Hi all,
That's exactly as Antonin says -- I have very little to add :-)
Only a few suggestions:
- With surfaces, both cluster and TFCE statistics tend to be slow. Consider
using the tail approximation ("-approx tail -n 500 -nouncorrected")
- Include -logp, so that the p-values are in log-10 scale. Significant
p-values are then those above 1.3 (i.e., -log10(0.05). This will help to
make the figures nicer later.
All the best,
Anderson
On 8 March 2017 at 00:19, Antonin Skoch <a...@ikem.cz> wrote:
> 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>
> > > >> > <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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