Dear Sahil,

I would suggest at first to make check of your GLM PALM setup by comparing mri_glmfit and PALM output files (using the same design and contrast):

1. values of gamma.mgh should correspond to values of *cope.mgh

2. values of F.mgh should be (*dpv_tstat.mgh) ^2.

3. values of sig.mgh should be {roughly) values of -log10(*dpv_tstat_uncp.mgh) - I am currently not sure why I do not get exact correspondence here.

4. When you threshold the sig.mgh by some threshold in freeview (let it be x) and use the same corresponding cluster-forming z-score threshold -C  in PALM computed as 
qnorm(1-10^-x/2)
(and use two-sided hypothesis by specifying -twotail), your *clustere_tstat.mgz should show the clusters with the same shape (regardless of their values, the clusters will be defined by non-zero value, other vertices would be zero) as the thresholded display of sig.mgh (computed by -two sided hypothesis).

If there is any inconsistence, then there is probably something wrong with your PALM setup.

Antonin


Dear Antonin,

Could you please have a look at the attached screen shot. This map is with
full number of permutations, without -approx tail -n 500 -nouncorrected

Here, I noticed that its only *_dpv_tstat.mgz which looks correct and
giving very high negative value, close to that big cluster, small positive
values at red clusters and the value changes when I change the position of
cursor.

*_dpv_tstat_fwep shows value of 1 mostly but shows between 0.97 and 1
close/at the red clusters and 1 elsewhere, even at the big blue negative
cluster.

Third, *_clustere_tstat_fwep and *_clustere_tstat shows 1 and 0
respectively everywhere, even at the big blue negative cluster.

If there is something fishy with the analysis, would you mind looking at
the data and the detailed commands I am using to run the analysis?

Thanks a lot,
Sahil

On Wed, Mar 8, 2017 at 11:54 PM, Antonin Skoch <ansk@ikem.cz> wrote:

> Dear Sahil,
>
> to assure that there is no other issue with your setup, I would recommend to obtain cluster-wise p-pvalue of that big cluster to see if it is reasonable, i.e. if it is somewhat close to the significance.
>
> Therefore, I would load *_clustere_tstat_fwep and click to the area of big cluster and see what the values of the vertices in that region are.
>
> Or, I would increase --thmax in mri_surfcluster to see the cluster-wise p-value(s). If you use --thmax 0.9999 (or maybe 1), you should see cluster-wise FWER corrected p-values of all clusters formed by used cluster-forming threshold.
>
> I would also maybe try to switch-off tail approximation and run it in full number of permutations (i.e. do not use -approx tail -n 500 -nouncorrected).
>
> If there is no other issue, then yes, the conclusion would be, that for the used cluster-extent inference and currently set cluster-forming threshold, none of the clusters survived FWER correction at cluster-wise p-value threshold of 0.05.
>
> Antonin
>
>
>
> Dear Antonin,
>
> Setting minimum to 1.3 for *_clustere_tstat_fwep doesn't show any
> significant cluster and similarly thresholded map *dpv_tstat.mgz also
> doesn't show anything at -log10(0.05) = 1.3. As you said, it seems like
> even though there is big cluster but after FWER correction, the
> significance goes away. Actually, even when I removed -logp, I still do not
> see any significant cluster.
>
> Next, I tried to use mri_surfcluster using following three commands
> following instructions from the link you sent:
>
> mri_binarize --i Results_Left_clustere_tstat_fwep.mgz --min 1 --o p_bin.mgz
>
> mris_calc --output pmap_filter.mgz Results_Left_clustere_tstat_fwep.mgz sub
> p_bin.mgz
>
> mri_surfcluster --in pmap_filter.mgz --subject fsaverage --hemi lh --surf
> white --annot aparc.a2009s --thmin 0.00000001 --thmax 0.05 --mask
> glmdir/mask.mgh --sum summary --nofixmni
>
> This gives me 'zero' cluster in the summary file.
>
> If the above steps are correct, would you conclude that the LGI results are
> not significant and un-reportable for publication purpose and I should give
> a try to thickness, volume and area maps?
>
> Thanks you so much Antonin for all your help.
> Sahil
>
>
>
> On Wed, Mar 8, 2017 at 3:05 PM, Antonin Skoch <a...@ikem.cz> wrote:
>
> > Dear Sahil,
> >
> > If you used -logp as Anderson suggested, you should set your min to 1.3 to
> > threshold your *_clustere_tstat_fwep map and see the clusters.
> >
> > What is the value of *_clustere_tstat_fwep in the region of the big
> > cluster seen at thresholded map *dpv_tstat.mgz ?  This should correspond to
> > your -log10(p) of your cluster.
> >
> > I personally did not use -logp and use the mri_surfcluster for the
> > reporting of the clusters, as I wrote in previous mail here:
> >
> > freesurfer@nmr.mgh.harvard.edu/msg52042.html" title="http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52042.html" target="_blank">http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52042.html
>
> >
> > But it is only matter of personal preference.
> >
> > And, beware, that the LGI is very smooth measure, therefore also rather
> > big cluster can be insignificant after FWER correction.
> >
> > Antonin
> >
> >
> >
> >
> > Hi Antonin,
> >
> > Here, I am sending you more information:
> >
> > (1). I used following command:
> > palm -i lh.Behav_LGI.10.mgh -s fsaverage/surf/lh.white
> > fsaverage/surf/lh.white.avg.
> area.mgh -d Xg_Behav.csv -t
> > Contrast_Behav.csv
> > -m lh.Behav_LGI.glmdir/mask.mgh -o Results_Left -Cstat extent -C 1.95
> > -approx tail -n 500 -nouncorrected -logp
> >
> > (2). Somehow, view of *_clustere_tstat_fwep is single colored, thresholded
> > 0 (min) and 1(max), which seems suspicious. Please find it attached.
> >
> > (3). Data showed in screen shot 1 is just partial correlation coefficient
> > (PCC, limiting between 0.30-0.35), obtained after running glm_fit command
> > and saved in glm directory.
> >
> > (4). *_clustere_tstat_fwep is attached here in this email.
> >
> > (5). If I load *dpv_tstat.mgz and threshold it between 1.3 (p = 0.05) and
> > 2
> > (max), I get the map attached 2nd in attached figure. I am not sure
> > how to "threshold
> > it by your cluster-forming threshold (I suppose that you should correctly
> > convert z value to t-value), to see your initial clusters after
> > thresholding".
> >
> > Thanks a lot Antonin.
> > Sahil
> >
> >
> >
> > On Wed, Mar 8, 2017 at 2:06 PM, Antonin Skoch <a...@ikem.cz> wrote:
> >
> > > Dear Sahil,
> > >
> > > could you send the full command-line and unthresholded view of
> > > *_clustere_tstat_fwep ?
> > >
> > > How the data showed in screenshot 1 were produced?
> > >
> > > How are the actual p-values of your clusters in *_clustere_tstat_fwep?
> > >
> > > You can also use -saveglm and inspect the files containing values of GLM
> > > fit.
> > > You can load the *dpv_tstat.mgz file and threshold it by your
> > > cluster-forming threshold (I suppose that you should correctly convert z
> > > value to t-value), to see your initial clusters after thresholding.
> > >
> > > Regards,
> > >
> > > Antonin
> > >
> > >
> > >
> > > Thanks a lot Anderson and Antonin, that's really useful.
> > >
> > > Actually, I am having trouble in interpreting the results. Could you
> > > please
> > > share any document explaining all these tests/outputs and their
> > > interpretation in simple terms?
> > >
> > > Here I am attaching a screen shot: (1) Simple partial correlations (I
> > > adjusted the color bar between 0.30 and 0.35 to visualize the high
> > > correlation coefficients, which is ~0.35) and (2) Results I get when I
> > > used cluster
> > > extent stats: *dpv_tstat
> > > But I do not see any significant clusters when I view
> > > *_clustere_tstat_fwep, *_dpv_tstat_fwep, which is very unexpected in my
> > > data set.
> > >
> > > So basically I really doubt if I am running the stats correctly because
> > > PCC
> > > looks high at that big cluster (shown in PCC in attached screen shot).
> > >
> > > Could you please suggest if there is any alternative (less stronger)
> > stat
> > > flag I can use here while running PALM command?
> > >
> > > I would be more than happy sharing any required files to interpret the
> > > results.
> > >
> > > Thanks.
> > >
> > > On Wed, Mar 8, 2017 at 10:20 AM, Sahil Bajaj <sahil.br...@gmail.com>
> > > wrote:
> > >
> > > > Thanks a lot Anderson and Antonin, that's really useful.
> > > >
> > > > Actually, I am having trouble in interpreting the results. Could you
> > > > please share any document explaining all these tests/outputs and their
> > > > interpretation in simple terms?
> > > >
> > > > Here I am attaching two screen shots: (1) Results I get when I used
> > > cluster
> > > > extent stats: *dpv_tstat and (2). Simple partial correlations (I
> > > adjusted
> > > > the color bar between 0.30 and 0.35 to visualize the high correlation
> > > > coefficients, which is ~0.35).
> > > > I do not see any significant clusters when I view
> > *_clustere_tstat_fwep,
> > > > *_dpv_tstat_fwep, which is very unexpected in my data set.
> > > >
> > > > So basically I really doubt if I am running the stats correctly
> > because
> > > > PCC looks high at that big cluster (shown in PCC in attached screen
> > > shot).
> > > >
> > > > Could you please suggest if there is any alternative (less stronger)
> > > stat
> > > > flag I can use here while running PALM command?
> > > >
> > > > I would be more than happy sharing any required files to interpret the
> > > > results.
> > > >
> > > > Thanks.
> > > >
> > > > On Wed, Mar 8, 2017 at 9:27 AM, Martin Juneja <mj70...@gmail.com>
> > > wrote:
> > > >
> > > >> Hi Antonin and Anderson,
> > > >>
> > > >> That's wonderful ! I am able to run PALM now, without any problem.
> > > >>
> > > >> Thank you so much for your help and time, I really appreciate that.
> > > >>
> > > >> Best,
> > > >> MJ
> > > >>
> > > >>
> > > >>
> > > >> On Wed, Mar 8, 2017 at 6:30 AM, Anderson M. Winkler <
> > > >> wink...@fmrib.ox.ac.uk> wrote:
> > > >>
> > > >>> 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 <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
> > > >>>> > > >> >     >
> > > >>>> > > >> >     >
> > > >>>> > >