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Hi Christian,

I have uploaded the data set 20130515_163011ep2dpacemocodyntp2s007a001.nii.gz.


Thank you very much for taking a look.

Ahmad

Ahmad Omar



On Wed, Jun 5, 2013 at 6:04 PM, Christian F. Beckmann <
[log in to unmask]> wrote:

> Hi
>
> The address is
> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C
>
> hth
> Christian
>
> On 5 Jun 2013, at 19:22, Ahmad Omar <[log in to unmask]> wrote:
>
> > Hi Steve,
> >
> > Would you please send me the web page address to upload a data set for
> you to look at?
> >
> > Thanks for your assistance.
> > Ahmad
> >
> > Ahmad Omar
> >
> >
> >
> > On Mon, Jun 3, 2013 at 5:44 PM, Ahmad Omar <[log in to unmask]> wrote:
> > Hi Christian,
> >
> > Would you please send me the web page address to upload a data set for
> you to look at?
> >
> > Thanks for your assistance.
> > Ahmad
> >
> > Ahmad Omar
> >
> >
> >
> > On Fri, May 31, 2013 at 9:10 PM, Ahmad Omar <[log in to unmask]> wrote:
> > Hi Christian,
> >
> > The runs we have been doing have been on a single subject. You suspect
> that the data set is bad, right? I will try to upload it from the center.
> >
> > Thanks for your help.
> > Ahmad
> >
> > Ahmad Omar
> >
> >
> >
> > On Fri, May 31, 2013 at 8:56 AM, Christian F. Beckmann <
> [log in to unmask]> wrote:
> > Hi,
> >
> > I suggest running single-subject ICAs first, just to see if the data
> quality per se is OK or if you happen to have strange artefacts in your
> data. If you cannot make this work then feel free to upload a single data
> set so we can see what's going on...
> >
> > hth
> > Christian
> >
> >
> >
> > On 31 May 2013, at 11:53, Ahmad Omar <[log in to unmask]> wrote:
> >
> > > Hi Steve,
> > >
> > > Thank you for your reply. Unfortunately, we are only getting what in
> some places are randomly scattered activations in the midbrain or
> concentrated activations in the frontal and orbito-frontal regions where
> there is already some epi-related distortions so not be relied upon  . I
> was meaning to ask this follow-up question. Shouldn't I turn off temporal
> high pass filtering as I am interested in the ultra-low frequency BOLD
> > > signals? I tried a run doing that and the activation areas changed a
> bit to being around the ventricles and in the putamen which also looked
> strange to us.
> > >
> > > We very much appreciate your help on this.
> > >
> > > Ahmad
> > >
> > > Ahmad Omar
> > >
> > >
> > >
> > > On Thu, May 30, 2013 at 1:00 AM, Stephen Smith <[log in to unmask]>
> wrote:
> > > Hi - there's nothing in this description or the log that jumps out at
> me - did you find *some* RSNs that you recognised?
> > > Steve.
> > >
> > > On 29 May 2013, at 16:31, Ahmad Omar <[log in to unmask]> wrote:
> > >
> > >>
> > >> Re-send. Thanks.
> > >>
> > >>
> > >> Ahmad Omar
> > >>
> > >>
> > >>
> > >> ---------- Forwarded message ----------
> > >> From: Ahmad Omar <[log in to unmask]>
> > >> Date: Mon, May 27, 2013 at 4:53 PM
> > >> Subject: Resting state fMRI using MELODIC
> > >> To: FSL Mailing List <[log in to unmask]>
> > >>
> > >>
> > >> Hello All,
> > >>
> > >> I am trying to apply MELODIC (ver. 3.13, FSL ver 5.0.4 on a virtual
> machine) to some resting-state fMRI data we are acquiring here at the
> radiology center. The scanner is a 3T Siemens Skyra. The sequence is the
> standard ep2d sequence acquiring 150 time points with TR = 2.57 sec, TE =
> 36 msec, flip angle = 75 deg, distance factor = 20, PAT = 2, Fat Sat. on,
> phase partial Fourier off, bandwidth = 1698 Hz/Px and 1.7mm x 1.7 mm x 5 mm
> (in the z-axis direction) resolution with interleaved slice acquisition.
> Motion correction and temporal high pass filtering were enabled in the
> scanner sequence. When I view and loop through the raw data in FSL View, it
> seems fine. No excessive translations or head rotation and no severe
> intensity variations. In MELODIC I set the following settings: Delete
> Volumes = 3, High pass filter cutoff (s) = 100, Motion Correction :
> MCFLIRT, Slice timing correction: Interleaved, spatial smoothing FWHM (mm)
> = 5, Temporal filtering: Highpass,  Threshold IC maps left at 0.5 and
> output the full stats folder was enabled. We were trying to reproduce the
> work done by  Tang, L et al. in the paper "Thalamic Resting-State
> Functional Networks: Disruption in Patients with Mild Traumatic Brain
> Injury". MELODIC finishes processing fine but we don't know why we are not
> seeing any meaningful activations in say the Default Mode Network areas let
> alone activations in the thalamus. I have included below a part of the
> log.txt file in the filtered_func_data.ica folder.
> > >>
> > >> Thanks and your help is much appreciated.
> > >>
> > >> Melodic Version 3.13
> > >>
> > >> /usr/local/fsl/bin/melodic -i filtered_func_data -o
> filtered_func_data.ica -v --nobet --bgthreshold=3 --tr=2.5699999332
> --report --guireport=../../report.html -d 0 --mmthresh=0.5 --Ostats
> > >> ---------------------------------------------
> > >>
> > >> Melodic results will be in filtered_func_data.ica
> > >>
> > >> Create mask ... done
> > >> Reading data file filtered_func_data  ...  done
> > >>   Estimating data smoothness ...  done
> > >>   Removing mean image ... done
> > >>   Normalising by voxel-wise variance ... done
> > >> Excluding voxels with constant value ... done
> > >>
> > >>   Data size : 147 x 106223
> > >>
> > >> Starting PCA  ... done
> > >> Start whitening using  49 dimensions ...
> > >>   retaining 88.3302 percent of the variability
> > >>  ... done
> > >>
> > >> Starting ICA estimation using symm
> > >>
> > >>   Step no. 1 change : 0.422912
> > >>   Step no. 2 change : 0.509312
> > >>   Step no. 3 change : 0.458818
> > >>   Step no. 4 change : 0.490924
> > >> .
> > >> .
> > >> .
> > >> Step no. 63 change : 5.50092e-05
> > >>   Step no. 64 change : 5.21687e-05
> > >>   Step no. 65 change : 5.06082e-05
> > >>   Step no. 66 change : 4.94706e-05
> > >>   Convergence after 66 steps
> > >>
> > >> Sorting IC maps
> > >>
> > >> Writing results to :
> > >>   filtered_func_data.ica/melodic_IC
> > >>   filtered_func_data.ica/melodic_Tmodes
> > >>   filtered_func_data.ica/melodic_mix
> > >>   filtered_func_data.ica/melodic_FTmix
> > >>   filtered_func_data.ica/melodic_PPCA
> > >>   filtered_func_data.ica/melodic_ICstats
> > >>   filtered_func_data.ica/mask
> > >> ...done
> > >> Creating report index page ...done
> > >>
> > >>
> > >> Running Mixture Modelling on Z-transformed IC maps ...
> > >>   IC map 1 ...
> > >>    calculating mixture-model fit
> > >>    saving probability map:    filtered_func_data.ica/stats/probmap_1
> > >>    saving mixture model fit:  filtered_func_data.ica/stats/MMstats_1
> > >>    re-scaling spatial maps ...
> > >>    thresholding ...
> > >>    alternative hypothesis test at p > 0.5
> > >>    saving thresholded Z-stats image:
>  filtered_func_data.ica/stats/thresh_zstat1
> > >>    creating report page ...    done
> > >> .
> > >> .
> > >> .
> > >>  IC map 49 ...
> > >>    calculating mixture-model fit
> > >>    saving probability map:    filtered_func_data.ica/stats/probmap_49
> > >>    saving mixture model fit:  filtered_func_data.ica/stats/MMstats_49
> > >>    re-scaling spatial maps ...
> > >>    thresholding ...
> > >>    alternative hypothesis test at p > 0.5
> > >>    saving thresholded Z-stats image:
>  filtered_func_data.ica/stats/thresh_zstat49
> > >>    creating report page ...    done
> > >>
> > >> Ahmad
> > >>
> > >
> > >
> > >
> ---------------------------------------------------------------------------
> > > Stephen M. Smith, Professor of Biomedical Engineering
> > > Associate Director,  Oxford University FMRIB Centre
> > >
> > > FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> > > +44 (0) 1865 222726  (fax 222717)
> > > [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
> > >
> ---------------------------------------------------------------------------
> > >
> > > Stop the cultural destruction of Tibet
> > >
> > >
> > >
> > >
> > >
> >
> >
> >
>