
out AFNI options for now, so I may need to hold fire on this. I'll look 
at your other suggestion today.


Thanks

John


Donna Dierker wrote:



Hi John,

On 09/19/2006 05:24 AM, [EMAIL PROTECTED] wrote:

  
Of course, I meant 'Radiological' rather than 'Neurological'! 
Apologies for any

confusion.


... and previously wrote:

On 09/19/2006 05:19 AM, [EMAIL PROTECTED] wrote:

  
When opening new .hdr data files exported from Brain Voyager QX, the 
volumes
require reorienting from neurological  LPI. I am using the 
'Orientation' tab
in the 'Volume attributes' editor to do this. However, although I am 
able to
flip around the X and Y axes without problems, both the 'Rotate 
Clockwise' and
'Convert to LPI' commands appear to introduce an error such that the 
'Resample'
tab displays  voxel dimensions of 0.000. If I then attempt to 
resample to 1 x 1
x 1, Caret crashes. Am I approaching the reorientation incorrectly or 
have

others experienced the same problem?
Any help appreciated

John Taylor
  

I was able to reproduce this behavior, so it seems like something John 
should look at.  Even after changing the Resample x spacing from 0.0 
to 1.0, I still get an OUT OF MEMORY stickup and must exit Caret.


Also, when I was playing around trying to solve John's problem, it 
seemed that changing the Orientation tab's X selection to 
right-to-left and pressing Convert to LPI didn't x-flip the volume as 
expected.  In the past, this button has worked as far as actually 
flipping the volume, but the slice display didn't update.  So I would 
then save my x-flipped volume file and reopen it in Caret, replacing 
any existing structural volumes that were currently loaded.  This used 
to work.  In my case just now, it didn't, and I tried using two 
different input volumes.


But there are a few ways to solve your problem.  If Brainvoyager can 
export NIfTI, then the header should provide Caret the orientation 
information it needs to do the appropriate flipping upon opening the 
volume.  If Brainvoyager can't export NIfTI, then complain -- loudly.


Other options include using AFNI utilities to convert Analyze to AFNI, 
then follow up using 3drefit to specify the existing orientation 
information.  Then you can use 3daxialize to actually do the flipping, 
although I'm guessing it shouldn't be necessary (i.e., I think Caret 
will flip it to LPI upon opening).


Finally, try playing around with caret_command's 
-volume-set-orientation feature.  Using FSL's very handy 
avg152T1_LR-marked.hdr, I found that this command caused Caret to 
display the right on the left:


caret_command -volume-set-orientation LPI avg152T1_LR-marked.hdr 
avg152T1_LR-marked_LPI+orig.HEAD


The attached right_on_right.jpg is what this volume looks like before 
running caret_command.  Since FSL uses a left-handed coordinate system 
(right-on-left), they use a negative pixdim[1] to specify the x-flip:


pixdim[1]: -2.

Caret knows to x-flip the volume when it sees negative pixdim[1] in 
the Analyze .hdr.  But if you use caret_command to tell Caret no, the 
orientation is actually LPI (as the above command is doing), then 
Caret won't x-flip the volume, so you get the result in the 
right_on_left.jpg capture.  Sorry if this is confusing, but it does 
serve to make the point that it's important to make sure your 
orientation is correct, using some

Re: [caret-users] left Hemisphere landmarks for registration with F99

2006-09-21 Thread Donna Dierker
To clarify, F6 is a six-subject macaque fascicularis atlas developed by 
a collaboration of wustl.edu researchers. See part 3 of the tutorial 
cited below for details.


On 09/20/2006 08:12 PM, David Vanessen wrote:

John (et al.),

I guess Donna wins a six-pack, because I do indeed have a response.

1) First, some general comments. Your questions come at a propitious 
time.


We are just completing a major revamping of the macaque F99 atlas 
along with many other changes to the macaque and human (PALS) atlas 
datasets, Caret 5.5 software, and a tutorial that illustrates many of 
the new features. Our intent is to announce this to the Caret user 
community in the coming week. (We just gave a successful 1-day 
workshop at Wash U and are now cleaning up on various details that 
emerged from this session.)


More specifically on the macaque atlas front, what we are calling the 
new 'F99' atlas differs from the old 'F99UA1' atlas in several ways. 
Most important is that both the left and right hemispheres are in a 
'standard-mesh' format (with 73730 nodes, same as our human PALS 
atlas). This greatly facilitates simultaneous visualization of the 
macaque left and right hemispheres (as well as concurrent 
macaque-human visualization) in a single Caret application.


Another aspect of this is that we registered the old F99UA1 left and 
right hemispheres to a 'hybrid' left-right target, in which the 
landmarks were generated by averaging the right and (mirror-flipped) 
left hemispheres, so it is not biased by one side or the other. Also, 
the number of landmarks used for registration to the older F99UA1 
surfaces is 26, larger than used previously. The number used for 
registering to F6 is smaller (24) and to the Paxinos (PHT) atlas is 23 
- i.e., they are case-specific, depending on what is reliably 
distinguishable in the source and target.


2) More specific to your starting question, the starting border 
projection file for the new F99 atlas is
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6590483archive_name=Macaque.F99UA1.LR.AVERAGE.LANDMARKS_Surfs-29407_29830_for_FULL-HEMISPHERE.73730.borderproj 



An archive containing all three LANDMARK borderproj files has just 
been uploaded to SumsDB and is available at:

http://sumsdb.wustl.edu/sums/directory.do?id=679531dir_name=MACAQUE
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6589983archive_name=Macaque.F99UA1.REGISTER-with-INDIVIDUAL.73730.spec 



If you view your individual hemisphere and the F99 atlas surface in 
separate Caret applications, determine how many of the 26 F99 
landmarks are reliably visible in your individual hemisphere. If some 
landmarks are unreliably (e.g., the posterior spur of the arcuate 
sulcus = ASp), delete it from the F99 borderproj file and save that by 
a different name. If other landmarks are visible in both hemispheres, 
but you judge the extent where there is 'correspondence' to be 
different, then you can 'nibble' the F99 landmarks (delete border 
points) or re-draw the landmark border, then reproject and re-save the 
modified F99 version while generating a corresponding landmark in the 
individual.


Before you attempt spherical registration, make sure that the number 
of borders in the individual and atlas borderprojection files are the 
same. Use the query (?) button in the open borderproj file or in the 
spec file, and select Border Names, which gives the total number as 
well as the individual names.


The datasets and the atlas tutorial are in
CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu/sums/directory.do?id=6585200

We are aiming for an update of the tutorial and datasets to be 
inserted/released by the weekend.



I hope this helps

David VE




On Sep 19, 2006, at 2:58 PM, John Arsenault wrote:


Hello,
I was wondering which .borderproj file was appropriate for the
registration of an individual macaque left hemisphere to the left
hemisphere of the F99 ATLAS. I found a file named
Macaque.F99UA1.LANDMARKS_for_RegWithMacaque.R.03-04-21.34132.borderproj 


in the left hemisphere section of the macaque atlas on SuMSDB. Is this
the correct file to use for spherical deformation? This .borderproj file
has more borders then there were for the .borderproj file I used for my
right hemisphere sperical deformation with the same monkey
(Macaque.F99UA1.R.LANDMARKS_for_FREESURFER-REGISTRATION.03-05.35946
.borderproj) incuding a posterior version of the AS border and
(LANDMARK.CaSv, LANDMARK.MW_HFtoTempCut, LANDMARK.PostOrb, LANDMARK.LOS,
LANDMARK.VLC, LANDMARK.DMC, LANDMARK.VMC, LANDMARK.OrbS,
LANDMARK.MW_POStoCaS). If I should use these borders then what
deformation map file should I use? If this is not the file I should use
then which file is correct for left hemisphere deformation? Also with 
the

updates to f99 what borders and .borderproj files will be used for
registration with the updated Atlas and when will that be available.
Thank you so much for your help,
John




Re: [caret-users] Assigning binary to ROI

2006-09-26 Thread Donna Dierker

On 09/25/2006 11:16 PM, DG MCLAREN wrote:

Yes, this can be done. There is paper that is under review that contains
this process in article format; however, I'll write the procedure below:

1) Create individual ROIs for each individual participant using their
own fiducial surface (I'm assuming you've done this already).

2) When you run the deformation (surface -- deformation -- apply
deformation; make sure you check the nearest neighbor option. Now the
deformed data, in standard space of 73730 nodes will be binary coded.

3) Under Attributes -- Metric -- Mathematical Operations; you can add
up the binary files to look at overlap on the average fiducial surface.
This is an excellent way to view the overlap.
  
Also be aware that AFNI/SUMA has some nice command line utilities that 
can save time when you have a bunch of files to sum. This command shows 
how I summed a bunch of binary volumes from the Zilles lab to make some 
probabilistic maps:


3dcalc -expr a+b+c+d+e+f+g+h+i+j+k+l -prefix 
wu_n=12_Brodmann_2_b_lin2StdMNI -a 
wu_pm14686_Brodmann_2_b_lin2StdMNI+orig.HEAD -b 
wu_pm1696_Brodmann_2_b_lin2StdMNI+orig.HEAD -c 
wu_pm18992_Brodmann_2_b_lin2StdMNI+orig.HEAD -d 
wu_pm20784_Brodmann_2_b_lin2StdMNI+orig.HEAD -e 
wu_pm2431_Brodmann_2_b_lin2StdMNI+orig.HEAD -f 
wu_pm28193_Brodmann_2_b_lin2StdMNI+orig.HEAD -g 
wu_pm295_Brodmann_2_b_lin2StdMNI+orig.HEAD -h 
wu_pm34083_Brodmann_2_b_lin2StdMNI+orig.HEAD -i 
wu_pm38281_Brodmann_2_b_lin2StdMNI+orig.HEAD -j 
wu_pm5694_Brodmann_2_b_lin2StdMNI+orig.HEAD -k 
wu_pm6895_Brodmann_2_b_lin2StdMNI+orig.HEAD -l 
wu_pm7186_Brodmann_2_b_lin2StdMNI+orig.HEAD


I haven't done this with metric/shape files, but if I needed to, I'd 
consider using AFNI's 1deval for this purpose. (Using shell scripts, 
you'd need to strip the header and node numbers and put them back on, 
but this isn't too hard to do.)

If you would like more detailed instructions, or the paper reference;
please contact me at [EMAIL PROTECTED]

Best Regards, Donald McLaren
=
D.G. McLaren
University of Wisconsin - Madison
Neuroscience Training Program
Tel: (773) 406 2464
=
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notify the sender via telephone at (773) 406 2464 or email.

- Original Message -
From: Akiko Ikkai [EMAIL PROTECTED]
Date: Monday, September 25, 2006 6:07 pm
Subject: [caret-users] Assigning binary to ROI
To: caret-users@brainvis.wustl.edu

  

Hello,

I'm trying to project ROI masks (where voxels in ROI= 1, outside 
ROI= 0)
onto a deformed surface. ROIs are in .hdr/img format, and the 
origin is

set at AC. I use attributes  map volume to surface to make metric
files, each of which contains just one ROI (e.g. L_FEF.metric,
L_IPS.metric, etc...). Then surface  deformation  apply deformation
map to create deformed metric file. 

Since the original ROI masks are binary, I'd like to rewrite the 
metricfile in binary as well (anything above 0 - 1). Is there any 
way to do

this in caret? If not, is there anyway to get to the .hdr file that is
enbedded in .metric file to binarise? My goal is to create binary ROIs
for each subject, overlay and see the degree of overlap across 
subjects.

Thanks in advance.

Akiko Ikkai
PhD Candidate 
Department of Psychology 
New York University 
6 Washington Place New York NY, 10003
 
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(Formerly Donna Hanlon; no change in marital status -- see 
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Re: [caret-users] strange problem with v 5.4 and 5.5

2006-10-11 Thread Donna Dierker

Hi Roland,

Try going to your home directory and doing this:

rm -rf .qt

See if this makes a difference.

You're not the first to report something like this, but I'm not sure 
it's the same problem exactly.  Veronica Smith reported segmentation 
faults when launching Caret (before trying to open a volume file, I 
think) when logged in either as herself or as a newly created user.  
When running as root, no problems.


In your case, was the other user root, or a completely different user?  
When Veronica created a new user, the idea was to get rid of any 
environment baggage that might be causing the wrong libraries to load, 
but it crashed for this new user, too.


Is there any difference in users' shells (e.g., tcsh vs bash)?

If using tcsh shell, could you copy your .cshrc to cshrc (same filename 
but without the leading .) and the upload it here:


http://pulvinar.wustl.edu/cgi-bin/upload.cgi

If using bash shell, could you copy your .bash_profile to bash_profile 
and the upload it there.


On 10/11/2006 05:08 AM, Roland Marcus Rutschmann wrote:

Hi,

I have a strange problem with version 5.4 and 5.5 (not with 5.3) which I 
cannot work out and would like an educated guess.


I am running caret on debian (sarge with updates). And have this problem only 
as a certain user (unfortunately my own account). 

Opening caret -debug - Open Data File - choose a analyze or nifti 
anatomical volume (e.g. 1 subj canonical of spm5) - Create Spec File No 


caret dies:
pc53469:~ setenv LC_ALL C  /misc/spm/bin/caret5.5 -debug
Set the environment variable CARET_DEBUG for debugging information.
little endian system
Screen size (1280, 1024)
/home/rur23430/.caret5_preferences is NOT an XML file.
Caret Home Directory: /misc/spm/caret-5.5
Mesa: _save_upgrade_vertex: dangling reference attr 2
NIFTI extension[0] 0
Unscaled range: 0 255
Scaled range: 0 1
VolumeFile flipping about axis: X
Time to assign colors to surface nodes was 0
failed rendering glyph 0 from font
ASSERT: !err in file qgl_x11.cpp, line 791
/misc/spm/bin/caret5.5: line 4:  7376 Aborted caret5 $*


The error it qt related but why only for certain users?

More Info:
As another user this works. I have deleted my .caret5_preferences - same 
result.
Another computer with almost identical configuration but different graphics 
card- same r.

slogin localhost vs. slogin [EMAIL PROTECTED] - same results
caret 5.4 - same results
kde vs. gnome - guess what same results

caret 5.3 works.
I unpack the caret versions into one directory and start them with a script:
#!/bin/sh
export CARET_HOME=/misc/spm/caret-5.3
export PATH=$CARET_HOME/bin:$PATH
caret5 $*


I'd love some ideas. Please,

Roland



  



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(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] Generate 3D coordinates list?

2006-10-24 Thread Donna Dierker
You may need to use File: Convert Data File Formats (or command line 
tool caret_file_convert) to convert the coord file to ASCII.


On 10/23/2006 04:18 PM, John Harwell wrote:

Try this,

* Select the nodes in your ROI.
* Change Normal Selection  to  Not Selection and then press the 
Select Nodes button.  You should now see all of the nodes in the ROI 
deselected and all nodes NOT in the ROI selected.
* Set the Operation Surface and Topology Surface to the surface in the 
main window.
* In the Operate on Selected Nodes section, set the Operation to 
Disconnect Selected Nodes and press the Disconnect Selected Nodes 
button.  All nodes except those in your original ROI will disappear.
* Save the coordinate and topology files for the surface remaining in 
the main window as ASCII (text) files.
* If you view the contents of the coordinate file, all disconnected 
nodes are moved to the origin and thus have a coordinate of (0.0, 0.0, 
0.0). The remaining nodes, which you are seeking, have valid coordinates.
* If you view the topology file, it contains the node indices that 
make up each of the remaining triangles.


I hope this helps.

--
John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.Box 8108
St. Louis, MO 63110   USA

On Oct 23, 2006, at 3:24 PM, Leeland Ekstrom wrote:


Hi,

Is there a way to export from Caret a 3D list of the coordinates of 
nodes contained in a ROI?  For example, using the 'Surface ROI' 
interface, I can select all the nodes within a given threshold range 
for a particular metric, but how can I export the (x,y,z) coordinates 
of those selected nodes into a text file or similar?


Thanks,
Leeland

--Leeland B. Ekstrom
PhD Candidate
Nuclear Science  Engineering / Health Sciences  Technology
Massachusetts Institute of Technology
P:617-899-0939

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(Formerly Donna Hanlon; no change in marital status -- see 
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Re: [caret-users] Fishy brainfish sampling

2006-10-30 Thread Donna Dierker

Graham,

1.  You're right:  BrainFish isn't mapping negative activity as 
intended.  I just mapped 
CARET_TUTORIAL_SEPT06/BURTON_04_VibroTactile_EARLY_BLIND+orig.HEAD onto 
PALS_B12 711-2C using BrainFish, and although this volume has big 
regions of negative activity, the metric file gets assigned 0.0 in these 
regions:


VOXEL IJK(78, 171, 96)   XYZ(-10.5, 47.5, 21.5)
   Anatomy: 1048.8
   Functional: -16.0
Node 30291
Metric: 0.0 0.0

MCW was happy with it back when we implemented it, but evidently they 
were mapping just positive data.  I'll figure out what lines need 
changing, but I'm not sure when this will be impemented.


Nor will I guarantee satisfaction, since these lines in the code suggest 
an MCW priority not entirely aligned with your suggestion #2 (which I 
interpret as most extreme voxel method -- not a bad alternative to have):


  //
  // Allow positive activity to override negative activity
  // Negative only overrides less negative
  //
  if (nearestNode = 0) {
 assigned[nearestNode] = true;
 const float nodeValue = activity[nearestNode];
 if (voxel  0.0) {
if (voxel  nodeValue) {
   activity[nearestNode] = voxel;
}
 }
 else if (nodeValue  0.0) {
if (voxel  nodeValue) {
   activity[nearestNode] = voxel;
}
 }
  }

Regarding converting Metric files to ASCII, DVE pointed out the 
caret_file_convert utility and the option when saving the metric, but 
there's a third alternative: File: Convert Data File Formats.


Also, on the D/C metric menu, there is a histogram with Min, Max, Range, 
etc.  (Also, the utilities under Attributes: Metric are handy.)


2.  Besides the comments above, I confess I'm not a big fan of the 
BrainFish algorithm.  I'm trying not to tell you what you want, but 
there are only a handful of cases in my experience where I deemed this 
voxel-centric algorithm the best tool for the job.  I suspect your 
choice of this method is related to your separate message regarding the 
average fiducial surface itself, so I'm going to focus my efforts on 
helping you better understand its nature (in a separate reply).


On 10/30/2006 08:53 AM, John Harwell wrote:


The MCW BrainFish algorithm was developed by a group at the Medical 
College of Wisconsin to meet a specific need they had.  Unless they 
tell me it is not working correctly, I am not going to dig into it.  I 
believe the enclosing voxel algorithm is the most popular, you might 
consider it.


--
John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.Box 8108
St. Louis, MO 63110   USA

On Oct 27, 2006, at 9:20 PM, Graham Wideman wrote:


Folks:

The brainfish algorithm is described here:
http://brainmap.wustl.edu/caret/html4.6/
map_fmri_to_surface/map_fmri_to_surface_dialog.html

... as picking up negative voxels if there are no positive ones 
around.  Couple of issues:


1. We don't seem to be able to get negative voxels to appear at all 
when using the brainfish mapping algorithm. This is for a volume that 
has been thresholded, hence lots of zero voxels, and it has well 
separated islands of positive and negative values.


(And applying mapping other than brainfish indeed shows the negative 
regions in caret -- so we *think* we know how to get the rest of the 
display settings right...)


So the question is: are you sure that the negative aspect of this 
mapping algorithm is currently working?


Also, is there a tool for inspecting metric files? (Or conversion to 
text?)


2. Would it make sense to have an alternative brainfish strategy 
which allocates to a node the voxel value with the highest *absolute* 
value, instead of any positive beats any negative?  This is 
particularly a concern for fMRI input that has not been thresholded.


Thanks,

Graham

--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] caret docs; Display Control especially

2006-10-31 Thread Donna Dierker

Hi Graham,

Burying your head in David's PALS paper is indeed the best way to get 
your head around this stuff.  It took me three careful reads before I 
really digested it.  (And you can't whip through in a short plane ride.)


To get a more hands-on feel for Caret/SureFit surfaces, consider
downloading and playing with these datasets in Caret:

PALS_VE05_FIG-11_FMRI_MFMapping.73730.spec
From PALS paper, figure 11
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6334372

Human.PALS.VE-et-al_JN06_WILLIAMS_Suppl_Fig-1_Volumes_Fiducials.spec
From WS paper (http://www.jneurosci.org/cgi/content/full/26/20/5470),
supplementary figure 1
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6473226

Also, notice in David's email replies:  You have taught him to say
voxel-wise statistics rather than volume-averaged fMRI results --
well done!

When mapping to the PALS_B12 surfaces, there's plenty of uncertainty to
go around.  Increasingly, there's consensus that reconstructing
individual surfaces and doing one's analysis in surface-land is an 
excellent complement to voxelwise-statistics for most cortical studies. 
 But for the majority of researchers not yet prepared to do so, this 
atlas is a useful visualization substrate for their group results.


Questions about which mapping method to use are valid, and reasonable
people can disagree about such things, but as you say, it's relatively
in the noise compared to what I would call doing it right.

Another source of variability stems from the degree to which the
PALS_B12 average fiducial surface represents your sample's average
anatomy well.  In a joint study with Dr. Csernansky and Deanna Barch's
lab, the PALS_B12 average fiducial represents the CONTROLS' anatomy 
well, but schizophrenics' anatomy less well.  Anatomical differences 
across groups almost certainly contribute (even where they may not quite 
reach statistical significance by our conservative method).  In the 
attached captures, the structural underlay is a mean SCZ volume for 
SCZ13anat_SFSdiff.jpg, mean CONTROL volume for CON19anat_SFSdiff.jpg. 
In both captures, the blue contour is the average CON fiducial (sample 
subjects -- not PALS_B12); the red contour is the average SCZ fiducial. 
 Not shown, the CON average fiducial overlaps the PALS_B12 fiducial 
much better than does the SCZ average fiducial.  Of course, you don't 
know how good a proxy PALS_B12 is for your sample unless you reconstruct 
all your subjects.  (Thanks to Dr. Lei Wang and Dr. Deanna Barch for 
allowing use of their prepublication data.)


On 10/27/2006 12:39 AM, Graham Wideman wrote:

David:


Further, my superficial understanding of MFM worries me that a weak
activation caught by all surfaces might produce the same appearance
as strong activation caught by only a small proportion of the MF
surfaces.


That is indeed possible.  However, this isn't necessarily a bad
thing.  Moreover, the same thing can occur during volume-based
statistical analyses - a voxel that shows weak but consistent
activation may show the same z-statistic as a voxel that has a strong
activation in a small proportion of individuals.


Not sure if it's important, but these seem somewhat different cases. 
In the voxel-based situation the confounding obscures the difference 
between a few strong activations vs many weak activations.


In the MFM situation, the confounding is at a subsequent stage: this 
is not about muddling strong and weak activations, but rather it's 
about the sampling strategy (fMRI-surface mapping) being more or less 
sensitive in different regions, depending on the variability of the MF 
surfaces in that region (ie: how many of the MF surfaces intersect an 
activation).


But all this may be relatively in the noise, I guess, compared to 
using surfaces derived from each individual subject.


(Again, time to read the paper in detail, and see in what ways you've 
been able to characterize the sensitivity of generic MFM vs using 
subjects' own surfaces.).


All very interesting.

Graham

--

Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



inline: SCZ13anat_SFSdiff.jpginline: CON19anat_SFSdiff.jpg

Re: [caret-users] Voxel Size for Macaque Anatomicals

2006-11-03 Thread Donna Dierker

Donald,

I hope Madison is treating you well.

Check out part 3 of this tutorial (PDF and zip file in this directory):

CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu/sums/directory.do?id=6585200

On 11/03/2006 12:22 PM, DG MCLAREN wrote:

David,

Awhile ago you mentioned that there were three macaque volumes (F99, F6, Paxinos) and that the F6 was probably best volume target. When I am searching for these, I can only seem to find F99 in SUMSDB. Do you know where the others are located? 


Also, what is the group surface borders based on?

Thank you in advance for your help.

Best Regards, Donald McLaren
=
D.G. McLaren
University of Wisconsin - Madison
Neuroscience Training Program
Tel: (773) 406 2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED 
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delivering it to the intended recipient, you are hereby notified that you are 
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- Original Message -
From: David Vanessen [EMAIL PROTECTED]
Date: Thursday, November 2, 2006 9:30 pm
Subject: Re: [caret-users] Voxel Size for Macaque Anatomicals
To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu

  

John,

On Nov 2, 2006, at 9:38 AM, John Arsenault wrote:



Hello,
  I have an anatomical image taken at .35mm isotropic.  For some  
reason I
was under the impression that one should resample there data to . 
5mm for

registration with the F99 surface.  Is this true or is this only for
data of resolution lower the .5mm?
  
The SureFit algorithm within Caret is designed to work best when 
the  
cortex is about 3 voxels thick.  This generally translates to 1 mm  
voxels for human and 0.5 mm voxels for macaque.


The algorithm is somewhat flexible, so you might nonetheless get  
decent segmentation with 0.35 mm voxels.  It's an empirical issue,  
and if your computer is fast it may be worthwhile to try it both  
ways, then compare segmentation quality.





As well I was wondering if it was
possible to view the latest segmentation of F99 as well as any
documentation on the smoothing performed after this segmentation? 
  

I

know the newest version is suppossed to be more faithful to layer 
  
4  


and
I am always interested in having my surfaces represent the 
  

surface as


faithfully as possible.  Thank you for your help,
  
  
  


John
  
http://sumsdb.wustl.edu/sums/archivelist.do? 
archive_id=6595443archive_name=Macaque.F99.BOTH-HEMS.STANDARD-
SCENES. 
73730.spec


has the latest version of the F99 surfaces (e.g.,  
Macaque.F99UA1.RIGHT.FIDUCIAL.Std-MESH.73730.coord,  
Macaque.F99UA1.LEFT.FIDUCIAL.Std-MESH.73730.coord)


http://sumsdb.wustl.edu/sums/directory.do? 
id=6585200dir_name=CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu/sums/archivelist.do? 
archive_id=6602379archive_name=Caret_Tutorial_Oct06.pdf


has the latest tutorial document, including a tutorial for the F99  
macaque atlas.


David




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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] Mapping Macaque SPM Functionals to a Caret Surface

2006-11-07 Thread Donna Dierker

Hi Simone,

Actually, when I look at it in Caret, the functional and anatomical 
appear aligned, so that's good.


When I use AFNI's to3d to create an AFNI .HEAD and .BRIK of 
rHerkules_1_18.hdr that specifies the orientation as ARI 
(anterior-to-posterior, right-to-left, inferior-to-superior), Caret 
flips it appropriately when opening.  The attached capture 
before_translation.jpg shows that the orientation is good at least in 
the y and z planes, although I'm not sure about the x-flipping.  (It 
might be left-to-right rather than right-to-left, as I asserted when 
using to3d.)  But the origin is off, no doubt because you set the AC in 
Caret.  The trick is finding the translation offset between the 
AC-centered and original volume.


Using my own guess at the AC (-53,-65,-85) in Caret, I can get the 
volume and surface closer, but I suspect the x-flipping may still be 
wrong and the AC is probably still not set identically to your actual 
setting.


I'm hoping you can take these clues and run with them on your own for a bit.

Eventually, you'll need to either translate and flip your surface 
coordinate file (using AFNI's Vecwarp or Caret's Window: Transformation 
matrix editor) to match your volume file, or write your volume out with 
an orientation and origin that matches your surface.  But first you need 
to get the magic numbers that specify the affine transform from your 
surface to your volume.


On 11/07/2006 10:27 AM, Simone Kamphuis wrote:

Donna Dierker schrieb:

Hi Simone,

In your case, your anatomical volume, functional volume, and surface 
are not aligned to one another.


The anatomical is in a different orientation (and probably different 
origin) than the surface (which is LPI - 
http://brainmap.wustl.edu/SureFit/orient.html, as Caret expects it to 
be).  The functional is in yet a different orientation.


Step one is to get the anatomical and surface aligned, and then find 
some way to align the functional with the anatomical.  This may 
require using some other software such as AFNI or SPM.  If your 
anatomical and functional volume are in some different orientation, 
but there is an AFNI or NIfTI header that tells Caret what the 
orientation actually is, then Caret can flip it accordingly.  But 
even if it gets the orientation right, there's still no guarantee the 
origins will align.


Unfortunately, I'm real busy for the next three weeks, so I can't 
play around with them to figure it out on my own.  See how far you 
can get on your end, and let me know tomorrow if you make no progress.


On 11/07/2006 05:46 AM, Simone Kamphuis wrote:

Dear Donna Dierker,

I have read your answer to John Arsenault's e-mail.
I also have problems to map functional data onto my monkey caret 
fiducial surface.


I was wondering if you could have a look at the files that I used.
(I will upload them to http://pulvinar.wustl.edu/cgi-bin/upload.cgi)

I used CARET v5.3 (Jun 20 2005).

Thank you in advance.
Simone Materna



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Dear Donna,

I guess I should have send you my '..AC_left+orig.HEAD' file as 
well (I uploaded this file now). This file is in the same orientation 
as the surface.
I used SPM to get the functional volume (T-map) in the same 
orientation as the anatomy (this might not seem to be the case at 
first sight, because the quality of the functional volume is not very 
good).


I don't know how to get the anatomy (and functional volume) in the 
same orientation as the surface, since I can't open the 
'..AC_left+orig.HEAD' file in SPM.


Thanks again,
Simone


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Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)

inline: after_translation.jpginline: before_translation.jpg

Re: [caret-users] Mapping Macaque SPM Functionals to a Caret Surface

2006-11-08 Thread Donna Dierker
I'm so glad.  I'm never happy with almost perfectly aligned or 
eyeballing the alignment.  I'm happy when I can figure out the magic 
numbers in a principled way.  I'm even happier when users do it 
themselves, as you did.


On 11/08/2006 10:16 AM, Simone Kamphuis wrote:

Dear Donna,

It all worked out fine!

The orientation of the anatomy and the functional volume was: 
anterior-posterior, left-right, inferior-superior. In SPM I changed 
this to LPI. Within SPM you can see the origin, which was -53, -65, 
-86 (you were almost right about them!) for the anatomy and -36, -52, 
-28 for the functional volume. I changed this back to 0 and that was all!


The activation I find in SPM matches very nicely with the activation I 
see in Caret, so I am very happy about that.


Thanks a lot!
Simone

Donna Dierker schrieb:

Hi Simone,

Actually, when I look at it in Caret, the functional and anatomical 
appear aligned, so that's good.


When I use AFNI's to3d to create an AFNI .HEAD and .BRIK of 
rHerkules_1_18.hdr that specifies the orientation as ARI 
(anterior-to-posterior, right-to-left, inferior-to-superior), Caret 
flips it appropriately when opening.  The attached capture 
before_translation.jpg shows that the orientation is good at least in 
the y and z planes, although I'm not sure about the x-flipping.  (It 
might be left-to-right rather than right-to-left, as I asserted when 
using to3d.)  But the origin is off, no doubt because you set the AC 
in Caret.  The trick is finding the translation offset between the 
AC-centered and original volume.


Using my own guess at the AC (-53,-65,-85) in Caret, I can get the 
volume and surface closer, but I suspect the x-flipping may still be 
wrong and the AC is probably still not set identically to your actual 
setting.


I'm hoping you can take these clues and run with them on your own for 
a bit.


Eventually, you'll need to either translate and flip your surface 
coordinate file (using AFNI's Vecwarp or Caret's Window: 
Transformation matrix editor) to match your volume file, or write 
your volume out with an orientation and origin that matches your 
surface.  But first you need to get the magic numbers that specify 
the affine transform from your surface to your volume.


On 11/07/2006 10:27 AM, Simone Kamphuis wrote:

Donna Dierker schrieb:

Hi Simone,

In your case, your anatomical volume, functional volume, and 
surface are not aligned to one another.


The anatomical is in a different orientation (and probably 
different origin) than the surface (which is LPI - 
http://brainmap.wustl.edu/SureFit/orient.html, as Caret expects it 
to be).  The functional is in yet a different orientation.


Step one is to get the anatomical and surface aligned, and then 
find some way to align the functional with the anatomical.  This 
may require using some other software such as AFNI or SPM.  If your 
anatomical and functional volume are in some different orientation, 
but there is an AFNI or NIfTI header that tells Caret what the 
orientation actually is, then Caret can flip it accordingly.  But 
even if it gets the orientation right, there's still no guarantee 
the origins will align.


Unfortunately, I'm real busy for the next three weeks, so I can't 
play around with them to figure it out on my own.  See how far you 
can get on your end, and let me know tomorrow if you make no progress.


On 11/07/2006 05:46 AM, Simone Kamphuis wrote:

Dear Donna Dierker,

I have read your answer to John Arsenault's e-mail.
I also have problems to map functional data onto my monkey caret 
fiducial surface.


I was wondering if you could have a look at the files that I used.
(I will upload them to http://pulvinar.wustl.edu/cgi-bin/upload.cgi)

I used CARET v5.3 (Jun 20 2005).

Thank you in advance.
Simone Materna



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Dear Donna,

I guess I should have send you my '..AC_left+orig.HEAD' file as 
well (I uploaded this file now). This file is in the same 
orientation as the surface.
I used SPM to get the functional volume (T-map) in the same 
orientation as the anatomy (this might not seem to be the case at 
first sight, because the quality of the functional volume is not 
very good).


I don't know how to get the anatomy (and functional volume) in the 
same orientation as the surface, since I can't open the 
'..AC_left+orig.HEAD' file in SPM.


Thanks again,
Simone


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Re: [caret-users] registration landmarks

2006-11-08 Thread Donna Dierker

On 11/08/2006 01:39 PM, Veronica S Smith wrote:

Hi,

I have attached a screen capture of the flat map, inflated map and 
spherical map with the 3 additional registration landmarks drawn.
Yeah, there are a lot of crossovers in the flat map near the sylvian, 
but they don't seem to have interfered with your drawing the sylvian 
border.  On the other hand, what looks like some folding over in the 
central sulcus is causing an undesirable zig-zag (or S shape between the 
middle and dorsal ends of the CeS) in that border.  Perhaps some 
judicious border point trimming may allow you to sidestep this problem, 
Moving border points will be tricky, because you can do that only on a 
flat map, and it looks like you have problems with the CeS creasing over 
in that region (i.e., what led to the zig-zag in the first place).


The flat map appears a bit more distorted than I am used to seeing and 
the sylvian fissure shape also seems atypical.
The flat map is borderline disaster, but unless you're using it for more 
than a tool to draw your registration borders, or it prevents you from 
drawing decent registration borders, I wouldn't worry about it.  If need 
be, you may be able to draw draw your CeS border on the very inflated 
surface (making sure you switch from 2D to 3D mode).  But I think I'd 
try deleting some points to rectify the zig-zag and see how that works.


To really judge your sylvian, we'd need the dataset.  Just eyeballing 
these captures, it does look a little weird, but it seems to be 
reflecting the anatomy reasonably well.  Your anterior termination looks 
too far superior and posterior -- roughly 15-30 degrees too far 
clockwise.  Can't just the posterior end without the dataset, but it 
looks reasonable.


I wanted to get a sanity check on the flat map and make sure I am not 
missing anything and constructive feedback on how my landmark borders 
look before moving forward.


Thanks in advance for your feedback,
Veronica

--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] registration landmarks

2006-11-08 Thread Donna Dierker

On 11/08/2006 02:12 PM, Donna Dierker wrote:
Your anterior termination looks too far superior and posterior -- 
roughly 15-30 degrees too far clockwise.

I should have specified when looking at the lateral inflated view.


Re: [caret-users] nifti images

2006-11-14 Thread Donna Dierker

Hi Mateus,

I can't address your original problem with the NIfTI 
orientation/rotation, but I did have a look at your volumes, and this 
statement confuses me:
The histogram of my images (3D_original.nii and 3D_resliced.nii) shows 
several noisy sharp peaks. 
The attached captures show the histograms of 3D_original.nii 
(histogram_orig.jpg) and 3D_resliced.nii (histogram_resliced.jpg).  The 
original has smoother looking peaks, but both have discernible gray and 
white matter peaks.  Neither look particularly bothersome.


Could you be more clear about what concerns you?

On 11/13/2006 05:43 AM, Mateus Joffily wrote:

John,

May I profit from the fact that I have already uploaded my images to 
ask you one more question about them? The histogram of my images 
(3D_original.nii and 3D_resliced.nii) shows several noisy sharp peaks. 
Do you know what do they mean? I know that, if I reslice the 
3D_resliced.nii to 1x1x1mm voxels size with Caret, they disappear. 
Thanks.


Mateus

John Harwell wrote:


Hi Mateus,

Can you upload the nifti volume that is not displayed correctly in  
Caret at http://pulvinar.wustl.edu/cgi-bin/upload.cgi;.  Also, can  
you capture and upload an image of the volume displayed correctly in  
SPM5 so that I know how it should appear.


After uploading the files, please email me the names of the files.   
It may be a few days before I can look into this problem.


--
John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.Box 8108
St. Louis, MO 63110   USA

On Nov 10, 2006, at 9:42 AM, Mateus Joffily wrote:


Hi,

I am having some trouble to load nifti images with caret5. The  
problem is the following:


1) When I try to load an image that has a rotation specified in the  
header, Caret seems not to apply it properly. The displayed image  
shows a strange orientation and the voxels size is wrong.


2) However, when the same image is resliced and no rotation is  
specified in its header, Caret displays the image correctly, the  
voxels size are correct and the image origin is also correctly  
located.


Those same images, (1) and (2), are both correctly displayed with  
SPM5.


The images extension is .nii, so I don't think this should be a  
problem related to image format interpretation (like interpreting  
nifti images as analyze and ignoring part of the header information).


Does anyone else has experienced this problem?  Thanks for your help.

Mateus
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inline: histogram_orig.jpginline: histogram_resliced.jpg

Re: [caret-users] nifti images

2006-11-15 Thread Donna Dierker

Hi Mateus,

See inline replies below.

On 11/14/2006 09:45 AM, Mateus Joffily wrote:

Hi Donna,

Thanks for your help. I am sending you two histograms of 3D_resliced.nii:
(1) histogram_resliced_1.jpg is the same histogram you already sent to 
me;
(2) histogram_resliced_2.jpg is the histogram of 3D_resliced.nii after 
resampling at 1x1x1mm with Caret.


We can see that the spikes disapear in (2). It looks like much closer 
to the histograms described in your 'Peak Tweaking' document. As I 
don't have much experience with image segmentation, I was wondering if 
there was any problem with my images. I am glad to know that they look 
fine for you.
Try segmenting both inputs using Caret and compare the results.  You 
don't have to patch the resulting hemispheres to get a good feel for the 
quality; just looking at the fiducial surfaces and segmentations is 
generally adequate for judging which input is better, and if the 
differences matter.  An unacceptably blurred structural MRI will have a 
smooth histogram, but probably won't produce a good segmentation.  In 
both histograms, I could detect peaks, so there's probably adequate 
GM/WM contrast to get a good segmentation.
May be the problem is the one pointed by Simon. If this is the case, 
adjusting the histogram bins could minimize the effect. Do we have 
control over the histogram bins with Caret interface?
It doesn't look like it; the only inputs are the voxdims.  To be honest, 
I rarely use Caret to resample my volumes.  I usually do this as part of 
a preprocessing protocol using AFNI, FSL, or SPM utilities.  They allow 
one to specify interpolation mode, etc.  (At wustl.edu, this is done 
when the volume is written to 711-2B space using Avi Snyder's imgreg and 
related utilities.)


Thanks,
Mateus



Dierker wrote:


Hi Mateus,

I can't address your original problem with the NIfTI 
orientation/rotation, but I did have a look at your volumes, and this 
statement confuses me:


The histogram of my images (3D_original.nii and 3D_resliced.nii) 
shows several noisy sharp peaks. 


The attached captures show the histograms of 3D_original.nii 
(histogram_orig.jpg) and 3D_resliced.nii (histogram_resliced.jpg).  
The original has smoother looking peaks, but both have discernible 
gray and white matter peaks.  Neither look particularly bothersome.


Could you be more clear about what concerns you?

On 11/13/2006 05:43 AM, Mateus Joffily wrote:


John,

May I profit from the fact that I have already uploaded my images to 
ask you one more question about them? The histogram of my images 
(3D_original.nii and 3D_resliced.nii) shows several noisy sharp 
peaks. Do you know what do they mean? I know that, if I reslice the 
3D_resliced.nii to 1x1x1mm voxels size with Caret, they disappear. 
Thanks.


Mateus

John Harwell wrote:


Hi Mateus,

Can you upload the nifti volume that is not displayed correctly in  
Caret at http://pulvinar.wustl.edu/cgi-bin/upload.cgi;.  Also, 
can  you capture and upload an image of the volume displayed 
correctly in  SPM5 so that I know how it should appear.


After uploading the files, please email me the names of the 
files.   It may be a few days before I can look into this problem.


--
John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.Box 8108
St. Louis, MO 63110   USA

On Nov 10, 2006, at 9:42 AM, Mateus Joffily wrote:


Hi,

I am having some trouble to load nifti images with caret5. The  
problem is the following:


1) When I try to load an image that has a rotation specified in 
the  header, Caret seems not to apply it properly. The displayed 
image  shows a strange orientation and the voxels size is wrong.


2) However, when the same image is resliced and no rotation is  
specified in its header, Caret displays the image correctly, the  
voxels size are correct and the image origin is also correctly  
located.


Those same images, (1) and (2), are both correctly displayed with  
SPM5.


The images extension is .nii, so I don't think this should be a  
problem related to image format interpretation (like interpreting  
nifti images as analyze and ignoring part of the header information).


Does anyone else has experienced this problem?  Thanks for your help.

Mateus
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Re: [caret-users] nifti images

2006-11-17 Thread Donna Dierker

Hi Mateus,

I think it's worth trying to segment both volumes using Caret to see if 
there is a noticeable effect on surface quality.  My guess is not much, 
but let us know if I'm wrong.


Just make sure you resample to cubic 1mm (preferrably using some 
scriptable utility as part of a preprocessing script that may also 
include bias correction, if needed).


On 11/16/2006 11:07 AM, Mateus Joffily wrote:

Hi Donna,

Usually, I also use SPM for resampling my images. When I resampled the 
3D_resliced.nii image with SPM, the histogram showed the same spiking 
as the original image (3D_original.nii). Only when I resliced the 
image with Caret, the histogram got smooth. I don't know exactly why...


To test the effects of the histogram bin on the final histogram 
distribution, I wrote a small matlab program (see attachment). As you 
can see, depending on the bin size, we can have a spiky histogram 
(top) or a smooth histogram (bottom). Both histograms were calculated 
from the same 3D_resliced.nii image. The spikes occur at bin intervals 
that encloses two successive integer intensity values. In my 
understanding, those spikes should happen whenever we have a discrete 
data set and non-integer bin size. What do you think?


Thanks,
Mateus


Donna Dierker wrote:


Hi Mateus,

See inline replies below.

On 11/14/2006 09:45 AM, Mateus Joffily wrote:


Hi Donna,

Thanks for your help. I am sending you two histograms of 
3D_resliced.nii:
(1) histogram_resliced_1.jpg is the same histogram you already sent 
to me;
(2) histogram_resliced_2.jpg is the histogram of 3D_resliced.nii 
after resampling at 1x1x1mm with Caret.


We can see that the spikes disapear in (2). It looks like much 
closer to the histograms described in your 'Peak Tweaking' document. 
As I don't have much experience with image segmentation, I was 
wondering if there was any problem with my images. I am glad to know 
that they look fine for you.


Try segmenting both inputs using Caret and compare the results.  You 
don't have to patch the resulting hemispheres to get a good feel for 
the quality; just looking at the fiducial surfaces and segmentations 
is generally adequate for judging which input is better, and if the 
differences matter.  An unacceptably blurred structural MRI will have 
a smooth histogram, but probably won't produce a good segmentation.  
In both histograms, I could detect peaks, so there's probably 
adequate GM/WM contrast to get a good segmentation.


May be the problem is the one pointed by Simon. If this is the case, 
adjusting the histogram bins could minimize the effect. Do we have 
control over the histogram bins with Caret interface?


It doesn't look like it; the only inputs are the voxdims.  To be 
honest, I rarely use Caret to resample my volumes.  I usually do this 
as part of a preprocessing protocol using AFNI, FSL, or SPM 
utilities.  They allow one to specify interpolation mode, etc.  (At 
wustl.edu, this is done when the volume is written to 711-2B space 
using Avi Snyder's imgreg and related utilities.)




Thanks,
Mateus



Dierker wrote:


Hi Mateus,

I can't address your original problem with the NIfTI 
orientation/rotation, but I did have a look at your volumes, and 
this statement confuses me:


The histogram of my images (3D_original.nii and 3D_resliced.nii) 
shows several noisy sharp peaks. 



The attached captures show the histograms of 3D_original.nii 
(histogram_orig.jpg) and 3D_resliced.nii (histogram_resliced.jpg).  
The original has smoother looking peaks, but both have discernible 
gray and white matter peaks.  Neither look particularly bothersome.


Could you be more clear about what concerns you?

On 11/13/2006 05:43 AM, Mateus Joffily wrote:


John,

May I profit from the fact that I have already uploaded my images 
to ask you one more question about them? The histogram of my 
images (3D_original.nii and 3D_resliced.nii) shows several noisy 
sharp peaks. Do you know what do they mean? I know that, if I 
reslice the 3D_resliced.nii to 1x1x1mm voxels size with Caret, 
they disappear. Thanks.


Mateus

John Harwell wrote:


Hi Mateus,

Can you upload the nifti volume that is not displayed correctly 
in  Caret at http://pulvinar.wustl.edu/cgi-bin/upload.cgi;.  
Also, can  you capture and upload an image of the volume 
displayed correctly in  SPM5 so that I know how it should appear.


After uploading the files, please email me the names of the 
files.   It may be a few days before I can look into this problem.


--
John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.Box 8108
St. Louis, MO 63110   USA

On Nov 10, 2006, at 9:42 AM, Mateus Joffily wrote:


Hi,

I am having some trouble to load nifti images with caret5. The  
problem is the following:


1) When I try to load an image that has a rotation specified in 
the  header, Caret seems

Re: [caret-users] Spherical registration

2006-11-28 Thread Donna Dierker

On 11/28/2006 11:48 AM, Mateus Joffily wrote:

Hi,

I am a little bit confused on how to proceed to register an individual 
surface into an Atlas.
The 'Caret5 Tutorial: Segmentation, Flattening, and Registration' 
explains how to perform a spherical registration using the 
'Human.colin.L.REGISTER-to-INDIVIDUAL.03-05.71785.spec' file. My 
questions are:


1) What spec file should I use to register into the right hemisphere?
2) If I choose to register into PALS-B12 atlas, what files should I use?
The answer to both 1) and 2) is use the PALS_B12 LR combo registration 
target dataset:


http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499

And use the template deform_map included in that dataset to preset your 
registration parameters.  See this page and Erin's cheat sheet (linked 
from the page below) for more details:


http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html

This is what we do.  There are separate landmark datasets for the left 
and right, but they differ very little, and using the LR combo enables 
you to do cross-hem or inter-hem analyses.  The way we look at it, 
there's very little down side to using the combo dataset, but a lot of 
up side to doing so.  So we routinely use the LR combo now.


We stopped using colin as a registration target a couple of years ago, 
but some documentation may still refer to it.


Thanks,
Mateus
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Re: [caret-users] Spherical registration

2006-11-28 Thread Donna Dierker

Mateus,

Yes -- that's the right archive.

I don't understand why you're getting the time out errors; I can't 
replicate the problem on my end.


What happens when you try this link (i.e., same, except port number 
omitted):


http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6057499

On 11/28/2006 01:03 PM, Mateus Joffily wrote:

Hi Donna,

I don't know if I am the only one experiencing this problem, but I am 
also unable to access the location: 
http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499. I 
still get a 'time out error'.


However, I can access the SuMS database from http://sumsdb.wustl.edu/. 
Could you, please, confirm me if this is the atlas that I need to 
download: 'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730'?


Thanks,
Mateus


Donna Dierker wrote:


On 11/28/2006 11:48 AM, Mateus Joffily wrote:


Hi,

I am a little bit confused on how to proceed to register an 
individual surface into an Atlas.
The 'Caret5 Tutorial: Segmentation, Flattening, and Registration' 
explains how to perform a spherical registration using the 
'Human.colin.L.REGISTER-to-INDIVIDUAL.03-05.71785.spec' file. My 
questions are:


1) What spec file should I use to register into the right hemisphere?
2) If I choose to register into PALS-B12 atlas, what files should I 
use?


The answer to both 1) and 2) is use the PALS_B12 LR combo 
registration target dataset:


http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499

And use the template deform_map included in that dataset to preset 
your registration parameters.  See this page and Erin's cheat sheet 
(linked from the page below) for more details:


http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html

This is what we do.  There are separate landmark datasets for the 
left and right, but they differ very little, and using the LR combo 
enables you to do cross-hem or inter-hem analyses.  The way we look 
at it, there's very little down side to using the combo dataset, but 
a lot of up side to doing so.  So we routinely use the LR combo now.


We stopped using colin as a registration target a couple of years 
ago, but some documentation may still refer to it.




Thanks,
Mateus
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(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] Caret Tutorial

2006-11-28 Thread Donna Dierker

On 11/28/2006 02:02 PM, Veronica S Smith wrote:

Hi,

I was just checking out the latest Caret Tutorial and wanted to 
clarify that the PDF file, Caret_Tutorial_Oct6, is a companion to 
the archive, CARET_TUTORIAL_SEPT06. It appears that the latter 
consists of data files only. Is that correct?

Yes -- correct.


Also, these two files are the most recent tutorials, yes?
Yes -- correct also.  The Oct 6 PDF reflects some typo and other minor 
document corrections noted at the MCW course in early October.


This is the latest and greatest dataset (same as in the 
CARET_TUTORIAL_SEPT-06 directory 
(http://sumsdb.wustl.edu/sums/directory.do?id=6585200 ):


CARET_TUTORIAL_SEPT06.zip
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030


Thanks,
Veronica




Re: [caret-users] Spherical registration

2006-11-29 Thread Donna Dierker
I did remove the port numbers from the list, which seemed to have no ill 
effect on my end.  Perhaps it resolved the problem on your end.


On 11/29/2006 03:15 AM, Mateus Joffily wrote:

Hi Donna,

I don't know what happened, but now all the links work.

Thanks,
Mateus

Donna Dierker wrote:


Mateus,

Yes -- that's the right archive.

I don't understand why you're getting the time out errors; I can't 
replicate the problem on my end.


What happens when you try this link (i.e., same, except port number 
omitted):


http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6057499

On 11/28/2006 01:03 PM, Mateus Joffily wrote:


Hi Donna,

I don't know if I am the only one experiencing this problem, but I 
am also unable to access the location: 
http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499. 
I still get a 'time out error'.


However, I can access the SuMS database from 
http://sumsdb.wustl.edu/. Could you, please, confirm me if this is 
the atlas that I need to download: 
'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730'?


Thanks,
Mateus


Donna Dierker wrote:


On 11/28/2006 11:48 AM, Mateus Joffily wrote:


Hi,

I am a little bit confused on how to proceed to register an 
individual surface into an Atlas.
The 'Caret5 Tutorial: Segmentation, Flattening, and Registration' 
explains how to perform a spherical registration using the 
'Human.colin.L.REGISTER-to-INDIVIDUAL.03-05.71785.spec' file. My 
questions are:


1) What spec file should I use to register into the right hemisphere?
2) If I choose to register into PALS-B12 atlas, what files should 
I use?



The answer to both 1) and 2) is use the PALS_B12 LR combo 
registration target dataset:


http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499

And use the template deform_map included in that dataset to preset 
your registration parameters.  See this page and Erin's cheat 
sheet (linked from the page below) for more details:


http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html

This is what we do.  There are separate landmark datasets for the 
left and right, but they differ very little, and using the LR combo 
enables you to do cross-hem or inter-hem analyses.  The way we look 
at it, there's very little down side to using the combo dataset, 
but a lot of up side to doing so.  So we routinely use the LR combo 
now.


We stopped using colin as a registration target a couple of years 
ago, but some documentation may still refer to it.




Thanks,
Mateus
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(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] distance from a node

2006-11-29 Thread Donna Dierker
If you were talking about geodesic distance (i.e., running along the 
contour of the fiducial surface -- not as the crow flies through the 
CSF/WM), then you could use the Surface: ROI feature for this purpose. 
(First operation Geodesic Distance, and then threshold the resulting 
metric at the desired distance.)


I'm not aware of something like that for 3D distances, but there's a 
Make Sphere feature in Window: Script Builder.  Worst case, you could 
generate a sphere around the enclosing voxel and map that ROI volume to 
the surface.


On 11/29/2006 11:18 AM, Mateus Joffily wrote:

Hi,

In Caret5.5, is there a way of selecting a node and finding all (or 
some) nodes that are at a given distance from it? I think I am looking 
for something similar to what is described in section 2.17.2 (Foci 
Data Searches) of the 'Caret Tutorial – the Basics'. But Section 
2.17.2 regards only WebCaret. Does it exist something similar to 
Caret5.5?


Thanks,
Mateus
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(Formerly Donna Hanlon; no change in marital status -- see 
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Re: [caret-users] crash of X KDE session

2006-11-29 Thread Donna Dierker

Hi Marco,

Although your problem is a bit different, another possible culprit is 
the .caret5_preferences file:


http://brainvis.wustl.edu/pipermail/caret-users/2006-November/000931.html

We're still struggling with this problem at University of Washington.  
Today I asked Veronica to try the attached script, which strips the 
recent files and directories from the caret preferences before launching 
caret.  I'm curious whether it helps in your case, in case the 
.fonts.conf trick fails.  Let us know what you find.


On 11/29/2006 11:19 AM, John Harwell wrote:

Marco,

Another user had a problem similar to this.  I believe it has to do 
with the FreeType library which gets used to create text characters 
that are drawn on the volume slices to show the voxel and its 
stereotaxic coordinate.


See if there is a file in your home directory named .fonts.conf 
(note that the file begins with a period so use the command ls -a to 
see the file).  If .fonts.conf exists, rename it, start Caret, and 
see if you can import a volume.


For more info:  
http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00892.html


--
John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.Box 8108
St. Louis, MO 63110   USA

On Nov 29, 2006, at 10:42 AM, marco tettamanti wrote:


Hi Donna and Hohn,
I am experiencing a severe problem with my caret installation in 
linux: whenever I try to import an Analyze Volume file, my entire X 
session immediately crashes, including all applications and I have to 
login in KDE from scratch.
I couldn't tell whether the problem is limited to the Import function 
only, because the system crashes so badly that I thought it would be 
better to obtain some feedback from you before doing some debugging. 
But all the other display functions of caret that I have tried out 
(rendering surfaces, overlaying metric maps and so on) seem to work 
fine.


I first encountered the problem a few days ago. I completely ignore 
what could be the origin of the problem. I had used the same 
installation without any problems before, including the Import 
function. I have also tried to do a fresh install, of both versions 
5.4 and 5.5, but the problem persists.


I did some updates of KDE and xorg recently, though, and I suspect 
that the problem may have arosen since then. All other applications 
run fine, though.


Also, I have installed the same .zip caret tar ball on another 
machine and there it runs fine...


This is the kernel of my machine:

Linux bll4 2.6.11-kanotix-11 #1 Sun May 29 22:32:10 CEST 2005 i686 
GNU/Linux



Any help would be greatly appreciated!


Best,
Marco

--Marco Tettamanti, Ph.D.
San Raffaele Scientific Institute
Facoltà di Psicologia
Via Olgettina 58
I-20132 Milano, Italy
Tel. ++39-02-26434888
Fax ++39-02-26434892
Email: [EMAIL PROTECTED]
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(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



caret_prefs_stripper.sh
Description: Bourne shell script


Re: [caret-users] distance from a node

2006-11-30 Thread Donna Dierker
Oh!  That's ridiculously easy.  Those reference distances are in mm on 
the inflated (except for the staring sylvian, which is relative to the 
flat surface).  You click one node on, say, the occipital pole; then you 
click a border point along the calcarine you guesstimate is about 24mm 
from the occipital pole; and you read out the Distance on the ID 
window.  This is a 3D distance (make sure you read the Inflated 
surface's distance, or flat if sylvian).  If your occipital pole point 
is offset significantly from the border point along the x or z axes, 
then use the Y component of the respective points and compute the 
difference.


For example, there's a pretty big x and z offset between this occipital 
pole (first) and candidate most-posterior calcarine border point:


Node 20734
   Main Window Inflated XYZ: 15.015987396, -110.156700134, -22.251829147
   Shape: -2.904558420 -2.124466896

Node 32819
   Main Window Inflated XYZ: 27.664737701, -77.988800049, -6.281192303 
Distance: 38.076580048

   Shape: -10.455765724 -8.209010124


So I compute -110 - -78 = 32 -- so this point is 32mm from the occipital 
pole, so we need to find one whose y component of the inflated 
coordinate is closer to like -110 + 24 = -86.


Hope this helps!

On 11/30/2006 06:53 AM, Mateus Joffily wrote:

Hi David,

Thanks for your reply. I asked for this capability because I am trying 
to perform a spherical registration. Many landmarks are defined as 
starting and terminating at a certain distance from an anatomical 
reference point. I thought that a tool, which allows the user to enter 
a reference point coordinate in the surface and, after, displays every 
node that is at a given geodesic distance from it, would be helpful
This capability is not essential for me. I was wondering if it was 
already implemented in Caret.


Best regards,
Mateus

David Vanessen wrote:


Mateus,

First, it is important to clarify whether your request pertains to  
nodes (as stated) or to foci.  In Caret terminology, nodes refers  
specifically to the points that make up a surface and have locations  
specified within a coordinate file.  Foci refers to stereotaxically  
identified locations (typically fMRI activation centers) that are  
specified within a foci file or foci projection file.  I'm guessing  
you are referring to foci, but let us  know.


At present, I don't think that the capability you are asking about  
exists for either nodes or foci.  If you can let us know what you  
will be using this for and whether this is a pressing need, it will  
help us to prioritize the request.  Also, if other Caret users would  
like to see this functionality, let us know.


Best regards,

David


On Nov 29, 2006, at 11:28 AM, Donna Dierker wrote:

If you were talking about geodesic distance (i.e., running along  
the contour of the fiducial surface -- not as the crow flies  
through the CSF/WM), then you could use the Surface: ROI feature  
for this purpose. (First operation Geodesic Distance, and then  
threshold the resulting metric at the desired distance.)


I'm not aware of something like that for 3D distances, but there's  
a Make Sphere feature in Window: Script Builder.  Worst case, you  
could generate a sphere around the enclosing voxel and map that ROI  
volume to the surface.


On 11/29/2006 11:18 AM, Mateus Joffily wrote:


Hi,

In Caret5.5, is there a way of selecting a node and finding all  
(or some) nodes that are at a given distance from it? I think I am  
looking for something similar to what is described in section  
2.17.2 (Foci Data Searches) of the 'Caret Tutorial – the Basics'.  
But Section 2.17.2 regards only WebCaret. Does it exist something  
similar to Caret5.5?


Thanks,
Mateus
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Re: [caret-users] crash of X KDE session

2006-11-30 Thread Donna Dierker

Marco,

Does the problem occur when you use File: Open Volume Anatomy (or 
functional) File to open the same file?


If so, does it occur if you convert the file to NIfTI and/or AFNI?  I'm 
guessing it will (e.g., suggesting a display issue, rather than a file 
I/O issue), but it helps to be sure.  If you have trouble converting to 
another file format, then upload the file here, and I'll provide you the 
converted version:


http://pulvinar.wustl.edu/cgi-bin/upload.cgi

On 11/30/2006 04:08 AM, marco tettamanti wrote:

Hi John and Donna,
I tried both of your methods, but unfortunately none solved my problem...
I have tried to rename the file .fonts.conf, alone and, following the 
thread between Roland and you, together with .fonts.cache-1 and 
.fontconfig/

I also tried running Donna's script sh ./caret_prefs_stripper.sh.
Helas, my entire X session always crashes when I import an Analyze 
image file.
My problem seem to be different form Roland's and Veronica's ones, in 
that the problem is not limited to Caret, but it affects the entire 
X environment.


Best,
Marco

John Harwell wrote:

Marco,

Another user had a problem similar to this.  I believe it has to do 
with the FreeType library which gets used to create text characters 
that are drawn on the volume slices to show the voxel and its 
stereotaxic coordinate.


See if there is a file in your home directory named .fonts.conf 
(note that the file begins with a period so use the command ls -a 
to see the file).  If .fonts.conf exists, rename it, start Caret, 
and see if you can import a volume.


For more info:  
http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00892.html


--
John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.Box 8108
St. Louis, MO 63110   USA

On Nov 29, 2006, at 10:42 AM, marco tettamanti wrote:


Hi Donna and Hohn,
I am experiencing a severe problem with my caret installation in 
linux: whenever I try to import an Analyze Volume file, my entire X 
session immediately crashes, including all applications and I have 
to login in KDE from scratch.
I couldn't tell whether the problem is limited to the Import 
function only, because the system crashes so badly that I thought it 
would be better to obtain some feedback from you before doing some 
debugging. But all the other display functions of caret that I have 
tried out (rendering surfaces, overlaying metric maps and so on) 
seem to work fine.


I first encountered the problem a few days ago. I completely ignore 
what could be the origin of the problem. I had used the same 
installation without any problems before, including the Import 
function. I have also tried to do a fresh install, of both versions 
5.4 and 5.5, but the problem persists.


I did some updates of KDE and xorg recently, though, and I suspect 
that the problem may have arosen since then. All other applications 
run fine, though.


Also, I have installed the same .zip caret tar ball on another 
machine and there it runs fine...


This is the kernel of my machine:

Linux bll4 2.6.11-kanotix-11 #1 Sun May 29 22:32:10 CEST 2005 i686 
GNU/Linux



Any help would be greatly appreciated!


Best,
Marco

--Marco Tettamanti, Ph.D.
San Raffaele Scientific Institute
Facoltà di Psicologia
Via Olgettina 58
I-20132 Milano, Italy
Tel. ++39-02-26434888
Fax ++39-02-26434892
Email: [EMAIL PROTECTED]
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Re: [caret-users] projecting PALS-B12 atlas into individual brain

2006-11-30 Thread Donna Dierker

On 11/30/2006 08:34 AM, Mateus Joffily wrote:

Hi,

I have concluded the spherical registration of one individual surface 
into PALS-B12. Three spec files have been created:


(1) Human.Isa.R.spec (original spec file);
(2) deformed_Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec;
(3) deformed_Human.Isa.R.spec;

Could you, please, precise me differences among those three specs and 
for what purpose should I use each one? Although the names seem to be 
informative, when I compare the surfaces linked to each one, they look 
very similar, if not the same.

1) The original is what you created during segmentation, flattening, etc.
2) The deformed_Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec 
should be in your individual's surface directory.  The dataset you 
downloaded is a stripped down version that contains no goodies (e.g., 
PALS border and paints, which you cite below).  To get such goodies to 
automagically deform to your subjects' directories when you run 
registration, put the goodies in the atlas target directory and add them 
to your target registration spec (i.e., 
Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec).  The one you 
currently have offers little, since it's designed more for the 
individual - atlas direction (e.g., getting a bunch of depth or fMRI 
maps on the PALS mesh).  But in your case, you care more about atlas - 
individual.
3) The deformed_Human.Isa.R.spec is in your atlas target directory.  
Other than sanity checking the deformed fiducial, I don't personally use 
this spec file much.  (And even when sanity checking, I use a 
SANITY_CHECK.spec that includes ALL my deformed fiducials and a single 
PALS closed topo.)  More typically, you're interested in a particular 
file type -- e.g., deformed surface shape for sulcal depth; deformed 
metric for fMRI; deformed fiducial coord file for average fiducials.  
One typically concatenates all the deformed shape/metric into composite 
files and does group statistics on them.


In the next step, I would like to project PALS_B12 atlas (borders and 
paints) into the non-deformed individual surface. Could you, please, 
point me the documentation that explains how to do that, and how do I 
use the deformation map files?
The hard part is figuring out exactly which goodies (e.g., PALS paint, 
border, metric) you want deformed.  Search for them in sumsdb.wustl.edu, 
or more likely find them in existing tutorials or datasets from figures 
in published papers that cite sumsdb links.  You may find that the 
goodies in the visualization specs off the landmarks page meet your 
needs.  If so, copy the appropriate paint, areacolor, border, 
bordercolor, metric, and/or palette files to your atlas target 
directory.  Then add them to your atlas target spec.  Then either re-run 
any registrations, or use Surface: Deformation: apply deformation map to 
apply the map in your individual's surface directory to the files in 
your atlas target directory.


Thanks again for your help.

Mateus

--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] Spherical registration

2006-11-30 Thread Donna Dierker

Here is the pecking order (believe in this order):

Landmark page 
(http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html)

Cheat sheet
Tutorial

On 11/30/2006 09:00 AM, Mateus Joffily wrote:

Hi,

In the 'Caret5 Tutorial', during the spherical registration procedure, 
it is instructed to use the 'Human to Human' standard parameters (in 
Surface: Deformation: Run Spherical Surface Deformation: Spherical 
Parameters: Set Parameters). However, in Erin's cheat sheet, it is 
instructed to read params from: Def Map File: 
'TEMPLATE_REG-with-POP-AVG_4k_NoFid.deform_map'.


If I am using 'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730' 
atlas, which procedure should I follow?


Thanks,
Mateus

Donna Dierker wrote:

I did remove the port numbers from the list, which seemed to have no 
ill effect on my end.  Perhaps it resolved the problem on your end.


On 11/29/2006 03:15 AM, Mateus Joffily wrote:


Hi Donna,

I don't know what happened, but now all the links work.

Thanks,
Mateus

Donna Dierker wrote:


Mateus,

Yes -- that's the right archive.

I don't understand why you're getting the time out errors; I can't 
replicate the problem on my end.


What happens when you try this link (i.e., same, except port number 
omitted):


http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6057499

On 11/28/2006 01:03 PM, Mateus Joffily wrote:


Hi Donna,

I don't know if I am the only one experiencing this problem, but I 
am also unable to access the location: 
http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499. 
I still get a 'time out error'.


However, I can access the SuMS database from 
http://sumsdb.wustl.edu/. Could you, please, confirm me if this is 
the atlas that I need to download: 
'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730'?


Thanks,
Mateus


Donna Dierker wrote:


On 11/28/2006 11:48 AM, Mateus Joffily wrote:


Hi,

I am a little bit confused on how to proceed to register an 
individual surface into an Atlas.
The 'Caret5 Tutorial: Segmentation, Flattening, and 
Registration' explains how to perform a spherical registration 
using the 
'Human.colin.L.REGISTER-to-INDIVIDUAL.03-05.71785.spec' file. My 
questions are:


1) What spec file should I use to register into the right 
hemisphere?
2) If I choose to register into PALS-B12 atlas, what files 
should I use?




The answer to both 1) and 2) is use the PALS_B12 LR combo 
registration target dataset:


http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499

And use the template deform_map included in that dataset to 
preset your registration parameters.  See this page and Erin's 
cheat sheet (linked from the page below) for more details:


http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html

This is what we do.  There are separate landmark datasets for the 
left and right, but they differ very little, and using the LR 
combo enables you to do cross-hem or inter-hem analyses.  The way 
we look at it, there's very little down side to using the combo 
dataset, but a lot of up side to doing so.  So we routinely use 
the LR combo now.


We stopped using colin as a registration target a couple of years 
ago, but some documentation may still refer to it.




Thanks,
Mateus
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Re: [caret-users] distance from a node

2006-11-30 Thread Donna Dierker
Come to think of it, I would benefit from that utility, too.;-)  Even 
better would be an accurate, automated border drawing utility.  Kidding 
aside, we recognize this is a highly desirable enhancement, but pretty 
tough to deliver right now.


John Harwell has added some caret_command features that can trim some of 
the easy ones (e.g., calcarine posterior, central dorsal/medial):


  SURFACE BORDER EXTREMA
 caret_command -surface-border-extrema \
input-topo-file input-coord-file input-border-file 
border-name


 List the extrema for the surface, the extrema for the border, and the
 difference between the extrema.
--
  SURFACE BORDER NIBBLER (remove border points within a distance to 
surface ext

rema)
 caret_command -surface-border-nibbler \
input-topo-file input-coord-file input-border-file 
border-name

output-border-file surface-extrema-name-or-node-indicator
 surface-extrema-offset-or-node-number pos-neg

 Remove points from the named border that are within that are on a .
 specified side of a surface extrema or node number.

But your idea is kind of interesting.

Meanwhile, if you choose reference points which differ primarily along 
the axis of interest, then the distance is a good proxy for the 
component difference, so no math required.  In either case, you'll be 
surprised how fast you get good at guessing.  Before long, you'll need 
only a few tries, and it's always fun when your first guess is right. ;-)


On 11/30/2006 12:52 PM, Mateus Joffily wrote:

Hi Donna,

That's exactly what I did (although, there are some details in your 
example that I didn't understand well, see below). But, instead of 
keep going forth and back selecting nodes and subtracting their 
coordinates values (I had to do it quite often), I was wondering if 
there was not an utility that would automatically highlight all the 
nodes that are at a given distance from my reference point. I am not 
saying that it is a necessary utility, but, if it was already 
implemented, I could benefit from it...


Thanks,
Mateus



For example, there's a pretty big x and z offset between this 
occipital pole (first) and candidate most-posterior calcarine border 
point:


In this example, I though that the biggest offset was for Y (dX: 
15-28=-13; dY: -110 --78=32; dZ: -22 --6=-16). That's why you first 
chose to adjust the Y distance, no?




Node 20734
   Main Window Inflated XYZ: 15.015987396, -110.156700134, -22.251829147
   Shape: -2.904558420 -2.124466896

Node 32819
   Main Window Inflated XYZ: 27.664737701, -77.988800049, 
-6.281192303 Distance: 38.076580048

   Shape: -10.455765724 -8.209010124


So I compute -110 - -78 = 32 -- so this point is 32mm from the 
occipital pole, so we need to find one whose y component of the 
inflated coordinate is closer to like -110 + 24 = -86.


Hope this helps!

On 11/30/2006 06:53 AM, Mateus Joffily wrote:


Hi David,

Thanks for your reply. I asked for this capability because I am 
trying to perform a spherical registration. Many landmarks are 
defined as starting and terminating at a certain distance from an 
anatomical reference point. I thought that a tool, which allows the 
user to enter a reference point coordinate in the surface and, 
after, displays every node that is at a given geodesic distance from 
it, would be helpful
This capability is not essential for me. I was wondering if it was 
already implemented in Caret.


Best regards,
Mateus

David Vanessen wrote:


Mateus,

First, it is important to clarify whether your request pertains to  
nodes (as stated) or to foci.  In Caret terminology, nodes refers  
specifically to the points that make up a surface and have 
locations  specified within a coordinate file.  Foci refers to 
stereotaxically  identified locations (typically fMRI activation 
centers) that are  specified within a foci file or foci projection 
file.  I'm guessing  you are referring to foci, but let us  know.


At present, I don't think that the capability you are asking about  
exists for either nodes or foci.  If you can let us know what you  
will be using this for and whether this is a pressing need, it 
will  help us to prioritize the request.  Also, if other Caret 
users would  like to see this functionality, let us know.


Best regards,

David


On Nov 29, 2006, at 11:28 AM, Donna Dierker wrote:

If you were talking about geodesic distance (i.e., running along  
the contour of the fiducial surface -- not as the crow flies  
through the CSF/WM), then you could use the Surface: ROI feature  
for this purpose. (First operation Geodesic Distance, and then  
threshold the resulting metric at the desired distance.)


I'm not aware of something like that for 3D distances, but 
there's  a Make Sphere feature in Window: Script Builder.  Worst 
case, you  could generate a sphere around the enclosing voxel and 
map that ROI  volume

Re: [caret-users] segmentation fails w/ uniformized data

2006-12-07 Thread Donna Dierker

Hi Rebecca,

As John said, uploading your volume is the quickest way for us to help, 
but here are some additional thoughts/factors:


* For very non-uniform volumes, 3dUniformize may not be enough. You 
might need a bigger gun like FSL's FAST 
(http://www.fmrib.ox.ac.uk/fsl/fast/index.html), which does better if 
you skull-strip with BET first. I have a script named fsl_bias_corr.sh 
that takes an input Analyze .hdr and runs BET and FAST on it. You may 
need to tweak your FIT and BIAS_SMOOTHING_ITERATIONS iterations to 
improve your result:


#!/bin/sh

INFNAME=$1
FSLDIR=/usr/local/fsl
FIT=0.10
BIAS_SMOOTHING_ITERATIONS=500

INBASENAME=`echo $INFNAME | sed 's/.hdr$//g'`
BETBASENAME=`echo $INFNAME | sed 's/.hdr$/_bet/g'`

COMMAND=$FSLDIR/bin/bet $INBASENAME $BETBASENAME -f $FIT -g 0
echo =; echo $COMMAND ; echo =
$COMMAND

COMMAND=$FSLDIR/bin/fast -t1 -c 3 -n -v5 -l $BIAS_SMOOTHING_ITERATIONS 
-or $BETBASENAME.hdr

echo =; echo $COMMAND ; echo =
$COMMAND

* After running FAST, you may find the problem disappears. It's likely 
failing during eye or hindbrain removal, both of which are rather 
brittle parts of the algorithm. Things that make this part break most 
often are:


-- rotation off AC-PC line (see AC work-around below, but there are 
definitely limits to how far off AC-PC the volume can be)

-- little CSF clearance between ventral occipital cortex and cerebellum
-- blood vessels or optic nerve preventing disconnection from skull

* Besides correcting for gain/bias field, other things that can help 
work around this problem are:


-- peak tweaking: sometimes the difference between WMpeak=75 and 
WMpeak=76 can be dramatic

-- adjusting the AC position, especially in the Z (axial) dimension

On 12/06/2006 04:48 PM, John Harwell wrote:

Rebecca,

Can you upload your volume to 
http://pulvinar.wustl.edu/cgi-bin/upload.cgi and we will see what is 
going on. Please let us know when you have uploaded your volume and 
the name of the volume file.


--
John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA

On Dec 6, 2006, at 2:48 PM, Rebecca Ebitz wrote:


Hi - I'm having a problem segmenting normalized scans.

I've got a very non-uniform volume (macaque, from a 4.7T w/ 0.5 mm 
voxels) and have used AFNI's 3dUniformize to correct these issues. 
However, when I try to segment the normalized data in CARET, it 
either gives me an error (usually that findBiggestObjectWithinMask 
failed in some way) or it simply crashes.


I can run a successful segmentation on the non-uniformized volume, it 
just requires a great deal of manual correction. I'm doing the same 
processing steps for both the normalized and non-uniform volumes.


Anything I should try here? I've tried to run several different 
normalizations and all of them cause segmentation to fail.


Please let me know what other information you need from me on this one.

-Rebecca

__
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Laboratory of Brain and Cognition
National Institute of Mental Health
Building 10, Room 4C214
Office: 301.4510.8509
[EMAIL PROTECTED]

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Re: [caret-users] tailarach coordinate

2006-12-07 Thread Donna Dierker

Hi Mateus,

Your question throws me a little bit, but I'll try to provide a helpful 
answer.


When you register your surface to PALS_B12.LR, one of the resulting 
files in the atlas target directory is a file named like 
def*Fiducial*coord -- what David calls the resampled fiducial.  (He 
doesn't like to use the word deformed, because that implies that the 
surface is being distorted to match some target; in fact, the file named 
like def*Fiducial*coord is indistinguishable from the original surface 
by eye.  It's actually slightly smoother than the original surface, 
resulting in a 7% surface area reduction.)  If you click on a node in 
the individual surface, you'll get a node number and 3D coordinate in 
the Identify Window.  If you click on roughly the same node in the 
resampled fiducial surface, you'll get a different node number -- even 
if you're extremely careful and pick the exact corresponding location, 
because your original surface has one mesh (e.g., say 54,040 nodes), 
while the PALS_B12.LR resampled surface has 73,730 nodes.  But you 
should get virtually the same 3D coordinate.


Now, you can also open PALS_B12.LR average fiducial surfaces in the same 
session as your def*Fid*coord file -- any of these coords included in 
your Caret data_files/fmri_mapping_files:


Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_711-2C.clean.align.73730.coord
Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_AFNI.clean.73730.coord
Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord
Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_MRITOTAL.clean.73730.coord
Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord
Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM95.clean.73730.coord
Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM96.clean.73730.coord
Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM99.clean.73730.coord

If you open one or more of these surfaces in a Window 2 and click on 
nodes, then you'll get two different 3D coordinates for the same node.  
Which you use to report your findings is your call.


David also encourages authors to report Latitude and Longitude, when 
available.  For PALS_B12.LR, make sure the latlon file is loaded when 
you run reports under Surface: ROI.


I hope this helps, but it probably won't.

On 12/07/2006 12:19 PM, Mateus Joffily wrote:

Hi,

I have registred one individual surface into PALS-B12 (using 
Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec). I would like 
to know the talairach coordinate of a voxel in the registered surface. 
Is it possible?


Thanks for your help,
Mateus
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Re: [caret-users] using caret for a meta-analysis

2006-12-08 Thread Donna Dierker

Hi Leon,

Shawn has done exactly what you want to do, so if anyone knows the 
pitfalls, he does. ;-)


Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 
of this tutorial, if you haven't done so already:


CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200

This tutorial includes a spec file intended for this purpose. The ones 
in the Caret fmri_mapping directory are not really intended for use as 
visualization specs; rather, Caret uses them when mapping fMRI data 
onto PALS_B12. You can, however, use the average fiducial surfaces in 
that directory for your foci-related purposes. Note that studies report 
results in stereotactic spaces other than MNI (e.g., AFNI users report 
true Talairach-Tournoux (T88) coordinates, which differs significantly 
from MNI -- see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach; 
wustl.edu researchers typically use 711-2* space -- somewhere between 
T88 and MNI). See 
http://brainvis.wustl.edu/help/pals_volume_normalization/ for additional 
details.


Reading tutorial section 5.2 may clarify some of this, but you're likely 
to have residual questions/confusion about these spaces.


On 12/08/2006 10:24 AM, Christ, Shawn E. wrote:


Hi Leon,

I have been working with David, Donna, and John on utilizing Caret for 
precisely this purpose with respect to an ALE-type meta-analysis on 
deception that we have submitted for publication. You can download a 
copy of our spec file, etc. at 
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996


I’ve also uploaded a copy of my personal notes on how to transform 
foci using Caret. They can be found at 
http://www.shawnchrist.com/FociTransform.pdf


I hope this helps!

Best,

-Shawn

--

Shawn Christ, Ph.D.

Assistant Professor

Department of Psychological Sciences

University of Missouri-Columbia

210 McAlester Hall

Columbia, MO 65211

[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]



*From:* [EMAIL PROTECTED] 
[mailto:[EMAIL PROTECTED] *On Behalf Of *Leon 
Deouell

*Sent:* Friday, December 08, 2006 9:50 AM
*To:* caret-users@brainvis.wustl.edu
*Subject:* [caret-users] using caret for a meta-analysis

Hi,

I am in the process of doing a meta-analysis of imaging data. I am a 
complete novice to Caret, but from a quick look it seems it's 
stereotaxic foci functions would be ideal to log the peak activity 
data from different studies. Eventually I would like to display 
symbols for each peak on a 3D brain rendering of some sort. Perhaps 
Naively, I thought I could load a template brain (open a spec file), 
add foci (assuming for a moment I have all coordinates in MNI space) 
using for example 'layersfocimap stererotaxic focus', and see them 
pop-out on the brain. However, at first pass, I run into the following 
questions:


a) What brain (spec file) should I load from the fMRI_mapping folder? 
There are so many of them. Is there anywhere a text file describing 
what these different files are?


b) If I enter a focus with coordinates which happen to be under the 
surface by a few millimeters, they don't show up on the surface. Is 
there a way to project them to the surface or to make the brain 
'transparent'?


c) Once I have the foci entered, can I project them to an inflated 
brain, and if so, how?


Finally, I assume I am not the first to want to use Caret for this 
purpose – does someone have a 'recipe' for such a project or tips on 
what pitfalls to avoid?


Thanks,

Leon



Dr. Leon Y Deouell, MD, PhD

Department of Psychology

The Hebrew University of Jerusalem

Jerusalem 91905

Israel

Tel: +972-2-5881739

Fax: +972-2-5825659

http://pissaro.soc.huji.ac.il/~leon/Lab 
http://pissaro.soc.huji.ac.il/%7Eleon/Lab




___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
  



--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] using caret for a meta-analysis

2006-12-08 Thread Donna Dierker

On 12/08/2006 11:44 AM, Leon Deouell wrote:

Dear Donna,

Thanks for the information. I realize the issue of different coordinate
spaces. What I am not sure of is this: If I specify the original space
(e.g., T88 or SPM2) for each study in the foci text file, or in the study
tab when entering individual foci using the GUI (5.2.2 in the tutorial),
will Caret take this into consideration when projecting to the PALS brain?
  

Yes

Or do I have to go through some intermediate of transforming from one space
to another? Originally I was considering using the tal2mni Matlab function
from the Cambridge imagers web site you mentioned to get all coordinates
into MNI space, but maybe this is redundant in Caret.
  
The idea is to make this unnecessary -- as long as the stereotaxic space 
in question is well-represented by one of these:


711-2C
AFNI
FLIRT
MRITOTAL
SPM2
SPM95
SPM96
SPM99

Thanks,

Leon   


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 08, 2006 6:34 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

Shawn has done exactly what you want to do, so if anyone knows the 
pitfalls, he does. ;-)


Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 
of this tutorial, if you haven't done so already:


CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200

This tutorial includes a spec file intended for this purpose. The ones 
in the Caret fmri_mapping directory are not really intended for use as 
visualization specs; rather, Caret uses them when mapping fMRI data 
onto PALS_B12. You can, however, use the average fiducial surfaces in 
that directory for your foci-related purposes. Note that studies report 
results in stereotactic spaces other than MNI (e.g., AFNI users report 
true Talairach-Tournoux (T88) coordinates, which differs significantly 
from MNI -- see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach; 
wustl.edu researchers typically use 711-2* space -- somewhere between 
T88 and MNI). See 
http://brainvis.wustl.edu/help/pals_volume_normalization/ for additional 
details.


Reading tutorial section 5.2 may clarify some of this, but you're likely 
to have residual questions/confusion about these spaces.


On 12/08/2006 10:24 AM, Christ, Shawn E. wrote:
  

Hi Leon,

I have been working with David, Donna, and John on utilizing Caret for 
precisely this purpose with respect to an ALE-type meta-analysis on 
deception that we have submitted for publication. You can download a 
copy of our spec file, etc. at 
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996


I've also uploaded a copy of my personal notes on how to transform 
foci using Caret. They can be found at 
http://www.shawnchrist.com/FociTransform.pdf


I hope this helps!

Best,

-Shawn

--

Shawn Christ, Ph.D.

Assistant Professor

Department of Psychological Sciences

University of Missouri-Columbia

210 McAlester Hall

Columbia, MO 65211

[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]



*From:* [EMAIL PROTECTED] 
[mailto:[EMAIL PROTECTED] *On Behalf Of *Leon 
Deouell

*Sent:* Friday, December 08, 2006 9:50 AM
*To:* caret-users@brainvis.wustl.edu
*Subject:* [caret-users] using caret for a meta-analysis

Hi,

I am in the process of doing a meta-analysis of imaging data. I am a 
complete novice to Caret, but from a quick look it seems it's 
stereotaxic foci functions would be ideal to log the peak activity 
data from different studies. Eventually I would like to display 
symbols for each peak on a 3D brain rendering of some sort. Perhaps 
Naively, I thought I could load a template brain (open a spec file), 
add foci (assuming for a moment I have all coordinates in MNI space) 
using for example 'layersfocimap stererotaxic focus', and see them 
pop-out on the brain. However, at first pass, I run into the following 
questions:


a) What brain (spec file) should I load from the fMRI_mapping folder? 
There are so many of them. Is there anywhere a text file describing 
what these different files are?


b) If I enter a focus with coordinates which happen to be under the 
surface by a few millimeters, they don't show up on the surface. Is 
there a way to project them to the surface or to make the brain 
'transparent'?


c) Once I have the foci entered, can I project them to an inflated 
brain, and if so, how?


Finally, I assume I am not the first to want to use Caret for this 
purpose - does someone have a 'recipe' for such a project or tips on 
what pitfalls to avoid?


Thanks,

Leon



Dr. Leon Y Deouell, MD, PhD

Department of Psychology

The Hebrew University of Jerusalem

Jerusalem 91905

Israel

Tel: +972-2-5881739

Fax: +972-2-5825659

http://pissaro.soc.huji.ac.il/~leon/Lab 
http

Re: [caret-users] (no subject)

2006-12-11 Thread Donna Dierker

Hi Dr. Ghosh,

I think you want the login and password for the download page:

http://brainmap.wustl.edu/pub/caret/index.html
login: Rabbit
password: Carrot

If you're talking about your caret-users mailing list options, you can 
get a password reminder here:


http://pulvinar.wustl.edu/mailman/options/caret-users

As for machine specs, I'm not sure whether there's a strict minimum 
memory or graphics card requirement.  If you're just using the machine 
for mapping foci or functional data, then memory and CPU are less 
important.  But if you're planning to to run segmentation and spherical 
registration, or any of the options under Attributes: Metric and Surface 
Shape Statistical Operations, then I'd aim for at least 2Gb memory and 
the fastest CPU you can afford (preferrably multiple processes).  We've 
had good luck with NVidia graphics cards, but plenty of people use other 
types of cards.  I'm sure you know to get plenty of disk space, since 
you're using SPM.


On 12/11/2006 07:45 AM, shantanu ghosh wrote:

hi Donna/David
I had downloaded the windows version of Caret5 sometime ago, but 
realized that I would be better off using the linux version. Since I 
was doing the analysis till now on spm, i really did not follow it 
up. Now that I require it to start doing metaanalysis and display, I 
would be needing it, but realized that I have forgotten my user id and 
p/w. Sorry to give you the trouble, but could you help me out!? I 
would be a starting user, and I have a linux O/S. I have not decided 
on the machine characteristics, so if you could give me something to 
start working on...

thanks


Shantanu Ghosh, PhD
Department of Humanities and Social Sciences
Indian Institute of Technology, Delhi
Hauz Khas
New Delhi 110016
INDIA
Tel.: +91-11-2659 6589
Fax: +91-11-2659 6509


Find out what India is talking about on - Yahoo! Answers India 
http://us.rd.yahoo.com/mail/in/yanswers/*http://in.answers.yahoo.com/
Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. 
Get it NOW 
http://us.rd.yahoo.com/mail/in/messengertagline/*http://in.messenger.yahoo.com 




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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] Flat surface crossovers

2006-12-11 Thread Donna Dierker
It means start on the outside and end on the inside, as shown in the 
attached capture, which shows an exaggeratedly thick red cut near some 
crossovers.


Both Erin and I would have left these minor, peripheral crossovers alone 
(i.e., no cuts), because we know from experience they tend to cause no 
trouble.  If there were tangles or fold-overs, then we'd cut them out.


On 12/11/2006 11:03 AM, Mateus Joffily wrote:

Dear experts,

I am trying to flatten a surface. After medial wall and calcarine cut 
corrections, I obtain the attached flat surface with some crossovers. 
The 'initial Flattening Dialog' informs that cuts used to excise 
errors should begin and end outside the map perimeter. I am not 
really sure about what it means. Should I draw the new cuts inside or 
outside the borders (perimeter?) of the initial flat map. Could 
someone clarify it to me?


Thanks for your help,
Mateus





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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)

inline: initial_flat_surface.jpg

Re: [caret-users] using caret for a meta-analysis

2006-12-22 Thread Donna Dierker

Hi Leon,

This looks like a bug to me.  I was able to replicate this behavior on 
my Caret 5.502 12/15/2006 Caret running RHEL.  The ID readout for these 
foci were just fine (readout followed by corresponding line from foci file):


Focus 2: MolholmEtAl05.pitch   Class: pitch
   Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0)
2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch

Focus 3: MolholmEtAl05.pitch   Class: pitch
   Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0)
3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrusPure,,pitch

But these foci had their x or y coordinate component zeroed out:

Focus 4: MolholmEtAl05.pitch   Class: pitch
   Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0)
4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch
[Note from Donna: If left SFG, then wouldn't it be -20?)

Focus 5: MolholmEtAl05.pitch   Class: pitch
   Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0)
5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal lobulePure,,pitch

Focus 6: MolholmEtAl05.pitch   Class: pitch
   Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0)
6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrusPure,,pitch

On 12/22/2006 03:26 AM, Leon Deouell wrote:

Hi,

I am finding something peculiar when looking at foci. To illustrate, I
created a smaller file with only one study (foci file attached). I went
through the following steps:

1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the
/CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder
2. Opened the foci file test1study.foci
3. Projected the foci using Layers/Foci/Project Foci to PALS atlas
(selecting 'project above surface [0.00]).

The projected foci can be viewed in the attached figure coordinates.jpg

Now I click on foci, and look the Identify Window. I find that for some, the
values in 'Original Sterotaxic Positions' match the coordinates in the foci
file. But for some (e.g., the one marked with a red ellipse in the figure) I
get one of the coordinates set to zero. For example for this focus, I get:

_
Focus 6: MolholmEtAl05.pitch  Class: pitch
 Original Stereotaxic Position (AFNI): 41.0 0.0 6.0
 Stereotaxic Position (FLIRT):  41.0 0.9 2.1
_

But focus 6 coordinates as specified in the foci file are 
actually [41, -75, 6]


The same happens to a few others (but not all) foci. Sometimes it is the y
coordinate that becomes zero, and sometimes the x coordinate. 


I verified that it is not something to do with the foci projection - the
same results are obtained if I click the foci before projection. 


Any idea what I may be doing wrong, or not interpreting correctly?

Thanks,

Leon







-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 08, 2006 7:49 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

On 12/08/2006 11:44 AM, Leon Deouell wrote:
  

Dear Donna,

Thanks for the information. I realize the issue of different coordinate
spaces. What I am not sure of is this: If I specify the original space
(e.g., T88 or SPM2) for each study in the foci text file, or in the study
tab when entering individual foci using the GUI (5.2.2 in the tutorial),
will Caret take this into consideration when projecting to the PALS brain?
  


Yes
  

Or do I have to go through some intermediate of transforming from one


space
  

to another? Originally I was considering using the tal2mni Matlab function
from the Cambridge imagers web site you mentioned to get all coordinates
into MNI space, but maybe this is redundant in Caret.
  

The idea is to make this unnecessary -- as long as the stereotaxic space 
in question is well-represented by one of these:


711-2C
AFNI
FLIRT
MRITOTAL
SPM2
SPM95
SPM96
SPM99
  

Thanks,

Leon   


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 08, 2006 6:34 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

Shawn has done exactly what you want to do, so if anyone knows the 
pitfalls, he does. ;-)


Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 
of this tutorial, if you haven't done so already:


CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200

This tutorial includes a spec file intended for this purpose. The ones 
in the Caret fmri_mapping directory are not really intended for use as 
visualization specs; rather, Caret uses them when mapping fMRI data 
onto PALS_B12. You can, however, use the average fiducial surfaces in 
that directory for your foci-related purposes. Note that studies report 
results in stereotactic spaces other than MNI (e.g., AFNI users report 
true Talairach

Re: [caret-users] using caret for a meta-analysis

2007-01-08 Thread Donna Dierker

Hi Leon,

Is it possible you have both a foci and fociproj file, both of which are 
loaded?


On 01/07/2007 03:37 AM, Leon Deouell wrote:

Hi,

I am displaying my foci now(post projection to PALS-B12) on the FIDUCIAL
Human.PALS_B12.LEFT_AVG_B1-12.FIDICUAL_FLIRT.clean.73730.coord. For some
reason, it looks like every  blob is doubled (see window capture attached).
I don't see this if I display the same foci on the inflated or hyperinflated
brains. Any idea why this is happening?

Thanks,

Leon

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 22, 2006 5:17 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

Thank YOU for figuring out your own problem -- a pretty obscure one, at 
that.


I agree both minus and long dash should read as minus; I hope it's not 
tough for John to do. Sometimes the I/O stuff is QT's domain and not so 
easy to control.


On 12/22/2006 09:05 AM, Leon Deouell wrote:
  

Dear Donna,

Thanks to your critical eye, I found out what the problem is. You noted


that
  

for focus 4 the description is L Superior Frontal Gyrus but the x


coordinate
  

was 20 in your readout. However, in the foci file I've sent, the line
actually says: 
4,-20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch


I am not sure what you used to read the foci file, but it seems this
software, like CARET, ignored the minus sign, and it turns out that all


the
  

numbers which were zeroed in CARET, where actually negative numbers in my
original foci file. I tracked the problem back to the character used for


the
  

minus sign. When I created the excel file (from which I created the CSV


foci
  

file), I have sometimes cut and paste from PDF files or HTML files of the
original articles. In some cases, the minus sign was a longer dash sign
rather than a real minus sign. They look very similar but the wrong
character is a slightly longer line if you look at it carefully. If you


open
  

the foci file I've sent before with Notepad (that is, if you use Windows)
you will see what I mean. When I replaced these characters with real minus
signs, the apparent bug was solved. 


I think this is a point to keep in mind because I am pretty sure many


would
  

cut and paste when creating large meta-analysis files (I have more than


100
  

points in the full file) rather than retype (which is also more prone to
errors). Maybe CARET can be configured to detect this somehow and either
report the problem or accept this other dash sign as minus. 

Many thanks for the quick response. 


Leon

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 22, 2006 4:19 PM
To: Leon Deouell
Cc: 'Caret, SureFit,and SuMS software users'
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

This looks like a bug to me.  I was able to replicate this behavior on 
my Caret 5.502 12/15/2006 Caret running RHEL.  The ID readout for these 
foci were just fine (readout followed by corresponding line from foci


file):
  

Focus 2: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0)
2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch

Focus 3: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0)
3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrusPure,,pitch

But these foci had their x or y coordinate component zeroed out:

Focus 4: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0)
4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch
[Note from Donna: If left SFG, then wouldn't it be -20?)

Focus 5: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0)
5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal


lobulePure,,pitch
  

Focus 6: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0)
6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrusPure,,pitch

On 12/22/2006 03:26 AM, Leon Deouell wrote:
  


Hi,

I am finding something peculiar when looking at foci. To illustrate, I
created a smaller file with only one study (foci file attached). I went
through the following steps:

1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the
/CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder
2. Opened the foci file test1study.foci
3. Projected the foci using Layers/Foci/Project Foci to PALS atlas
(selecting 'project above surface [0.00]).

The projected foci can be viewed in the attached figure coordinates.jpg

Now I click on foci, and look the Identify Window. I find that for some,

  

the
  


values in 'Original Sterotaxic Positions' match the coordinates

Re: [caret-users] metric file stats

2007-01-10 Thread Donna Dierker

Hi Clayton,

1. A reasonable question, but I'm afraid this document is both 
incomplete and obsolete:


http://brainvis.wustl.edu/courses/Caret_5_332_Tutorial_Analysis.doc

For example, Find Significant Clusters is now called Two-Sample T-test. 
But maybe it will still prove helpful. This submenu is one of the 
fastest changing in Caret right now, so it's very much a moving target. 
The two sample t-test is spelled out in the methods of our Williams 
Syndrome (WS) paper:


Van Essen, D.C., Dierker, D., Snyder, A., Raichle, M.E., Reiss, A., and 
Korenberg, J. (2006) Symmetry of cortical folding abnormalities in 
Williams syndrome revealed by surface-based analyses. J. Neuroscience 
26:5470-5483.

http://brainvis.wustl.edu/resources/WmsJNsci.pdf

It's basically the surface equivalent of the suprathreshold cluster test 
described in Nichols  Holmes primer paper. The interhemispheric test 
also is described in our WS paper.


If you have questions about other tests, let us know.

2. Thanks to John Harwell, the following tests are available via command 
line:


vp.wustl.edu 22% caret_command -help | grep metric-or-shape-stat

INFO: To see command line options, Run with -help

METRIC/SHAPE STATISTICS COORDINATE DIFFERENCE 
-metric-or-shape-stat-coord-diff
METRIC/SHAPE STATISTICS INTERHEMISPHERIC CLUSTERS 
-metric-or-shape-stat-interhemispheric-clusters
METRIC/SHAPE STATISTICS ONE SAMPLE T-TEST 
-metric-or-shape-stat-one-sample-t-test

METRIC/SHAPE STATISTICS PAIRED T-TEST -metric-or-shape-stat-paired-t-test
METRIC/SHAPE STATISTICS TWO SAMPLE T-TEST and WILCOXON 
-metric-or-shape-stat-two-sample-t-test


But these weren't added until 12/15, so you probably will need to 
download a new version; let us know which platform you use.


On 01/10/2007 12:34 PM, Clayton E Curtis wrote:

Hi,

I have two quick questions. 


1.  What's the best place to get documentation on the new metric/surface
shape statistical operations?  We've looked at the documentation at
http://brainmap.wustl.edu/caret/caret5.5_help/statistics/ 
but would like to have some more details, especially about the

permuation analyses.

2.  Are there command line options (e.g., caret_command) for performing
these statistical tests on metric files?  


Thanks!

Clayton Curtis

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--
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(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] metric file stats

2007-01-11 Thread Donna Dierker

On 01/10/2007 10:45 PM, Clayton Curtis wrote:

Dear Donna,

Thanks for your reply.

The command line options will be really useful for scripting stat 
tests. I'm going to download and install the update asap. My lab uses 
mac osx (intel) and linux platforms. I hope the new versions are 
available for these platforms. Thanks John!


Also, just a quick check with regard to the permutation analysis when 
doing a one-sample t-test. Obviously in this case you cannot permute 
the experimental conditions (because you are testing that t  0). I am 
assuming the spatial positions of the nodes of the surface are 
randomly reordered to compute the permuted distribution. Right? Or is 
there a random sign flipping of the values of the nodes? These are two 
common methods used in permutation tests that I know about. Thank again!
The signs of the metric columns are randomly flipped. This excerpt from 
an old email may help:


Paired t-test and single sample t-test specifications: The single sample 
t-test tests whether the mean of a normal population is different from 
some constant. The paired t-test is a special case of the single sample 
t-test, where you have two matched groups (in this case, two composite 
files, each with the same group of subjects: One for task A, one for 
task B). You subtract the B columns from the A columns to get n 
difference columns. Example:


Composite A:
cope1_prob1_sub1_sess1_L.hdr
cope1_prob1_sub2_sess1_L.hdr
...
cope1_prob1_sub8_sess1_L.hdr

Composite B:
cope1_prob2_sub1_sess1_L.hdr
cope1_prob2_sub2_sess1_L.hdr
...
cope1_prob2_sub8_sess1_L.hdr

Difference:
cope1_prob1_sub1_sess1_L.hdr - cope1_prob2_sub1_sess1_L.hdr
cope1_prob1_sub2_sess1_L.hdr - cope1_prob2_sub2_sess1_L.hdr
...
cope1_prob1_sub8_sess1_L.hdr - cope1_prob2_sub8_sess1_L.hdr

Now you test whether the differences are different from 0.
First, we generate this real t-map:

i = node index
n = number of subjects/columns
T_i = (Mean_diff_i - UserInputConstant)/(sample_std_dev_i/square_root(n))
degrees of freedom = n-1

Computing this t-map is very straightforward, but the multiple 
comparisons / thresholding issues take more work. If we don't rely on 
parametric methods, then we can get around the normality assumption. 
Nichols and Holmes' Primer Paper 
(http://www.fil.ion.ucl.ac.uk/spm/doc/papers/NicholsHolmes.pdf) 
Multi-Subject fMRI: Activation example on page 18 describes a very 
clever nonparametric strategy:


a) Permutation strategy: Now we just have a single composite: The 
difference columns. Since there are no longer two groups, we can't 
exchange labels; instead, we randomly flip the signs of the columns, 
essentially tossing a coin to see whether difference column[k] should 
have its sign flipped. (As Nichols and Holmes say, we make the weak 
assumption that the distribution is symmetric, which won't work for our 
depth data, but is probably entirely appropriate for most fMRI data.) In 
this example, n=8, so we have 2 to the eighth power or 256 ways of 
assigning +1 or -1 to a subject. We multiply column k by -1 or +1 based 
on the current relabeliing, and generate a t-map using the T_i equation 
above. (In general, we would let the user specify the randomization 
iterations, as we do now, but we'd check to make sure the user-input 
iterations doesn't exceed 2 to the nth power; if it does, then Caret 
overrules the user and uses 2 to the nth power, which is an exhaustive 
list of the possible relabelings.)


b) Algorithm:

* We do this for all 256 (min of 2 to the nth power or user input 
iterations) relabelings and save the maximum and minimum t-stat for each 
map.
* We get the value of the 13th largest maximum (256 * .05 =12.8) to find 
our significance threshold.
* We threshold our real difference map at this threshold and find any 
clusters (regardless of surface area). We output the same info (number 
of nodes, corrected surface area, COG-[XYZ], lat-lon, and p-value) as we 
currently do for our Find Significant Cluster feature.


Clayton Curtis

On Jan 10, 2007, at 4:23 PM, Donna Dierker wrote:


Hi Clayton,

1. A reasonable question, but I'm afraid this document is both 
incomplete and obsolete:


http://brainvis.wustl.edu/courses/Caret_5_332_Tutorial_Analysis.doc

For example, Find Significant Clusters is now called Two-Sample 
T-test. But maybe it will still prove helpful. This submenu is one of 
the fastest changing in Caret right now, so it's very much a moving 
target. The two sample t-test is spelled out in the methods of our 
Williams Syndrome (WS) paper:


Van Essen, D.C., Dierker, D., Snyder, A., Raichle, M.E., Reiss, A., 
and Korenberg, J. (2006) Symmetry of cortical folding abnormalities 
in Williams syndrome revealed by surface-based analyses. J. 
Neuroscience 26:5470-5483.

http://brainvis.wustl.edu/resources/WmsJNsci.pdf

It's basically the surface equivalent of the suprathreshold cluster 
test described in Nichols  Holmes primer paper. The interhemispheric 
test also is described in our WS paper

Re: [caret-users] [SPAM] finding a local maximum

2007-01-12 Thread Donna Dierker

Hi Akiko,

Try this: Copy your metric file to a surface_shape file and load it as a 
surface shape. (The formats are identical.)


Then, try Surface: Region of Interest: Surface Shape cluster analysis. 
You'll need to do this for each tail (i.e., once at thresh=3.0 and once 
at thresh=-3, or whatever thresh you specify).


On 01/11/2007 07:42 PM, Akiko Ikkai wrote:

Hello,

I have a question regarding finding a local maximum on a deformed surface.
We projected t-values (.metric, based on one-sample T operations) onto a
deformed veryinflated surface, and set threshold to get nice
visualization of the activations. We are able to guesstimate where the
peak lies by comparing against the color bar, but we would like to know
the exact coordinates of the peak, each cluster separately.   


I was exploring Surface ROI operations that gives the statistical
report on the selected nodes, such as min, max, and rage, but it does
not show the coordinates.

Thanks in advance! 


Akiko Ikkai
PhD Candidate 
Department of Psychology 
New York University 
6 Washington Place New York NY, 10003  



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Re: [caret-users] metric file stats

2007-01-12 Thread Donna Dierker

Hi Adam,

It looks like John Harwell has 12/15/2006 versions of caret_command_exe 
for each platform here:


http://brainvis.wustl.edu/pub/john/
login pub
password download

Once extracted, these go in your caret bin directory.  We usually save 
the old version in case we don't like the new one, but I've been running 
the new one on Linux with no complaints.  My problems are usually of the 
PEBKAC variety (problem exists between keyboard and chair).


On 01/11/2007 08:56 AM, Adam Riggall wrote:

Donna,

I'm in charge of maintaining the systems in Clay's lab, and was 
wondering where I could get a version of Caret that includes the new 
command line stats functions mentioned below.  They will make some of 
the work we are doing right now much easier.  We have a mix of Linux 
machines and Intel Macs in the lab.


Thanks very much,
Adam

Begin forwarded message:

*From: *Clayton Curtis [EMAIL PROTECTED] 
mailto:[EMAIL PROTECTED]

*Date: *January 10, 2007 7:38:51 PM EST
*To: *Adam C. Riggall [EMAIL PROTECTED] 
mailto:[EMAIL PROTECTED]

*Subject: **Fwd: Re: [caret-users] metric file stats*

*From: *Donna Dierker [EMAIL PROTECTED] 
mailto:[EMAIL PROTECTED]

*Date: *January 10, 2007 4:23:59 PM EST
*To: *Caret, SureFit, and SuMS software users 
caret-users@brainvis.wustl.edu mailto:caret-users@brainvis.wustl.edu

*Subject: **Re: [caret-users] metric file stats*
*Reply-To: *Caret, SureFit, and SuMS software users 
caret-users@brainvis.wustl.edu mailto:caret-users@brainvis.wustl.edu



Hi Clayton,

1. A reasonable question, but I'm afraid this document is both 
incomplete and obsolete:


http://brainvis.wustl.edu/courses/Caret_5_332_Tutorial_Analysis.doc

For example, Find Significant Clusters is now called Two-Sample 
T-test. But maybe it will still prove helpful. This submenu is one of 
the fastest changing in Caret right now, so it's very much a moving 
target. The two sample t-test is spelled out in the methods of our 
Williams Syndrome (WS) paper:


Van Essen, D.C., Dierker, D., Snyder, A., Raichle, M.E., Reiss, A., 
and Korenberg, J. (2006) Symmetry of cortical folding abnormalities 
in Williams syndrome revealed by surface-based analyses. J. 
Neuroscience 26:5470-5483.

http://brainvis.wustl.edu/resources/WmsJNsci.pdf

It's basically the surface equivalent of the suprathreshold cluster 
test described in Nichols  Holmes primer paper. The interhemispheric 
test also is described in our WS paper.


If you have questions about other tests, let us know.

2. Thanks to John Harwell, the following tests are available via 
command line:


vp.wustl.edu 22% caret_command -help | grep metric-or-shape-stat

INFO: To see command line options, Run with -help

METRIC/SHAPE STATISTICS COORDINATE DIFFERENCE 
-metric-or-shape-stat-coord-diff
METRIC/SHAPE STATISTICS INTERHEMISPHERIC CLUSTERS 
-metric-or-shape-stat-interhemispheric-clusters
METRIC/SHAPE STATISTICS ONE SAMPLE T-TEST 
-metric-or-shape-stat-one-sample-t-test

METRIC/SHAPE STATISTICS PAIRED T-TEST -metric-or-shape-stat-paired-t-test
METRIC/SHAPE STATISTICS TWO SAMPLE T-TEST and WILCOXON 
-metric-or-shape-stat-two-sample-t-test


But these weren't added until 12/15, so you probably will need to 
download a new version; let us know which platform you use.


On 01/10/2007 12:34 PM, Clayton E Curtis wrote:

Hi,

I have two quick questions. 
1.  What's the best place to get documentation on the new metric/surface

shape statistical operations?  We've looked at the documentation at
http://brainmap.wustl.edu/caret/caret5.5_help/statistics/ but would 
like to have some more details, especially about the

permuation analyses.

2.  Are there command line options (e.g., caret_command) for performing
these statistical tests on metric files?  
Thanks!


Clayton Curtis

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(Formerly Donna Hanlon; no change in marital status -- see 
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http://home.att.net/%7Edonna.hanlon for details.)


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(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] finding a local maximum

2007-01-12 Thread Donna Dierker
I meant type cp my_metric.metric my_metric.surface_shape at the 
command line.


You'll select all nodes, but enter a thresh when you select surface 
shape cluster report.


On 01/12/2007 11:05 AM, Akiko Ikkai wrote:

Hi Donna,

hm... by copy metric file, you mean to save it as a surface_shape
file? When I did that, and re-open it as a surface shape, it showed
options of creating new columns (deformed Depth/ deformed Smoothed
Depth/ deformed Folding (Mean Curvature)/ deformed Gaussian Curvature).
In D/C, I set Secondary Overlay to Shape and chose one of the surface
shapes, but nothing happened. 


Also in Surface  ROI, I could not choose clusters, but one node.
I think the problem is that I'm not copying into the right format.
Could you elaborate on that?

thanks!  


Akiko Ikkai
PhD Candidate 
Department of Psychology 
New York University 
6 Washington Place New York NY, 10003   


- Original Message -
From: Donna Dierker [EMAIL PROTECTED]
Date: Friday, January 12, 2007 9:11 am
Subject: Re: [caret-users] [SPAM]  finding a local maximum

  

Hi Akiko,

Try this: Copy your metric file to a surface_shape file and load it 
as a 
surface shape. (The formats are identical.)


Then, try Surface: Region of Interest: Surface Shape cluster 
analysis. 
You'll need to do this for each tail (i.e., once at thresh=3.0 and 
once 
at thresh=-3, or whatever thresh you specify).


On 01/11/2007 07:42 PM, Akiko Ikkai wrote:


Hello,

I have a question regarding finding a local maximum on a deformed 
  
surface. We projected t-values (.metric, based on one-sample T 
operations) onto a


deformed veryinflated surface, and set threshold to get nice
visualization of the activations. We are able to guesstimate 
  

where the

peak lies by comparing against the color bar, but we would like 
  

to know

the exact coordinates of the peak, each cluster separately.   


I was exploring Surface ROI operations that gives the statistical
report on the selected nodes, such as min, max, and rage, but it 
  

does not show the coordinates.

Thanks in advance! 


Akiko Ikkai
PhD Candidate 
Department of Psychology 
New York University 
6 Washington Place New York NY, 10003  



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(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)


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Re: [caret-users] import and registration questions

2007-01-16 Thread Donna Dierker

Hi Remya,

See inline replies below.

On 01/15/2007 01:36 PM, Remya Nair wrote:

Hi Donna

I am new to Caret, so any help would be greatly appreciated.
There are a number of things that I intend to do.
1. View macaque data sets in Caret. These are in Dicom format and so I 
understand that they cannot be imported to Caret directly. Is that true?
True, I'm afraid. I confess when I've needed to do this I've used 3rd 
party converters (e.g., Freesurfer's mri_convert and AFNI's to3d).
I tried converting my data to Analyze format using rDICOM2ANALYZE 
command and then importing the resulting file in Caret.
I'm not familiar with this command; I'm guessing it's your local 
institution's conversion utility.
This displayed a small image in one corner of the Caret main window 
and not the whole window. What am I doing wrong?
Probably nothing, but the Analyze format typically lacks origin and 
orientation information that Caret needs. You can compensate for this 
using the Volume: Edit Volume Attributes menu. If you don't know your 
actual origin setting, then try using -xdim/2, -ydim/2, -zdim/2. At 
least then, you will probably see something reasonable in the Caret window.
2. Next, I want to register my anatomical to the F6 or F99 atlas. How 
is this done?How do I specify my own Origin when I do this?
One way is to use Caret to segment your anatomical and then use 
spherical registration to deform your macaque's surface to the F99 
atlas. Another way is to use some third party volume registration tool 
(e.g., FSL's flirt) to register your anatomical volume to the atlas volume.


If you haven't already looked at this tutorial, there are sections on 
the new macaque F6 atlas:


CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu/sums/directory.do?id=6585200

Before doing a lot of work, I'd at least scan the tutorial document.


Thanks in advance!

Caret Newbie
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Re: [caret-users] Brodmann areas in transaxial slices

2007-01-22 Thread Donna Dierker

Hi Lena,

I think there may be multiple atlases that serve this purpose, but it 
sounds like you're looking for something more volume than 
surface-based.  You might try the SPM Anatomy toolbox:


http://www.fz-juelich.de/ime/spm_anatomy_toolbox

Dr. Van Essen has the Brodmann areas mapped onto our PALS_B12 
surface-based atlas, but I don't think we have mapped those maps 
projected back to volume-land.  It's not too hard to do so, but first 
see if this Eickhoff data suits your needs.


Donna

On 01/22/2007 05:02 AM, Lena wrote:

Dear Caret users,

I'm looking for an atlas that can show me the location of the various
Brodmann areas in transaxial slices. Is this possible with the Caret
software?

Sincerely,
Lena Edström



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Re: [caret-users] ROI - borders around clusters

2007-01-24 Thread Donna Dierker
The only thing I can think to try is to restart Caret and repeat your 
selection of all nodes within threshold 1.0 to 5.0.  I can see from 
your capture that you did this and your green nodes include clusters for 
which it didn't draw borders.  My only guess is that perhaps somehow the 
create borders is still acting on a previous nodes connected to node 
number 33651 selection, even though this radio button isn't selected 
(and the green nodes show select nodes was pressed with All nodes within 
threshold selected).  Restarting simply removes any previous selections, 
if there is a bug lurking here.


Otherwise, my only other guess is that Caret has a minimum area for 
clusters, before it will generate a border around it, and the smaller 
ones fall below that threshold.  I'm not aware of such a limit.


If you upload your spec file (including coord, topo, and metric), I can 
see if my luck is any better than yours:


http://pulvinar.wustl.edu/cgi-bin/upload.cgi

On 01/24/2007 10:55 AM, Mateus Joffily wrote:

Hi,

I am trying to use 'Surface Region of Interest' to create borders 
around metric clusters. The nodes on the surface are correctly 
selected, but when I select 'Create Borders Around Clusters'  only one 
of the clusters is surrounded by a border. I have tried the same 
operation with other metric columns and the program seems to work 
fine. I don't know why, for this specific metric, some clusters are 
left out.
I am attaching an image of caret windows. Any suggestion is well 
appreciated.


Thanks,
Mateus





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Re: [caret-users] ROI - borders around clusters

2007-01-25 Thread Donna Dierker

Hi Mateus,

I replicated your probelm exactly with the roi.zip archive you 
uploaded.  It contained only the flat coord and cut topo; have you tried 
using the fiducial coord with closed topo?  It may not help, but it's 
worth a try.


Although the clusters using metric2 appear smaller in area than the 
metric1 clusters, the nodes within the metric2 clusters are denser, 
which probably is a factor.  See the attached captures, shows the dense 
metric 2 clusters and the sparser metric 1 clusters, using drawing mode: 
Links (No Backside) on the D/C surface misc menu.  The top two clusters 
are only a single tile wide, so I'm not surprised Caret would have 
trouble drawing a border around them.  The two bottom ones also have 
places where they're only a tile wide, so maybe that's the problem.  If 
so, and switching coord/topo combos fails, then Im not sure what else 
to suggest.


Doing a very small amount of metric smoothing (Average neighbors, 1 
iteration, strength 1.0)  and reducing the threshold a tad would 
probably help (primarily just making the clusters larger), but I'm 
guessing this is something you'd be very hesitant to do.


On 01/25/2007 08:33 AM, Mateus Joffily wrote:

Hi Donna,

I restarted Caret and I created a new Spec file, including only the 
topology, flat coordinates, metric and surface shape files, and the 
problem persists. I did the following tests until now:


1) I tried the same operation, selecting only one of the clusters for 
which the program didn't draw borders before, but the program 
complains No clusters were found.


2) I tried the same operation with another metric that has even 
smaller cluster, and the program draws the borders correctly.


3) I tried some other operations on the selected nodes (e.g. Assign 
metric column to selected nodes, and Statistical report), and the 
program works fine for every cluster. Only 'Create Borders Around 
Clusters' doesn't work.


I uploaded my new Spec file (roi.zip)  with the two metrics included 
('metric1': problematic one; and 'metric2': with smaller clusters that 
works fine). If you have any other idea about what can be the problem...


Thank you very much,
Mateus


Donna Dierker wrote:

The only thing I can think to try is to restart Caret and repeat your 
selection of all nodes within threshold 1.0 to 5.0.  I can see 
from your capture that you did this and your green nodes include 
clusters for which it didn't draw borders.  My only guess is that 
perhaps somehow the create borders is still acting on a previous 
nodes connected to node number 33651 selection, even though this 
radio button isn't selected (and the green nodes show select nodes 
was pressed with All nodes within threshold selected).  Restarting 
simply removes any previous selections, if there is a bug lurking here.


Otherwise, my only other guess is that Caret has a minimum area for 
clusters, before it will generate a border around it, and the smaller 
ones fall below that threshold.  I'm not aware of such a limit.


If you upload your spec file (including coord, topo, and metric), I 
can see if my luck is any better than yours:


http://pulvinar.wustl.edu/cgi-bin/upload.cgi

On 01/24/2007 10:55 AM, Mateus Joffily wrote:


Hi,

I am trying to use 'Surface Region of Interest' to create borders 
around metric clusters. The nodes on the surface are correctly 
selected, but when I select 'Create Borders Around Clusters'  only 
one of the clusters is surrounded by a border. I have tried the same 
operation with other metric columns and the program seems to work 
fine. I don't know why, for this specific metric, some clusters are 
left out.
I am attaching an image of caret windows. Any suggestion is well 
appreciated.


Thanks,
Mateus

 



 



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inline: metric2_small_but_dense.jpginline: metric1_skinny.jpg

Re: [caret-users] ROI - borders around clusters

2007-01-26 Thread Donna Dierker

Hi Mateus,

It's true the top cluster is mostly dense, but look at the node I've 
highlighed in red in the attached capture.  I wonder whether nodes like 
this that cinch the cluster cause the algorithm to give up.


Attached is some code I dug out of the source that might be what Caret 
is actually using.  (John would know for sure.)  Maybe it will prove 
helpful in deciphering what is the bottleneck, so to speak.


On 01/26/2007 07:14 AM, Mateus Joffily wrote:

Hi Donna,

I replicated your probelm exactly with the roi.zip archive you 
uploaded.  It contained only the flat coord and cut topo; have you 
tried using the fiducial coord with closed topo?  It may not help, 
but it's worth a try.


Yes, the problem persists.



Although the clusters using metric2 appear smaller in area than the 
metric1 clusters, the nodes within the metric2 clusters are denser, 
which probably is a factor.  See the attached captures, shows the 
dense metric 2 clusters and the sparser metric 1 clusters, using 
drawing mode: Links (No Backside) on the D/C surface misc menu.  The 
top two clusters are only a single tile wide, so I'm not surprised 
Caret would have trouble drawing a border around them.  The two 
bottom ones also have places where they're only a tile wide, so maybe 
that's the problem.  If so, and switching coord/topo combos fails, 
then Im not sure what else to suggest.


Yes, probably the number of tiles is a limitation for drawing the 
borders. I see that borders are usualy not drawn around single tile 
metrics. However, I have other metrics with denser clusters that it 
doesn't draw the border neither (compare the top cluster (no border)  
with the bottom cluster (cyan border) in the attached capture). May be 
there is some other reason too... I will think a bit more about the 
problem and, if I find something new, I will let you know.


Thanks a lot for your help,
Mateus



Doing a very small amount of metric smoothing (Average neighbors, 1 
iteration, strength 1.0)  and reducing the threshold a tad would 
probably help (primarily just making the clusters larger), but I'm 
guessing this is something you'd be very hesitant to do.


On 01/25/2007 08:33 AM, Mateus Joffily wrote:


Hi Donna,

I restarted Caret and I created a new Spec file, including only the 
topology, flat coordinates, metric and surface shape files, and the 
problem persists. I did the following tests until now:


1) I tried the same operation, selecting only one of the clusters 
for which the program didn't draw borders before, but the program 
complains No clusters were found.


2) I tried the same operation with another metric that has even 
smaller cluster, and the program draws the borders correctly.


3) I tried some other operations on the selected nodes (e.g. Assign 
metric column to selected nodes, and Statistical report), and the 
program works fine for every cluster. Only 'Create Borders Around 
Clusters' doesn't work.


I uploaded my new Spec file (roi.zip)  with the two metrics included 
('metric1': problematic one; and 'metric2': with smaller clusters 
that works fine). If you have any other idea about what can be the 
problem...


Thank you very much,
Mateus


Donna Dierker wrote:

The only thing I can think to try is to restart Caret and repeat 
your selection of all nodes within threshold 1.0 to 5.0.  I can 
see from your capture that you did this and your green nodes 
include clusters for which it didn't draw borders.  My only guess 
is that perhaps somehow the create borders is still acting on a 
previous nodes connected to node number 33651 selection, even 
though this radio button isn't selected (and the green nodes show 
select nodes was pressed with All nodes within threshold 
selected).  Restarting simply removes any previous selections, if 
there is a bug lurking here.


Otherwise, my only other guess is that Caret has a minimum area for 
clusters, before it will generate a border around it, and the 
smaller ones fall below that threshold.  I'm not aware of such a 
limit.


If you upload your spec file (including coord, topo, and metric), I 
can see if my luck is any better than yours:


http://pulvinar.wustl.edu/cgi-bin/upload.cgi

On 01/24/2007 10:55 AM, Mateus Joffily wrote:


Hi,

I am trying to use 'Surface Region of Interest' to create borders 
around metric clusters. The nodes on the surface are correctly 
selected, but when I select 'Create Borders Around Clusters'  only 
one of the clusters is surrounded by a border. I have tried the 
same operation with other metric columns and the program seems to 
work fine. I don't know why, for this specific metric, some 
clusters are left out.
I am attaching an image of caret windows. Any suggestion is well 
appreciated.


Thanks,
Mateus


inline: dense_but_no_border.jpg/*LICENSE_START*/
/*
 *  Copyright 1995-2002 Washington University School of Medicine
 *
 *  http://brainmap.wustl.edu
 *
 *  This file is part of CARET.
 *
 *  CARET is free software; you can

Re: [caret-users] caret question

2007-01-26 Thread Donna Dierker

Hi Gene,

It sounds like you've actually created a new coord file -- an inflated 
version of a the colin SPM2 fiducial.  So if you wanted to use this 
later, you'd need to save it as a separate coord file.  Then you could 
use D/C: Scene to append a scene using this coord file, and then save 
the corresponding scene file.


In practice, unless your sole subject is Colin Holmes, I'd recommend 
using PALS_B12 as a mapping target instead of colin.  And if there's a 
very good reason for sticking with colin, the existing inflated surfaces 
that come with the old colin atlas should work perfectly well as a 
visualization substrate, which is the typical usage for an inflated 
surface; one maps to the fiducial, but visualizes on the inflated.  Did 
you have an alternative application for the inflated surface?


Just as it's possible to map on fiducial, render on inflated, it's 
possible to go the other way.  For example, you can draw borders on the 
existing colin flat or inflated maps; project them; and then save them 
using the SPM2 reference fiducial, if you want your border points in MNI152.


On 01/26/2007 01:52 PM, Eugene Tunik wrote:

Hello,
I'm new to caret. I've created an inflated surface using the
Colin-SPM2-L/R fiducial and would like to save this inflated surface for
future mapping of functionals data.

If I'm correct, it's simply a matter of File - save data file - save as
a scene.

However, when reloading the spec file afterward, I don't see the
inflated scene that I created.

Please help...

Many thanks,
Gene


Eugene Tunik, PhD, PT
Dept. of Physical Therapy, NYU
http://homepages.nyu.edu/~et38/
  




Re: [caret-users] A Question about Spherical Registration

2007-02-21 Thread Donna Dierker

Hi Reza,

The atlas target dataset you used was the right one, but it is a 
stripped down version that minimizes the number of files that get 
deformed from the atlas to the individual's directory.  (Some people 
want to look at the atlas paint or border files on their individual's 
surface, so then you would need to put those files in the atlas target 
directory and add them to your atlas spec file; then, they would 
automatically deform to the individual's directory during registration.)


Since you want to visualize on the atlas target, there's no need to 
re-register; rather, just download one or more of these datasets:


PALS_B12.LEFT.STANDARD-SCENES.73730.spec
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595803

PALS_B12.RIGHT.STANDARD-SCENES.73730.spec
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595827

There are quite a few other options/documents listed here:

CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu/sums/directory.do?id=6585200

You can move your deformed results to the extracted directory, or move 
the extracted files to your atlas target directory -- your choice.  I 
tend to create separate right and left subdirectories under my atlas 
target directory, which has lots of files, but when I run registration I 
use the single parent atlas target directory.


Often, we want to do group analysis of functional (metric) or anatomical 
(surface_shape) data; in these cases, we create composite metric or 
depth files.  This command line utility (caret_command -help-full) can 
be helpful:


 caret_command -metric-or-shape-composite
 caret_command -metric-or-shape-composite-named-column

If you're going to use the tools under Attributes: Metric and Surface 
Shape Statistical Operations, then the spec files above lack the 
distortion metrics and OPEN topo files included in these analysis datasets:


   * Visualization/Analysis spec LEFT: 
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6486316
   * Visualization/Analysis spec RIGHT: 
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6486393


Most of the tests can be run using the caret_command utility.

Donna

On 02/21/2007 01:25 AM, Reza Rajimehr wrote:

Dear caret-users,

I did the spherical registration of an individual human brain to the human
PALS atlas. I used the following dataset as the target atlas brain:

http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499

A new deformed .spec file has been generated. However, it has only one new
surface, which is a deformed sphere. I would like to visualize the
functional activities of the individual brain on the atlas brain (e.g. on
the atlas flat map). Should I download a more elaborate PALS dataset and
add them to the current directory? If so, should I redo the spherical
registration, or the new PALS surfaces (e.g. inflated, flattened, ...)
will be automatically linked to the deformed spherical surface that I
already have?

Thanks,
Reza


Reza Rajimehr, MD

NMR Athinoula A. Martinos Center
Department of Radiology
Massachusetts General Hospital (MGH)
Building 149, 13th St.
Charlestown, MA 02129

Email: [EMAIL PROTECTED]



Re: [caret-users] installation problems

2007-02-23 Thread Donna Dierker

Hi Erik,

When John comes in, he'll probably be more help, but until then here are 
some thoughts:


* On my new 64-bit Linux workstation, find /usr -name libGLU.so.1 
returns this output:


/usr/X11R6/lib/libGLU.so.1
/usr/X11R6/lib64/libGLU.so.1
/usr/lib/libGLU.so.1
/usr/lib64/libGLU.so.1

* The Linux version of Caret is 32-bit, so maybe 64-bit GLU libs (e.g., 
/usr/X11R6/lib64/libGLU.so.1) won't work with Caret.


* If you have a 32-bit GLU lib installed somewhere, try setting your 
LD_LIBRARY_PATH to make sure Caret looks there first.  Example for csh/tcsh:


setenv LD_LIBRARY_PATH /usr/lib32:$LD_LIBRARY_PATH

* Caret runs fine on my 64-bit machine, but ldd output shows it's 
finding a 32-bit GLU lib:


/usr/lib/libGL.so.1.0.8756: ELF 32-bit LSB shared object, Intel 80386, 
version 1 (SYSV), stripped


Donna

On 02/22/2007 05:44 PM, [EMAIL PROTECTED] wrote:

Hello,
I recentrly downloaded Caret5 and followed the installation instructions
carefully. I am using a 64-bit Linux machine (Fedora core), and have
successfully installed many other softwares before.

After installing, I attempt to start caret and it gives me the error:

caret5: error while loading shared libraries: libGLU.so.1: cannot open
shared object file: No such file or directory

Of course, these lib files are there where they are supposed to be. I am
not the only one over here who gets this error, so we thought we would ask
what the problem is and how to get around it.

Thanks,
Erik Edwards
Univ. California Berkeley 
Univ. California San Francisco

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Re: [caret-users] lesions

2007-02-26 Thread Donna Dierker

On 02/23/2007 10:16 PM, Joan Fisher wrote:

Dear Caret users:

I have a group of MRIs of children with unilateral brain injury that I 
would like to get morphometric measurements on.  Specifically, I would 
like to know how the gray and white matter in each hemisphere compare 
overall (for the whole hemisphere) and how they compare for specific 
regions (especially the traditional language areas and the white 
matter tracts feeding these areas).
Can Caret give me estimates of the amount of gray and white matter in 
each hemisphere (and/or for each region) with patients that have brain 
lesions?
Not really.  Caret generates a midthickness or layer 4 segmentation 
-- midway between the gray/white boudary and the GM/CSF boundary.  I 
know of no way to generate GM or WM volumes with Caret/SureFit's default 
outputs.


FreeSurfer generates both boundaries, and it should be possible to get 
volume estimates; I think it even gives you these by default.
Would it be feasible to get this data whether the patient has 
periventricular lesions (that don't affect the cortex) as well as 
patients where the lesions do affect the cortical surface?
There will be issues with the lesions, but I'm under the impression it 
can still be done using FreeSurfer.


With Caret, you can still segment lesioned brains, but you'll probably 
need to do manual patching in the area surrounding the lesion.
Finally, if I were to draw the lesioned area (as I have already done 
in AFNI, for example), would Caret be able to normalize the brains 
around the lesion (according to an atlas or averaged brain)?  Or do 
you have your own way of handling lesioned brains?
A few people here at wustl.edu have segmented and registered lesioned 
brains using Caret/SureFit.  There's no standard recipe, and it's 
lesion-specific.  Some are more troublesome than others.  One idea 
Donald McLaren (now at wisc.edu) had was to draw a border around the 
lesion and use this during registration to contain it.  This seems 
pretty reasonable to me, but you need a semi-principled way to draw the 
corresponding target lesion region on the PALS_B12 target (probably 
using the very inflated surface, but with the average fiducial loaded in 
a window 2 for reference).
I have had a terrible time finding a method to analyze the structural 
MRI information in these brain-lesioned brains, so I would appreciate 
your input on this issue.

You're not alone, if that's any consolation. ;-)


Many thanks,
Joan Fisher
University of Chicago

Donna L. Dierker



Re: [caret-users] Flattening and Spherical Registration of the Monkey Brain

2007-02-26 Thread Donna Dierker

On 02/23/2007 02:05 PM, Reza Rajimehr wrote:

Dear Donna and David,

Thank you for the helpful comments and suggestions. I successfully
finished flattening of an individual human brain and its spherical
registration to the human PALS atlas, and the registration is perfect. Now
I want to start flattening of an individual monkey brain and its spherical
registration to the macaque F99UA1 atlas. Before starting this process, I
just wanted to make sure that I am using the correct (and the most
up-to-date) files. In particular, I would appreciate if you provide me
with the SumsDB links for the following files:

1) Macaque template cuts for flattening (border file and border color file).
  
These files come with the Caret distribution and should load 
automagically when you select Macaque standard cuts left or right:


caret/data_files/flatten_borders/Macaque.TEMPLATE-CUTS.LEFT-HEM.SPHERE.border
caret/data_files/flatten_borders/Macaque.TEMPLATE-CUTS.RIGHT-HEM.SPHERE.border
caret/data_files/flatten_borders/Macaque.TEMPLATE-CUTS.STANDARD.bordercolor

2) Macaque landmarks for registration (border color file and border
projection file).
  
Going to the SumsDB home page (http://sumsdb.wustl.edu/sums/index.jsp) 
and clicking the Macaque left Go to Data directory link, then EXTENDED 
DATA SETS, I see this spec:


Macaque.F99UA1.L.ForREG-with-F99UA1.R.03-03.34132.spec
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6094474

The dataset for the right is less clear; I'll need to do some digging.  
This might be it:


Macaque.F99UA1.R.LOBAR.35946.spec
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6094366


3) F99UA1 atlas for registration (.spec, .deform_map, and sphere.coord
files).
  
See above.  You need to draw the borders for the source (individual) 
macaque, but the atlas target exists somewhere in sumsdb.

4) The complete F99UA1 atlas containing various .coord files (and other
Caret files) for surface visualization.
  
Try the standard scenes and other macaque specs from the Sep 2006 
tutorial (part 3):


CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu/sums/directory.do?id=6585200



and a brief question about flattening: where is the location of temporal
and frontal cuts on the macaque cortex, and how can I draw them? (i.e.
where are the recommended start and end points for these cuts?)
  
I'm not sure.  Unless they're in the landmark border set used during 
registration, it doesn't matter that much.  Not all flattening cuts are 
used during registration (e.g., only calcarine and medial wall are used 
in humans).  In monkeys, there are multiple landmark sets out there, 
with varying numbers of borders.


If they just affect flattening -- not registration -- then drawing a cut 
from the medial wall to the temporal pole will reduce distortion.  For 
the frontal cut, try drawing one from the medial wall along the medial 
orbital gyrus to the frontal pole.

Thanks,
Reza


  

Hi Reza,

The atlas target dataset you used was the right one, but it is a
stripped down version that minimizes the number of files that get
deformed from the atlas to the individual's directory.  (Some people
want to look at the atlas paint or border files on their individual's
surface, so then you would need to put those files in the atlas target
directory and add them to your atlas spec file; then, they would
automatically deform to the individual's directory during registration.)

Since you want to visualize on the atlas target, there's no need to
re-register; rather, just download one or more of these datasets:

PALS_B12.LEFT.STANDARD-SCENES.73730.spec
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595803

PALS_B12.RIGHT.STANDARD-SCENES.73730.spec
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595827

There are quite a few other options/documents listed here:

CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu/sums/directory.do?id=6585200

You can move your deformed results to the extracted directory, or move
the extracted files to your atlas target directory -- your choice.  I
tend to create separate right and left subdirectories under my atlas
target directory, which has lots of files, but when I run registration I
use the single parent atlas target directory.

Often, we want to do group analysis of functional (metric) or anatomical
(surface_shape) data; in these cases, we create composite metric or
depth files.  This command line utility (caret_command -help-full) can
be helpful:

  caret_command -metric-or-shape-composite
  caret_command -metric-or-shape-composite-named-column

If you're going to use the tools under Attributes: Metric and Surface
Shape Statistical Operations, then the spec files above lack the
distortion metrics and OPEN topo files included in these analysis
datasets:

* Visualization/Analysis spec LEFT:
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6486316
* Visualization/Analysis spec RIGHT:
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6486393

Most of the 

Re: [caret-users] A Problem with .borderproj files

2007-03-02 Thread Donna Dierker

Reza,

The only thing I'd add to John's advice is that the text editor part is 
for identifying which borders are dups -- not for deleting them.  You 
can delete them from the border file, but then you'll need to tweak 
other lines.  For example, the number of borders is in a line by itself 
right after the EndHeader line.  If you don't delete from the end, then 
you'll need to reindex the border numbers.  Typically, if you use the 
text editor to find the dup borders, it's easier to then use Layers: 
Borders: Delete border with mouse to delete the top one.


Problems like this can occur when borderproj files mistakenly get loaded 
twice.  For example, say you somehow have a borderproj loaded with just 
the medial wall and calcarine borders.  Then if you append a borderproj 
file that also includes those landmarks, now you have dup borders.  This 
is where the Append and Replace buttons are important when loading 
borderproj files.


Donna

On 03/01/2007 04:44 PM, John Harwell wrote:

Reza,

Since it states that there are 16 border with 14 border names, that 
seems to indicate that there are multiple borders with the same name.  
You can correct this by loading the border projection file into a text 
editor, finding the duplicate borders, and deleting them duplicate 
that you do not need.  It may require trial and error to determine 
which of the duplicate borders to delete so be sure to back up your 
file before editing it.


Good Luck.

--
John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.Box 8108
St. Louis, MO 63110   USA

On Mar 1, 2007, at 4:22 PM, Reza Rajimehr wrote:


Hi caret-users,

I am doing a spherical registration of the individual monkey brain to 
the
F99UA1 atlas, and I am experiencing a problem. I drew 14 landmarks on 
the
individual flat coord, did border projection, and saved it as a 
borderproj
file. When checking the borderproj file by ? in the individual spec 
file,

it confirms that it has 14 borders, and there are 14 border names. I
selected the same landmarks on the atlas flat coord, deleted the rest of
the borders, did border projection, and saved it as a borderproj file.
When checking the borderproj file by ? in the atlas spec file, it says
that there are 16 borders. However, there are only 14 border names in 
the

? box. It seems that there are 2 additional landmarks on the atlas brain
that are not visible to me in the Caret window and have no name. I 
get an
error when doing the deformation, complaining that the number of 
landmarks

in the individual and atlas brains are different.

Thanks for any help,

Best,
Reza


Reza Rajimehr, MD

NMR Athinoula A. Martinos Center
Department of Radiology
Massachusetts General Hospital (MGH)
Building 149, 13th St.
Charlestown, MA 02129

Email: [EMAIL PROTECTED]

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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] Map SPM volume

2007-03-07 Thread Donna Dierker

Hi Julian,

When mapping to atlas, are you selecting a spec file created from this 
dataset:


CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu/sums/directory.do?id=6585200

... using steps as described in Section 5.1 of this tutorial:

Caret_Tutorial_Oct06.pdf
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379

It's tough to see how you could get this error under those 
circumstances, since the files in that spec file (or derivative thereof) 
all have the same 73730 standard mesh.


While this spec won't have a pial surface, it will have left and right 
versions of the following configurations:


PALS_B12 average fiducial
inflated
very inflated
flat

Since you're using SPM2, I'd suggest replacing the average fiducial 
coord files with these files:


Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord
Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord

To do so, after opening 
Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec, select File: 
Open Data File: and select 
Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord.  Repeat 
for Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord.  
Then, select Toolbar: Spec and use the X buttons to delete these 
versions, which are similar but not as optimal as the SPM2 versions in 
your case:


Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord
Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord

Both the SPM2 and FLIRT versions are in mni152 space, but the 
contributing PALS_B12 anatomicals were normalized using SPM2 for the 
SPM2 versions, while FSL's flirt (affine only) was used to normalize the 
FLIRT versions.


Donna

On 03/07/2007 08:33 AM, Julianm Macoveanu wrote:


Hi guys,

I need some help with basic stuff. I just want to use Caret to 
visualize my SPM2 activations on inflated/Fiducial surfaces. So I have 
the normalized volume file to start with.


 

I have opened a spec file from the Caret tutorial, use the map volume 
to surface function, choose my volume, then Map to spec file with 
atlas (and without). I have also tried not to open any spec file to 
begin with, and then just open the one I chose as output during the 
mapping procedure


 

As space I tried the SPM2, as this is the kind of volume I have (but 
also 711-sc).


 

After the metric file is generated, I just try to open it, but I get 
the error that my metric file contains different number of nodes.


 

What I would like to have is a spec file that have all different 
surfaces (including pial and multi-fiducial which I could not find in 
any examples of spec files) and then just create metric files from my 
SPM volumes in order to visualize the activations.


 


Cheers,

Julian

 





Re: [caret-users] Map SPM volume

2007-03-07 Thread Donna Dierker

On 03/07/2007 10:27 AM, Julianm Macoveanu wrote:

Yes, I use the CARET_TUTORIAL_SEPT06/MAPPNING_PROCEDURES files, and load the
Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec file.

I think I got the hang of it. The break through was, after creating the
metric file load one of the predefined scenes before trying to open my
metric file. In this way it didn't complain anymore about different number
of nodes.

If I understand it right if I want now to see the activation on a pial
surface I should just open the coord file and add it to my template spec
file. Do you know where I could find this? I think it should also be
something between pial and fiducial.
  
The PALS_B12 atlas (and the colin atlas before it) has no pial 
surfaces.  One can generate pseudo-pial surfaces by using Surface: 
Geometry: Expand or Shrink surface to expand a fiducial surface, but 
I've never tried this with an average fiducial surface, and I don't 
really recommend it.  We prefer the inflated surface for visualization, 
unless you have activity in the operculum or insula that is difficult to 
see; in such cases, we then use the Very Inflated surface.  Activity in 
buried sulci isn't visible when viewed on a pial or a regular fiducial 
(less so with an average fiducial).


I realize some people still prefer looking at a highly structured pial 
surface, but considering this is group data you're mapping, the 
structure of any one individual is not really representative of the 
group structure of your subjects.  We believe mapping to PALS_B12 and 
viewing the results on the inflated surface is a more faithful 
representation of your results than viewing them on, say, colin27's pial 
surface.  Slowly, we're hoping to win you over. ;-)



Also, L and R are overlaid wrong, what SPM reports as left, I see it on the
right hemisphere in Caret. How can this be changed?
  
Use File: Open Data File: volume functional file and check the Volume is 
an SPM2 Volume with Right on Left checkbox.

Thanks,
Julian

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Wednesday, March 07, 2007 4:05 PM
To: Caret, SureFit, and SuMS software users
Subject: [BULK] Re: [caret-users] Map SPM volume
Importance: Low

Hi Julian,

When mapping to atlas, are you selecting a spec file created from this 
dataset:


CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu/sums/directory.do?id=6585200

... using steps as described in Section 5.1 of this tutorial:

Caret_Tutorial_Oct06.pdf
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379

It's tough to see how you could get this error under those 
circumstances, since the files in that spec file (or derivative thereof) 
all have the same 73730 standard mesh.


While this spec won't have a pial surface, it will have left and right 
versions of the following configurations:


PALS_B12 average fiducial
inflated
very inflated
flat

Since you're using SPM2, I'd suggest replacing the average fiducial 
coord files with these files:


Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord
Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord

To do so, after opening 
Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec, select File: 
Open Data File: and select 
Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord.  Repeat 
for Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord.  
Then, select Toolbar: Spec and use the X buttons to delete these 
versions, which are similar but not as optimal as the SPM2 versions in 
your case:


Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord
Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord

Both the SPM2 and FLIRT versions are in mni152 space, but the 
contributing PALS_B12 anatomicals were normalized using SPM2 for the 
SPM2 versions, while FSL's flirt (affine only) was used to normalize the 
FLIRT versions.


Donna

On 03/07/2007 08:33 AM, Julianm Macoveanu wrote:
  

Hi guys,

I need some help with basic stuff. I just want to use Caret to 
visualize my SPM2 activations on inflated/Fiducial surfaces. So I have 
the normalized volume file to start with.


 

I have opened a spec file from the Caret tutorial, use the map volume 
to surface function, choose my volume, then Map to spec file with 
atlas (and without). I have also tried not to open any spec file to 
begin with, and then just open the one I chose as output during the 
mapping procedure


 

As space I tried the SPM2, as this is the kind of volume I have (but 
also 711-sc).


 

After the metric file is generated, I just try to open it, but I get 
the error that my metric file contains different number of nodes.


 

What I would like to have is a spec file that have all different 
surfaces (including pial and multi-fiducial which I could not find in 
any examples of spec files) and then just create metric files from my 
SPM volumes in order to visualize the activations.


 


Cheers,

Julian

Re: [BULK] Re: [caret-users] Map SPM volume

2007-03-08 Thread Donna Dierker
 hem is in a different window. (For more details, take the full 
September 2006 tutorial 
http://sumsdb.wustl.edu/sums/directory.do?id=6585200.) I don't know of 
any plans to un-split the hemispheres (i.e., combine them into a 
single coord file). David seems to think of the hemispheres as mostly 
independent entities.


I'm sure you are not alone in your questions/concerns.

Donna

On 03/07/2007 04:39 PM, [EMAIL PROTECTED] wrote:

Thanks Donna, everything seems to work now, so I’m happy :)

About the surfaces, I saw something in the archive, is it a white brain,
or deflated pial:
http://sumsdb.wustl.edu:8081/sums/search.do?category_id=6
and then click the first option with a brain icon on it that is possible
to view in the web browser.

There are 12 versions of each hemisphere so I presume that it is an
individual brain. Do you think is ok to use one of them, or do you happen
to have an average surface?

I think you are right, inflated brains may be best suited for visualizing
purposes, however, just in case some stubborn SPM guy would like once in a
while see he’s activation the way he is used to….
I think Freesurfer has a pial surface. Maybe it works to import that somehow?

Also, it would be nice to have the option to see the whole brain at once
(the non-split way) even inflated, but I guess that’s not yet possible….

Cheers,
Julian


  

On 03/07/2007 10:27 AM, Julianm Macoveanu wrote:


Yes, I use the CARET_TUTORIAL_SEPT06/MAPPNING_PROCEDURES files, and load
the
Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec file.

I think I got the hang of it. The break through was, after creating the
metric file load one of the predefined scenes before trying to open my
metric file. In this way it didn't complain anymore about different
number
of nodes.

If I understand it right if I want now to see the activation on a pial
surface I should just open the coord file and add it to my template spec
file. Do you know where I could find this? I think it should also be
something between pial and fiducial.

  

The PALS_B12 atlas (and the colin atlas before it) has no pial
surfaces.  One can generate pseudo-pial surfaces by using Surface:
Geometry: Expand or Shrink surface to expand a fiducial surface, but
I've never tried this with an average fiducial surface, and I don't
really recommend it.  We prefer the inflated surface for visualization,
unless you have activity in the operculum or insula that is difficult to
see; in such cases, we then use the Very Inflated surface.  Activity in
buried sulci isn't visible when viewed on a pial or a regular fiducial
(less so with an average fiducial).

I realize some people still prefer looking at a highly structured pial
surface, but considering this is group data you're mapping, the
structure of any one individual is not really representative of the
group structure of your subjects.  We believe mapping to PALS_B12 and
viewing the results on the inflated surface is a more faithful
representation of your results than viewing them on, say, colin27's pial
surface.  Slowly, we're hoping to win you over. ;-)



Also, L and R are overlaid wrong, what SPM reports as left, I see it on
the
right hemisphere in Caret. How can this be changed?

  

Use File: Open Data File: volume functional file and check the Volume is
an SPM2 Volume with Right on Left checkbox.


Thanks,
Julian

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna
Dierker
Sent: Wednesday, March 07, 2007 4:05 PM
To: Caret, SureFit, and SuMS software users
Subject: [BULK] Re: [caret-users] Map SPM volume
Importance: Low

Hi Julian,

When mapping to atlas, are you selecting a spec file created from this
dataset:

CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu/sums/directory.do?id=6585200

... using steps as described in Section 5.1 of this tutorial:

Caret_Tutorial_Oct06.pdf
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379

It's tough to see how you could get this error under those
circumstances, since the files in that spec file (or derivative thereof)
all have the same 73730 standard mesh.

While this spec won't have a pial surface, it will have left and right
versions of the following configurations:

PALS_B12 average fiducial
inflated
very inflated
flat

Since you're using SPM2, I'd suggest replacing the average fiducial
coord files with these files:

Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord
Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord

To do so, after opening
Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec, select File:
Open Data File: and select
Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord.  Repeat
for Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord.
Then, select Toolbar: Spec and use the X buttons to delete these
versions, which are similar but not as optimal as the SPM2 versions in
your case:

Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord

Re: [caret-users] resizeunderlayvolume

2007-03-09 Thread Donna Dierker

Hi Florian,

To my surprise, no -- I don't think there is.  Seems like a useful 
option, but currently John is working on other things.


You might download AFNI (http://afni.nimh.nih.gov/afni) and try 
3dZeropad.  Even if you don't use AFNI for analysis, it has some really 
handy command line utilities.


Donna

On 03/09/2007 04:20 AM, Florian Gerstl wrote:

Dear Caret-Users,
I'm trying to find something equal to the resize underlay volume menu
in  caret_command ..
I'm trying to automatically segment a bunch of occipital lobes and just
masking out the non-occipital areas wouldn't work...

Is there a caret_command spell for resizing the anatomy volume?

thanks, florian
  




Re: [caret-users] Registering Individual Macaque to F99 template

2007-03-12 Thread Donna Dierker

See inline replies below (both in Donald's and Hamied's messages).

On 03/12/2007 12:00 PM, DG MCLAREN wrote:
Sterling Johnson's lab here at UW-Madison is working on creating a group averaged macaque atlas for volume registration. However, we aren't quite ready to make them public as there are a few bugs still being worked out. We have been using SPM to coregister T2W and T1W images. I'd assume FSL-FLIRT would have similar results. 


The best approach might be as follows:
1) Register T2W to T1W
2) Register T1W to F99 (downloadable from SUMS); if you need .img format there 
are many tools available to convert HEAD/BRIK to hdr/img. I believe you can 
load them in CARET and save them as an img file, although I might be wrong.
  
Yes, you can save them as SPM/MedX (which is really Analyze) in Caret, 
or use AFNI's 3dANALYZEtoAFNI or FSL's afni2avw to convert 
Macaque.F99UA1.LR.03-11+orig.HEAD to Analyze.

3) Multiple the 2 transforms to get the T2W to F99 brain; Apply the transform 
using FSL.
  

FSL's ConcatXFM and ApplyXFM will be useful for these purposes.

Hope this helps.

Best Regards, Donald McLaren

- Original Message -
From: Hamied Haroon [EMAIL PROTECTED]
Date: Monday, March 12, 2007 10:31 am
Subject: [caret-users] Registering Individual Macaque to F99 template
To: caret-users@brainvis.wustl.edu

  

Hello,

I'm a completely fresh novice learning how to use Caret 5.5.

I was wondering if anyone could give me some advice on the following,
please...

I have a single whole-brain T2-weighted structural MRI dataset acquired
in a post-mortem macaque brain. My dataset is in Analyze format.

At first, I thought you wanted to used surface-based registration to 
register your monkey to F99, but creating a surface reconstruction 
(segmentation) from a post-mortem T2 scan would be quite challenging in 
Caret.


After refreshing my memory of the tutorial, I now am guessing you want 
to use volume-based registration to get your T2 aligned with 
Macaque.F99UA1.BOTH.LewisVE00+orig.HEAD, the volumetric replresentation 
of the LVE00 parcellation scheme.  It's not probabilistic, but it's a 
reasonable goal.

How can I register/deform my individual macaque dataset to the F99
dataset so that I can then parcellate the temporal lobe according to the
probabilistic atlases available in CARET_TUTORIAL_SEPT06\MACAQUE?

 


If I should use FLIRT in FSL to do the registration then

how can I get the F99 dataset in Analyze-format to do the registration,
and


See above: Save in Caret or use AFNI's 3dANALYZEtoAFNI or FSL's afni2avw.

what options are suggested to be chosen in FLIRT to get the best
registration results?

The FSL flirt page (http://www.fmrib.ox.ac.uk/analysis/research/flirt) 
advertises inter-modal registration, so it's worth a shot.  This is 
something I've never done, so I'm afraid I can't help you here.  The 
output of flirt -help didn't mention mode-specific inputs/outputs, so I 
think I'd just try it and hope for the best.  Check your results using 
fslview, Caret, or AFNI.
 


I look forward to receiving your kind advice.

 


Thanking you in anticipation.

 


Hamied

 




 


 Hamied Ahmad Haroon   PhD  AMInstP

 Research Associate in MR Neuroimaging

 Division of Imaging Science and Biomedical Engineering

 Faculty of Medical and Human Sciences

 The University of Manchester

 Room G.603 Stopford Building, Oxford Road,

 Manchester   M13 9PT

 England, United Kingdom

 Tel: +44 (0)161 275 6871   Fax: +44 (0)161 275 5145



 

 

 


___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users


___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users

  



--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] the name

2007-03-13 Thread Donna Dierker

Hi Ervin,

I think the confusion stemmed from receiving a caret-users mailing list 
confirmation with a more personalized login and password around the same 
time you receive the download information.  To download Caret, use this 
access information:



To obtain the Caret software, use this login ID and password
 login: Rabbit
 password: Carrot

Donna

The Caret software can be downloaded from 
http://brainmap.wustl.edu/caret#DownloadCaret;.


On 03/13/2007 08:01 AM, Ervin Berényi wrote:

What is my name?
 
The password is correct.
 
I can't login to the downloading area.
 
Ervin Berényi






Re: [caret-users] About Monkey to Human Deformation

2007-03-14 Thread Donna Dierker

Hi Reza,

Hmmm.  I can almost replicate this behavior.  When I load 
CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN/RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-LDMK-VE.73730.spec.deform_map, 
both the individual and atlas directory buttons are disabled, but Data 
File and Deformed File... are both enabled (see attached capture).  I 
thought perhaps this might be because the deform_map was read-only, but 
I get the same behavior with a copy that is writeable.  Normally, one 
can change the individual and atlas directories, as one must do when 
using a deform_map from one of our datasets (unless you're David Van 
Essen, in which case the paths work fine).


Using the Data File button, I could navigate to an input metric and 
successfully deform the data file.  But if your buttons are disabled, 
then you might try using the following two caret commands to get the job 
done:


  DEFORMATION MAP FILE SOURCE/TARGET PATH UPDATE
 caret_command -def-map-path \
deformation-map-file source-path target-path

  SURFACE APPLY DEFORMATION MAP
 caret_command -surface-deformation-apply \
deformation-map-file file-type \
input-file  output-file \
[source-topo-file]  [source-deformed-topo-file] \
[atlas-topo-file]
   
 Deform a data file.


 Note: source-topo-file, source-deformed-topo-file and
 atlas-topo-file are only required when deforming
 coordinate files.

 file-type is one of:
AREAL_ESTIMATION
BORDER_FLAT
BORDER_PROJECTION
BORDER_SPHERICAL
CELL
CELL_PROJECTION
COORDINATE
COORDINATE_FLAT
FOCI
FOCI_PROJECTION
LAT_LON
METRIC
PAINT
PROB_ATLAS
RGB_PAINT
SURFACE_SHAPE
TOPOGRAPHY

Donna

On 03/14/2007 03:11 AM, Reza Rajimehr wrote:

Dear David,

In the Apply Deformation Map dialog box, I specified the following items:

1) Deformation Map File: the 23-LDMK deform_map file
2) File Type: Metric
3) Flat Max Edge Length: 10.00
4) Metric Deformation: Nearest Node (not sure which one is better?)
5) Smooth One Iteration (Except Flat)

The other buttons were not clickable (the dialog box does not allow me to
use them).

When I click the Apply button, I immediately receive the following error
message:

Deform Error
Is deformation map file valid? You must select a data file for
deformation. You must select the output name for the deformed file.

I tried to apply deformation map from two different .spec files:

1) Macaque F99 atlas directory, which has deformed metric files (from
individual macaque to F99). I added/appended the .deform_map file to this
.spec file before applying deformation.

2) COMPARE_MACAQUE_HUMAN directory (as a part of CARET_TUTORIAL_SEPT06
directory). I added/appended my metric files to this .spec file before
applying deformation.

In both cases, I got the same error.


Thanks for your helpful comments/suggestions,

Reza


  

Reza,

On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote:



Dear caret-users,

David Van Essen suggested me to use the following .deform_map file for
deformation of macaque F99 to Human PALS:

RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-
LDMK-VE.73730.spec.deform_map
  

Once you have a deform_map file, you can use it to register data
sets  from monkey to human WITHOUT re-running a registration.  This
is done using the Surface: Deformation: Apply Deformation Map
option.  If you want to register paint files, metric files, and most
other files, you don't need anything other than the deform_map file
to get the job done, and the dialog window is fairly self-
explanatory.  If you want to register a border projection file or a
coordinate file, then you need additional coordinate and topology
files that are available as part of the Caret Sept_06 tutorial dataset:
http://sumsdb.wustl.edu/sums/archivelist.do?
archive_id=6595051archive_name=COMPARE_PALS_MacaqueF99.73730.spec

The only reason to actually re-run an interspecies registration is IF
you don't like the particular set of landmarks used and you want to
try your own.  If so, you should start with borderproj files also in:
http://sumsdb.wustl.edu/sums/archivelist.do?
archive_id=6595051archive_name=COMPARE_PALS_MacaqueF99.73730.spec
and make your additions and subtractions from there.

See Part 4 of the latest Caret tutorial for more details on monkey-
human comparisons.
http://sumsdb.wustl.edu/sums/directory.do?
id=6585200dir_name=CARET_TUTORIAL_SEPT-06



I specified this as my .deform_map file in the Spherical Parameters
tab in
the Spherical Surface Deformation dialog box. My question is what I
should
specify as .borderproj file. I have a borderproj file in my F99
directory
(that I used for the registration of individual macaque to F99). I
also
have a borderproj file in my PALS directory (that I used for the
registration of individual human to PALS). Should I use these
borderproj

Re: [caret-users] Announcement: open access MR data (OASIS)

2007-03-14 Thread Donna Dierker
In case it becomes useful to anyone, these 12 OASIS subjects comprise 
the PALS_B12:


OAS1_0006_MR1 Human_Buckner_Case06
OAS1_0009_MR1 Human_Buckner_Case04
OAS1_0054_MR1 Human_Buckner_Case01
OAS1_0061_MR1 Human_Buckner_Case11
OAS1_0111_MR1 Human_Buckner_Case07
OAS1_0152_MR1 Human_Buckner_Case05
OAS1_0163_MR1 Human_Buckner_Case03
OAS1_0350_MR1 Human_Buckner_Case08
OAS1_0361_MR1 Human_Buckner_Case10
OAS1_0368_MR2 Human_Buckner_Case12
OAS1_0448_MR1 Human_Buckner_Case02
OAS1_0450_MR1 Human_Buckner_Case09

Donna Dierker
http://brainmap.wustl.edu/

On 03/14/2007 12:37 PM, Daniel Marcus wrote:


Dear Colleagues,

The Open Access Series of Imaging Studies (OASIS) is now available at 
www.oasis-brains.org http://www.oasis-brains.org/. The data are 
publicly available under to a liberal Data Use Agreement available 
here: http://www.oasis-brains.org/app/template/UsageAgreement.vm. The 
first data set includes structural MR obtained from 416 subjects aged 
18 to 96, including 100 subjects diagnosed with very mild to moderate 
Alzheimer’s Disease. A longitudinal data set will be released in the 
coming months. A manuscript describing the project is currently in 
press at Journal of Cognitive Neuroscience. For more information, 
please visit the website.


Regards,

Dan Marcus

[EMAIL PROTECTED]

Neuroinformatics Research Group

Washington University School of Medicine

http://nrg.wustl.edu http://nrg.wustl.edu/





Re: [caret-users] Monkey Atlas and stereotaxic

2007-03-14 Thread Donna Dierker

Hi Remya,

Glad to hear you got your hands on a T1 scan.

There's no documentation I know of that covers what you want to do, but 
it's not that hard (if I understand it correctly).


I think you'll just need two versions of your volumes (one AC-centered, 
one inter-aural) and two versions of your fiducial surface (ditto).  
You'll need the AC-centered volume to create your fiducial surface, 
which also will be AC-centered.  When you're happy with your AC-centered 
surface, then translate both volume and surface back to inter-aural.


The hard part is calculating the x,y,z translation offsets between the 
AC-centered origin and your inter-aural origin.  Sometimes it takes a 
sign flip or two to get it right, but only you can compute the magnitude 
of these shifts.  I'll call them shiftx, shifty, shiftz.


Change your volume back to inter-aural like so:

Volume: Edit volume attributes: coordinates: origin: Adjust x,y,z by 
shiftx,shifty,shiftz.  After applying change, hit toolbar: R (with 
volume view in main window) to reset the volume to the new origin, to 
make sure it's correct.  This may take trial and error to get the sign 
right.


Once the volume view accurately reflects the inter-aural origin, save 
the translated volume: File: Save Data File: volume files: NIFTI (or 
AFNI or SPM/MedX, which is basically Analyze): my_interaural.nii


Now, translate your surface:

* switch to fiducial view in main window
* Window: Transformation matrix editor
* Translate: enter shiftx, shifty, shiftz (again -- sign-flipping as needed)
* Apply matrix to main window

In this case, if you get it wrong, then you'll need to use Toolbar: spec 
to reload the fiducial after each trial, to get back to the original AC 
origin.


Once you get it right, use File: Save data file: coord file to save the 
translated coord file as a name like my.fiducial.inter-aural.coord.


Good luck.

Donna

On 03/14/2007 02:44 PM, Remya Nair wrote:

Hi Caret-Gods...!

I have a question regarding Caret and monkey atlas. I apologize for 
the basic nature of these questions, but I am a newbie to Caret and 
that is all i have to say in my defense!!!
We have T1 weighted 0.5 isotropic resolution anatomical images of 
monkey brain. The final aim is to be able to reconstruct surfaces as 
well as find the co-ordinates of points of interest w.r.t our 
stereotaxic coord system. We are working with the inter-aural 
stereotaxic system.
Ideally, apart from viewing the surface , we will need stereotaxic 
coordinates to know exactly where the AP0 is, mediolateral coordinates 
etc.
I have ,as per the Caret segmentation tutorial, segmented the volume 
and created the surfaces. But, the way i have done it, the volume has 
been centered at the AC (as per the tutorial instructions). What 
should I do to center it to the inter-aural origin? is there any caret 
documentation on this... if yes, could you please point me to them? 
Consequently what would be the next steps I should perform (perhaps 
registration?) to be able to read off the stereo-coords of interest as 
per my coordinate system? Please do point me to the appropriate 
tutorials/spec files that i may need.


Thanks in advance!!

RN




Re: [caret-users] About Monkey to Human Deformation

2007-03-14 Thread Donna Dierker

Hi Reza,

See inline reply below.

Donna

On 03/14/2007 03:40 PM, Reza Rajimehr wrote:

Hi Donna,

The Data File button is disabled in my Caret, so I think I have to use the
caret commands. Just a question: what are source and target paths in
the first caret command. I assume that the source path is a monkey
(macaque F99) directory, which has the input metric file, and the target
path is a human PALS directory. Is this correct?
  
Correct, but in this case, I'm wondering whether you can set both source 
and target directories to CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN 
and simply use the deform_map in that directory.


This directory contains some, but not all of the source and target files 
cited in the deform_map file.

I have already added the .deform_map file to the directory, which has the
input metric file.
  
This is not normally necessary.  Typically, the file you want to deform 
is in the source directory, while the deform_map you use is in the 
target (atlas) directory.  The output file (usually the same as the 
input file with deformed_ prepended) usually is written to the atlas 
target directory.


But in your case, setting both source and target directories to the 
absolute path of your CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN 
directory may work.  Then you could navigate to your data file as 
needed, and let Caret write your deformed data file to your 
CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN directory.

Thanks for your help,
Reza


  

Hi Reza,

Hmmm.  I can almost replicate this behavior.  When I load
CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN/RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-LDMK-VE.73730.spec.deform_map,
both the individual and atlas directory buttons are disabled, but Data
File and Deformed File... are both enabled (see attached capture).  I
thought perhaps this might be because the deform_map was read-only, but
I get the same behavior with a copy that is writeable.  Normally, one
can change the individual and atlas directories, as one must do when
using a deform_map from one of our datasets (unless you're David Van
Essen, in which case the paths work fine).

Using the Data File button, I could navigate to an input metric and
successfully deform the data file.  But if your buttons are disabled,
then you might try using the following two caret commands to get the job
done:

   DEFORMATION MAP FILE SOURCE/TARGET PATH UPDATE
  caret_command -def-map-path \
 deformation-map-file source-path target-path

   SURFACE APPLY DEFORMATION MAP
  caret_command -surface-deformation-apply \
 deformation-map-file file-type \
 input-file  output-file \
 [source-topo-file]  [source-deformed-topo-file] \
 [atlas-topo-file]

  Deform a data file.

  Note: source-topo-file, source-deformed-topo-file and
  atlas-topo-file are only required when deforming
  coordinate files.

  file-type is one of:
 AREAL_ESTIMATION
 BORDER_FLAT
 BORDER_PROJECTION
 BORDER_SPHERICAL
 CELL
 CELL_PROJECTION
 COORDINATE
 COORDINATE_FLAT
 FOCI
 FOCI_PROJECTION
 LAT_LON
 METRIC
 PAINT
 PROB_ATLAS
 RGB_PAINT
 SURFACE_SHAPE
 TOPOGRAPHY

Donna

On 03/14/2007 03:11 AM, Reza Rajimehr wrote:


Dear David,

In the Apply Deformation Map dialog box, I specified the following
items:

1) Deformation Map File: the 23-LDMK deform_map file
2) File Type: Metric
3) Flat Max Edge Length: 10.00
4) Metric Deformation: Nearest Node (not sure which one is better?)
5) Smooth One Iteration (Except Flat)

The other buttons were not clickable (the dialog box does not allow me
to
use them).

When I click the Apply button, I immediately receive the following
error
message:

Deform Error
Is deformation map file valid? You must select a data file for
deformation. You must select the output name for the deformed file.

I tried to apply deformation map from two different .spec files:

1) Macaque F99 atlas directory, which has deformed metric files (from
individual macaque to F99). I added/appended the .deform_map file to
this
.spec file before applying deformation.

2) COMPARE_MACAQUE_HUMAN directory (as a part of CARET_TUTORIAL_SEPT06
directory). I added/appended my metric files to this .spec file before
applying deformation.

In both cases, I got the same error.


Thanks for your helpful comments/suggestions,

Reza



  

Reza,

On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote:




Dear caret-users,

David Van Essen suggested me to use the following .deform_map file for
deformation of macaque F99 to Human PALS:

RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-
LDMK-VE.73730.spec.deform_map

  

Once you have a deform_map file, you can use it to register data
sets  from monkey to human WITHOUT re-running a registration.  This
is done using the Surface: Deformation: Apply 

Re: [caret-users] Surface Flattening

2007-03-19 Thread Donna Dierker

Hi Rishi,

You can safely ignore this warning.  You only need the area color if you 
actually want to view the paint file.  In your case, you're just 
humoring the flattening algorithm.  But if you want to view the paint 
file, a generic area color file is attached.


Donna

On 03/19/2007 09:51 AM, Rishi Kalwani wrote:

hi,
i'm about the flatten my macaque's right hemisphere surfaceand it 
says that i need to have my paint file loaded in my spec filewhen 
i load the paint file, it says that i also need to have an area color 
file loaded, but i don't have an area color file...is this a 
critical file that is necessary for surface flattening?if so, is there 
a way to generate an area color file?  thanks

rishi



?xml version=1.0 encoding=UTF-8?
Area_Color_File
   FileHeader
  Element
 Name![CDATA[caret-version]]/Name
 Value![CDATA[5.501]]/Value
  /Element
  Element
 Name![CDATA[date]]/Name
 Value![CDATA[Tue Dec 12 16:25:19 2006]]/Value
  /Element
  Element
 Name![CDATA[encoding]]/Name
 Value![CDATA[XML]]/Value
  /Element
   /FileHeader
   Color
  name![CDATA[???]]/name
  red170/red
  green170/green
  blue170/blue
  alpha255/alpha
  pointSize2.00/pointSize
  lineSize1.00/lineSize
  symbol![CDATA[POINT]]/symbol
   /Color
   Color
  name![CDATA[GYRAL]]/name
  red170/red
  green170/green
  blue170/blue
  alpha1/alpha
  pointSize2.00/pointSize
  lineSize1.00/lineSize
  symbol![CDATA[POINT]]/symbol
   /Color
   Color
  name![CDATA[MEDIAL.WALL]]/name
  red255/red
  green0/green
  blue0/blue
  alpha1/alpha
  pointSize2.00/pointSize
  lineSize1.00/lineSize
  symbol![CDATA[POINT]]/symbol
   /Color
/Area_Color_File


Re: [caret-users] Identifying Medial Wall for Flattening

2007-03-21 Thread Donna Dierker

On 03/21/2007 08:08 AM, Rishi Kalwani wrote:

hi,

after flattening i get a compressed medial wall surface with an 
orange border(along with blue borders)


how well does this orange border demark the medial wall?  is it 
necessary to make corrections?
We ALWAYS redraw the medial wall and calcarine sulcus borders.  
Sometimes, we redraw other flattening cuts (e.g., frontal, cingulate, 
sylvian, or temporal) if we might use the flat map to draw borders 
around surface-based regions of interest in that area.  For most 
purposes, though, redrawing the calcarine and medial wall borders suffices.


from the caret 5 core6 landmark web page, i saw that the ventral 
extent of the medial wall is more lateral than the dorsal extent.


so the medial wall does not lie on a single medial plane, right?
Correct:  It curves quite a bit along the sagittal plane all along the 
ventral segment, but especially from the amygdala to the olfactory 
sulcus.  The dorsal segment is more stable along the x axis.


None of this is cause for concern.  Just draw on the compressed medial 
wall, but use an inflated view in Window 2 to orient yourself.  After 
drawing, project the border, so you can see how it looks on the inflated 
surface.


Just curious:  Are you still working with monkeys, or is this a human 
subject?


thanks

rishi




Re: [caret-users] Calcarine Sulcus and Border Drawing

2007-03-22 Thread Donna Dierker

Rishi,

See inline replies below.

Donna

On 03/22/2007 10:45 AM, Rishi Kalwani wrote:

hi,

in the core6 landmark website it says not to draw the calcarine sulcus 
if it makes a hard ventral turn.

This means as it extends from the medial wall toward the occipital pole.


the CaSu on my monkey makes a ventral turn below the medial wall, but 
it's about 20-30 degrees off from the medial wall..should i draw 
the full extent of the CaSu?
This isn't too uncommon.  Your calcarine border/cut MUST intersect the 
medial wall, or the Caret demons will visit you.  If your calcarine 
sulcus starts curving ventrally as it approaches the medial wall, almost 
parallel with the parahippocampal gyrus for a while, then you'll need to 
deviate from the fundus and cross over to the medial wall, near the 
margins of the cortex inferior to the splenium.


The attached captures range_inflated.jpg and range_fiducial.jpg show my 
best guess of the ballpark intersection location.  I'm copying Erin 
Reid, who draws many more monkey borders than I do.  Other monkey people 
may also weigh in here if I'm off.


does the CaSu nearly stretch to the most ventral extent of the surface?
Not at either end.  I'm not sure I understand what you mean.  (Some 
captures with well-placed ID nodes will help me get it if my captures 
don't clear things up.)


also, a separate problem is that when i press the apply button in the 
DRAW Borders dialog and begin to click the left mouse button to trace 
the medial wall on the surface in the main window, it doesn't show me 
a border being drawn.is there something else i need to do?
This used to happen when you somehow rotated a flat surface, such as the 
compressed medial wall surface.  Slight rotations that aren't evident to 
the user can prevent draw borders from working properly.  Hitting 
Toolbar: R (reset) usually fixes the problem (but undoes any 
zooming/panning).  But I thought John added a warning if you applied 
draw borders and there was a rotation to the surface.  How old is your 
Caret version?  I thought you just got a new version, but I'm not certain.


thanks

rishi


inline: range_inflated.jpginline: range_fiducial.jpg

[Fwd: Re: [caret-users] Macaque Neuroanatomy]

2007-03-23 Thread Donna Dierker
Passing on Jim Lewis' reply about Hamied's query, which DVE and Rolf 
Kotter also covered.


 Original Message 
Subject:Re: [caret-users] Macaque Neuroanatomy
Date:   Fri, 23 Mar 2007 15:49:10 -0400
From:   James Lewis [EMAIL PROTECTED]
To: Donna Dierker [EMAIL PROTECTED]
References: 
[EMAIL PROTECTED] 
[EMAIL PROTECTED]




Donna (others),
  The brain area acronyms below are largely derived from non-English 
terminology, typically German, and thus I didn't include the full names in some 
of those cases.  However, my recollection is roughly:
IPa  = intraparietal, anterior
PA =  no idea
TAa - is some temporal cortex subdivision, anterior
TE, Tx = similarly are temporal subdivisions, but of unclear actual 
nomenclature.

My experience in finding/using such terminology was that if some study had cited a reasonable looking homologue to what I was observing in our monkey slice sections then I would use their nomenclature. If there were competing potential names then I went with that which seemed closest to what I was seeing. In the case of these latter names, I couldn't find any more recent refernces, and thus stook with their nomenclature even though they didn't explicitly state what their acronyms stood for--often times these were transcribed from German or the like. 
 The nomenclature issue was a BIG issue indeed, and will likely continue to evolve as newer and better methods of segregating brain regions develop.  The problem only gets worse when dealing with human brain areas/regions.


hope this helps.

jim


James W. Lewis, PhD.
Dept. Physiology and Pharmacology
West Virginia University
PO Box 9229
Morgantown, WV 26506-9229

Phone: (304) 293-1517
Fax: (304) 293-3850
Email: [EMAIL PROTECTED]
http://www.hsc.wvu.edu/wvucn/people/Lewis



Donna Dierker [EMAIL PROTECTED] 3/22/2007 1:54 PM 

Hi Jim,

Thought you might know the answer to this user's query; I don't, and DVE 
is out of the office.


Donna

On 03/22/2007 12:27 PM, Hamied Haroon wrote:


Hello,

I’m not a neuroanatomist, but I want to find the neuroanatomical names 
for the temporal areas in the F99UA1 macaque parcellated according to 
C:\Caret5\CARET_TUTORIAL_SEPT06\MACAQUE\Macaque.F99UA1.BOTH.LewisVE00+orig


Most of the abbreviations given in the associated paint colour key are 
listed explicitly in the “LVE00” reference paper (Lewis JW and Van 
Essen DC, /J Comp Neurol/, *428*:112-37, 2000). Unfortunately the 
following abbreviations don’t appear to be given in full in this 
reference paper or in the other references cited (Seltzer B and Pandya 
DN, /Brain Res/, *149*:1-24, 1978, and Cusick CG et al., /J Comp 
Neurol/, *360*:513-35, 1995):


IPa

PA

TAa

TE

Ts

I would be very grateful if anyone could please let me know what these 
abbreviations are in full.


Many thanks in anticipation.

Hamied



Hamied Ahmad Haroon PhD AMInstP

Research Associate in MR Neuroimaging

Division of Imaging Science and Biomedical Engineering

Faculty of Medical and Human Sciences

The University of Manchester

Room G.603 Stopford Building, Oxford Road,

Manchester M13 9PT

England, United Kingdom

Tel: +44 (0)161 275 6871 Fax: +44 (0)161 275 5145

Email: [EMAIL PROTECTED] 
mailto:[EMAIL PROTECTED]


Web: www.isbe.man.ac.uk/~hharoon http://www.isbe.man.ac.uk/%7Ehharoon





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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)





--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] mapping SPM5 volumes in Caret

2007-03-26 Thread Donna Dierker

Hi Tobias,

I don't recognize this problem.  Hmmm.  How about if I give it a try on 
my end.  Can you upload one or more of your volumes here:


http://pulvinar.wustl.edu/cgi-bin/upload.cgi

From the 'QEventDispatcherUNIX::unregisterTimer error, I guess you're 
running Linux.  We'll see if my Linux box acts the same.


Also, would you mind also uploading one of the metric files?  Or you can 
just verify that it is all zeros like so:


caret_file_convert -text my.metric

cut -f2 -d' ' my.metric |sort -un

If you get a bunch of lines with scalars in them, then the metric file 
contains non-zero nodes; however, if you just get a bunch of lines with 
alpha characters, one line with 0.00, and one with 73730, then it is 
all zeroes.


Donna

On 03/24/2007 03:08 PM, Tobias Egner wrote:

Dear all,

I am trying (unsuccessfully) to display some SPM T-images generated in
SPM5 in Caret 5.5. Here's what I am doing:

The T-images are in nifti1 format (with .img and .hdr extensions), and
the original functional data were converted to nifti via the DICOM
import function in SPM5. The images are normalized (and resliced) to
the SPM5 MNI T1.nii template (voxel size 2x2x2, dimensions: 91x109x91,
origin: 46 64 37).

In Caret 5.5, I follow the steps indicated in the
Caret_Tutorial_Sep22.pdf section 5.1. (and using the Caret Tutorial
Sept06 data set).

1- I open the fMRI mapping template Spec file, select all, then save
under a new name, and load scenes.
2- Attributes: Map volumes to surface, then add my SPM t-maps and set
thresholds.
3- Map to spec file with atlas: As output I select my newly created
spec file, and then I select the SPM2 space, and the corresponding
SPM2 left hem atlas, then repeat those steps with the SPM2 right hem
atlas. I accept the default settings on the next page.
4- The I name my metric files (left, right) in accrodance with the
left/right aspects of the 'surface family'.
5-  As Mapping Algorithm, I accept the 'enclosing voxel' default, then
I press Finish and the computing starts...

At the end of the number crunching, I get a little warning sound and
in the command line window it reads:

'QEventDispatcherUNIX::unregisterTimer: invalid argument'

Regardless, I next load the Scene No 4 (FLAT etc..), and then open the
two metric files I have created. I then also load the SPM2 fiducial
coord files. I select Metric as the Primary Overlay, and select L-to-L
R-to-R matching. With great anticipation, I select one of my metric
files, but no cigar: I don't see any surface overlays whatsoever.

Any idea where I am going wrong? Many thanks for any advice!
Best wishes,

Tobias.




--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)



Re: [caret-users] mapping SPM5 volumes in Caret

2007-03-26 Thread Donna Dierker

Hi Tobias,

Your metric files were only 30 lines long -- header but no data.  
Anyway, I suspect this is a case where Caret doesn't recognize your 
nifti1 .img and .hdr format.  It's reading it as Analyze, which works, 
except you need to then set the origin.  The attached captures 
overlay_bad.jpg and overlay_good.jpg show how the volume intersects the 
average fiducial surface before and after using Volume: Edit Volume 
Attributes: to set the origin to -90,-126,-72.  (I didn't double-check 
that this is precisely the right origin!)  Saving the volume with the 
tweaked origin results in a reasonable looking metric, as the attached 
capture shows.


If you can export a flavor of NIFTI that gets along better with Caret, 
then perhaps a way around this problem is to do this one; save the .hdr 
as something like make_caret_happy.hdr; and copy this .hdr over your 
existing (or copied) .hdr for mapping purposes.  If you do this, please 
check two things:  1) The left-right orientation is good; 2) the origin 
is exactly right.


For what it's worth, I've used the .nii style NIFTI files with good success.

Donna

On 03/26/2007 08:37 AM, Tobias Egner wrote:

Dear Donna,

thanks for your help: I've uploaded a couple of volumes
('Tobias_feature.hdr', etc) and the metric files (note that in the
metric files, my volumes are referred to by different names). I'm
actually using Windows though, not Linux.

Many thanks and best wishes,

Tobias.

On 3/26/07, Donna Dierker [EMAIL PROTECTED] wrote:

Hi Tobias,

I don't recognize this problem.  Hmmm.  How about if I give it a try on
my end.  Can you upload one or more of your volumes here:

http://pulvinar.wustl.edu/cgi-bin/upload.cgi

 From the 'QEventDispatcherUNIX::unregisterTimer error, I guess you're
running Linux.  We'll see if my Linux box acts the same.

Also, would you mind also uploading one of the metric files?  Or you can
just verify that it is all zeros like so:

caret_file_convert -text my.metric

cut -f2 -d' ' my.metric |sort -un

If you get a bunch of lines with scalars in them, then the metric file
contains non-zero nodes; however, if you just get a bunch of lines with
alpha characters, one line with 0.00, and one with 73730, then it is
all zeroes.

Donna

On 03/24/2007 03:08 PM, Tobias Egner wrote:
 Dear all,

 I am trying (unsuccessfully) to display some SPM T-images generated in
 SPM5 in Caret 5.5. Here's what I am doing:

 The T-images are in nifti1 format (with .img and .hdr extensions), and
 the original functional data were converted to nifti via the DICOM
 import function in SPM5. The images are normalized (and resliced) to
 the SPM5 MNI T1.nii template (voxel size 2x2x2, dimensions: 91x109x91,
 origin: 46 64 37).

 In Caret 5.5, I follow the steps indicated in the
 Caret_Tutorial_Sep22.pdf section 5.1. (and using the Caret Tutorial
 Sept06 data set).

 1- I open the fMRI mapping template Spec file, select all, then save
 under a new name, and load scenes.
 2- Attributes: Map volumes to surface, then add my SPM t-maps and set
 thresholds.
 3- Map to spec file with atlas: As output I select my newly created
 spec file, and then I select the SPM2 space, and the corresponding
 SPM2 left hem atlas, then repeat those steps with the SPM2 right hem
 atlas. I accept the default settings on the next page.
 4- The I name my metric files (left, right) in accrodance with the
 left/right aspects of the 'surface family'.
 5-  As Mapping Algorithm, I accept the 'enclosing voxel' default, then
 I press Finish and the computing starts...

 At the end of the number crunching, I get a little warning sound and
 in the command line window it reads:

 'QEventDispatcherUNIX::unregisterTimer: invalid argument'

 Regardless, I next load the Scene No 4 (FLAT etc..), and then open the
 two metric files I have created. I then also load the SPM2 fiducial
 coord files. I select Metric as the Primary Overlay, and select L-to-L
 R-to-R matching. With great anticipation, I select one of my metric
 files, but no cigar: I don't see any surface overlays whatsoever.

 Any idea where I am going wrong? Many thanks for any advice!
 Best wishes,

 Tobias.


inline: overlay_bad.jpginline: overlay_good.jpginline: origin_fixed.jpg

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