New subject: Error viewing corrected results

7 Mar 2017


      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,

== ...

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
    >
    >

Re: [Freesurfer] Error viewing corrected results