Freesurfer

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

08 Mar '17

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>>> 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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Uploading masks on data processed by freesurfer
by Lionel Giriteka 08 Mar '17

08 Mar '17

Hi I have processed my data with freesurfer. And an expert have made manual segmentations and sendt it to me as masks (analyze format = img & hdr). I now want to view these masks with the data I have run through freesurfer, but I am not sure how to proceed. Any advices? Thanks a lot. Best Regards, Lionel

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VL: Freesurfer labeling problem?
by Reetta-Liina Säilä 08 Mar '17

08 Mar '17

Hello All, I have done the hippocampus segmentation with dev version 6 (Downloaded on 26th March 2016). I have difficulties in determing what the output labels consist of. The outputfile names are these: left_Hippocampal_tail left_subiculum left_CA1 left_hippocampal-fissure left_presubiculum left_parasubiculum left_molecular_layer_HP left_GC-ML-DG left_CA3 left_CA4 left_fimbria left_HATA left_Whole_hippocampus (and the same on the right side) But, there are some discrepancies between these output labels and Eugenio Iglesias' article (attached). First, more often I see GC-ML-DG labeled as GC-DG, what is the difference between these two? Is the dentate gyrus' molecular layer included in GC-ML-DG / GC-DG or not? In summary, my question is: what structures exactly are included in the labels of dev version 6: - GC-ML-DG - molecular_layer_HP -CA3 And which labels correspond these on the final version of Freesurfer 6? These are the discrepancies on the article attached on pages 2, and 7. 1) The article says on page 2: - The T2 images are often acquired anisotropically, such that resolution along the direction of the major axis of the hippocampus is reduced in exchange for higher in-plane resolution within each coronal slice. This design choice is motivated by the internal structure of the hippocampus: resembling a Swiss roll, its spiral structure changes less rapidly along its major axis, which is almost parallel to the anterior-posterior direction. In in vivo T2-weighted data, part of this spiral becomes visible as a hypointense band that corresponds to the stratum radiatum, lacunosum moleculare, hippocampal sulcus and molecular layer of the dentate gyrus. These layers separate the hippocampus from the dentate gyrus. Henceforth, for simplicity in writing, we will refer to this band as the “molecular layer”. 2) On page 7: "Molecular layer: This label consists of two parts, molecular layer for subiculum or molecular layer for CA fields. The molecular layer appears as dark contrast that lies directly underneath the hippocampal fissure and above the subiculum. The molecular layer of the hippocampus continues as dark contrast that forms between the CA regions and the GC-DG as well as the hippocampal fissure. The molecular layer follows the shape of the hippocampal folds." I am little confused of this 'molecular layer' term in the previous contexts, and what the actual output label 'molecular layer' consists of. Has someone gone through this already? Thank you! Best, Reetta-Liina

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Different segmentation atlas
by Julie Hall 08 Mar '17

08 Mar '17

Dear all, I would like to use the Gordon Parcellation as segmentation atlas for my subjects. I have warped this atlas into individual subject space. Then I wanted to use mris_sample_parc to apply this parcallation, but I have a few questions.. 1. Is this the right command to use? 2. When I use this command, I get the following error: could not open translation file /Applications/freesurfer/cma_parcellation_colors.txt I don’t have this color table, should I create one (and how?)? Thank you Julie

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Re: [Freesurfer] Error viewing corrected results
by Antonin Skoch 07 Mar '17

07 Mar '17

Dear Martin, thinking of that further, my advice for negative cluster-forming threshold was probably wrong in this context. Instead, I think that you can achieve negative one-side hypothesis by specifying positive cluster-forming threshold and inverting the sign of your contrast vector. Antonin 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>>> 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 > >> > > > >> > >

1 0

Re: [Freesurfer] Error viewing corrected results
by Antonin Skoch 07 Mar '17

07 Mar '17

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>>> wrote: > >> > > >> > This is a problem with using LGI in that it is already extremely > >> > smooth > >> > that the smoothness exceeds the limit of the look up table that we > >> > supply. I recommend that you not use a gaussian-based correction for > >> > LGI. Instead, use permutation (see mri_glmfit-sim --help). > >> > > >> > > >> > > >> > On 03/06/2017 01:36 PM, Martin Juneja wrote: > >> > > Hello everyone, > >> > > > >> > > I am trying to extract clusters showing significant correlation > >> > > between LGI and a behavioral measure. I am able to extract PCC and > >> > > sig.mgh but at the last step when I try to run simulation command > >> > to > >> > > view corrected results and I run: > >> > > > >> > > mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 > >> > > --2spaces > >> > > > >> > > I get following error: > >> > > > >> > > ERROR: cannot find > >> > > > >> > > >> > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd > >> > > > >> > > But I can see mc-z.csd file in fwhm30 etc. > >> > > > >> > > Full message on terminal window is attached following. > >> > > > >> > > Any help would be really appreciated. > >> > > > >> > > ----- Full message ---- > >> > > > >> > > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd > >> > dods --C > >> > > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir > >> > lh.MEQ_LGI.glmdir > >> > > > >> > > WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin > >> > > > >> > > SURFACE: fsaverage lh > >> > > > >> > > log file is lh.MEQ_LGI.glmdir/cache.mri_glmfit-sim.log > >> > > > >> > > /usr/local/freesurfer/bin/mri_glmfit-sim > >> > > > >> > > --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 --2spaces > >> > > > >> > > $Id: mri_glmfit-sim,v 1.60 2016/04/30 15:13:36 greve Exp $ > >> > > > >> > > Mon Mar 6 11:11:13 MST 2017 > >> > > > >> > > setenv SUBJECTS_DIR > >> > > /data/emot/Freesurfer/FreeSurferSegmentation/SB_AgingAll > >> > > > >> > > FREESURFER_HOME /usr/local/freesurfer > >> > > > >> > > Original mri_glmfit command line: > >> > > > >> > > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd > >> > dods --C > >> > > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir > >> > lh.MEQ_LGI.glmdir > >> > > > >> > > DoSim = 0 > >> > > > >> > > UseCache = 1 > >> > > > >> > > DoPoll = 0 > >> > > > >> > > DoPBSubmit = 0 > >> > > > >> > > DoBackground = 0 > >> > > > >> > > DiagCluster = 0 > >> > > > >> > > gd2mtx = dods > >> > > > >> > > fwhm = 35.073391 > >> > > > >> > > ERROR: cannot find > >> > > > >> > > >> > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd > >> > > > >> > > > >

2 1

GLM-error
by Limachia, Gaurang (NIH/NINDS) [F] 07 Mar '17

07 Mar '17

Dear Freesurfer Experts, I was running qdec, and encountered an error while I was running the analyze button on the qdec. Subsequently, if you can help with the following error would greatly appreciate it. Continuous Variable Means (all subjects) 0 Intracranial_volume 1.53095e+06 157812 1 Gender 1.75728 0.428726 Class Means of each Continuous Variable 1 Main 1530945.8883 1.7573 INFO: gd2mtx_method is dods Reading source surface /raids/hmcsraid3/silvina/PMD_FATCAT2015/fsaverage/surf/lh.white MRISread(/raids/hmcsraid3/silvina/PMD_FATCAT2015/fsaverage/surf/lh.white): could not open file No such file or directory mri_glmfit: could not read surface /raids/hmcsraid3/silvina/PMD_FATCAT2015/fsaverage/surf/lh.white No such file or directory Error in Analyze: command failed: mri_glmfit --y /raids/hmcsraid3/silvina/PMD_FATCAT2015/qdec/Untitled/y.mgh --fsgd /raids/hmcsraid3/silvina/PMD_FATCAT2015/qdec/Untitled/qdec.fsgd dods --glmdir /raids/hmcsraid3/silvina/PMD_FATCAT2015/qdec/Untitled --surf fsaverage lh --C /raids/hmcsraid3/silvina/PMD_FATCAT2015/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /raids/hmcsraid3/silvina/PMD_FATCAT2015/qdec/Untitled/contrasts/lh-Avg-thickness-Intracranial_volume-Cor.mat Thanks, Gaurang Shyam Limachia

2 1

Re: [Freesurfer] Error viewing corrected results
by Antonin Skoch 07 Mar '17

07 Mar '17

Dear Martin, input -i input file is lh.MEQ_LGI.10.mgh file in your glmdir directory (for left hemisphere). As you could read in following messages in the referenced thread in FSL discussion forum, cluster-forming threshold need to be specified in z, not in t. Therefore, you would have to select cluster forming threshold and specify it as a z score. I think that your z-score for your original mri_glmfit-sim commandline argument --cache 4 negwill be -qnorm(1-10^-4)=-3.719016. (I am not perfectly sure since I never tried negative one-side hypothesis testing in PALM). You could also use other statistics, such as cluster mass, or TFCE. See PALM user guide. Do not include -pmethodp none and -pmethodr none, since you would need the partitioning due your non-orthogonal design matrix. ?h.white.avg.area.mgh file (which you will find under fsaverage directory) goes as second argument after -s option. Therefore I suppose the commandline for cluster extent inference with cluster forming threshold p=0.0001, negative one-sided hypothesis, left hemisphere, will be hopefully something like palm -i y.mgh -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh -d Xg.csv -t your_contrasts.csv -n number_of_permutations -m mask.mgh -o output_basename -Cstat extent -C -3.719016 -saveglm -savedof -savemetrics The last 3 commandline options are only for diagnostical purposes. The output is surface overlay you can visualize in freeview. I use following code snippet for the reporting significant clusters in MNI coordinates: # PALM output cluster extent p maps have 1 outside cluster - problem with mri_surfcluster and also for display in freeView #here we set values 1 to 0 in pmaps. #done by binarizing and subtracting if [[ $# -ne 2 ]]; then echo "get cluster summary of PALM statistics. Expecting 2 arguments: 1- input p-map, 2- hemisphere (lh/rh)" exit fi mri_binarize --i $1 --min 1 --o p_bin.mgz mris_calc --output ${1%%.mgz}_filtered.mgz $1 sub p_bin.mgz mri_surfcluster --in ${1%%.mgz}_filtered.mgz --subject fsaverage --hemi $2 --surf white --annot aparc --thmin 0.000000001 --thmax 0.05 --mask mask.mgh --sum ${1%%.mgz}_cluster.summary --nofixmni rm p_bin.mgz They are not Bonferroni-corrected for 2 hemispheres (--2spaces). Regarding your design and contrast: Design has to be matrix of values. You can use qdec to produce Xg.dat file with design matrix, then rename it to Xg.csv to be correctly readable by PALM. Regards, Antonin Hi Antonin, As you suggested in discussion forum, I tried to run following command after mri_glmfit:palm -s fsaverage/surf/lh.white -n 10000 -m mask.mgh -Cstat extent -C 1.974975 -pmethodp none -pmethodr none -twotail -d Design_MEQ.txt -t Contrast_MEQ.txt Running PALM alpha104 using MATLAB 9.0.0.341360 (R2016a) with the following options: -s fsaverage/surf/lh.white -n 10000 -m mask.mgh -Cstat extent -C 1.974975 -pmethodp none -pmethodr none -twotail -d Design.txt -t Contrast.txt Found FSL in /usr/share/fsl/5.0 Found FreeSurfer in /usr/local/freesurfer Found SPM in /usr/local/spm12 Error using palm_takeargs (line 1141) Missing input data (missing "-i"). Error in palm_core (line 33) [opts,plm] = palm_takeargs(varargin{:}); Error in palm (line 81) palm_core(varargin{:}); Looks like error is because its missing -i input here, I am not sure what's input file here? Also, I am trying to correlate LGI versus behavioral score, regressing out the effect of sex and age. So I just wanted to confirm if my design.txt and contrast.txt files are correct here. Please find both following: Design file (Variables Behav, Age) as following: S001 Male 60 36 S003 Female 73 29 S004 Male 48 39 .......so on...... Contrast file as following: 0 0 0.5 0.5 0 0 (same as *.mtx file used for glm_fit) Thank you so much for your help and time. On Tue, Mar 7, 2017 at 10:49 AM, Martin Juneja <mj70...(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>>> 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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tracula stats
by Jacobs H (NP) 07 Mar '17

07 Mar '17

Hi FreeSurfer, I have analyzed my diffusion data using Tracula and combined the voxelwise diffusion measures across all subjects in one file (following the guidelines online). In this text file, I saw that on some of these voxels some people have NAs, so their tract is most likely shorter there. I now would like to do t-tests for each voxel and plot these in freeview. Would you recommend to only take those voxels that have a value in each subject? Look forward to your thoughts on this. Best wishes Heidi

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Re: [Freesurfer] Error viewing corrected results
by Antonin Skoch 07 Mar '17

07 Mar '17

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&… 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>> 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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