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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 > > > > > > > > > > >