Going to /path/to/spm5/src and typing "make && make install" did the
trick. On Saturday I only tried "make all"... So, case closed.
Thanks,
Chris
elise metereau wrote:
> Hello
>
> I think you need to compile SPM5 in order to make it work with your
> matlab version. (change the variable MEX_BIN in spm5/src/Makefile file).
>
> Hope this helps
>
> Elise
>
> Chris Watson a écrit :
>> 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
>>>
>>
>
>
|
