[caret-users] mapping functional data from SPM5
Donna Dierker
donna at brainvis.wustl.edu
Thu Feb 21 16:11:40 CST 2008
Hi Amy,
I'm increasingly convinced this is a NIFTI volume. See if you have
better luck mapping this volume:
http://pub:download@brainmap.wustl.edu/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 <donna at brainvis.wustl.edu>
> Date: Thursday, February 21, 2008 3:36 pm
> Subject: Re: [caret-users] mapping functional data from SPM5
> To: On-Yee Lo <oyl201 at nyu.edu>, caret-users <caret-users at brainvis.wustl.edu>
>
>
>
>> 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
>>>>>> caret-users at brainvis.wustl.edu
>>>>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>
>>>
>
>
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