20 Apr
2017
20 Apr
'17
10:10 a.m.
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 greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 thismatlab
> 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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:
> > > > You have a table of data, so no template is needed. Ifyou
> put the > > --surf before the --table, it probably runs, but it will ignore > > the surface > > > > > > On 4/18/17 9:58 PM, miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> > > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>
<mailto:miracooloz@gmail.com <mailto:miracooloz@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 --tableaparc_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
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