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Hi Christian, I was wondering if you got a chance to take a look at and process the resting state fMRI data I uploaded a couple of days ago? 20130515_163011ep2dpacemocodyntp2s007a001.nii.gz Thanks you for your assistance. Ahmad Ahmad Omar On Thu, Jun 6, 2013 at 8:44 PM, Ahmad Omar <[log in to unmask]> wrote: > 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 >> > > >> > > >> > > >> > > >> > > >> > >> > >> > >> > >