The 5 condition analysis is not all that well conditioned either. I have
an (arbitrary) threshold of 10^6 max for the condition number. The
5-condition design is safely below the threshold, the 10-condition is
well above. Unfortunately, this threshold is hardwired. Do you really
need to do the 10-condition? The results may not be very good even if
you can analyze it.
doug
On 10/24/2013 12:08 PM, preci...@nmr.mgh.harvard.edu wrote:
> Xtmp.mat Attached
>
>
>> Hi Ronny, you added 5 new conditions, so it should have increased by at
>> least 5. However, if you are using a derivative with the HRF, then you
>> will have 2 regressors for each condition and it will increase by 10.
>>
>> I don't know why it does not like the 2nd one. Can you send me the
>> Xtmp.mat file?
>>
>> doug
>>
>> On 10/23/2013 12:16 PM, preci...@nmr.mgh.harvard.edu wrote:
>>> I have two sets of identical blocks within each fMRI run, so conditions
>>> {1,2,3,4,5,1,2,3,4,5}, and there are three separate runs of the two
>>> blocks.
>>>
>>> If I run the analysis treating each with the contrasts set up with this
>>> numbering scheme (e.g. 3 vs 1 has two occurrences) , I get the following
>>> output from /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m
>>>
>>> ...
>>> ntptot = 687, nX = 136, DOF = 551
>>> Saving X matrix to
>>> /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008/bold/improv.sm05.lh/Xtmp.mat
>>> XCond = 2926.01 (normalized)
>>>
>>> However, if I want to treat the two sets of blocks separately, i.e.,
>>> {1,2,3,4,5,6,7,8,9,10}
>>> so I can look at contrasts such as 3 vs 1 as well as 8 vs 6 then
>>> fast_selxavg3.m gives:
>>>
>>> ntptot = 687, nX = 146, DOF = 541
>>> Saving X matrix to
>>> /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh/Xtmp.mat
>>> XCond = 4.33238e+08 (normalized)
>>> ERROR: design is ill-conditioned
>>>
>>> 1) why does nX increase by 10 in the 2nd case?
>>> 2) why is fast_selxavg3.m unhappy and XCond so large? Can it not handle
>>> 10
>>> separate blocks?
>>>
>>> The entire log file in the 2nd case is attached.
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> >
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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