Doug, please correct me if i am wrong and add if need to. > Hi, > After wrestling with this a bit, I think I get the idea (finally!). > Just to confirm: > > 1- set a primary threshold in the mri_glmfit command, e.g., --sim > perm 5000 1.3 will run 5000 permutations with the primary cluster > forming threshold set at .05.
Correct [thres value = -log10(pvalue)] > 2- Look up the cluster summary table and identify clusters with CWP > < .05 (if alpha=.04). These CWP values are corrected based on the > maximal cluster size statistics generated during the permutations. Yes, identify clusters with CWP < .05 if you have --sim perm 5000 1.3 > 3 - Visualize clusters in tksurfer - one way is to load the --cwsig > file, where each cluster is assigned a corrected p-value. Seeting the > overlay display to min=1.3 will then show you all clusters that are > significant at the clusterwise corrected .05 level. You are right > Am I right so far? > > Couple more questions regarding smoothing: > > 1 - If I input data obtaioned from qdec into mri_glmfit just to run > the permutations, do I need to specify the --fwhm? Does this > correspond to the one used for the analysis (i.e., the one specific > in qdec), or the residual fwhm obtained from the y.fsgd file? (Note, > I see that you need to specify the residual fwhm for the monte-carlo > sims, by I wanted to check whether a fwhm is required for the --sim > perm option) The fwhm value needed for mc simulation is(either from fwhm.dat or y.fsgd file--both have same value, which is usually a little higher than the fwhm used at Qdec. ) > 2 - does the --var-fwhm option corresond to the variance smoothing > described in the Nichols and Holmes Hum Brain Mapp paper? If so, it > seems this would be useful for --sim perm. Does anyone have any > recommendations for what a good value would be? Should it be the same > fwhm as that used to smooth the thickness values; i.e., is I specify > 15mm in qdec, should I use 15mm for --var-fwhm? --var-fwhm is Smooth residual variance. while the fwhm at qdec is to smooth input > Thanks again for your help, > Alex > > > On 11/12/2007, at 12:49 PM, Doug Greve wrote: > >> >> >> Alex Fornito wrote: >>> >>> Sorry Doug, I'm a bit thick , so pls let me clarify :) >>> >>> The threshold set in mri_glmfit with --sim perm 5000 1.3 >>> corresponds to the primary (1) vertex-wise threshold; (2) the >>> cluster-based threshold; or (3) both? >> Just #1, the vertex-wise. The simulation is done to figure out #2. >>> >>> I'm a little confused, as in you previous response you stated: >>> >>>>> Thus, if I set --sim perm 5000 1.3, vertices significant at p<. >>>>> 05 will first be identified, and those that are connected will >>>>> be assigned to clusters. >>>> Correct so far. >>> >>> But then later said the vertex-wise values are uncorrected. In >>> that case, and based on your response re: data contained in >>> the .csd file, I assume that the '1.3' threshold corresponds to >>> that determined by the permutation distribution for the group >>> difference statistic at each vertex, rather than the maxima across >>> all vertices, which corrects for multiple comparisons as detailed >>> in the Nichols & Holmes (2001) paper. This is why the vertex-wise >>> values are uncorrected? >> The 1.3 is what you determined and specified on the command-line. >> The maxima across all vertices is stored in the CSD and can in >> principle be used to compute a vertex-wise threshold (instead of >> using a cluster-wise correction). In this case, the 1.3 you spec on >> the cmd line would be meaningless. >> >>> >>> If the above is the case, than how and when is the cluster-wise >>> threshold selected? I noted that you said any cluster-wise >>> threshold can be selected, by mri_surfcluster does not allow me to >>> set a --thmin different to that passed to mri_glmfit when using >>> a .csd file. >> By default, mri_surfcluster will print out all clusters along with >> their cluster-wise p-value. You then look at the list and only >> report the ones that meet the threshold that you feel comfortable >> with. >>> >>> Thanks again. >>> >>> On 11/12/2007, at 12:03 PM, Doug Greve wrote: >>> >>>> >>>> >>>> Alex Fornito wrote: >>>>> >>>>> Ok, so sounds like that is not possible - thanks for clarifying. >>>>> >>>>> I have been playing with the --sim perm option and was wondering >>>>> how cluster-level inferences are determined. From what I >>>>> understand, a primary (voxel-level) threshold generally needs to >>>>> be specified to form clusters, prior to some statistics >>>>> assessing a particular property of the suprathreshold clusters >>>>> (e.g., size or mass) being tested again its null distribution. >>>>> >>>>> I know that the --sim perm requires specification of a >>>>> threshold, but I am presuming that this if for cluster-level >>>>> inference. mri_surfcluster obtains threshold information from >>>>> the .csd file with no further user input, making me wonder how >>>>> the 'primary', vertex-level threshold for determining supra- >>>>> threshold clusters is set. I see two possible options: >>>>> >>>>> 1 - You are implementing the Threshold-Free Cluster Enhancement >>>>> (TFCE) technique described on the Randomize website. >>>>> >>>> Never heard of it. >>>>> 2 - The primary, vertex-wise threshold is determined by the >>>>> permutation distribution of the maximal statistic for the >>>>> difference between two groups (in a 2-group comparison). All >>>>> connected suprathreshold vertices are then assigned to different >>>>> clusters, and the size of these clusters is then tested against >>>>> the permutation distribution for cluster size. >>>>> Thus, if I set --sim perm 5000 1.3, vertices significant at p<. >>>>> 05 will first be identified, and those that are connected will >>>>> be assigned to clusters. >>>> Correct so far. >>>> >>>>> Clusters will then be determined significant if p<05, as >>>>> evaluated against the permutation distribution for the maximal >>>>> cluster size statistic. >>>> You can choose any cluster-wise sig threshold you want (ie, it is >>>> distinct from the vertex-wise threshold). >>>>> Is this what the MaxStat and MaxClusterSize columns in the .csd >>>>> file correspond to? >>>> I've programmed mri_glmfit to keep track of both the max cluster >>>> size and the maximum statistic. The latter can be used to do a >>>> vertex-wise correction for muliple comparisons instead of a >>>> cluster-wise. This avoids having to set an arbitrary vertex-wise >>>> threshold needed when clustering. I'm still missing a piece of >>>> code that will apply the CSD in this way. >>>>> If this is the case, is using 2 corrected thresholds (for >>>>> primary, vertex-wise, and then cluster-level inferences) seems >>>>> to be relatively conservative? I have noted that in many fMR >>>>> experiments, it seems customary to use an uncorrected primary >>>>> threshold based on signal intensity, coupled with an extent >>>>> threshold to form clusters, prior to making FWE-corrected >>>>> cluster-level inferences. >>>> The vertex-wise theshold is not corrected in any way. >>>> >>>> doug >>>> >>>> >>>>> >>>>> Appreciate help on this and sorry for all the questions - much >>>>> of this is new to me!! >>>>> Alex >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 07/12/2007, at 5:59 AM, Doug Greve wrote: >>>>> >>>>>> FDR assumes that the collection of values has both positives >>>>>> and negatives. It assumes that the pvalues of the negatives are >>>>>> uniformly distributed between 0 and 1, and this model is used >>>>>> to estimate the total number of positives (both true and >>>>>> false). When you cluster, you are setting all voxels below a >>>>>> certain threshold to 0, thus invalidating the assumption about >>>>>> the distribution of the negatives. >>>>>> >>>>>> doug >>>>>> >>>>>> Alexander Fornito wrote: >>>>>>> >>>>>>> Sorry, can I ask why the clustering step would invalidate FDR? >>>>>>> >From my understanding, FDR allows you set a limit on the >>>>>>> number of false >>>>>>> positive in a family of contrasts reaching significance at a >>>>>>> nominal >>>>>>> threshold. I would like to this nominal threshold using >>>>>>> cluster stats >>>>>>> (e.g., p<.05, cluster extent 30mm), and then use FDR to >>>>>>> correct for >>>>>>> comparisons at vertices exceeding this initial threshold, >>>>>>> therefore >>>>>>> avoiding running FDR on each vertex of the surface. Is this >>>>>>> not possible? >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> That does not sound right, I think that the first clustering >>>>>>>> step will >>>>>>>> probably invalidate FDR. You can use FDR to set the voxel- >>>>>>>> wise threshold >>>>>>>> when you run mri_surfcluster, but I'm not sure you can do it >>>>>>>> afterwards. >>>>>>>> >>>>>>>> Alex Fornito wrote: >>>>>>>> >>>>>>>> >>>>>>>>> I retract the last email - it seems like I was entering the >>>>>>>>> wrong >>>>>>>>> sig.mgh file as input. Sorry for the confusion!!! >>>>>>>>> >>>>>>>>> On a separate issue, I would like to check that I have the >>>>>>>>> following >>>>>>>>> correct: >>>>>>>>> >>>>>>>>> I have extracted a cluster image using mri_surfcluster withouth >>>>>>>>> running simulations. Say, for e.g., I use thmin 2 and >>>>>>>>> minarea 30. I >>>>>>>>> load the resulting output.mgh file into tksurfer. >>>>>>>>> I would then like to perform FDR correction on the resulting >>>>>>>>> clusters. >>>>>>>>> I'm guessing that pressing the FDR button in the Overlay >>>>>>>>> config menu >>>>>>>>> will do the trick, since (from what I understand) the >>>>>>>>> output.mgh file >>>>>>>>> I have loaded assigns a zero to all vertices not in a >>>>>>>>> cluster. I >>>>>>>>> figure that this will therefore result in an FDR correction >>>>>>>>> that >>>>>>>>> accounts only for the vertices within my clusters. >>>>>>>>> >>>>>>>>> However, I'm uncertain how the 'only marked' checkbox fits >>>>>>>>> in. If I >>>>>>>>> tick it, I get an error calculating the FDR. I'm guessing >>>>>>>>> this option >>>>>>>>> is relevant if you combined a stat map with a label file. >>>>>>>>> >>>>>>>>> Am I on the right track? >>>>>>>>> >>>>>>>>> Thanks again, >>>>>>>>> Alex >>>>>>>>> >>>>>>>>> On 05/12/2007, at 9:52 AM, Alex Fornito wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>>> <Pic.png> >>>>>>>>>> >>>>>>>>>> Thanks for all your help guys, but I am still having >>>>>>>>>> trouble (!). >>>>>>>>>> This time I've tried a different dataset, again just a >>>>>>>>>> simple 2 group >>>>>>>>>> comaprison with no covariates. >>>>>>>>>> >>>>>>>>>> Running this in qdec, and visualizing with a low threshold >>>>>>>>>> (min=1.3), >>>>>>>>>> I see a whole bunch of clusters (see attached). However, >>>>>>>>>> when I run >>>>>>>>>> mri_surfcluster, I only get one whole brain cluster again (see >>>>>>>>>> below). This time I smoothed with 15 mm in qdec, although I >>>>>>>>>> get the >>>>>>>>>> same if I smooth with 10mm. I have kept the thresholds low on >>>>>>>>>> purpose, because I expect that something should come out?? >>>>>>>>>> I did not >>>>>>>>>> run simulations in this instance, to cut processing time. >>>>>>>>>> >>>>>>>>>> mri_surfcluster --in qdec/MF_lh_15mm/contrasts.sig.mgh -- >>>>>>>>>> no-adjust >>>>>>>>>> --subject fsaverage/ --hemi l h --thmin 1.3 --minarea 15 --sum >>>>>>>>>> TestClusters >>>>>>>>>> >>>>>>>>>> thsign = abs, id = 0 >>>>>>>>>> version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 >>>>>>>>>> greve Exp $ >>>>>>>>>> hemi = lh >>>>>>>>>> srcid = qdec/MF_lh_15mm/contrasts.sig.mgh paint >>>>>>>>>> srcsubjid = fsaverage/ >>>>>>>>>> srcsurf = white >>>>>>>>>> srcframe = 0 >>>>>>>>>> thsign = abs >>>>>>>>>> thmin = 1.3 >>>>>>>>>> thmax = -1 >>>>>>>>>> fdr = -1 >>>>>>>>>> minarea = 15 >>>>>>>>>> xfmfile = talairach.xfm >>>>>>>>>> nth = -1 >>>>>>>>>> sumfile = TestClusters >>>>>>>>>> subjectsdir = /data/kang/work/struct/alex/freesurfer/ >>>>>>>>>> subjects_cann >>>>>>>>>> FixMNI = 1 >>>>>>>>>> ------------- XFM matrix (RAS2RAS) --------------- >>>>>>>>>> /data/kang/work/struct/alex/freesurfer/subjects_cann/ >>>>>>>>>> fsaverage//mri/transforms/t >>>>>>>>>> alairach.xfm >>>>>>>>>> 1.000 0.000 0.000 0.000; >>>>>>>>>> 0.000 1.000 0.000 0.000; >>>>>>>>>> 0.000 0.000 1.000 0.000; >>>>>>>>>> 0.000 0.000 0.000 1.000; >>>>>>>>>> ---------------------------------------------------- >>>>>>>>>> Reading source surface >>>>>>>>>> /data/kang/work/struct/alex/freesurfer/subjects_cann/fsav >>>>>>>>>> erage//surf/lh.white >>>>>>>>>> reading group avg surface area 822 cm^2 from file >>>>>>>>>> Reading in average area >>>>>>>>>> /data/kang/work/struct/alex/freesurfer/subjects_cann/fsa >>>>>>>>>> verage//surf/lh.white.avg.area.mgh >>>>>>>>>> Done reading source surface >>>>>>>>>> Computing metric properties >>>>>>>>>> Loading source values >>>>>>>>>> number of voxels in search space = 163842 >>>>>>>>>> Done loading source values (nvtxs = 163842) >>>>>>>>>> overall max = 1e+10 at vertex 26 >>>>>>>>>> overall min = 1.75775 at vertex 126983 >>>>>>>>>> surface nvertices 163842 >>>>>>>>>> surface area 65416.985991 >>>>>>>>>> surface area 65416.985976 >>>>>>>>>> NOT Adjusting threshold for 1-tailed test >>>>>>>>>> Searching for Clusters ... >>>>>>>>>> thmin=1.300000 (1.300000), thmax=-1.000000 (-1), thsignid=0, >>>>>>>>>> minarea=15.000000 >>>>>>>>>> Found 1 clusters >>>>>>>>>> Max cluster size 103339.460938 >>>>>>>>>> INFO: fixing MNI talairach coordinates >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 05/12/2007, at 4:19 AM, Doug Greve wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> There's really no such thing as an opt kernel size. The >>>>>>>>>>> best size >>>>>>>>>>> depends on the underlying signal and can be space variant. >>>>>>>>>>> >>>>>>>>>>> doug >>>>>>>>>>> >>>>>>>>>>> Alex Fornito wrote: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> Yes, I selected 25 mm on qdec, based on the Lerch paper >>>>>>>>>>>> suggesting >>>>>>>>>>>> this was a generally 'optimal' kernel size. The 34.309.. >>>>>>>>>>>> was the >>>>>>>>>>>> residual output to y.fsgd. >>>>>>>>>>>> >>>>>>>>>>>> Do you recommend a smaller kernel? >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On 04/12/2007, at 5:41 PM, Pratap Kunwar wrote: >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>> I think, one reason for getting only one big cluster is >>>>>>>>>>>>> because >>>>>>>>>>>>> your fwhm >>>>>>>>>>>>> value is very high. By the way how did you get fwhm >>>>>>>>>>>>> 34.309616??, >>>>>>>>>>>>> was it >>>>>>>>>>>>> produced by selecting fwhm 25 (max on Qdec)on Qdec? >>>>>>>>>>>>> >>>>>>>>>>>>> Did you try fwhm 10 or 15? >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks for your help Pratap. >>>>>>>>>>>>>> I've actually been trying to follow the tutorial and >>>>>>>>>>>>>> was running >>>>>>>>>>>>>> simulations initially, but when I tried to re-trace my >>>>>>>>>>>>>> steps I >>>>>>>>>>>>>> ended >>>>>>>>>>>>>> omitted them because I forgot they were necessary for >>>>>>>>>>>>>> mri_surfcluster. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Either way, the results are the same- I still get one >>>>>>>>>>>>>> whole surface >>>>>>>>>>>>>> cluster as output even after running simulations. In >>>>>>>>>>>>>> this case, I >>>>>>>>>>>>>> re- >>>>>>>>>>>>>> ran it copying your commands, except I used perm >>>>>>>>>>>>>> because I have low >>>>>>>>>>>>>> numbers and no covariates. I also ran 1000 >>>>>>>>>>>>>> permutations, to get a >>>>>>>>>>>>>> quick initial result for testing. My commands and >>>>>>>>>>>>>> output are below. >>>>>>>>>>>>>> >>>>>>>>>>>>>> I would appreciate further help on this, as I'm not >>>>>>>>>>>>>> sure where I'm >>>>>>>>>>>>>> going wrong! >>>>>>>>>>>>>> >>>>>>>>>>>>>> also, I noticed that after your mri_glmfit command, you >>>>>>>>>>>>>> added --i >>>>>>>>>>>>>> divided into 5000 each. Sorry, but I'm not sure what >>>>>>>>>>>>>> you meant by >>>>>>>>>>>>>> that. >>>>>>>>>>>>>> >>>>>>>>>>>>> ---> i had split simulation (10,000 iterations)into >>>>>>>>>>>>> multiple runs >>>>>>>>>>>>> csd1* >>>>>>>>>>>>> (5000 iterations) and csd2* (5000 iterations) since mc-z >>>>>>>>>>>>> relatively takes >>>>>>>>>>>>> long time comparing to permutation. >>>>>>>>>>>>> More on, >>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/ >>>>>>>>>>>>> FsTutorial_2fGroupAnalysis?action=highlight&value=fsgd >>>>>>>>>>>>> <https://surfer.nmr.mgh.harvard.edu/fswiki/ >>>>>>>>>>>>> FsTutorial_2fGroupAnalysis?action=highlight&value=fsgd> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>>> mri_glmfit --y qdec/MF_group_rh/y.mgh --fsgd qdec/ >>>>>>>>>>>>>> MF_group_rh/ >>>>>>>>>>>>>> qdec.fsgd doss --surf fsaverage rh --fwhm 34.309616 --C >>>>>>>>>>>>>> qdec/ >>>>>>>>>>>>>> MF_group_rh/contrasts/Diff-1-2-Intercept.mat --sim perm >>>>>>>>>>>>>> 1000 2 >>>>>>>>>>>>>> stats/ >>>>>>>>>>>>>> newperm_rh/newperm_rh --glmdir stats/newperm_rh/ >>>>>>>>>>>>>> >>>>>>>>>>>>>> gdfReadHeader: reading qdec/MF_group_rh/qdec.fsgd >>>>>>>>>>>>>> INFO: demeaning continous variables >>>>>>>>>>>>>> Continuous Variable Means (all subjects) >>>>>>>>>>>>>> Class Means of each Continuous Variable >>>>>>>>>>>>>> 1 group1 >>>>>>>>>>>>>> 2 group2 >>>>>>>>>>>>>> INFO: gd2mtx_method is doss >>>>>>>>>>>>>> Reading source surface /data/kang/work/struct/alex/ >>>>>>>>>>>>>> freesurfer/ >>>>>>>>>>>>>> subjects_cann/fsaverage/surf/rh.white >>>>>>>>>>>>>> reading group avg surface area 822 cm^2 from file >>>>>>>>>>>>>> Reading in average area /data/kang/work/struct/alex/ >>>>>>>>>>>>>> freesurfer/ >>>>>>>>>>>>>> subjects_cann/fsaverage/surf/rh.white.avg.area.mgh >>>>>>>>>>>>>> simbase stats/newperm_rh/newperm_rh >>>>>>>>>>>>>> Number of vertices 163842 >>>>>>>>>>>>>> Number of faces 327680 >>>>>>>>>>>>>> Total area 65020.765625 >>>>>>>>>>>>>> AvgVtxArea 0.396850 >>>>>>>>>>>>>> AvgVtxDist 0.717994 >>>>>>>>>>>>>> StdVtxDist 0.193566 >>>>>>>>>>>>>> reading group avg surface area 822 cm^2 from file >>>>>>>>>>>>>> Reading in average area /data/kang/work/struct/alex/ >>>>>>>>>>>>>> freesurfer/ >>>>>>>>>>>>>> subjects_cann/fsaverage/surf/rh.white.avg.area.mgh >>>>>>>>>>>>>> INFO: fwhm2niters: Fixing group surface area >>>>>>>>>>>>>> Surface smoothing by fwhm=34.309616, niters=866.000000 >>>>>>>>>>>>>> >>>>>>>>>>>>>> $Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks >>>>>>>>>>>>>> Exp $ >>>>>>>>>>>>>> cwd /data/kang/work/struct/alex/freesurfer/subjects_cann >>>>>>>>>>>>>> cmdline mri_glmfit --y qdec/MF_group_rh/y.mgh --fsgd >>>>>>>>>>>>>> qdec/MF_group_rh/ >>>>>>>>>>>>>> qdec.fsgd doss --surf fsaverage rh --fwhm 34.309616 --C >>>>>>>>>>>>>> qdec/ >>>>>>>>>>>>>> MF_group_rh/contrasts/Diff-1-2-Intercept.mat --sim perm >>>>>>>>>>>>>> 1000 2 >>>>>>>>>>>>>> stats/ >>>>>>>>>>>>>> newperm_rh/newperm_rh --glmdir stats/newperm_rh/ >>>>>>>>>>>>>> sysname Linux >>>>>>>>>>>>>> hostname kang >>>>>>>>>>>>>> machine i686 >>>>>>>>>>>>>> user alex >>>>>>>>>>>>>> FixVertexAreaFlag = 1 >>>>>>>>>>>>>> UseMaskWithSmoothing 1 >>>>>>>>>>>>>> fwhm 34.309616 >>>>>>>>>>>>>> niters 866.000000 >>>>>>>>>>>>>> OneSampleGroupMean 0 >>>>>>>>>>>>>> y /data/kang/work/struct/alex/freesurfer/ >>>>>>>>>>>>>> subjects_cann/qdec/ >>>>>>>>>>>>>> MF_group_rh/y.mgh >>>>>>>>>>>>>> logyflag 0 >>>>>>>>>>>>>> usedti 0 >>>>>>>>>>>>>> FSGD qdec/MF_group_rh/qdec.fsgd >>>>>>>>>>>>>> glmdir stats/newperm_rh/ >>>>>>>>>>>>>> DoFFx 0 >>>>>>>>>>>>>> Loading y from >>>>>>>>>>>>>> /data/kang/work/struct/alex/freesurfer/subjects_cann/ >>>>>>>>>>>>>> qdec/MF_group_rh/y.mgh >>>>>>>>>>>>>> Matrix condition is 1 >>>>>>>>>>>>>> search space = 82167.6 >>>>>>>>>>>>>> Smoothing input by fwhm 34.309616 >>>>>>>>>>>>>> Smoothing done, nsteps = 866, tsec = 1236.17 >>>>>>>>>>>>>> ... done >>>>>>>>>>>>>> DOF = 28 >>>>>>>>>>>>>> thresh = 2, threshadj = 2 >>>>>>>>>>>>>> Starting simulation sim over 1000 trials >>>>>>>>>>>>>> 1/1000 t=0 >>>>>>>>>>>>>> ------------------------------------------------ >>>>>>>>>>>>>> Starting fit and test >>>>>>>>>>>>>> 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% >>>>>>>>>>>>>> Diff-1-2-Intercept 0 nc=3 maxcsize=1910.81 >>>>>>>>>>>>>> sigmax=-3.00831 >>>>>>>>>>>>>> Fmax=13.551 >>>>>>>>>>>>>> 2/1000 t=0.0572833 >>>>>>>>>>>>>> ------------------------------------------------ >>>>>>>>>>>>>> Starting fit and test >>>>>>>>>>>>>> 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% >>>>>>>>>>>>>> Diff-1-2-Intercept 1 nc=0 maxcsize=0 sigmax=1.36036 >>>>>>>>>>>>>> Fmax=4.46612 >>>>>>>>>>>>>> 3/1000 t=0.0994333 >>>>>>>>>>>>>> ------------------------------------------------ >>>>>>>>>>>>>> >>>>>>>>>>>>>> ... and so on... then >>>>>>>>>>>>>> >>>>>>>>>>>>>> mri_surfcluster --src qdec/MF_group_lh/ >>>>>>>>>>>>>> contrasts.sig.mgh --csd >>>>>>>>>>>>>> stats/ >>>>>>>>>>>>>> newperm_lh/newperm_lh-Diff-1-2-Intercept.csd --sum >>>>>>>>>>>>>> stats/newperm_lh/ >>>>>>>>>>>>>> newperm_lh --ocp stats/newperm_lh/newperm_lh.mgh >>>>>>>>>>>>>> >>>>>>>>>>>>>> thsign = abs, id = 0 >>>>>>>>>>>>>> version $Id: mri_surfcluster.c,v 1.39 2007/07/31 >>>>>>>>>>>>>> 00:34:19 greve Exp >>>>>>>>>>>>>> $ >>>>>>>>>>>>>> hemi = rh >>>>>>>>>>>>>> srcid = qdec/MF_group_lh/contrasts.sig.mgh paint >>>>>>>>>>>>>> srcsubjid = fsaverage >>>>>>>>>>>>>> srcsurf = white >>>>>>>>>>>>>> srcframe = 0 >>>>>>>>>>>>>> thsign = abs >>>>>>>>>>>>>> thmin = 2 >>>>>>>>>>>>>> thmax = -1 >>>>>>>>>>>>>> fdr = -1 >>>>>>>>>>>>>> minarea = 0 >>>>>>>>>>>>>> xfmfile = talairach.xfm >>>>>>>>>>>>>> nth = -1 >>>>>>>>>>>>>> sumfile = stats/newperm_lh/newperm_lh >>>>>>>>>>>>>> subjectsdir = >>>>>>>>>>>>>> /data/kang/work/struct/alex/freesurfer/subjects_cann >>>>>>>>>>>>>> FixMNI = 1 >>>>>>>>>>>>>> ------------- XFM matrix (RAS2RAS) --------------- >>>>>>>>>>>>>> /data/kang/work/struct/alex/freesurfer/subjects_cann/ >>>>>>>>>>>>>> fsaverage/mri/ >>>>>>>>>>>>>> transforms/talairach.xfm >>>>>>>>>>>>>> 1.000 0.000 0.000 0.000; >>>>>>>>>>>>>> 0.000 1.000 0.000 0.000; >>>>>>>>>>>>>> 0.000 0.000 1.000 0.000; >>>>>>>>>>>>>> 0.000 0.000 0.000 1.000; >>>>>>>>>>>>>> ---------------------------------------------------- >>>>>>>>>>>>>> Reading source surface /data/kang/work/struct/alex/ >>>>>>>>>>>>>> freesurfer/ >>>>>>>>>>>>>> subjects_cann/fsaverage/surf/rh.white >>>>>>>>>>>>>> reading group avg surface area 822 cm^2 from file >>>>>>>>>>>>>> Reading in average area /data/kang/work/struct/alex/ >>>>>>>>>>>>>> freesurfer/ >>>>>>>>>>>>>> subjects_cann/fsaverage/surf/rh.white.avg.area.mgh >>>>>>>>>>>>>> Done reading source surface >>>>>>>>>>>>>> Computing metric properties >>>>>>>>>>>>>> Loading source values >>>>>>>>>>>>>> number of voxels in search space = 163842 >>>>>>>>>>>>>> Done loading source values (nvtxs = 163842) >>>>>>>>>>>>>> overall max = 43.1907 at vertex 101931 >>>>>>>>>>>>>> overall min = 7.66111 at vertex 28089 >>>>>>>>>>>>>> surface nvertices 163842 >>>>>>>>>>>>>> surface area 65020.838384 >>>>>>>>>>>>>> surface area 65020.838382 >>>>>>>>>>>>>> NOT Adjusting threshold for 1-tailed test >>>>>>>>>>>>>> Searching for Clusters ... >>>>>>>>>>>>>> thmin=2.000000 (2.000000), thmax=-1.000000 (-1), >>>>>>>>>>>>>> thsignid=0, >>>>>>>>>>>>>> minarea=0.000000 >>>>>>>>>>>>>> Found 1 clusters >>>>>>>>>>>>>> Max cluster size 103836.125000 >>>>>>>>>>>>>> INFO: fixing MNI talairach coordinates >>>>>>>>>>>>>> Saving cluster pval stats/newperm_lh/newperm_lh.mgh >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On 04/12/2007, at 11:30 AM, Pratap Kunwar wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Alex, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> You have to do simulations using mri_glmfit before youdo >>>>>>>>>>>>>>> mri_surfcluster, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [more info in this link at >>>>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/ >>>>>>>>>>>>>>> FsTutorial_2fGroupAnalysis?action=highlight&value=fsgd >>>>>>>>>>>>>>> go down to [4.0 Using mri_glmfit to correct for multiple >>>>>>>>>>>>>>> comparisons: ] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> USAGE: ./mri_glmfit >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> --glmdir dir : save outputs to dir >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> --y inputfile **y.mgh >>>>>>>>>>>>>>> --fsgd FSGDF <gd2mtx> : freesurfer descriptor file >>>>>>>>>>>>>>> **qdec.fsgd >>>>>>>>>>>>>>> --C contrast1.mat <--C contrast2.mat ...> >>>>>>>>>>>>>>> --fwhm fwhm : smooth input by fwhm ** your >>>>>>>>>>>>>>> smoothing value from >>>>>>>>>>>>>>> " >>>>>>>>>>>>>>> fwhm.dat" >>>>>>>>>>>>>>> --surf subject hemi <surfname> : needed for some >>>>>>>>>>>>>>> flags (uses >>>>>>>>>>>>>>> white by >>>>>>>>>>>>>>> default) **lh or rh >>>>>>>>>>>>>>> --sim nulltype nsim thresh csdbasename : simulation >>>>>>>>>>>>>>> perm, mc- >>>>>>>>>>>>>>> full, mc-z >>>>>>>>>>>>>>> **mc-z (i used) is faster than mc-full, minimum >>>>>>>>>>>>>>> threshold value >>>>>>>>>>>>>>> ( i.e. >>>>>>>>>>>>>>> 1.3 for 0.05), >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> My command was more like this, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> mri_glmfit --y y.mgh --fsgd qdec.fsgd doss --surf >>>>>>>>>>>>>>> fsaverage rh -- >>>>>>>>>>>>>>> fwhm < ?? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> --C contrast/contrastname.mat --sim mc-z 5000 1.3 f11/ >>>>>>>>>>>>>>>> csd1 -- >>>>>>>>>>>>>>>> glmdir f11 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> mri_glmfit --y y.mgh --fsgd qdec.fsgd doss --surf >>>>>>>>>>>>>>> fsaverage rh >>>>>>>>>>>>>>> --fwhm >>>>>>>>>>>>>>> 14.504073 --C contrast/contrastname.mat --sim mc-z >>>>>>>>>>>>>>> 5000 1.3 >>>>>>>>>>>>>>> f11/csd2 >>>>>>>>>>>>>>> --glmdir f11 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> --i divided into 5000 each >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> from above mri_glmfit, i got two files starting with >>>>>>>>>>>>>>> csd1* .csd >>>>>>>>>>>>>>> and >>>>>>>>>>>>>>> csd2*.csd. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Next one is >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> mri_surfcluster, >>>>>>>>>>>>>>> mri_surfcluster --src contrastname/sig.mgh --csd >>>>>>>>>>>>>>> csd1* .csd --csd >>>>>>>>>>>>>>> csd2* >>>>>>>>>>>>>>> ..csd --sum <text summary file --sum <*.sum> --ocp >>>>>>>>>>>>>>> <*.mgh> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> the output file *.sum can be opened in text editor >>>>>>>>>>>>>>> and *.mgh can >>>>>>>>>>>>>>> be seen >>>>>>>>>>>>>>> using tksurfer. Check the link above link for more >>>>>>>>>>>>>>> details (i just >>>>>>>>>>>>>>> followed that link when i did last month). >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> let me know if you get into more problems. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> pratap >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On 11/28/2007 07:43 PM, Alex Fornito wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>> I have run qdec for a simple contrast comparing >>>>>>>>>>>>>>>>>> thickness >>>>>>>>>>>>>>>>>> across >>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>> cortical surface between a patient and control >>>>>>>>>>>>>>>>>> group. Not much >>>>>>>>>>>>>>>>>> survives vertex-wise FDR correction, and I would >>>>>>>>>>>>>>>>>> like to try >>>>>>>>>>>>>>>>>> cluster-based thresholding. I would like to make >>>>>>>>>>>>>>>>>> sure I >>>>>>>>>>>>>>>>>> understand the >>>>>>>>>>>>>>>>>> inputs to the command. Am I correct on the following? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> --in = the signifcance values (i.e., >>>>>>>>>>>>>>>>>> contrast_name.sig.mgh >>>>>>>>>>>>>>>>>> file) >>>>>>>>>>>>>>>>>> --thmin = the vertexwise threshold for determining >>>>>>>>>>>>>>>>>> clusters, >>>>>>>>>>>>>>>>>> where 2 >>>>>>>>>>>>>>>>>> corresponds to p=.01 >>>>>>>>>>>>>>>>>> --minarea = the cluster extent threshold - Am I >>>>>>>>>>>>>>>>>> correct in >>>>>>>>>>>>>>>>>> assuming >>>>>>>>>>>>>>>>>> this should not be smaller than the smoothing kernel? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> When I run the command below, I get the following >>>>>>>>>>>>>>>>>> output. >>>>>>>>>>>>>>>>>> Only one >>>>>>>>>>>>>>>>>> (whole hemi) cluster is identified. I'm not sure if >>>>>>>>>>>>>>>>>> its a >>>>>>>>>>>>>>>>>> problem in >>>>>>>>>>>>>>>>>> my command line, or with my data. Also, I seem to >>>>>>>>>>>>>>>>>> have the >>>>>>>>>>>>>>>>>> --cwsig >>>>>>>>>>>>>>>>>> flag wrong, but can't figure out the error >>>>>>>>>>>>>>>>>> (appending .w >>>>>>>>>>>>>>>>>> or .label to >>>>>>>>>>>>>>>>>> the end of the output filename does not change the >>>>>>>>>>>>>>>>>> error). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I greatly appreciate your help. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> mri_surfcluster --in qdec/MF_group_lh/ >>>>>>>>>>>>>>>>>> contrasts.sig.mgh >>>>>>>>>>>>>>>>>> --subject >>>>>>>>>>>>>>>>>> fsaverage --hemi lh --surf white --annot aparc -- >>>>>>>>>>>>>>>>>> sign abs >>>>>>>>>>>>>>>>>> --thmin 2 >>>>>>>>>>>>>>>>>> --minarea 25 --sum stats/qdec_run/cluster/ >>>>>>>>>>>>>>>>>> summary.txt --o >>>>>>>>>>>>>>>>>> stats/qdec_run/cluster/cluster_output --cwsig >>>>>>>>>>>>>>>>>> stats/qdec_run/cluster/cwsig --olab >>>>>>>>>>>>>>>>>> stats/qdec_run/cluster/MF_group_lh_thk >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> thsign = abs, id = 0 >>>>>>>>>>>>>>>>>> version $Id: mri_surfcluster.c,v 1.39 2007/07/31 >>>>>>>>>>>>>>>>>> 00:34:19 greve >>>>>>>>>>>>>>>>>> Exp $ >>>>>>>>>>>>>>>>>> hemi = lh >>>>>>>>>>>>>>>>>> srcid = qdec/MF_group_lh/contrasts.sig.mgh >>>>>>>>>>>>>>>>>> paint >>>>>>>>>>>>>>>>>> srcsubjid = fsaverage >>>>>>>>>>>>>>>>>> srcsurf = white >>>>>>>>>>>>>>>>>> srcframe = 0 >>>>>>>>>>>>>>>>>> thsign = abs >>>>>>>>>>>>>>>>>> thmin = 2 >>>>>>>>>>>>>>>>>> thmax = -1 >>>>>>>>>>>>>>>>>> fdr = -1 >>>>>>>>>>>>>>>>>> minarea = 25 >>>>>>>>>>>>>>>>>> xfmfile = talairach.xfm >>>>>>>>>>>>>>>>>> nth = -1 >>>>>>>>>>>>>>>>>> outid = stats/qdec_run/cluster/cluster_output paint >>>>>>>>>>>>>>>>>> sumfile = stats/run2/cluster/summary.txt >>>>>>>>>>>>>>>>>> subjectsdir = /data/kang/work/struct/alex/ >>>>>>>>>>>>>>>>>> freesurfer/ >>>>>>>>>>>>>>>>>> subjects_cann >>>>>>>>>>>>>>>>>> FixMNI = 1 >>>>>>>>>>>>>>>>>> ------------- XFM matrix (RAS2RAS) --------------- >>>>>>>>>>>>>>>>>> /data/kang/work/struct/alex/freesurfer/ >>>>>>>>>>>>>>>>>> subjects_cann/fsaverage/ >>>>>>>>>>>>>>>>>> mri/transforms/talairach.xfm >>>>>>>>>>>>>>>>>> 1.000 0.000 0.000 0.000; >>>>>>>>>>>>>>>>>> 0.000 1.000 0.000 0.000; >>>>>>>>>>>>>>>>>> 0.000 0.000 1.000 0.000; >>>>>>>>>>>>>>>>>> 0.000 0.000 0.000 1.000; >>>>>>>>>>>>>>>>>> ---------------------------------------------------- >>>>>>>>>>>>>>>>>> Reading source surface >>>>>>>>>>>>>>>>>> /data/kang/work/struct/alex/freesurfer/ >>>>>>>>>>>>>>>>>> subjects_cann/fsaverage/ >>>>>>>>>>>>>>>>>> surf/lh.white >>>>>>>>>>>>>>>>>> reading group avg surface area 822 cm^2 from file >>>>>>>>>>>>>>>>>> Reading in average area >>>>>>>>>>>>>>>>>> /data/kang/work/struct/alex/freesurfer/ >>>>>>>>>>>>>>>>>> subjects_cann/fsaverage/ >>>>>>>>>>>>>>>>>> surf/lh.white.avg.area.mgh >>>>>>>>>>>>>>>>>> Done reading source surface >>>>>>>>>>>>>>>>>> Reading annotation >>>>>>>>>>>>>>>>>> /data/kang/work/struct/alex/freesurfer/ >>>>>>>>>>>>>>>>>> subjects_cann/fsaverage/ >>>>>>>>>>>>>>>>>> label/lh.aparc.annot >>>>>>>>>>>>>>>>>> reading colortable from annotation file... >>>>>>>>>>>>>>>>>> colortable with 35 entries read (originally >>>>>>>>>>>>>>>>>> /space/amaebi/26/users/buckner_cortical_atlas/scripts/ >>>>>>>>>>>>>>>>>> colortable_final.txt) >>>>>>>>>>>>>>>>>> Computing metric properties >>>>>>>>>>>>>>>>>> Loading source values >>>>>>>>>>>>>>>>>> number of voxels in search space = 163842 >>>>>>>>>>>>>>>>>> Done loading source values (nvtxs = 163842) >>>>>>>>>>>>>>>>>> overall max = 43.1907 at vertex 101931 >>>>>>>>>>>>>>>>>> overall min = 7.66111 at vertex 28089 >>>>>>>>>>>>>>>>>> surface nvertices 163842 >>>>>>>>>>>>>>>>>> surface area 65416.985991 >>>>>>>>>>>>>>>>>> surface area 65416.985976 >>>>>>>>>>>>>>>>>> NOT Adjusting threshold for 1-tailed test >>>>>>>>>>>>>>>>>> Searching for Clusters ... >>>>>>>>>>>>>>>>>> thmin=2.000000 (2.000000), thmax=-1.000000 (-1), >>>>>>>>>>>>>>>>>> thsignid=0, >>>>>>>>>>>>>>>>>> minarea=25.000000 >>>>>>>>>>>>>>>>>> Found 1 clusters >>>>>>>>>>>>>>>>>> Max cluster size 103339.460938 >>>>>>>>>>>>>>>>>> INFO: fixing MNI talairach coordinates >>>>>>>>>>>>>>>>>> Saving thresholded output to >>>>>>>>>>>>>>>>>> stats/qdec_run/cluster/cluster_output >>>>>>>>>>>>>>>>>> avg = 35.029, stdev = 4.669, min = 7.661, max = 43.191 >>>>>>>>>>>>>>>>>> Saving cluster pval stats/qdec_run/cluster/cwsig >>>>>>>>>>>>>>>>>> unknown file type for file (stats/qdec_run/cluster/ >>>>>>>>>>>>>>>>>> cwsig) >>>>>>>>>>>>>>>>>> LabelWrite: saving to stats/qdec_run/cluster/ >>>>>>>>>>>>>>>>>> MF_group_lh_thk-0001.label >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Alex Fornito >>>>>>>>>>>>>>>>>> JN Peters Research Fellow >>>>>>>>>>>>>>>>>> Melbourne Neuropsychiatry Centre >>>>>>>>>>>>>>>>>> Department of Psychiatry >>>>>>>>>>>>>>>>>> The University of Melbourne >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Postal address: >>>>>>>>>>>>>>>>>> Melbourne Neuropsychiatry Centre >>>>>>>>>>>>>>>>>> National Neuroscience Facility >>>>>>>>>>>>>>>>>> Levels 2 & 3, 161 Barry St >>>>>>>>>>>>>>>>>> Carlton South Vic 3053 Australia >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Ph: +61 3 8344 1861 >>>>>>>>>>>>>>>>>> Fax: +61 3 9348 0469 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [EMAIL PROTECTED] >>>>>>>>>>>>>>>>>> <mailto:[EMAIL PROTECTED]> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ------------------------------------------------------ >>>>>>>>>>>>>>>>>> ------------- >>>>>>>>>>>>>>>>>> ----- >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ >>>>>>>>>>>>>>>>>> freesurfer >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ >>>>>>>>>>>>>>>> freesurfer >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>> Alex Fornito >>>>>>>>>>>>>> JN Peters Research Fellow >>>>>>>>>>>>>> Melbourne Neuropsychiatry Centre >>>>>>>>>>>>>> Department of Psychiatry >>>>>>>>>>>>>> The University of Melbourne >>>>>>>>>>>>>> >>>>>>>>>>>>>> Postal address: >>>>>>>>>>>>>> Melbourne Neuropsychiatry Centre >>>>>>>>>>>>>> National Neuroscience Facility >>>>>>>>>>>>>> Levels 2 & 3, 161 Barry St >>>>>>>>>>>>>> Carlton South Vic 3053 Australia >>>>>>>>>>>>>> >>>>>>>>>>>>>> Ph: +61 3 8344 1861 >>>>>>>>>>>>>> Fax: +61 3 9348 0469 >>>>>>>>>>>>>> >>>>>>>>>>>>>> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>> Alex Fornito >>>>>>>>>>>> JN Peters Research Fellow >>>>>>>>>>>> Melbourne Neuropsychiatry Centre >>>>>>>>>>>> Department of Psychiatry >>>>>>>>>>>> The University of Melbourne >>>>>>>>>>>> >>>>>>>>>>>> Postal address: >>>>>>>>>>>> Melbourne Neuropsychiatry Centre >>>>>>>>>>>> National Neuroscience Facility >>>>>>>>>>>> Levels 2 & 3, 161 Barry St >>>>>>>>>>>> Carlton South Vic 3053 Australia >>>>>>>>>>>> >>>>>>>>>>>> Ph: +61 3 8344 1861 >>>>>>>>>>>> Fax: +61 3 9348 0469 >>>>>>>>>>>> >>>>>>>>>>>> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>>>> MGH-NMR Center >>>>>>>>>>> [EMAIL PROTECTED] >>>>>>>>>>> Phone Number: 617-724-2358 >>>>>>>>>>> Fax: 617-726-7422 >>>>>>>>>>> >>>>>>>>>>> In order to help us help you, please follow the steps in: >>>>>>>>>>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> Alex Fornito >>>>>>>>>> JN Peters Research Fellow >>>>>>>>>> Melbourne Neuropsychiatry Centre >>>>>>>>>> Department of Psychiatry >>>>>>>>>> The University of Melbourne >>>>>>>>>> >>>>>>>>>> Postal address: >>>>>>>>>> Melbourne Neuropsychiatry Centre >>>>>>>>>> National Neuroscience Facility >>>>>>>>>> Levels 2 & 3, 161 Barry St >>>>>>>>>> Carlton South Vic 3053 Australia >>>>>>>>>> >>>>>>>>>> Ph: +61 3 8344 1861 >>>>>>>>>> Fax: +61 3 9348 0469 >>>>>>>>>> >>>>>>>>>> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> <Pic.png>_______________________________________________ >>>>>>>>>> Freesurfer mailing list >>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>> >>>>>>>>> Alex Fornito >>>>>>>>> JN Peters Research Fellow >>>>>>>>> Melbourne Neuropsychiatry Centre >>>>>>>>> Department of Psychiatry >>>>>>>>> The University of Melbourne >>>>>>>>> >>>>>>>>> Postal address: >>>>>>>>> Melbourne Neuropsychiatry Centre >>>>>>>>> National Neuroscience Facility >>>>>>>>> Levels 2 & 3, 161 Barry St >>>>>>>>> Carlton South Vic 3053 Australia >>>>>>>>> >>>>>>>>> Ph: +61 3 8344 1861 >>>>>>>>> Fax: +61 3 9348 0469 >>>>>>>>> >>>>>>>>> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> -- >>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> [EMAIL PROTECTED] >>>>>>>> Phone Number: 617-724-2358 >>>>>>>> Fax: 617-726-7422 >>>>>>>> >>>>>>>> In order to help us help you, please follow the steps in: >>>>>>>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> [EMAIL PROTECTED] >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> >>>>>> In order to help us help you, please follow the steps in: >>>>>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> Alex Fornito >>>>> JN Peters Research Fellow >>>>> Melbourne Neuropsychiatry Centre >>>>> Department of Psychiatry >>>>> The University of Melbourne >>>>> >>>>> Postal address: >>>>> Melbourne Neuropsychiatry Centre >>>>> National Neuroscience Facility >>>>> Levels 2 & 3, 161 Barry St >>>>> Carlton South Vic 3053 Australia >>>>> >>>>> Ph: +61 3 8344 1861 >>>>> Fax: +61 3 9348 0469 >>>>> >>>>> [EMAIL PROTECTED] >>>>> >>>>> >>>>> >>>>> >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> [EMAIL PROTECTED] >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> In order to help us help you, please follow the steps in: >>>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> >>>> >>> >>> Alex Fornito >>> JN Peters Research Fellow >>> Melbourne Neuropsychiatry Centre >>> Department of Psychiatry >>> The University of Melbourne >>> >>> Postal address: >>> Melbourne Neuropsychiatry Centre >>> National Neuroscience Facility >>> Levels 2 & 3, 161 Barry St >>> Carlton South Vic 3053 Australia >>> >>> Ph: +61 3 8344 1861 >>> Fax: +61 3 9348 0469 >>> >>> [EMAIL PROTECTED] >>> >>> >>> >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> [EMAIL PROTECTED] >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> In order to help us help you, please follow the steps in: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > Alex Fornito > JN Peters Research Fellow > Melbourne Neuropsychiatry Centre > Department of Psychiatry > The University of Melbourne > > Postal address: > Melbourne Neuropsychiatry Centre > National Neuroscience Facility > Levels 2 & 3, 161 Barry St > Carlton South Vic 3053 Australia > > Ph: +61 3 8344 1861 > Fax: +61 3 9348 0469 > > [EMAIL PROTECTED] > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
