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...@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...@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...@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...@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...@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...@ikem.cz> wrote: > > >>> > > >>>> Dear Sahil, > > >>>> > > >>>> I suppose, for qcache 1.3 the equivalent cluster-forming threshold > > >>>> z-value is > > >>>> > > >>>> two-tailed test: > > >>>> qnorm(1-10^-1.3/2)=1.958949 > > >>>> > > >>>> for one-tailed test: > > >>>> qnorm(1-10^-1.3)=1.643704 > > >>>> > > >>>> (qnorm is R function call for quantile function of normal > > distribution, > > >>>> you can compute this by using other methods or use statistical > > z-tables) > > >>>> > > >>>> And, the directionality of the hypothesis is I suppose specified by > > the > > >>>> sign of your contrast vector, as I wrote in my previous mail. > > >>>> > > >>>> As for the output files, you can look at the documentation: > > >>>> > > >>>> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide#Output_files > > >>>> > > >>>> For example, if you are looking for the p-values, used cluster > extent > > >>>> inference and used t-contrast, the file with FWER-corrected > p-values > > would > > >>>> be something like > > >>>> > > >>>> output_basename_clustere_tstat_fwep.mgz > > >>>> > > >>>> Antonin > > >>>> > > >>>> > > >>>> > > >>>> > > >>>> Hello Martin and Antonin, > > >>>> > > >>>> I was following this conversation very closely to understand how to > > use > > >>>> PALM in FreeSurfer. > > >>>> > > >>>> Can any of you please confirm in case I am interested in checking > > >>>> correlation between gyrification index (LGI) and behavioral measure > > using > > >>>> two tailed, p < 0.05: > > >>>> Step 1: I used --cache 1.3 > > >>>> Step 2: Because (1-10^-1.3)= 0.95, so I will have to use -C 0.95 in > > palm > > >>>> command > > >>>> > > >>>> Could you please confirm if thats correct and the output > *_tstat.mgz > > is the > > >>>> final two-tailed corrected significant correlation map between LGI > > and > > >>>> behavioral data? > > >>>> > > >>>> Thanks a lot for this wonderful discussion. > > >>>> Sahil > > >>>> > > >>>> PS: For one-tailed: it will be -C -0.95 in palm command, correct? > > >>>> > > >>>> > > >>>> > > >>>> On Tue, Mar 7, 2017 at 3:48 PM, Antonin Skoch <a...@ikem.cz> > wrote: > > >>>> > > >>>> > Dear Martin, > > >>>> > > > >>>> > after -s option, there have to be 2 arguments, as I specified in > my > > previous > > >>>> > mail: > > >>>> > > > >>>> > -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh > > >>>> > > > >>>> > And beware that -C has to have negative sign, if your hypothesis > is > > >>>> > one-tailed negative. > > >>>> > > > >>>> > Antonin > > >>>> > > > >>>> > > > >>>> > > > >>>> > Hi Antonin, > > >>>> > > > >>>> > Thank you so much for this detailed explanation, that's really > > useful. > > >>>> > > > >>>> > Following your instructions, I ran: > > >>>> > > > >>>> > palm -i lh.MEQ_LGI.10.mgh -s fsaverage/surf/lh.white.avg.area.mgh > > > -d > > >>>> > check.csv -t Contrast_MEQ.csv -n 5000 -m > lh.MEQ_LGI.glmdir/mask.mgh > > -o > > >>>> > myresults -Cstat extent -C 3.719016 > > >>>> > > > >>>> > but I am getting following error: > > >>>> > > > >>>> > Running PALM alpha104 using MATLAB 9.0.0.341360 (R2016a) with the > > following > > >>>> > options: > > >>>> > -i lh.MEQ_LGI.10.mgh > > >>>> > -s fsaverage/surf/lh.white.avg.area.mgh > > >>>> > -d check.csv > > >>>> > -t Contrast_MEQ.csv > > >>>> > -n 5000 > > >>>> > -m lh.MEQ_LGI.glmdir/mask.mgh > > >>>> > -o myresults > > >>>> > -Cstat extent > > >>>> > -C 3.719016 > > >>>> > Loading surface 1/1: fsaverage/surf/lh.white.avg.area.mgh > > >>>> > Reading input 1/1: lh.MEQ_LGI.10.mgh > > >>>> > > > >>>> > Struct contents reference from a non-struct array object. > > >>>> > > > >>>> > Error in palm_takeargs (line 1632) > > >>>> > if any(size(plm.srf{s}.data.vtx, > > >>>> > 1) == ... > > >>>> > > > >>>> > Error in palm_core (line 33) > > >>>> > [opts,plm] = palm_takeargs(varargin{:}); > > >>>> > > > >>>> > Error in palm (line 81) > > >>>> > palm_core(varargin{:}); > > >>>> > > > >>>> > Could you please help me in resolving this error? > > >>>> > > > >>>> > Thanks much. > > >>>> > > > >>>> > On Tue, Mar 7, 2017 at 2:55 PM, Antonin Skoch <a...@ikem.cz> > > wrote: > > >>>> > > > >>>> > > Dear Martin, > > >>>> > > > > >>>> > > input -i input file is > > >>>> > > > > >>>> > > lh.MEQ_LGI.10.mgh file in your glmdir directory (for left > > hemisphere). > > >>>> > > > > >>>> > > As you could read in following messages in the referenced > thread > > in FSL > > >>>> > > discussion forum, cluster-forming threshold need to be > specified > > in z, not > > >>>> > > in t. > > >>>> > > > > >>>> > > Therefore, you would have to select cluster forming threshold > and > > specify > > >>>> > > it as a z score. > > >>>> > > > > >>>> > > I think that your z-score for your original mri_glmfit-sim > > commandline > > >>>> > > argument > > >>>> > > > > >>>> > > --cache 4 neg > > >>>> > > > > >>>> > > will be -qnorm(1-10^-4)=-3.719016. (I am not perfectly sure > > since I never > > >>>> > > tried negative one-side hypothesis testing in PALM). > > >>>> > > > > >>>> > > You could also use other statistics, such as cluster mass, or > > TFCE. See > > >>>> > > PALM user guide. > > >>>> > > > > >>>> > > Do not include -pmethodp none and -pmethodr none, since you > would > > need the > > >>>> > > partitioning due your non-orthogonal design matrix. > > >>>> > > > > >>>> > > ?h.white.avg.area.mgh file (which you will find under fsaverage > > directory) > > >>>> > > goes as second argument after -s option. > > >>>> > > > > >>>> > > Therefore I suppose the commandline for cluster extent > inference > > with > > >>>> > > cluster forming threshold p=0.0001, negative one-sided > > hypothesis, left > > >>>> > > hemisphere, will be hopefully something like > > >>>> > > > > >>>> > > palm > > >>>> > > -i y.mgh > > >>>> > > -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh > > > >>>> > > -d Xg.csv > > >>>> > > -t your_contrasts.csv > > >>>> > > -n number_of_permutations > > >>>> > > -m mask.mgh > > >>>> > > -o output_basename > > >>>> > > -Cstat extent > > >>>> > > -C -3.719016 > > >>>> > > -saveglm > > >>>> > > -savedof > > >>>> > > -savemetrics > > >>>> > > > > >>>> > > The last 3 commandline options are only for diagnostical > > purposes. > > >>>> > > > > >>>> > > The output is surface overlay you can visualize in freeview. > > >>>> > > > > >>>> > > I use following code snippet for the reporting significant > > clusters in MNI > > >>>> > > coordinates: > > >>>> > > > > >>>> > > # PALM output cluster extent p maps have 1 outside cluster - > > problem with > > >>>> > > mri_surfcluster and also for display in freeView > > >>>> > > #here we set values 1 to 0 in pmaps. > > >>>> > > #done by binarizing and subtracting > > >>>> > > if [[ $# -ne 2 ]]; then > > >>>> > > echo "get cluster summary of PALM statistics. Expecting 2 > > arguments: 1- > > >>>> > > input p-map, 2- hemisphere (lh/rh)" > > >>>> > > exit > > >>>> > > fi > > >>>> > > mri_binarize --i $1 --min 1 --o p_bin.mgz > > >>>> > > mris_calc --output ${1%%.mgz}_filtered.mgz $1 sub p_bin.mgz > > >>>> > > mri_surfcluster --in ${1%%.mgz}_filtered.mgz --subject > fsaverage > > --hemi $2 > > >>>> > > --surf white --annot aparc --thmin 0.000000001 --thmax 0.05 > > --mask mask.mgh > > >>>> > > --sum ${1%%.mgz}_cluster.summary --nofixmni > > >>>> > > rm p_bin.mgz > > >>>> > > > > >>>> > > They are not Bonferroni-corrected for 2 hemispheres > (--2spaces). > > >>>> > > > > >>>> > > Regarding your design and contrast: > > >>>> > > > > >>>> > > Design has to be matrix of values. You can use qdec to produce > > Xg.dat file > > >>>> > > with design matrix, then rename it to Xg.csv to be correctly > > readable by > > >>>> > > PALM. > > >>>> > > > > >>>> > > Regards, > > >>>> > > > > >>>> > > Antonin > > >>>> > > > > >>>> > > > > >>>> > > > > >>>> > > > > >>>> > > > > >>>> > > Hi Antonin, > > >>>> > > > > >>>> > > As you suggested in discussion forum, I tried to run following > > command > > >>>> > > after mri_glmfit: > > >>>> > > > > >>>> > > palm -s fsaverage/surf/lh.white -n 10000 -m mask.mgh -Cstat > > extent -C > > >>>> > > 1.974975 -pmethodp none -pmethodr none -twotail -d > Design_MEQ.txt > > -t > > >>>> > > Contrast_MEQ.txt > > >>>> > > > > >>>> > > Running PALM alpha104 using MATLAB 9.0.0.341360 (R2016a) with > the > > following > > >>>> > > options: > > >>>> > > > > >>>> > > -s fsaverage/surf/lh.white > > >>>> > > > > >>>> > > -n 10000 > > >>>> > > > > >>>> > > -m mask.mgh > > >>>> > > > > >>>> > > -Cstat extent > > >>>> > > > > >>>> > > -C 1.974975 > > >>>> > > > > >>>> > > -pmethodp none > > >>>> > > > > >>>> > > -pmethodr none > > >>>> > > > > >>>> > > -twotail > > >>>> > > > > >>>> > > -d Design.txt > > >>>> > > > > >>>> > > -t Contrast.txt > > >>>> > > > > >>>> > > Found FSL in /usr/share/fsl/5.0 > > >>>> > > > > >>>> > > Found FreeSurfer in /usr/local/freesurfer > > >>>> > > > > >>>> > > Found SPM in /usr/local/spm12 > > >>>> > > > > >>>> > > Error using palm_takeargs (line 1141) > > >>>> > > > > >>>> > > Missing input data (missing "-i"). > > >>>> > > > > >>>> > > Error in palm_core (line 33) > > >>>> > > > > >>>> > > [opts,plm] = palm_takeargs(varargin{:}); > > >>>> > > > > >>>> > > Error in palm (line 81) > > >>>> > > > > >>>> > > palm_core(varargin{:}); > > >>>> > > > > >>>> > > Looks like error is because its missing -i input here, I am not > > sure what's > > >>>> > > input file here? > > >>>> > > > > >>>> > > Also, I am trying to correlate LGI versus behavioral score, > > regressing out > > >>>> > > the effect of sex and age. So I just wanted to confirm if my > > design.txt and > > >>>> > > contrast.txt files are correct here. Please find both > following: > > >>>> > > > > >>>> > > Design file (Variables Behav, Age) as following: > > >>>> > > > > >>>> > > S001 Male 60 36 > > >>>> > > > > >>>> > > S003 Female 73 29 > > >>>> > > > > >>>> > > S004 Male 48 39 > > >>>> > > > > >>>> > > .......so on...... > > >>>> > > > > >>>> > > Contrast file as following: > > >>>> > > 0 0 0.5 0.5 0 0 (same as *.mtx file used for glm_fit) > > >>>> > > > > >>>> > > Thank you so much for your help and time. > > >>>> > > > > >>>> > > On Tue, Mar 7, 2017 at 10:49 AM, Martin Juneja < > mj70...@gmail.com> > > wrote: > > >>>> > > > > >>>> > > > Hi Antonin, > > >>>> > > > > > >>>> > > > Thanks a lot for your reply. > > >>>> > > > > > >>>> > > > Somehow, in the link you sent, I could not find any response > to > > your > > >>>> > > > email. But I can see your email to Anderson and command line > > parameters. > > >>>> > > > > > >>>> > > > As I am not an expert in using FreeSurfer, so would it be > > possible for you > > >>>> > > > to share detailed step-by-step guide and PALM command after I > > run > > >>>> > > > mri_glmfit > > >>>> > > > command and how and where to include '?h.white.avg.area.mgh' > > file? > > >>>> > > > > > >>>> > > > I would really appreciate any help. > > >>>> > > > > > >>>> > > > On Mon, Mar 6, 2017 at 4:28 PM, Antonin Skoch <a...@ikem.cz> > > wrote: > > >>>> > > > > > >>>> > > >> Dear Martin, > > >>>> > > >> > > >>>> > > >> I think yes, you can use PALM with FreeSurfer surfaces, see > my > > >>>> > > >> conversation with Anderson on FSL list: > > >>>> > > >> > > >>>> > > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1604&L=FSL > > >>>> > > >>>> > > > >>>> > > > > >>>> > > >> &D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=239088 > > > >>>> > > >> > > >>>> > > >> but beware not to forget to include average the vertex area > > >>>> > > >> (?h.white.avg.area.mgh) file. > > >>>> > > >> > > >>>> > > >> Antonin > > >>>> > > >> > > >>>> > > >> > > >>>> > > >> If you don't have an orthogonal design, then you can't use > > >>>> > > >> mri_glmfit-sim. I think you can use PALM: > > >>>> > > >> > > >>>> > > >> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM > > >>>> > > >> > > >>>> > > >> I have not tried it yet. > > >>>> > > >> > > >>>> > > >> Anderson, can you use PALM with surfaces? > > >>>> > > >> > > >>>> > > >> > > >>>> > > >> > > >>>> > > >> > > >>>> > > >> > > >>>> > > >> > > >>>> > > >> On 03/06/2017 05:23 PM, Martin Juneja wrote: > > >>>> > > >> > Hi Dr. Greve, > > >>>> > > >> > > > >>>> > > >> > I tried to run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir > > --sim perm > > >>>> > > >> > 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 > > >>>> > > >> > It gives error that ERROR: design matrix is not > orthogonal, > > cannot be > > >>>> > > >> > used with permutation. > > >>>> > > >> > > > >>>> > > >> > But when I run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir > > --sim perm > > >>>> > > >> > 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 > > --perm-force, it > > >>>> > > >> > works. > > >>>> > > >> > > > >>>> > > >> > I am not sure whether I will have to make the design > matrix > > >>>> > > >> > orthogonal. If so, could you please tell me how that can > be > > done? > > >>>> > > >> > > > >>>> > > >> > Or using --perm-force should be fine? > > >>>> > > >> > > > >>>> > > >> > Thanks. > > >>>> > > >> > > > >>>> > > >> > On Mon, Mar 6, 2017 at 1:58 PM, Douglas N Greve > > >>>> > > >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard. > edu > > <gr...@nmr.mgh.harvard.edu> > > >>>> > > >> > <gr...@nmr.mgh.harvard.edu> > > >>>> > > >> > <gr...@nmr.mgh.harvard.edu> > > >>>> > > >> > <gr...@nmr.mgh.harvard.edu>>> wrote: > > >>>> > > >> > > > >>>> > > >> > This is a problem with using LGI in that it is already > > extremely > > >>>> > > >> > smooth > > >>>> > > >> > that the smoothness exceeds the limit of the look up > > table that we > > >>>> > > >> > supply. I recommend that you not use a gaussian-based > > correction > > >>>> > > >> > for > > >>>> > > >> > LGI. Instead, use permutation (see mri_glmfit-sim > > --help). > > >>>> > > >> > > > >>>> > > >> > > > >>>> > > >> > > > >>>> > > >> > On 03/06/2017 01:36 PM, Martin Juneja wrote: > > >>>> > > >> > > Hello everyone, > > >>>> > > >> > > > > >>>> > > >> > > I am trying to extract clusters showing significant > > correlation > > >>>> > > >> > > between LGI and a behavioral measure. I am able to > > extract PCC > > >>>> > > >> > and > > >>>> > > >> > > sig.mgh but at the last step when I try to run > > simulation command > > >>>> > > >> > to > > >>>> > > >> > > view corrected results and I run: > > >>>> > > >> > > > > >>>> > > >> > > mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cache 4 > > neg --cwp > > >>>> > > >> > 0.05 > > >>>> > > >> > > --2spaces > > >>>> > > >> > > > > >>>> > > >> > > I get following error: > > >>>> > > >> > > > > >>>> > > >> > > ERROR: cannot find > > >>>> > > >> > > > > >>>> > > >> > > > >>>> > > >> > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/ > > cortex/fwhm35/neg/th40/mc-z.csd > > >>>> > > >> > > > > >>>> > > >> > > But I can see mc-z.csd file in fwhm30 etc. > > >>>> > > >> > > > > >>>> > > >> > > Full message on terminal window is attached > following. > > >>>> > > >> > > > > >>>> > > >> > > Any help would be really appreciated. > > >>>> > > >> > > > > >>>> > > >> > > ----- Full message ---- > > >>>> > > >> > > > > >>>> > > >> > > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd > > MEQ.fsgd > > >>>> > > >> > dods --C > > >>>> > > >> > > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex > --glmdir > > >>>> > > >> > lh.MEQ_LGI.glmdir > > >>>> > > >> > > > > >>>> > > >> > > WARNING: unrecognized mri_glmfit cmd option > > mri_glmfit.bin > > >>>> > > >> > > > > >>>> > > >> > > SURFACE: fsaverage lh > > >>>> > > >> > > > > >>>> > > >> > > log file is lh.MEQ_LGI.glmdir/cache.mri_glmfit-sim.log > > > > > >>>> > > >> > > > > >>>> > > >> > > /usr/local/freesurfer/bin/mri_glmfit-sim > > >>>> > > >> > > > > >>>> > > >> > > --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 > > --2spaces > > >>>> > > >> > > > > >>>> > > >> > > $Id: mri_glmfit-sim,v 1.60 2016/04/30 15:13:36 greve > > Exp $ > > >>>> > > >> > > > > >>>> > > >> > > Mon Mar 6 11:11:13 MST 2017 > > >>>> > > >> > > > > >>>> > > >> > > setenv SUBJECTS_DIR > > >>>> > > >> > > /data/emot/Freesurfer/FreeSurferSegmentation/SB_AgingAll > > > > > >>>> > > >> > > > > >>>> > > >> > > FREESURFER_HOME /usr/local/freesurfer > > >>>> > > >> > > > > >>>> > > >> > > Original mri_glmfit command line: > > >>>> > > >> > > > > >>>> > > >> > > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd > > MEQ.fsgd > > >>>> > > >> > dods --C > > >>>> > > >> > > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex > --glmdir > > >>>> > > >> > lh.MEQ_LGI.glmdir > > >>>> > > >> > > > > >>>> > > >> > > DoSim = 0 > > >>>> > > >> > > > > >>>> > > >> > > UseCache = 1 > > >>>> > > >> > > > > >>>> > > >> > > DoPoll = 0 > > >>>> > > >> > > > > >>>> > > >> > > DoPBSubmit = 0 > > >>>> > > >> > > > > >>>> > > >> > > DoBackground = 0 > > >>>> > > >> > > > > >>>> > > >> > > DiagCluster = 0 > > >>>> > > >> > > > > >>>> > > >> > > gd2mtx = dods > > >>>> > > >> > > > > >>>> > > >> > > fwhm = 35.073391 > > >>>> > > >> > > > > >>>> > > >> > > ERROR: cannot find > > >>>> > > >> > > > > >>>> > > >> > > > >>>> > > >> > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/ > > cortex/fwhm35/neg/th40/mc-z.csd > > >>>> > > >> > > > > >>>> > > >> > > > > >>>> > > > > >>>> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@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. > >
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