setenv FS_USE_OCTAVE 4.0.3 setenv FS_OCTAVE_LIB /Applications/octave/lib setenv FS_OCTAVE_BIN /Application/octave/binary
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 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
> > <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. If you
> > 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 --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
> > <mailto:Freesurfer@nmr.mgh.> > > <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/ >>> Thefreesurfer
> > > 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 >
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
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu >
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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/
> > _______________________________________________ > <mailto:Freesurfer@nmr.mgh.
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu >
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
> greve@nmr.mgh.harvard.edu <mailto:greve@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:Freesurfer@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
greve@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