Freesurfer

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30132 discussions

Results from R to Freesurfer
by Dorian P. 09 Mar '17

09 Mar '17

Hi Freesurfers, I am using R to perform thickness analyses. All subjects are transformed in fsaverage space and all values are placed in a matrix with 327684 columns (163842 for each hemisphere). I put the results back in a surface file (.asc format) and then convert it to a binary Freesurfer format. I then open the files in Freesurfer to view them. Overall the results make sense and fall in the right places. But I am concerned that some results fall into the corpus callosum, which, if I remember correctly should not have any thickness value, and therefore no results. Here is a screenshot: [image: Inline image 1] Can someone help my understand what might be wrong? Or, if this is normal, why I am finding thickness results where there is no thickness? Is there a way to find label numbers for each vertex in fsaverage space (i.e. list of parcel number for each vertex). This might be useful to exclude certain vertices or compute summery statistics of the results directly in R. Third question, is it possible to threshold the above map based on minimal cluster area (i.e., in mri_surfcluster). If yes, do I need to prepare a binary file with p-values for thresholding (0-1), or can I use mri_surfcluster with t-score maps (0-Inf)? Thank you for your help. Dorian

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Re: [Freesurfer] Error viewing corrected results
by Antonin Skoch 09 Mar '17

09 Mar '17

Dear Sahil, I would suggest at first to make check of your GLM PALM setup by comparing mri_glmfit and PALM output files (using the same design and contrast): 1. values of gamma.mgh should correspond to values of *cope.mgh 2. values of F.mgh should be (*dpv_tstat.mgh) ^2. 3. values of sig.mgh should be {roughly) values of -log10(*dpv_tstat_uncp.mgh) - I am currently not sure why I do not get exact correspondence here. 4. When you threshold the sig.mgh by some threshold in freeview (let it be x) and use the same corresponding cluster-forming z-score threshold -C in PALM computed as qnorm(1-10^-x/2) (and use two-sided hypothesis by specifying -twotail), your *clustere_tstat.mgz should show the clusters with the same shape (regardless of their values, the clusters will be defined by non-zero value, other vertices would be zero) as the thresholded display of sig.mgh (computed by -two sided hypothesis). If there is any inconsistence, then there is probably something wrong with your PALM setup. Antonin Dear Antonin, Could you please have a look at the attached screen shot. This map is with full number of permutations, without -approx tail -n 500 -nouncorrected Here, I noticed that its only *_dpv_tstat.mgz which looks correct and giving very high negative value, close to that big cluster, small positive values at red clusters and the value changes when I change the position of cursor. *_dpv_tstat_fwep shows value of 1 mostly but shows between 0.97 and 1 close/at the red clusters and 1 elsewhere, even at the big blue negative cluster. Third, *_clustere_tstat_fwep and *_clustere_tstat shows 1 and 0 respectively everywhere, even at the big blue negative cluster. If there is something fishy with the analysis, would you mind looking at the data and the detailed commands I am using to run the analysis? Thanks a lot, Sahil On Wed, Mar 8, 2017 at 11:54 PM, Antonin Skoch <ansk(a)ikem.cz> wrote: > Dear Sahil, > > to assure that there is no other issue with your setup, I would recommend to obtain cluster-wise p-pvalue of that big cluster to see if it is reasonable, i.e. if it is somewhat close to the significance. > > Therefore, I would load *_clustere_tstat_fwep and click to the area of big cluster and see what the values of the vertices in that region are. > > Or, I would increase --thmax in mri_surfcluster to see the cluster-wise p-value(s). If you use --thmax 0.9999 (or maybe 1), you should see cluster-wise FWER corrected p-values of all clusters formed by used cluster-forming threshold. > > I would also maybe try to switch-off tail approximation and run it in full number of permutations (i.e. do not use -approx tail -n 500 -nouncorrected). > > If there is no other issue, then yes, the conclusion would be, that for the used cluster-extent inference and currently set cluster-forming threshold, none of the clusters survived FWER correction at cluster-wise p-value threshold of 0.05. > > Antonin > > > > Dear Antonin, > > Setting minimum to 1.3 for *_clustere_tstat_fwep doesn't show any > significant cluster and similarly thresholded map *dpv_tstat.mgz also > doesn't show anything at -log10(0.05) = 1.3. As you said, it seems like > even though there is big cluster but after FWER correction, the > significance goes away. Actually, even when I removed -logp, I still do not > see any significant cluster. > > Next, I tried to use mri_surfcluster using following three commands > following instructions from the link you sent: > > mri_binarize --i Results_Left_clustere_tstat_fwep.mgz --min 1 --o p_bin.mgz > > mris_calc --output pmap_filter.mgz Results_Left_clustere_tstat_fwep.mgz sub > p_bin.mgz > > mri_surfcluster --in pmap_filter.mgz --subject fsaverage --hemi lh --surf > white --annot aparc.a2009s --thmin 0.00000001 --thmax 0.05 --mask > glmdir/mask.mgh --sum summary --nofixmni > > This gives me 'zero' cluster in the summary file. > > If the above steps are correct, would you conclude that the LGI results are > not significant and un-reportable for publication purpose and I should give > a try to thickness, volume and area maps? > > Thanks you so much Antonin for all your help. > Sahil > > > > On Wed, Mar 8, 2017 at 3:05 PM, Antonin Skoch <a...(a)ikem.cz> wrote: > > > Dear Sahil, > > > > If you used -logp as Anderson suggested, you should set your min to 1.3 to > > threshold your *_clustere_tstat_fwep map and see the clusters. > > > > What is the value of *_clustere_tstat_fwep in the region of the big > > cluster seen at thresholded map *dpv_tstat.mgz ? This should correspond to > > your -log10(p) of your cluster. > > > > I personally did not use -logp and use the mri_surfcluster for the > > reporting of the clusters, as I wrote in previous mail here: > > > > freesurfer(a)nmr.mgh.harvard.edu/msg52042.html" title="http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52042.html" target="_blank">http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52042.html > > > > > But it is only matter of personal preference. > > > > And, beware, that the LGI is very smooth measure, therefore also rather > > big cluster can be insignificant after FWER correction. > > > > Antonin > > > > > > > > > > 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 <a...(a)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.br...(a)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 <mj70...(a)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 < > > > >> wink...(a)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 <a...(a)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...(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, > > > >>>> > 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...(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...(a)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...(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...(a)nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard <gr...(a)nmr.mgh.harvard>. > > edu > > > <gr...(a)nmr.mgh.harvard.edu> > > > >>>> > > >> > <gr...(a)nmr.mgh.harvard.edu> > > > >>>> > > >> > <gr...(a)nmr.mgh.harvard.edu> > > > >>>> > > >> > <gr...(a)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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Re: [Freesurfer] Error viewing corrected results
by Antonin Skoch 09 Mar '17

09 Mar '17

Dear Sahil, to assure that there is no other issue with your setup, I would recommend to obtain cluster-wise p-pvalue of that big cluster to see if it is reasonable, i.e. if it is somewhat close to the significance. Therefore, I would load *_clustere_tstat_fwep and click to the area of big cluster and see what the values of the vertices in that region are. Or, I would increase --thmax in mri_surfcluster to see the cluster-wise p-value(s). If you use --thmax 0.9999 (or maybe 1), you should see cluster-wise FWER corrected p-values of all clusters formed by used cluster-forming threshold. I would also maybe try to switch-off tail approximation and run it in full number of permutations (i.e. do not use -approx tail -n 500 -nouncorrected). If there is no other issue, then yes, the conclusion would be, that for the used cluster-extent inference and currently set cluster-forming threshold, none of the clusters survived FWER correction at cluster-wise p-value threshold of 0.05. Antonin Dear Antonin, Setting minimum to 1.3 for *_clustere_tstat_fwep doesn't show any significant cluster and similarly thresholded map *dpv_tstat.mgz also doesn't show anything at -log10(0.05) = 1.3. As you said, it seems like even though there is big cluster but after FWER correction, the significance goes away. Actually, even when I removed -logp, I still do not see any significant cluster.Next, I tried to use mri_surfcluster using following three commands following instructions from the link you sent: mri_binarize --i Results_Left_clustere_tstat_fwep.mgz --min 1 --o p_bin.mgz mris_calc --output pmap_filter.mgz Results_Left_clustere_tstat_fwep.mgz sub p_bin.mgz mri_surfcluster --in pmap_filter.mgz --subject fsaverage --hemi lh --surf white --annot aparc.a2009s --thmin 0.00000001 --thmax 0.05 --mask glmdir/mask.mgh --sum summary --nofixmni This gives me 'zero' cluster in the summary file. If the above steps are correct, would you conclude that the LGI results are not significant and un-reportable for publication purpose and I should give a try to thickness, volume and area maps? Thanks you so much Antonin for all your help. Sahil On Wed, Mar 8, 2017 at 3:05 PM, Antonin Skoch <a...(a)ikem.cz> wrote: > Dear Sahil, > > If you used -logp as Anderson suggested, you should set your min to 1.3 to > threshold your *_clustere_tstat_fwep map and see the clusters. > > What is the value of *_clustere_tstat_fwep in the region of the big > cluster seen at thresholded map *dpv_tstat.mgz ? This should correspond to > your -log10(p) of your cluster. > > I personally did not use -logp and use the mri_surfcluster for the > reporting of the clusters, as I wrote in previous mail here: > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52042.html > > But it is only matter of personal preference. > > And, beware, that the LGI is very smooth measure, therefore also rather > big cluster can be insignificant after FWER correction. > > Antonin > > > > > 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 <a...(a)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.br...(a)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 <mj70...(a)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 < > > >> wink...(a)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 <a...(a)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...(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, > > >>>> > 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...(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...(a)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...(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...(a)nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard. > edu > > <gr...(a)nmr.mgh.harvard.edu> > > >>>> > > >> > <gr...(a)nmr.mgh.harvard.edu> > > >>>> > > >> > <gr...(a)nmr.mgh.harvard.edu> > > >>>> > > >> > <gr...(a)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 > > >>>> > > >> > > > > >>>> > > >> > > > > >>>> > >

2 1

glmfit error / group analysis
by teodora petrova 09 Mar '17

09 Mar '17

Hello, I am trying to test for the effect of different variables on cortical thickness. The variables (with type) are: index (continuous). Gender(factor), Age(continuous), Years of education (continuous), Depression (factor), Vascular comorbidity (factor), and MMSE (continuous). Later, I need to correlate thickness with my variable of interest (index). Depending on the results of the current analysis, I will choose which of the other variables will be my covariates. Here is what I attempted to do so far and the error I got: I have constructed the fsgd file according to the example with one group and covariates (see attahced to this email). My contrasts look like, for example: 0 1 0 0 0 0 0 (to test effects of gender), and 0 0 1 0 0 0 0 (to test for the effects of age). I am following the commands in the Group Analysis tutorial. I pass successfully mris_preproc and mri_surf2surf. When I get to mri_glmfit, I receive the error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. 1. My command line is mri_glmfit --y lh.newindex.thickness.10.mgh --fsgd FSGD.fsgd dods --C index.mtx --C gender.mtx --C age.mtx --C education.mtx --C depression.mtx --C vascularc.mtx --C MMSE.mtx --surf fsaverage lh --cortex --glmdir lh.newindex.glmdir2. Please find attachced my fsgd file 3. Find attached the Design matrix What is the best way to construct the fsgd and contrasts? In the version I am sending, I have demeaned all continuous variables. Is that something you will recommend to do? (I tried the group analysis with a fsgd file containing the normal, non-demeaned values, but got the same error). Thank you for the help! Best,Teodora

2 1

Issue with mri_segstats to extract cortical thickness from a volume ROI
by Elodie Boudes 09 Mar '17

09 Mar '17

Hello FreeSurfer community, I am trying to extract the cortical thickness from a specific ROI. I followed the pipeline: cortical thickness of a volume-defined ROI. But for the last step: mri_segstats \ --seg $SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh \ --in lh.thickness.fsaverage.mgh \ --sum segstats-ROI5.txt I encountered an error: ERROR: dimension inconsistency in source data Number of surface vertices = 126983 Number of value vertices = 163842 I tried as suggested in the forum the reshape-factor option as well as the noreshape option for mri_vol2surf and mri_surf2surf. With no success, I obtained a similar error. The ROI is extracted from another acquisition and is registered to the T1. The T1 has been processed by following the classic pipeline using recon-all … -all Any suggestions on how to fix that error or another pipeline that will allow me to get the cortical thickness from inside my ROI? Thank you Elodie Boudes University of Calgary

2 1

mri_label2vol error: could not scan # of lines from label file
by Burks, Joshua D (HSC) 09 Mar '17

09 Mar '17

Hello FreeSurfer Developers, I’m attempting to convert a dlabel file from the Human Connectome Project to a volumetric ROI that I can use for fiber tractography on other platforms. I followed the tutorial provided by HCP (hcp-users FAQ #9: How do I map data between FreeSurfer ... - HCP Wiki<https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uac…>) for resampling HCP-derived data for use in FreeSurfer. When I run the mri_label2vol command: mri_label2vol: could not scan # of lines from label file ERROR reading /home/neuroresearch/workbench/test1.label.gii Does anyone have thoughts on how to troubleshoot this? I have not seen any similar errors described in the list. 1) FreeSurfer version: freesurfer-x86_64-apple-darwin16.4.0-dev-20170302 2) Platform: MacOS 10.12.3

2 1

Yet another freeview coordinates question
by Peled, Noam 08 Mar '17

08 Mar '17

Hey all, When loading two T1 in freeview, one for a subject and one for fsaverage, and switching between them, only the tkreg RAS coordinates changes while moving the mouse, not the RAS. Does it mean that the RAS in freeview is always in MNI305? Thanks, Noam

1 1

Re: [Freesurfer] Error viewing corrected results
by Antonin Skoch 08 Mar '17

08 Mar '17

Dear Sahil, If you used -logp as Anderson suggested, you should set your min to 1.3 to threshold your *_clustere_tstat_fwep map and see the clusters. What is the value of *_clustere_tstat_fwep in the region of the big cluster seen at thresholded map *dpv_tstat.mgz ? This should correspond to your -log10(p) of your cluster. I personally did not use -logp and use the mri_surfcluster for the reporting of the clusters, as I wrote in previous mail here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52042.html But it is only matter of personal preference. And, beware, that the LGI is very smooth measure, therefore also rather big cluster can be insignificant after FWER correction. Antonin 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(a)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(a)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(a)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(a)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(a)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...(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, > >>>> > 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...(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...(a)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...(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...(a)nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > <gr...(a)nmr.mgh.harvard.edu> > >>>> > > >> > <gr...(a)nmr.mgh.harvard.edu> > >>>> > > >> > <gr...(a)nmr.mgh.harvard.edu> > >>>> > > >> > <gr...(a)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 > >>>> > > >> > > > >>>> > > >> > > > >>>> > > > >>>> > >

2 1

Re: [Freesurfer] Error viewing corrected results
by Antonin Skoch 08 Mar '17

08 Mar '17

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(a)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(a)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(a)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(a)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...(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, >>>> > 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...(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...(a)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...(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...(a)nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu <gr...(a)nmr.mgh.harvard.edu> >>>> > > >> > <gr...(a)nmr.mgh.harvard.edu> >>>> > > >> > <gr...(a)nmr.mgh.harvard.edu> >>>> > > >> > <gr...(a)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(a)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. >>>> >>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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. >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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. >> >>

2 1

one group in RepeatedMeasuresAnova or Paird Analysis
by 刘丽 08 Mar '17

08 Mar '17

Dear FS Experts, I have one group to compare the difference between their preoperative and postoperative after one month. I followed http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial to process data. I run these command in number 2.* Longitudinal Image Processing*： 1. recon-all –s sub01_MR1 –all / recon-all –s sub01_MR2 –all 2. recon-all -base sub01 -tp sub01_MR1 -tp sub01_MR2 –all 3. recon-all -long sub01_MR1 sub01 –all / recon-all -long sub01_MR2 sub01 –all I am confused about choosing which kind of analysis in the page http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics And I tried http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova The “rmanova.fsgd”: GroupDescriptorFile 1 Class sub01 Class sub02 … Variables TP1-vs-TP2 Input sub01_MR1 sub01 1 Input sub01_MR2 sub01 -1 Input sub02_MR1 sub02 1 Input sub02_MR2 sub02 -1 … “tp1-va-tp2.mtx”: 0 0 … 1 And I look in one mail in the list, say “one group to use Paird Analysis easier”. http://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis “pairs.fsgd”: GroupDescriptorFile 1 Class Main Input sub04_MR1 Main Input sub04_MR2 Main Input sub05_MR1 Main Input sub05_MR2 Main … “paird-diff.fsgd” : GroupDescriptorFile 1 Class Main Variables Age Input sub04pair Main 24 Input sub05pair Main 27 … “mean.mtx”: 1 0 My question： 1. Are the above several files I set up correct？？There are inconsistent results in them… So which one should I choose?? 2. I found the increase or decrease a subjects had a great influence on the analysis result, how to filter the participants?? Looking forward to reply, and thanks very much! Kind regards, Livia

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