Hello Doug,
I downloaded and installed octave. However, I can't find the
annotval2surfoverlay.m
file in the matlab directory of freesurfer. Does it come with FS v6 or do i
need to download the file? Also, I was looking into the
annotval2surfoverlay file and I have couple of questions.
% Run these commands in matlab
% annotnames = strvcat('superiortemporal','insula','postcentral');
% annotvals = [1.1 2.2 3.7];
% annotfile = '~/subjects/fsaverage/label/lh.aparc.annot';
% surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile);
% clear mri
% mri.vol = surfoverlay;
% MRIwrite(mri,'vals.mgh');
%
1) Are the annotation values (annotvals) from results after correcting for
multiple comparisons using mri_fdr?
2) Do I need to add octave path to freesurfer PATH like the example below?setenv FS_USE_OCTAVE 4.0.3 setenv FS_OCTAVE_LIB /Applications/octave/lib setenv FS_OCTAVE_BIN /Application/octave/binary On Wed, Apr 19, 2017 at 3:39 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > I think that will work > > > On 04/19/2017 03:33 PM, miracle ozzoude wrote: > > Hello Doug, > > Do you think writing the script with octave can substitute for matlab? > > I am using FS v6.0 and I have the annotval2surfoverlay.m. Thanks > > Best, > > Paul > > > > On Wed, Apr 19, 2017 at 1:47 PM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > Sorry, I don't have another solution for you. > > > > > > On 04/19/2017 01:42 PM, miracle ozzoude wrote: > > > Thanks Doug. However, I am running freesurfer analysis on my > > personal > > > computer and I don't have matlab. Also, I don't know how this > matlab > > > script works/ matlab works. Any instructions on how to use it or > > > alternate? Please and thank you. > > > Best, > > > Paul. > > > > > > On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve > > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > > > It is a table of data, so you can't visualize it directly on > > anything. > > > You can try using annotval2surfoverlay.m to create a surface > > > overlay of > > > the data. > > > > > > > > > On 04/19/2017 10:05 AM, miracle ozzoude wrote: > > > > Hello Doug, > > > > It worked. The issue was due to formatting error with the > > aparc > > > file. > > > > Also, I was trying to visualize the result on the surface > > using > > > > freeview -f fsaverage/lh.pial -viewport 3d (clicking > > overlay on > > > > freeview and loading the sig.mgh). However, i got an error " > > > failed to > > > > display overlay". How can I visualize the result? Thanks > > > > Best, > > > > Paul > > > > > > > > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve > > > > <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > >> > > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > > <mailto:gr...@nmr.mgh.harvard.edu <mailto: > gr...@nmr.mgh.harvard.edu>>>> wrote: > > > > > > > > You have a table of data, so no template is needed. If > you > > > put the > > > > --surf before the --table, it probably runs, but it > > will ignore > > > > the surface > > > > > > > > > > > > On 4/18/17 9:58 PM, miracoo...@gmail.com > > <mailto:miracoo...@gmail.com> > > > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>> > > > > <mailto:miracoo...@gmail.com <mailto: > miracoo...@gmail.com> > > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>> wrote: > > > >> Thanks doug. Does it mean when using the --table > > flag, you > > > can't > > > >> use the fsaverage template? I came across several > > post in the > > > >> forum that used "--surf fsaverage lh " and it worked. > > > >> Best, > > > >> Paul > > > >> > > > >> Sent from my BlackBerry 10 smartphone. > > > >> *From: *Douglas Greve > > > >> *Sent: *Tuesday, April 18, 2017 9:52 PM > > > >> *To: *freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > >> <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > >> *Reply To: *Freesurfer support list > > > >> *Subject: *Re: [Freesurfer] mri_glmfit error with aparc > > > table flag > > > >> > > > >> > > > >> Don't include --surf fsaverage lh. It thinks the > > input is a > > > >> surface, not a table > > > >> > > > >> > > > >> > > > >> On 4/18/17 9:21 PM, miracle ozzoude wrote: > > > >>> Hello freesurfer, > > > >>> I am trying to run mri_glmfit with the --table flag. My > > > >>> aparc_lh_thick_stats.txt contain entorhinal and > > > parahippocampal > > > >>> thickness values for 32 subjects. I ran the glm > > command and > > > >>> received an error. Please, how can i solve this > > issue? I have > > > >>> included my command, fsgd file, contrast matrix and > > error > > > below. > > > >>> Thanks > > > >>> Best, > > > >>> Paul > > > >>> > > > >>> GLM command: mri_glmfit --table > aparc_lh_thick_stats.txt > > > --fsgd > > > >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh > > > --cortex > > > >>> --glmdir lh.thickness.glmdir > > > >>> > > > >>> > > > >>> ERROR= "gdfRead(): reading age.fsgd > > > >>> > > > >>> INFO: DeMeanFlag keyword not found, DeMeaning will > > NOT be > > > done. > > > >>> > > > >>> Continuous Variable Means (all subjects) > > > >>> > > > >>> 0 Age 39.9375 17.3312 > > > >>> > > > >>> Class Means of each Continuous Variable > > > >>> > > > >>> 1 Group1 35.6316 > > > >>> > > > >>> 2 Group2 46.2308 > > > >>> > > > >>> INFO: gd2mtx_method is dods > > > >>> > > > >>> Reading source surface > > > >>> > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/ > fsaverage/surf/lh.white > > > >>> > > > >>> Number of vertices 163842 > > > >>> > > > >>> Number of faces 327680 > > > >>> > > > >>> Total area 65416.984375 > > > >>> > > > >>> AvgVtxArea 0.399269 > > > >>> > > > >>> AvgVtxDist 0.721953 > > > >>> > > > >>> StdVtxDist 0.195470 > > > >>> > > > >>> > > > >>> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 > > zkaufman > > > Exp $ > > > >>> > > > >>> cwd /Users/MiracleOz/Documents/improvervsdeclinermri > > > >>> > > > >>> cmdline mri_glmfit.bin --table > > aparc_lh_thick_stats.txt --fsgd > > > >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh > > > --cortex > > > >>> --glmdir lh.thickness.glmdir > > > >>> > > > >>> sysname Darwin > > > >>> > > > >>> hostname MacBook-Pro.local > > > >>> > > > >>> machine x86_64 > > > >>> > > > >>> user MiracleOz > > > >>> > > > >>> FixVertexAreaFlag = 1 > > > >>> > > > >>> UseMaskWithSmoothing 1 > > > >>> > > > >>> OneSampleGroupMean 0 > > > >>> > > > >>> y > > > >>> > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_ > lh_thick_stats.txt > > > >>> > > > >>> logyflag 0 > > > >>> > > > >>> usedti 0 > > > >>> > > > >>> FSGD age.fsgd > > > >>> > > > >>> labelmask > > > >>> > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/ > fsaverage/label/lh.cortex.label > > > >>> > > > >>> maskinv 0 > > > >>> > > > >>> glmdir lh.thickness.glmdir > > > >>> > > > >>> IllCondOK 0 > > > >>> > > > >>> ReScaleX 1 > > > >>> > > > >>> DoFFx 0 > > > >>> > > > >>> Creating output directory lh.thickness.glmdir > > > >>> > > > >>> Loading y from > > > >>> > > > > > /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_ > lh_thick_stats.txt > > > >>> > > > >>> Found 66 data colums > > > >>> > > > >>> Found 0 data rows > > > >>> > > > >>> INFO: gd2mtx_method is dods > > > >>> > > > >>> Saving design matrix to lh.thickness.glmdir/Xg.dat > > > >>> > > > >>> Computing normalized matrix > > > >>> > > > >>> Normalized matrix condition is 32.2165 > > > >>> > > > >>> Matrix condition is 20734.7 > > > >>> > > > >>> Found 149955 points in label. > > > >>> > > > >>> ERROR: mri_reshape: number of elements cannot change > > > >>> > > > >>> nv1 = 163842, nv1 = 66 > > > >>> > > > >>> search space = 82219.962936 > > > >>> > > > >>> ERROR: dimension mismatch between y and X. > > > >>> > > > >>> y has 0 inputs, X has 32 rows." > > > >>> > > > >>> FSGD file: GroupDescriptorFile 1 > > > >>> > > > >>> Title MOT > > > >>> > > > >>> Class Group1 > > > >>> > > > >>> Class Group2 > > > >>> > > > >>> Variables Age > > > >>> > > > >>> Input 01053p Group1 23 > > > >>> > > > >>> Input 01054p Group1 43 > > > >>> > > > >>> Input 01061p Group2 39 > > > >>> > > > >>> Input 01062p Group2 19 > > > >>> > > > >>> Input 01074p Group2 28 > > > >>> > > > >>> .............. (I have more participants) > > > >>> > > > >>> > > > >>> CONTRAST MATRIX: 1 -1 0 0 > > > >>> > > > >>> > > > >>> > > > >>> _______________________________________________ > > > >>> Freesurfer mailing list > > > >>> Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > >>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > >>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > >> > > > >> _______________________________________________ > > > >> Freesurfer mailing list > > > >> Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > >> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > _______________________________________________ > Freesurfer > > > mailing > > > > list Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ > freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 > > <http://www.partners.org/complianceline> > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline>> > > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline> > > > <http://www.partners.org/complianceline > > <http://www.partners.org/complianceline>>> . If the e-mail was sent > > > > to you in error but does not contain patient > > information, please > > > > contact the sender and properly dispose of the e-mail. > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > >> > > > Phone Number: 617-724-2358 <tel:617-724-2358> > > <tel:617-724-2358 <tel:617-724-2358>> > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > > <tel:617-726-7422>> > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > > Outgoing: > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ > greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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