Dear Sahil, I suppose, for qcache 1.3 the equivalent cluster-forming threshold z-value is
two-tailed test: qnorm(1-10^-1.3/2)=1.958949 for one-tailed test: qnorm(1-10^-1.3)=1.643704 (qnorm is R function call for quantile function of normal distribution, you can compute this by using other methods or use statistical z-tables) And, the directionality of the hypothesis is I suppose specified by the sign of your contrast vector, as I wrote in my previous mail. As for the output files, you can look at the documentation: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide#Output_files For example, if you are looking for the p-values, used cluster extent inference and used t-contrast, the file with FWER-corrected p-values would be something like output_basename_clustere_tstat_fwep.mgz Antonin Hello Martin and Antonin, I was following this conversation very closely to understand how to use PALM in FreeSurfer.Can any of you please confirm in case I am interested in checking correlation between gyrification index (LGI) and behavioral measure using two tailed, p < 0.05: Step 1: I used --cache 1.3 Step 2: Because (1-10^-1.3)= 0.95, so I will have to use -C 0.95 in palm command Could you please confirm if thats correct and the output *_tstat.mgz is the final two-tailed corrected significant correlation map between LGI and behavioral data? Thanks a lot for this wonderful discussion. Sahil PS: For one-tailed: it will be -C -0.95 in palm command, correct? On Tue, Mar 7, 2017 at 3:48 PM, Antonin Skoch <a...@ikem.cz> wrote: > Dear Martin, > > after -s option, there have to be 2 arguments, as I specified in my previous > mail: > > -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh > > And beware that -C has to have negative sign, if your hypothesis is > one-tailed negative. > > Antonin > > > > Hi Antonin, > > Thank you so much for this detailed explanation, that's really useful. > > Following your instructions, I ran: > > palm -i lh.MEQ_LGI.10.mgh -s fsaverage/surf/lh.white.avg.area.mgh -d > check.csv -t Contrast_MEQ.csv -n 5000 -m lh.MEQ_LGI.glmdir/mask.mgh -o > myresults -Cstat extent -C 3.719016 > > but I am getting following error: > > Running PALM alpha104 using MATLAB 9.0.0.341360 (R2016a) with the following > options: > -i lh.MEQ_LGI.10.mgh > -s fsaverage/surf/lh.white.avg.area.mgh > -d check.csv > -t Contrast_MEQ.csv > -n 5000 > -m lh.MEQ_LGI.glmdir/mask.mgh > -o myresults > -Cstat extent > -C 3.719016 > Loading surface 1/1: fsaverage/surf/lh.white.avg.area.mgh > Reading input 1/1: lh.MEQ_LGI.10.mgh > > Struct contents reference from a non-struct array object. > > Error in palm_takeargs (line 1632) > if any(size(plm.srf{s}.data.vtx, > 1) == ... > > Error in palm_core (line 33) > [opts,plm] = palm_takeargs(varargin{:}); > > Error in palm (line 81) > palm_core(varargin{:}); > > Could you please help me in resolving this error? > > Thanks much. > > On Tue, Mar 7, 2017 at 2:55 PM, Antonin Skoch <a...@ikem.cz> wrote: > > > Dear Martin, > > > > input -i input file is > > > > lh.MEQ_LGI.10.mgh file in your glmdir directory (for left hemisphere). > > > > As you could read in following messages in the referenced thread in FSL > > discussion forum, cluster-forming threshold need to be specified in z, not > > in t. > > > > Therefore, you would have to select cluster forming threshold and specify > > it as a z score. > > > > I think that your z-score for your original mri_glmfit-sim commandline > > argument > > > > --cache 4 neg > > > > will be -qnorm(1-10^-4)=-3.719016. (I am not perfectly sure since I never > > tried negative one-side hypothesis testing in PALM). > > > > You could also use other statistics, such as cluster mass, or TFCE. See > > PALM user guide. > > > > Do not include -pmethodp none and -pmethodr none, since you would need the > > partitioning due your non-orthogonal design matrix. > > > > ?h.white.avg.area.mgh file (which you will find under fsaverage directory) > > goes as second argument after -s option. > > > > Therefore I suppose the commandline for cluster extent inference with > > cluster forming threshold p=0.0001, negative one-sided hypothesis, left > > hemisphere, will be hopefully something like > > > > palm > > -i y.mgh > > -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh > > -d Xg.csv > > -t your_contrasts.csv > > -n number_of_permutations > > -m mask.mgh > > -o output_basename > > -Cstat extent > > -C -3.719016 > > -saveglm > > -savedof > > -savemetrics > > > > The last 3 commandline options are only for diagnostical purposes. > > > > The output is surface overlay you can visualize in freeview. > > > > I use following code snippet for the reporting significant clusters in MNI > > coordinates: > > > > # PALM output cluster extent p maps have 1 outside cluster - problem with > > mri_surfcluster and also for display in freeView > > #here we set values 1 to 0 in pmaps. > > #done by binarizing and subtracting > > if [[ $# -ne 2 ]]; then > > echo "get cluster summary of PALM statistics. Expecting 2 arguments: 1- > > input p-map, 2- hemisphere (lh/rh)" > > exit > > fi > > mri_binarize --i $1 --min 1 --o p_bin.mgz > > mris_calc --output ${1%%.mgz}_filtered.mgz $1 sub p_bin.mgz > > mri_surfcluster --in ${1%%.mgz}_filtered.mgz --subject fsaverage --hemi $2 > > --surf white --annot aparc --thmin 0.000000001 --thmax 0.05 --mask mask.mgh > > --sum ${1%%.mgz}_cluster.summary --nofixmni > > rm p_bin.mgz > > > > They are not Bonferroni-corrected for 2 hemispheres (--2spaces). > > > > Regarding your design and contrast: > > > > Design has to be matrix of values. You can use qdec to produce Xg.dat file > > with design matrix, then rename it to Xg.csv to be correctly readable by > > PALM. > > > > Regards, > > > > Antonin > > > > > > > > > > > > Hi Antonin, > > > > As you suggested in discussion forum, I tried to run following command > > after mri_glmfit: > > > > palm -s fsaverage/surf/lh.white -n 10000 -m mask.mgh -Cstat extent -C > > 1.974975 -pmethodp none -pmethodr none -twotail -d Design_MEQ.txt -t > > Contrast_MEQ.txt > > > > Running PALM alpha104 using MATLAB 9.0.0.341360 (R2016a) with the following > > options: > > > > -s fsaverage/surf/lh.white > > > > -n 10000 > > > > -m mask.mgh > > > > -Cstat extent > > > > -C 1.974975 > > > > -pmethodp none > > > > -pmethodr none > > > > -twotail > > > > -d Design.txt > > > > -t Contrast.txt > > > > Found FSL in /usr/share/fsl/5.0 > > > > Found FreeSurfer in /usr/local/freesurfer > > > > Found SPM in /usr/local/spm12 > > > > Error using palm_takeargs (line 1141) > > > > Missing input data (missing "-i"). > > > > Error in palm_core (line 33) > > > > [opts,plm] = palm_takeargs(varargin{:}); > > > > Error in palm (line 81) > > > > palm_core(varargin{:}); > > > > Looks like error is because its missing -i input here, I am not sure what's > > input file here? > > > > Also, I am trying to correlate LGI versus behavioral score, regressing out > > the effect of sex and age. So I just wanted to confirm if my design.txt and > > contrast.txt files are correct here. Please find both following: > > > > Design file (Variables Behav, Age) as following: > > > > S001 Male 60 36 > > > > S003 Female 73 29 > > > > S004 Male 48 39 > > > > .......so on...... > > > > Contrast file as following: > > 0 0 0.5 0.5 0 0 (same as *.mtx file used for glm_fit) > > > > Thank you so much for your help and time. > > > > On Tue, Mar 7, 2017 at 10:49 AM, Martin Juneja <mj70...@gmail.com> wrote: > > > > > Hi Antonin, > > > > > > Thanks a lot for your reply. > > > > > > Somehow, in the link you sent, I could not find any response to your > > > email. But I can see your email to Anderson and command line parameters. > > > > > > As I am not an expert in using FreeSurfer, so would it be possible for you > > > to share detailed step-by-step guide and PALM command after I run > > > mri_glmfit > > > command and how and where to include '?h.white.avg.area.mgh' file? > > > > > > I would really appreciate any help. > > > > > > On Mon, Mar 6, 2017 at 4:28 PM, Antonin Skoch <a...@ikem.cz> wrote: > > > > > >> Dear Martin, > > >> > > >> I think yes, you can use PALM with FreeSurfer surfaces, see my > > >> conversation with Anderson on FSL list: > > >> > > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1604&L=FSL > > > > > >> &D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=239088 > > >> > > >> but beware not to forget to include average the vertex area > > >> (?h.white.avg.area.mgh) file. > > >> > > >> Antonin > > >> > > >> > > >> If you don't have an orthogonal design, then you can't use > > >> mri_glmfit-sim. I think you can use PALM: > > >> > > >> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM > > >> > > >> I have not tried it yet. > > >> > > >> Anderson, can you use PALM with surfaces? > > >> > > >> > > >> > > >> > > >> > > >> > > >> On 03/06/2017 05:23 PM, Martin Juneja wrote: > > >> > Hi Dr. Greve, > > >> > > > >> > I tried to run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm > > >> > 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 > > >> > It gives error that ERROR: design matrix is not orthogonal, cannot be > > >> > used with permutation. > > >> > > > >> > But when I run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm > > >> > 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 --perm-force, it > > >> > works. > > >> > > > >> > I am not sure whether I will have to make the design matrix > > >> > orthogonal. If so, could you please tell me how that can be done? > > >> > > > >> > Or using --perm-force should be fine? > > >> > > > >> > Thanks. > > >> > > > >> > On Mon, Mar 6, 2017 at 1:58 PM, Douglas N Greve > > >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > > >> > <gr...@nmr.mgh.harvard.edu> > > >> > <gr...@nmr.mgh.harvard.edu> > > >> > <gr...@nmr.mgh.harvard.edu>>> wrote: > > >> > > > >> > This is a problem with using LGI in that it is already extremely > > >> > smooth > > >> > that the smoothness exceeds the limit of the look up table that we > > >> > supply. I recommend that you not use a gaussian-based correction > > >> > for > > >> > LGI. Instead, use permutation (see mri_glmfit-sim --help). > > >> > > > >> > > > >> > > > >> > On 03/06/2017 01:36 PM, Martin Juneja wrote: > > >> > > Hello everyone, > > >> > > > > >> > > I am trying to extract clusters showing significant correlation > > >> > > between LGI and a behavioral measure. I am able to extract PCC > > >> > and > > >> > > sig.mgh but at the last step when I try to run simulation command > > >> > to > > >> > > view corrected results and I run: > > >> > > > > >> > > mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp > > >> > 0.05 > > >> > > --2spaces > > >> > > > > >> > > I get following error: > > >> > > > > >> > > ERROR: cannot find > > >> > > > > >> > > > >> > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd > > >> > > > > >> > > But I can see mc-z.csd file in fwhm30 etc. > > >> > > > > >> > > Full message on terminal window is attached following. > > >> > > > > >> > > Any help would be really appreciated. > > >> > > > > >> > > ----- Full message ---- > > >> > > > > >> > > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd > > >> > dods --C > > >> > > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir > > >> > lh.MEQ_LGI.glmdir > > >> > > > > >> > > WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin > > >> > > > > >> > > SURFACE: fsaverage lh > > >> > > > > >> > > log file is lh.MEQ_LGI.glmdir/cache.mri_glmfit-sim.log > > >> > > > > >> > > /usr/local/freesurfer/bin/mri_glmfit-sim > > >> > > > > >> > > --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 --2spaces > > >> > > > > >> > > $Id: mri_glmfit-sim,v 1.60 2016/04/30 15:13:36 greve Exp $ > > >> > > > > >> > > Mon Mar 6 11:11:13 MST 2017 > > >> > > > > >> > > setenv SUBJECTS_DIR > > >> > > /data/emot/Freesurfer/FreeSurferSegmentation/SB_AgingAll > > >> > > > > >> > > FREESURFER_HOME /usr/local/freesurfer > > >> > > > > >> > > Original mri_glmfit command line: > > >> > > > > >> > > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd > > >> > dods --C > > >> > > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir > > >> > lh.MEQ_LGI.glmdir > > >> > > > > >> > > DoSim = 0 > > >> > > > > >> > > UseCache = 1 > > >> > > > > >> > > DoPoll = 0 > > >> > > > > >> > > DoPBSubmit = 0 > > >> > > > > >> > > DoBackground = 0 > > >> > > > > >> > > DiagCluster = 0 > > >> > > > > >> > > gd2mtx = dods > > >> > > > > >> > > fwhm = 35.073391 > > >> > > > > >> > > ERROR: cannot find > > >> > > > > >> > > > >> > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd > > >> > > > > >> > > > > > >
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