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 Warning: FINITE is obsolete and will be removed in future versions.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
>>
>>
>> ------------------------------------------------------------------------
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>
>
>> 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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