Freesurfer March 2017

freesurfer@nmr.mgh.harvard.edu

148 participants
263 discussions

3D T1 DICOM to NII
by shi yao wang 12 Mar '17

12 Mar '17

Dear FS experts: I am using MRICron software to convert DICOM to NII. However, one 3D MRI DICOM will generate three nii files: Such as xxxx.nii, *co*XXX.nii, *o*XXX.nii When I use MRIcron to preview these files, some files show entire 3D MRI, but others only show some parts of images. (See attached sample). I am wondering which files should be loaded into FS analysis. thanks Lawrence Emory University.

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-dura_thresh
by Octavian Lie 11 Mar '17

11 Mar '17

Dear All, In FS6.0.0, this flag is added to manually adjust watershed threshold instead of its automatic calculation. I went back to the original paper by Segonne et al, and I could identify the prefllooding height h and the post watershed threshold t. I assume the flag refers to the latter. Since the threshold varies between subjects, where is it specified in the log file of a recon-all run? Also, could you indicate a (narrow) range one could start with if trying to manually adjust a run, based on your experience? Also, what is the watershed direction based on t (higher t values lead to more aggressive dura removal, or the other way around? Thank you very much, Octavian

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MRI intensity normalize
by shi yao wang 11 Mar '17

11 Mar '17

Dear FS experts, I am wondering the process of MRI intensity normalization. Before I am running recon -all, can I run following process to normalize our MRI images. mri_normalize SUBJECT/mri/nu SUBJECT/mri/wm or any other preprocessing methods to avoid bias. thanks Lawrence Emory University

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Intensity normalization in longitudinal processing
by Jaiashre Sridhar 11 Mar '17

11 Mar '17

Hello FreeSurfer Team, For a longitudinal study, we processed the cross-sectional scans through FS v5.1 and ran the longitudinal stream in FS v6.0. The voxel intensities in wm.mgz of the long timepoints are variable and are much lower (not in the range of 110). I have attached the image of a longitudinal timepoint created in v6.0 and compared it to the one created in v5.1 (The cross brain recons for both of them were done in v5.1). The white and pial surfaces look similar across versions but the long created in v6.0 does not have a uniform intensity compared to the one created in v5.1. Should this matter as long as the surfaces look fine? I tried to use expert options with ‘mri_normalize –gentle’ while creating the long in v6.0 but it did not help. Any suggestions to achieve a better intensity normalization? Thank you, Jaiashre.

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Error mri_surf2surf FS6
by Juergen Haenggi 11 Mar '17

11 Mar '17

Dear FS experts we are trying to run statistics in FS6 Linux. Everthing worked fine until we applied the command mris_preproc that called mri_surf2surf and produced the following error: ############################################################# --------------------------------------------------- #@# 1/98 s1006_01.long.s1006_base Thu Mar 9 13:20:16 CET 2017 -------------- ----------------------- mri_surf2surf --srcsubject s1006_01.long.s1006_base --srchemi rh --srcsurfreg average_AN_FS6_long_split.sphere.reg --trgsubject average_AN_FS6_long_split --trghemi rh --trgsurfreg sphere.reg --tval ./average_AN_FS6_long_split/stats/lme_preproc/tmp.mris_preproc.3575/s1006_01.long.s1006_base.1.mgh --sval /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.volume --jac --sfmt curv --noreshape --cortex MRISread(/usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg): could not open file Source registration surface changed to average_AN_FS6_long_split.sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects mri_surf2surf --srcsubject s1006_01.long.s1006_base --srchemi rh --srcsurfreg average_AN_FS6_long_split.sphere.reg --trgsubject average_AN_FS6_long_split --trghemi rh --trgsurfreg sphere.reg --tval ./average_AN_FS6_long_split/stats/lme_preproc/tmp.mris_preproc.3575/s1006_01.long.s1006_base.1.mgh --sval /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.volume --jac --sfmt curv --noreshape --cortex sysname Linux hostname psy-neuro-clt-Monster machine x86_64 user ego srcsubject = s1006_01.long.s1006_base srcval = /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.volume srctype = curv trgsubject = average_AN_FS6_long_split trgval = ./average_AN_FS6_long_split/stats/lme_preproc/tmp.mris_preproc.3575/s1006_01.long.s1006_base.1.mgh trgtype = srcsurfreg = average_AN_FS6_long_split.sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg No such file or directory mri_surf2surf: could not read surface /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg No such file or directory ############################################################### this line is odd: MRISread(/usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg): could not open file we are wondering why FS6 introduced the name of the target average (average_AN_FS6_long_split) into the name of the individual subject (rh.average_AN_FS6_long_split.sphere.reg) when looking for s1006_01.long.s1006_base/surf/rh.sphere.reg. When using FS5.3.0 mris_preproc worked without this error. Any idea? Thanks in advance Best regards Jürgen ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. -----------------------------------------------------------------------------------------------------

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Re: [Freesurfer] Error viewing corrected results
by Antonin Skoch 10 Mar '17

10 Mar '17

Dear Sahil, thinking of that, the comparisons I suggested in previous mail are probably valid only for the case of orthogonal design. And even with the orthogonal design as Anderson said, the values can a bit differ: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1604&L=FSL&D=0&1=FSL&9=A&… As I did my own tests with orthogonal design, the values were equal to the reasonable precision, apart from the case 3. So you could produce some testing orthogonal design and make similar tests on that. Antonin 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] Issue with mri_segstats to extract cortical thickness from a volume ROI
by Elodie Boudes 10 Mar '17

10 Mar '17

Dear Douglas , I used mri_vol2surf \ --mov /path/to/ROI5.nii \ --reg TT_avg152T1_to_fsaverage.dat \ --projdist-max 0 1 0.1 \ --interp nearest \ --hemi lh \ --out lh.fsaverage.ROI5.mgh \ --reshape And I got lh.thickness.fseaverage.mgh from the normal pipeline using recon-all. It’s the patient specific thickness average. Elodie On Mar 8, 2017, at 7:27 PM, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Error viewing corrected results (Antonin Skoch) 2. Re: mri_concat pet images into 1 template image (Douglas Greve) 3. Re: mri_concat pet images into 1 template image (Shane S) 4. Re: Error viewing corrected results (Sahil Bajaj) 5. Issue with mri_segstats to extract cortical thickness from a volume ROI (Elodie Boudes) 6. mri_label2vol error: could not scan # of lines from label file (Burks, Joshua D (HSC)) 7. Re: Yet another freeview coordinates question (Peled, Noam) 8. Results from R to Freesurfer (Dorian P.) ---------------------------------------------------------------------- Message: 1 Date: Wed, 8 Mar 2017 23:05:07 +0100 From: Antonin Skoch <ansk(a)ikem.cz> Subject: Re: [Freesurfer] Error viewing corrected results To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <2951470448-17194(a)posta.medicon.cz> Content-Type: text/plain; charset="utf-8" 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 ? ? > ? ? > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170308/b… ------------------------------ Message: 2 Date: Wed, 8 Mar 2017 17:30:40 -0500 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_concat pet images into 1 template image To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <fd5d66bf-1067-1125-f8cf-9a1e713c9c9c(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" No, the template is a within subject template used for registration. If your pet data only has one frame (eg, FDG SUV), then you don't need to run mri_convert or mri_concat, just use your pet image as the template On 3/8/17 11:11 AM, Shane S wrote: Hello Freesurfer, I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper. On the PetSurfer link, there are 2 methods. mri_convert pet.nii.gz ?frame frameno template.nii.gz or mri_concat pet.nii.gz --mean ?0 template.nii.gz What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz ?mean ?o template.nii.gz? correct? Thank you for helping. Best Wishes, S -- Shane Schofield _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170308/1… ------------------------------ Message: 3 Date: Wed, 8 Mar 2017 22:33:48 +0000 From: Shane S <shane.schofield(a)yahoo.com> Subject: Re: [Freesurfer] mri_concat pet images into 1 template image To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <etPan.58c086cc.19a42184.2b9(a)yahoo.com> Content-Type: text/plain; charset="utf-8" Dear Doug, My PET data is 3 x 5 minute acquisitions. Each subject has? subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am supposed to align and average them. Please advise. Thanks! --? Shane Schofield On 8 March 2017 at 22:31:06, Douglas Greve (greve(a)nmr.mgh.harvard.edu) wrote: No, the template is a within subject template used for registration. If your pet data only has one frame (eg, FDG SUV), then you don't need to run mri_convert or mri_concat, just use your pet image as the template On 3/8/17 11:11 AM, Shane S wrote: Hello Freesurfer, I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper.? On the PetSurfer link, there are 2 methods. mri_convert pet.nii.gz ?frame frameno template.nii.gz? or mri_concat pet.nii.gz --mean ?0 template.nii.gz What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz ?mean ?o template.nii.gz? correct? Thank you for helping. Best Wishes, S --? Shane Schofield _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170308/d… ------------------------------ Message: 4 Date: Wed, 8 Mar 2017 16:25:06 -0700 From: Sahil Bajaj <sahil.brain(a)gmail.com> Subject: Re: [Freesurfer] Error viewing corrected results To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAAvfsVj7FM0ogSTO-secc1nzFLiZE9yLjq2JLkJ=cdRJ4ou=CA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" 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 <ansk(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 <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 _______________________________________________ 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170308/0… ------------------------------ Message: 5 Date: Thu, 9 Mar 2017 01:15:26 +0000 From: Elodie Boudes <elodie.boudes(a)ucalgary.ca> Subject: [Freesurfer] Issue with mri_segstats to extract cortical thickness from a volume ROI To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <2B77FD35-72A8-4A94-BDA9-B6A62DC5E316(a)ucalgary.ca> Content-Type: text/plain; charset="utf-8" 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170309/1… ------------------------------ Message: 6 Date: Thu, 9 Mar 2017 01:26:46 +0000 From: "Burks, Joshua D (HSC)" <Joshua-Burks(a)ouhsc.edu> Subject: [Freesurfer] mri_label2vol error: could not scan # of lines from label file To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <685F1E2D-5597-4F0B-BEEB-2CB32FFD8812(a)ouhsc.edu> Content-Type: text/plain; charset="utf-8" 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170309/1… ------------------------------ Message: 7 Date: Thu, 9 Mar 2017 02:17:13 +0000 From: "Peled, Noam" <NPELED(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Yet another freeview coordinates question To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <F77601247B59244F9311E7776B9DAE9618464DB0(a)PHSX10MB10.partners.org> Content-Type: text/plain; charset="windows-1256" ok, I've figured out that this is indeed the case: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23348.html Also, following these instructions I was able to get RAS from the tkreg RAS in FreeView: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024293.html Thanks, Noam ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Peled, Noam [NPELED(a)mgh.harvard.edu] Sent: Wednesday, March 08, 2017 9:27 AM To: Freesurfer support list ?[freesurfer(a)nmr.mgh.harvard.edu]? Subject: [Freesurfer] Yet another freeview coordinates question 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170309/c… ------------------------------ Message: 8 Date: Wed, 8 Mar 2017 21:27:02 -0500 From: "Dorian P." <alb.net(a)gmail.com> Subject: [Freesurfer] Results from R to Freesurfer To: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAF9pfmZN7VXYjotbDzoxFihwNXq7gKDp3eVr4gx9QMPZVcbY+w(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170308/e… -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 390528 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170308/e… ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 157, Issue 26 *******************************************

1 0

FS v6.0 recon-all freezes
by Andrius 10 Mar '17

10 Mar '17

Hi, Maybe some could give advice regarding my problem with FS v6.0. Now I am running recon-all for my patients cohort on Linux Centos 6, FS v6.0. It is PC with i5 intel, 4 Core, 8 Gb RAM. 80% of my subjects finished recon-all process without errors pretty fast (it takes about 11-14 hours per subject). But about 20% subjects hang at the same point of recon all : #@# Fix Topology Copy lh Wed Mar 8 11:22:47 EET 2017 #@# Fix Topology Copy rh Wed Mar 8 11:22:47 EET 2017 #@# Fix Topology lh Wed Mar 8 11:22:47 EET 2017 #@# Fix Topology rh Wed Mar 8 11:22:47 EET 2017 It hangs for infinity at this point. Tried to do it on other PC with same parameters but it stucks at the same point. Any ideas what is wrong? Thank you very much Andrius

3 2

Inflation of one hemi only
by Kang, XJ 10 Mar '17

10 Mar '17

Hi, I am trying to inflate right hemisphere only using the commands: recon-all -autorecon2 -hemi rh -subjid 160526 recon-all -autorecon3 -hemi rh -subjid 160526 The inflation stopped at the step: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 160526 SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could not open file The program "mris_volmask" needs to read "lh.white", which is not generated. Any expert has any suggestions? Maybe I didn't use the commands correctly? Thank you for your help. XJ Kang

3 6

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

3 6

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Freesurfer March 2017