Re: [Freesurfer] Error viewing corrected results

Dear Martin,

thinking of that further, my advice for negative cluster-forming threshold was probably wrong in this context. Instead, I think that you can achieve negative one-side hypothesis by specifying positive cluster-forming threshold and inverting the sign of your contrast vector.

Antonin

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 > >