Sorry for the bombardment. I tried displaying even the template images
that come with SPM5 (e.g. EPI.nii), and I get:
Running "Display Image"
Image "/occipital/matlab/spm5/templates/EPI.nii" can not be resampled
Image "/occipital/matlab/spm5/templates/EPI.nii" can not be resampled
I'm all out of ideas, too.
Chris Watson wrote:
> A little more information.
> We use Freesurfer to convert our DICOM images (from GE 3T scanner) to
> Analyze 7.5 format. Should I be converting to nifti instead? I get the
> same error when manually trying to do, e.g. slice timing using the GUI
> (that is, bad image handle dimensions). So, as of right now, I guess I
> can't view previous results or analyze new data.
>
> If it helps any, I attached a text file of the output to
> 'analyze75info('foo.img')', and output of commands per this email :
> http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710&L=SPM&D=0&P=29198
>
> Happy Saturday,
> Chris
>
> Chris Watson wrote:
>> I downloaded the most recent update, and untarred it. Now when I try
>> to view an SPM.mat, I get the following error message:
>> ??? Error using ==> spm_sample_vol
>> Bad image handle dimensions.
>>
>> Error in ==> spm_get_data at 41
>> Y(i,:) = spm_sample_vol(V(i),XYZ(1,:),XYZ(2,:),XYZ(3,:),0);
>>
>> Error in ==> spm_getSPM at 540
>> Z = min(Z,spm_get_data(xCon(i).Vspm,XYZ));
>>
>> Error in ==> spm_results_ui at 274
>> [SPM,xSPM] = spm_getSPM;
>>
>> ??? Error while evaluating uicontrol Callback
>>
>> This won't require re-analyzing all the data, will it?
>> Chris
>>
>> Simon Durrant wrote:
>>> Hi Chris,
>>>
>>> The fast and dirty solution is simply to turn the warning off by
>>> entering the following at the command prompt:-
>>>
>>> warning('off','MATLAB:FINITE:obsoleteFunction')
>>>
>>> This will stop it slowing down the processing. It's caused by the
>>> Matlab guys changing the "finite" function name to "isfinite" to
>>> make it more consistent with their other type-check functions, but
>>> unfortunately all code using the old version subsequently gets a
>>> warning. I'm sure the SPM authors know about it and will be
>>> updating that and many other version-specific issues (mex files
>>> compiled with older versions of Matlab are another notable example)
>>> in SPM8.
>>>
>>> Best,
>>>
>>> Simon
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>>
>>> > Date: Fri, 8 Aug 2008 12:17:56 -0400
>>> > From: [log in to unmask]
>>> > Subject: [SPM] Warning, using Matlab 7.6 (R2008a)
>>> > To: [log in to unmask]
>>> >
>>> > Hello,
>>> > While doing preprocessing for a dataset, I receive this warning (I
>>> just
>>> > upgraded to Matlab 7.6):
>>> >
>>> > Warning: FINITE is obsolete and will be removed in future
>>> versions. Use
>>> > ISFINITE instead.
>>> > > In file_array.subsasgn>subfun at 95
>>> > In file_array.subsasgn at 63
>>> > In spm_write_plane at 33
>>> > In spm_slice_timing at 261
>>> > In spm_config_slice_timing>slicetiming at 170
>>> > In spm_jobman>run_struct1 at 1540
>>> > In spm_jobman>run_struct1 at 1548
>>> > In spm_jobman>run_struct1 at 1548
>>> > In spm_jobman>run_job at 469
>>> > In spm_jobman at 85
>>> >
>>> > This warning is spit out for just about every slice, and slows
>>> down the
>>> > process quite a bit. This is what a tech support guy from The
>>> Mathworks
>>> > had to say: (I originally thought the Matlab built-in 'subsasgn'
>>> was to
>>> > blame)
>>> >
>>> > "It is true that FINITE function has been deprecated in MATLAB and we
>>> > promote using ISFINITE instead of FINITE. As you mentioned that spm_*
>>> > files are from the SPM5 package, you will probably need to contact
>>> SPM
>>> > to incorporate the necessary changes about replacing the FINITE
>>> > functions to INFINITE in the files.
>>> > From the error messages, it does not seem that SUBASGN is using
>>> FINITE.
>>> > Although it is hard to say by looking at the error messages alone,
>>> but
>>> > it looks like SUBASGN has been overloaded for the FILE_ARRAY
>>> object in
>>> > SPM5 package. Hence, in this case as well, you will probably need to
>>> > contact SPM for further information."
>>> >
>>> > I already changed all instances of "finite" to "isfinite" in the spm
>>> > files. Is there anything else to be done? (I'm using SPM5 on
>>> RHEL4, for
>>> > reference).
>>> >
>>> > Thanks,
>>> > Chris Watson
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> Find out how to make Messenger your very own TV! Try it Now!
>>> <http://clk.atdmt.com/UKM/go/101719648/direct/01/>
>>
>>
>
> ------------------------------------------------------------------------
>
>
>>> analyze75info('/raid2/fmri5/realsubs_visclos_stroop/CARDIAC/metcalf_b/visclos/vc/bold/image001.img')
>>>
>
> ans =
>
> Filename: '/raid2/fmri5/realsubs_visclos_stroop/CARDIAC/metcalf_b/visclos/vc/bold/image001.hdr'
> FileModDate: '08-Aug-2008 14:46:51'
> HdrFileSize: 348
> ImgFileSize: 196608
> Format: 'Analyze'
> FormatVersion: '7.5'
> Width: 64
> Height: 64
> BitDepth: 16
> ColorType: 'grayscale'
> ByteOrder: 'ieee-le'
> HdrDataType: ''
> DatabaseName: ''
> Extents: 0
> SessionError: 0
> Regular: 0
> Dimensions: [64 64 24 1]
> VoxelUnits: 'mm'
> CalibrationUnits: ''
> ImgDataType: 'DT_SIGNED_SHORT'
> PixelDimensions: [3.7500 3.7500 6 2]
> VoxelOffset: 0
> CalibrationMax: 0
> CalibrationMin: 0
> Compressed: 0
> Verified: 0
> GlobalMax: 8191
> GlobalMin: 0
> Descriptor: ''
> AuxFile: ''
> Orientation: 'Transverse flipped'
> Originator: ' ''
> Generated: ''
> Scannumber: ''
> PatientID: ''
> ExposureDate: ''
> ExposureTime: ''
> Views: 0
> VolumesAdded: 0
> StartField: 0
> FieldSkip: 0
> OMax: 0
> OMin: 0
> SMax: 0
> SMin: 0
>
>
>>> N =
>>> nifti('/raid2/fmri5/realsubs_visclos_stroop/CARDIAC/metcalf_b/visclos/vc/
>>> bold/image001.img');
>>> N.dat
>>>
>
> ans =
>
> fname: [1x83 char]
> dim: [64 64 24]
> dtype: 'INT16-LE'
> offset: 0
> scl_slope: 1
> scl_inter: 0
>
>
>
>>> size(N.dat)
>>>
>
> ans =
>
> 64 64 24
>
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