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 <ansk@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>>> 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
> >> >     >
> >> >     >
>
>

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.