It's a boxcar design so 20.265.
mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh
-fwhm 5 -event-related -paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 2
-refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 7
-tpexclude tpexclude.dat
On Jul 17, 2013, at 3:50 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:
> when you ran mkanalysis-sess, what did you set --refeventdur to?
> On 07/17/2013 02:50 PM, Joseph Dien wrote:
>> then I get on the order of .02% difference between the contrasted conditions.
>> The run mean values are in my expected ballpark of about 100 or so.
>> The condition betas are just very very small.
>> Or perhaps this is typical of FSFAST analyses?
>>
>> On Jul 17, 2013, at 2:00 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>>>
>>> The beta's have already been scaled. What do you get if you just
>>> beta/runmean ?
>>>
>>>
>>>
>>> On 07/17/2013 01:45 PM, Joseph Dien wrote:
>>>> I implemented the ROI percent signal change formula following the
>>>> MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values
>>>> I'm getting seem too small (on the order of .0002%). Basically the
>>>> formula is the (beta * peak absolute value of the canonical HRF
>>>> regressor * 100)/(run mean). No derivatives in this case as it is a
>>>> boxcar design.
>>>>
>>>> I took the mean across all the runs since FSFAST uses the same
>>>> regressor across the entire experiment (unlike SPM).
>>>> I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF
>>>> as you suggested (where m equals the condition+1).
>>>>
>>>> Is it possible that I'm missing something in the scaling here?
>>>> Especially with a boxcar design, the signal change should be much
>>>> larger than this for a significant cluster, I think. For example, the
>>>> peak HRF value for one of the conditions is 0.0092. If the betas are
>>>> already scaled according to the peak value, then it would come out as
>>>> .02%, which is more reasonable, although still too small.
>>>>
>>>> Thanks for your help with this!
>>>>
>>>> Joe
>>>>
>>>>
>>>>
>>>> On May 31, 2013, at 5:02 PM, Douglas N Greve
>>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>>>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>>>
>>>>>
>>>>> Oh, right, it is probably not there for subcortical. I don't know what I
>>>>> would have to do to write it out. It won't be something that happens
>>>>> before I get back from HBM. Can you remind me after HBM?
>>>>> doug
>>>>>
>>>>> On 05/31/2013 04:44 PM, Joseph Dien wrote:
>>>>>> It looks like the corrected vertex p-values
>>>>>> (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the
>>>>>> surface-based lh and rh spaces. For the subcortical volume-based
>>>>>> analysis I don't see the corresponding corrected voxel p-values being
>>>>>> available?
>>>>>>
>>>>>> On May 31, 2013, at 2:46 PM, Joseph Dien <jdie...@mac.com
>>>>>> <mailto:jdie...@mac.com>
>>>>>> <mailto:jdie...@mac.com>
>>>>>> <mailto:jdie...@mac.com>> wrote:
>>>>>>
>>>>>>>
>>>>>>> On May 31, 2013, at 12:11 PM, Douglas N Greve
>>>>>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>
>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>> On 05/31/2013 01:49 AM, Joseph Dien wrote:
>>>>>>>>> I was able to make more progress so I'm mostly good at this point but
>>>>>>>>> I have a remaining question:
>>>>>>>>>
>>>>>>>>> I assume the contents of sig.nii.gz (which I assume are the vertex
>>>>>>>>> p-values) are not FWE corrected. Is it possible to get FWE-corrected
>>>>>>>>> vertex p-values? Or are only clusterwise corrections available?
>>>>>>>> There should be something like cache.th13.abs.sig.voxel.mgh which is
>>>>>>>> corrected on a voxelwise basis (the th13 is just part of the name
>>>>>>>> but it
>>>>>>>> should be the same regardless of the threshold you choose)
>>>>>>>> doug
>>>>>>>
>>>>>>> Excellent! Thanks! :)
>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks again for your patience!
>>>>>>>>>
>>>>>>>>> Joe
>>>>>>>>>
>>>>>>>>> On May 30, 2013, at 4:37 PM, Joseph Dien <jdie...@mac.com
>>>>>>>>> <mailto:jdie...@mac.com>
>>>>>>>>> <mailto:jdie...@mac.com>
>>>>>>>>> <mailto:jdie...@mac.com>
>>>>>>>>> <mailto:jdie...@mac.com>> wrote:
>>>>>>>>>
>>>>>>>>>> Just to make sure I'm doing this right, I'm going to summarize what
>>>>>>>>>> I've taken away from your answers and to ask some new questions. In
>>>>>>>>>> order to present the results, I need two things:
>>>>>>>>>>
>>>>>>>>>> 1) A set of histograms (with error bars) for each cluster figure to
>>>>>>>>>> show the % signal change for each of the four contrasts of interest.
>>>>>>>>>> The cache.th20.pos.y.ocn.dat file only gives it for the condition
>>>>>>>>>> where the cluster was significant so I can't use that.
>>>>>>>>>> So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot
>>>>>>>>>> from the group level analysis to generate a mask for each cluster of
>>>>>>>>>> interest.
>>>>>>>>>> Then I could extract the value of the voxels from each
>>>>>>>>>> subject's cespct file for each contrast, average them across the
>>>>>>>>>> cluster ROI, then average them across each subject, to generate the
>>>>>>>>>> histogram?
>>>>>>>>>> This would suffice to give me the %age signal change?
>>>>>>>>>> I would be doing these computations in Matlab using MRIread.
>>>>>>>>>>
>>>>>>>>>> 2) A results table with the headings:
>>>>>>>>>>
>>>>>>>>>> Cluster p (FWE corrected)
>>>>>>>>>> Cluster size
>>>>>>>>>> Peak Voxel p (FWE corrected)
>>>>>>>>>> Peak Voxel T
>>>>>>>>>> Peak Voxel Coords
>>>>>>>>>> BA
>>>>>>>>>> Anatomical Landmark
>>>>>>>>>>
>>>>>>>>>> I can get the first two from
>>>>>>>>>> the cache.th20.pos/neg.sig.cluster.summary files from the group
>>>>>>>>>> level
>>>>>>>>>> analysis.
>>>>>>>>>> I can get the peak voxel coordinates from the summary files as well.
>>>>>>>>>> I can use this to get the peak voxel p from the group
>>>>>>>>>> level sig.nii.gz file. Is this FWE corrected? If not, how can
>>>>>>>>>> I get
>>>>>>>>>> this information?
>>>>>>>>>> I can use these coordinates to get the peak voxel T by getting the
>>>>>>>>>> value from the group level F.nii.gz file and taking its square root.
>>>>>>>>>> How can I get the sign of the T statistic?
>>>>>>>>>> I can use the Lancaster transform to convert the MNI305 peak voxel
>>>>>>>>>> coordinates into the Atlas coordinates to look up the putative
>>>>>>>>>> BA and
>>>>>>>>>> landmarks (unless there is a better way with Freesurfer? I'm seeing
>>>>>>>>>> some references to some BA labels in the forum but it doesn't look
>>>>>>>>>> like this is a complete set yet?).
>>>>>>>>>>
>>>>>>>>>> Sorry for all these questions! I got some nice results from FSFAST
>>>>>>>>>> and would like to get them written up.
>>>>>>>>>>
>>>>>>>>>> Cheers!
>>>>>>>>>>
>>>>>>>>>> Joe
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On May 29, 2013, at 10:53 PM, Douglas Greve
>>>>>>>>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>
>>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>
>>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 5/29/13 10:42 PM, Joseph Dien wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> On May 29, 2013, at 11:40 AM, Douglas N Greve
>>>>>>>>>>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>>>>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>
>>>>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>
>>>>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Joe,
>>>>>>>>>>>>>
>>>>>>>>>>>>> On 05/29/2013 01:00 AM, Joseph Dien wrote:
>>>>>>>>>>>>>> I need to extract the beta weights from a cluster identified
>>>>>>>>>>>>>> with
>>>>>>>>>>>>>> FS-Fast in order to compute percentage signal change.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 1) I see a file called beta.nii.gz that appears to have the beta
>>>>>>>>>>>>>> weight information. It has a four dimensional structure and the
>>>>>>>>>>>>>> fourth dimension appears to be the beta weights. Is there an
>>>>>>>>>>>>>> index
>>>>>>>>>>>>>> somewhere as to which beta weight is which? Or if not, how
>>>>>>>>>>>>>> are they
>>>>>>>>>>>>>> organized?
>>>>>>>>>>>>> For the first level analysis, the first N beta weights correspond
>>>>>>>>>>>>> to the
>>>>>>>>>>>>> N conditions in the paradigm file. The rest are nuisance
>>>>>>>>>>>>> variables.
>>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Ah, very good! In order to compute the percent signal change
>>>>>>>>>>>> statistic (I'm following the MarsBaR approach:
>>>>>>>>>>>> http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated)
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> I'm also going to need the beta weights for the session mean
>>>>>>>>>>>> regressors. How are the nuisance regressors organized?
>>>>>>>>>>> You can just use the meanfunc.nii.gz. Also, each contrasts is
>>>>>>>>>>> computed as the simple contrast (ces) and as a percent of the
>>>>>>>>>>> baseline at the voxel (cespct, cesvarpct).
>>>>>>>>>>>>
>>>>>>>>>>>>>> 2) In order to extract the cluster, it looks like I would
>>>>>>>>>>>>>> use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a
>>>>>>>>>>>>>> volume where the voxels are tagged with the number of the
>>>>>>>>>>>>>> corresponding cluster.
>>>>>>>>>>>>> Is that from a group analysis?
>>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Yes, that's right.
>>>>>>>>>>>>
>>>>>>>>>>>>>> I could then use that to generate masks to extract the
>>>>>>>>>>>>>> information I
>>>>>>>>>>>>>> need for each cluster from beta.nii.gz.
>>>>>>>>>>>>> If this is from a group analysis, then there should already be
>>>>>>>>>>>>> a file
>>>>>>>>>>>>> there (something.y.ocn.dat) that has a value for each subject
>>>>>>>>>>>>> in the
>>>>>>>>>>>>> rows and a value for each cluster in the columns.
>>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> I see it. Are these values already scaled as percent signal
>>>>>>>>>>>> change? If so, that would be wonderful! :)
>>>>>>>>>>> Only if you specified it when you ran isxconcat-sess. Note that the
>>>>>>>>>>> "non-scaled" values are actually scaled to percent of grand mean
>>>>>>>>>>> intensity.
>>>>>>>>>>>>
>>>>>>>>>>>>>> Is that correct?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 3) The final information that I would need is the canonical hrf
>>>>>>>>>>>>>> shape
>>>>>>>>>>>>>> generated by FSFAST for a single event. I guess I could
>>>>>>>>>>>>>> generate
>>>>>>>>>>>>>> that
>>>>>>>>>>>>>> by setting up a dummy analysis run with a single event of the
>>>>>>>>>>>>>> desired
>>>>>>>>>>>>>> duration and then look in the X variable in the resulting
>>>>>>>>>>>>>> X.mat file?
>>>>>>>>>>>>> try this
>>>>>>>>>>>>> plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf)
>>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Perfect! :)
>>>>>>>>>>>>
>>>>>>>>>>>>>> Sorry for all the questions!
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Joe
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Douglas N. Greve, Ph.D.
>>>>> MGH-NMR Center
>>>>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>>>>> <mailto: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
>>>>> <http://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
>>>>>
>>>>>
>>>>> The information in this e-mail is intended only for the person to
>>>>> whom it is
>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>> the e-mail
>>>>> contains patient information, please contact the Partners Compliance
>>>>> HelpLine at
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>>>>> but does not contain patient information, please contact the sender
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>>>>> dispose of the e-mail.
>>>>>
>>>>
>>>>
>>>> --------------------------------------------------------------------------------
>>>>
>>>> Joseph Dien,
>>>> Senior Research Scientist
>>>> University of Maryland
>>>>
>>>> E-mail: jdie...@mac.com <mailto:jdie...@mac.com> <mailto:jdie...@mac.com>
>>>> Phone: 202-297-8117
>>>> http://joedien.com//
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu <mailto: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
>>
>>
>> --------------------------------------------------------------------------------
>>
>> Joseph Dien,
>> Senior Research Scientist
>> University of Maryland
>>
>> E-mail: jdie...@mac.com <mailto:jdie...@mac.com>
>> Phone: 202-297-8117
>> http://joedien.com//
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
> --
> 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/
>
--------------------------------------------------------------------------------
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 202-297-8117
http://joedien.com//
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