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 negwill 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>>> 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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