Hi, Mark and Christian

Just coming back for reporting a thing during my testing on the codes in
fslpspec. I am still wandering there were some bugs in the codes regarding
the test. The test is described below.

I have a 4D bold data with 197 vols. The previous reported error was met
when this data computed by using 

fslpspec bold-4d.nii.gz bold-4d-ps.nii.gz.

Further, I used the same command to calc the psd of the bold data with less
vols which is achieved by using command below:

fslroi bold-4d.nii.gz bold-4d196.nii.gz 0 196

Then the fslpspec works on the vols-reduced data (The speed of this command
is really improved than that before!): 

fslpspec bold-4d196.nii.gz bold-4d-ps.nii.gz.

I am confused by that. I read the source codes in fslpspec and found
potential problems in following lines (line 82, 'Mat.Nrows()/2') when the
number of vols is odd. 

     80 ReturnMatrix calcFFT(const Matrix& Mat)
     81 {
     82   Matrix res(Mat.Nrows()/2,Mat.Ncols()), empty(1,1);
     83   empty=0;
     84   ColumnVector tmpCol;

In a word, there could be an error relevant to an incompatible dimension of
processing 4d bold-data with odd vols. The even sounds ok. Hope a reply
about this, thanks!

All the best
Xinian

On Fri, 19 Sep 2008 08:55:51 +0100, Mark Jenkinson <[log in to unmask]> wrote:

>Hi,
>
>It looks to me like your syntax is wrong too.
>The version of fslpsec here does not have a -m option.
>In fact it doesn't an option for a mask at all.
>
>So you should try:
>   fslpspec 4d-bold.nii.gz 4d-bold-ps.nii.gz
>and then if you want to mask it, do it afterwards with fslmaths.
>
>As for you compiling problems, I am not familiar enough with
>the altix compilers to know how to deal with your specific errors.
>Maybe someone else on the list can help.  Here are some sample
>errors just in case:
>
>standard input}: Assembler messages:
>{standard input}:2257: Warning: Use of 'ld8' may violate WAW
>dependency 'GR%, % in 1 - 127' (impliedf), specific resource number is
>77
>{standard input}:2257: Warning: Only the first path encountering the
>conflict is reported
>{standard input}:2254: Warning: This is the location of the
>conflicting usage
>
>
>/tmp/ccDniEw0.s: Assembler messages:
>/tmp/ccDniEw0.s:1242: Warning: Additional NOP may be necessary to
>workaround Itanium processor A/B step errata
>/tmp/ccDniEw0.s:1551: Warning: Additional NOP may be necessary to
>workaround Itanium processor A/B step errata
>
>
>/tmp/ccjI4bFi.s: Assembler messages:
>/tmp/ccjI4bFi.s:6084: Warning: Use of 'mov' may violate WAW dependency
>'GR%, % in 1 - 127' (impliedf), specific resource number is 14
>/tmp/ccjI4bFi.s:6083: Warning: This is the location of the conflicting
>usage
>
>As these also occur in third-party code (not FSL code) then I think it
>is a more
>general problem that needs to be fixed with your compiler and possibly
>the options you are using for it.
>
>All the best,
>	Mark
>
>
>
>
>
>On 19 Sep 2008, at 08:18, Christian F. Beckmann wrote:
>
>> Hi Xinian,
>>
>> did you check that the original 4d data and the mask have the same
>> dimensions? What do you get from fslsize on these two files?
>> ta
>> Christian
>>
>> _______________________________________________
>> Christian F. Beckmann, DPhil
>>
>> Senior Lecturer, Clinical Neuroscience Department
>> Division of Neuroscience and Mental Health
>> Imperial College London
>> Hammersmith Hospital - London W12 0NN
>> Tel.: +44 (0) 208 383 3722   ---   Fax: +44 (0) 208 383 2029
>> Email: [log in to unmask]
>> http://www.imperial.ac.uk/medicine/people/c.beckmann/
>>
>> Senior Research Fellow, FMRIB Centre
>> University of Oxford
>> JR Hospital - Oxford OX3 9DU
>> Tel.: +44 (0) 1865 222551 --- Fax: +44 (0) 1865 222717
>> Email: [log in to unmask]
>> http://www.fmrib.ox.ac.uk/~beckmann
>>
>>
>>
>>
>> On 19 Sep 2008, at 02:37, Xinian Zuo wrote:
>>
>>> Hi, Mark
>>>
>>> Thanks for the response and zealous helps at all times. I am using a
>>> pre-compiled version of FSL (CentOS4.0) under RedHat-9.0 and
>>> employing
>>> fslpspec cmd for computation of the PSD of a 4D BOLD fMRI data with
>>> around
>>> 190 time points. I retested this using another pre-compiled vesrion
>>> (CentOS5.0) under RedHat-AS 3.4 and got the same matter. As you
>>> suggested,
>>> it would be a good choice to compile it from source release. The
>>> cmd I used
>>> like below,
>>> #---------------------------------------
>>> fslpspec 4d-bold.nii.gz -m example_func_brain_mask.nii.gz 4d-bold-
>>> ps.nii.gz
>>> #---------------------------------------
>>> and the output is only a message written in previous post. If you
>>> need
>>> further information or data transfer for a diagnostic usage, please
>>> let me know.
>>>
>>> btw: I compiled source under altix platform using intel C++ 9.0 and
>>> failed.
>>> I am wandering all this may be related with the specific
>>> architecture of our
>>> machine...
>>>
>>> All the best
>>> Xinian
>>>
>>> On Thu, 18 Sep 2008 11:56:44 +0100, Mark Jenkinson <[log in to unmask]
>>> > wrote:
>>>
>>>> Hi,
>>>>
>>>> I cannot replicate this here.
>>>>
>>>> What exactly are you doing?
>>>> And is this a pre-compiled version of FSL or not?
>>>> Probably best to send us the result of running
>>>> fslerrorreport (on the input file).
>>>>
>>>> All the best,
>>>> Mark
>>>>
>>>>
>>>>
>>>> Xinian Zuo wrote:
>>>>> Hi, folks
>>>>>
>>>>> Is there anyone to test the work of fslpspec in 4.1 version
>>>>> right? I just
>>>>> let it calculate a 4D fmri data and got an error below:
>>>>>
>>>>> terminate called after throwing an instance of
>>>>> 'NEWMAT::IncompatibleDimensionsException'
>>>>>
>>>>> and exit...
>>>>>
>>>>> btw: I displayed my bold timeseries by using fslview and checked
>>>>> potential
>>>>> data flaw, but they looks good.
>>>>>
>>>>> Is this a bug? Hope any words about this.
>>>>>
>>>>> Thanks
>>>>> Xinian
>>>>>
>>>>>
>>