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.brain@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 mj70481@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 < winkler@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 ansk@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,
- == ...
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 >> > 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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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 ansk@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.brain@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 mj70481@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 < winkler@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 ansk@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,
- == ...
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
> >> > > > >> > > > >
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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.
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-
Antonin Skoch -
Sahil Bajaj