[caret-users] mapping functional data from SPM5
Donna Dierker
donna at brainvis.wustl.edu
Thu Feb 21 14:35:59 CST 2008
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 <donna at brainvis.wustl.edu>
> Date: Thursday, February 21, 2008 2:34 pm
> Subject: Re: [caret-users] mapping functional data from SPM5
> To: On-Yee Lo <oyl201 at nyu.edu>
> Cc: Eugene Tunik <eugene.tunik at nyu.edu>
>
>
>
>> 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 <eugene.tunik at nyu.edu>
>>>> Date Wed, 20 Feb 2008 14:59:11 -0500
>>>> To "On-Yee (Amy) Lo" <oyl201 at nyu.edu>
>>>> 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 <donna at brainvis.wustl.edu>
>>>> Date Wed, 20 Feb 2008 13:40:56 -0600
>>>> To "Caret, SureFit, and SuMS software users" <caret-users at brainvis.wustl.edu>
>>>> 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 <donna at brainvis.wustl.edu>
>>>>> Date: Wednesday, April 11, 2007 9:28 am
>>>>> Subject: Re: [caret-users] mapping functional data from SPM5
>>>>> To: "Caret, SureFit, and SuMS software users" <caret-users at brainvis.wustl.edu>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> Hi Gene,
>>>>>>
>>>>>> It might take you 15 minutes to wade through this whole thread,
>>>>>>
>> but
>>
>>>>>>
>>>>>>
>>>> it
>>>>
>>>>
>>>>>> will resonate:
>>>>>>
>>>>>> http://www.mail-archive.com/caret-users@brainvis.wustl.edu/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/
>>>>>>> _______________________________________________
>>>>>>> caret-users mailing list
>>>>>>> caret-users at 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.)
>>>>>>
>>>>>> _______________________________________________
>>>>>> caret-users mailing list
>>>>>> caret-users at brainvis.wustl.edu
>>>>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> caret-users mailing list
>>>>> caret-users at brainvis.wustl.edu
>>>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>
>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> caret-users mailing list
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>>>>
>>>>
>>>
>>>
>
>
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