Hi Amy,
I'm increasingly convinced this is a NIFTI volume. See if you have
better luck mapping this volume:
http://pub:[EMAIL PROTECTED]/pub/donna/ARCHIVE/CARET_USERS/test.nii
login pub
password download
Using nifti_tool (which comes with the AFNI distribution, but is
available elsewhere -- might even be in your SPM distribution), I
converted your NIFTI .hdr/.img pair to .nii:
nifti_tool -copy_im -prefix /tmp/test.nii -infiles MB_spmT_0001.hdr
I'm hoping you have better luck with it.
Donna
On 02/21/2008 02:57 PM, On-Yee Lo wrote:
Hi Donna,
I am not sure "original info missing" part. How could I check if my origin was
set correctly? How could I fix this problem?
Besides, I'll try to combine hdr./img. file together as nii. file and try it again after I get the software.
Also, i selected "metric/functional" not "ROI' when I mapped.
What else can I do? Is it possible that the installation was not set
appropriately? How can I check it?
Thanks,
Amy
----- Original Message -----
From: Donna Dierker <[EMAIL PROTECTED]>
Date: Thursday, February 21, 2008 3:36 pm
Subject: Re: [caret-users] mapping functional data from SPM5
To: On-Yee Lo <[EMAIL PROTECTED]>, caret-users <[email protected]>
Hi Amy,
These files don't quite look like what I'd expect out of SPM2. If
they
were, I'd see something like this when I execute AFNI's mayo_analyze
on
the .hdr:
orient: <0>
SPM originator decodes to 40 57 26
originator: <(>
Instead, I get the attached output for this volume:
/upload/MB_spmT_0001.hdr
/upload/MB_spmT_0001.img
While this is not uncommon for FSL, it wasn't for SPM2, as far as I know:
pixdim[0]: <-1.0000>
There also are characters that suggest that this might really be a
NIFTI
volume written as .hdr/.img, rather than as .nii. If this is a SPM5
volume, then write it as .nii and try again.
All this said, I was able to open the volume on my end and map it.
The
origin wasn't set correctly, because the origin info missing. (But if
it's really a NIFTI volume, the origin info is there; Caret just
doesn't
support .hdr/.img NIFTI yet. It does support nii.)
One other thing: When you mapped, which did you select: metric /
functional or ROI/paint/probabilistic atlas on the first page of the
Map data dialog? If you selected ROI / prob atlas, then your mapping
is
output as paint -- not metric.
Donna
On 02/21/2008 02:12 PM, On-Yee Lo wrote:
Hi Donna,
I am sorry to reply to you again. Could you forward this mail to
John or David? Thanks!
When I open data file, there is an error showing:" xxx.hdr: unalbe
to open with ZLIB for reading."
Did you check my uploaded files? How're them?
Thanks,
Amy
----- Original Message -----
From: Donna Dierker <[EMAIL PROTECTED]>
Date: Thursday, February 21, 2008 2:34 pm
Subject: Re: [caret-users] mapping functional data from SPM5
To: On-Yee Lo <[EMAIL PROTECTED]>
Cc: Eugene Tunik <[EMAIL PROTECTED]>
Hi Amy,
Do you mind if I copy caret-users on subsequent replies? We've got
icy
conditions in STL, and I may be headed home soon and stay home
tomorrow. John or David might be able to help you that way,
although
the weather may impact them, too.
It definitely sounds like the mapping is failing, if metric isn't
outputting, if it can't be selected on the D/C menu.
Some things come to mind:
* .hdr is really a NIFTI file masquerading as Analyze .img
* it can't find the .img
Try File: Open Data File: type Volume Functional
Are there any errors in the command window from which Caret was launched?
You might also try enabling debug on your File : Preferences.
I'd like to have a look at your functional volume. Upload .hdr and
.img
here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
Donna
On 02/21/2008 01:15 PM, On-Yee Lo wrote:
Hello Donna,
I've checked the files and we do have those files in the
caret/data_files/fmri_mapping_files. but I still can not active the
"Metric" icon and do the next step.
I followed the below sequences and try to map functional volume to
surface:
1.Open "Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec"
2.Load --> Attributes --> Map Functional Volumes To Surfaces
3.Add volumes From Disk (spmT_0001.hdr)
<Here comes a message:If this ".hdr" file does not contain an SPM
originator, it is unlikely that it will get mapped to
the surface correctly.> I think our file contain SPM originator.
4."Map to Caret with Atlas.." --> chose "Space-SPM2" and "Atlas-
PALS_B12 Multi-Fid Map LEFT hemisphere(73730 nodes), SPM2 space"
5.And then when we tried to open D/C, Metric icon can not be
selected for overlay.
Any other suggestion for our problem?
Thanks so much,
Amy
(RA for Dr. Eugene Tunik)
----- Original Message -----
From Eugene Tunik <[EMAIL PROTECTED]>
Date Wed, 20 Feb 2008 14:59:11 -0500
To "On-Yee (Amy) Lo" <[EMAIL PROTECTED]>
Subject Fwd: Re: [caret-users] mapping functional data from SPM5
Amy, can you check on this...
Eugene Tunik, PhD, PT
Dept. of Physical Therapy, NYU
http://homepages.nyu.edu/~et38/
----- Original Message -----
From Donna Dierker <[EMAIL PROTECTED]>
Date Wed, 20 Feb 2008 13:40:56 -0600
To "Caret, SureFit, and SuMS software users" <[email protected]>
Subject Re: [caret-users] mapping functional data from SPM5
Hi Gene,
There's an important distinction between the Caret distribution
and
the
latest Caret snapshot. If you downloaded only the latest Caret
snapshot, and did not previously install the entire distribution,
then
important files in the caret/data_files/fmri_mapping_files won't
be
found. When I extract this archive, it contains those files:
/146Gb/www/html/pub/caret/caret_distribution.v5.51.windows.zip
This extracted subdirectory contains over 200 files:
caret/data_files/fmri_mapping_files/
Do you have that directory and those files?
Donna
On 02/20/2008 11:36 AM, Eugene Tunik wrote:
Hi Donna,
I have a quick question about a caret problem.
I installed v.5.51 on a new windows machine. (and the tutorial
sept
06 toolbox).
I just want to map functional volume to surface so I do the following:
1) load spec file (in mapping procedures->PALs for fmri mapping
2) attributes-=> map to surface...and go through the whole deal
of
loading my image file (SPM space).
When the whole thing is done, and I click D/C, the metric icon
doesn't become active so I cannot overlay anything.
(The same functional works fine on a different machine that has
an
older installation of caret).
Any suggestions?
Thanks and best,
Gene
Eugene Tunik, PhD, PT
Dept. of Physical Therapy, NYU
http://homepages.nyu.edu/~et38/
----- Original Message -----
From: Donna Dierker <[EMAIL PROTECTED]>
Date: Wednesday, April 11, 2007 9:28 am
Subject: Re: [caret-users] mapping functional data from SPM5
To: "Caret, SureFit, and SuMS software users" <[email protected]>
Hi Gene,
It might take you 15 minutes to wade through this whole thread,
but
it
will resonate:
http://www.mail-archive.com/[email protected]/msg01088.html
Here are the highlights:
* Caret only reads NIFTI files that are a single file with the
".nii"
extension. The next release of Caret will be able to read NIFTI
files
that are in an Analyze hdr/img pair. Caret still reads the
files
as
if
they were Analyze, but without the SPM99/SPM2-style
"originator"
info
in
the .hdr, it's clueless about the location of the origin.
* Use Volume: Edit volume attributes to set the origin to -90,-126,-72.
* When opening the functional volume in Caret, select the
"Volume
is
an
SPM2 Volume with Right on Left" if your volume is stored in a
left-handed coordinate system (aka radilogical or right on left
--
see
http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q15). If
you
need
to map several functional volumes and want to use the
caret_map_fmri
command line utility, then you'll probably need to convert your
volumes
to *.nii, AFNI, or SPM2-style .hdr.
Donna
On 04/11/2007 07:50 AM, Eugene Tunik wrote:
Dear all,
I am mapping a contrast image (the spmT.hdr/img) that is
output
in
SPM5.
However, Caret is not mapping it to the fiducial. This works
fine
using an spmT image output from SPM2.
Is there something special about the SPM5 output that makes it
incompatible with caret?
Any suggestions are appreciated.
Best,
Gene
Eugene Tunik, PhD, PT
Dept. of Physical Therapy, NYU
http://homepages.nyu.edu/~et38/
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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see
http://home.att.net/~donna.hanlon for details.)
_______________________________________________
caret-users mailing list
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_______________________________________________
caret-users mailing list
[email protected]
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
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