If you use
thick = fast_vol2mat(MRIread('file.mgh'));
thick will be a matrix of nsubjects-by-nvertices.
Note that the vertex indices from labels are 0-based whereas matlab
expects 1-based.
doug
On 03/27/2013 09:08 AM, Gabriel Gonzalez Escamilla wrote:
> That makes much more sense than the thing I was looking for.
>
> Now I have a problem reading the lh.lh-rh.thickness.mgh with the
> load_mgh.m function, as I have no idea of how to read it to get the
> vertex by vertex thickness value of each subject.
>
> I tryed as [thick, ~,~,~]=load_mgh('file.mgh',[],[1:nSubjs])
> then reading: subjIDthick=thick(vtxID,1,1,subjID);
> where vtxID es the vertex of the .label file I want, and subjID is the
> number of the subject.
> is that correct?
>
> All this is because I will use it as a covariate in the statistical
> analysis as suggested in
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27129.html
>
>
> Regards,
> Gabriel.
>
>
>
> El 26/03/13, *Douglas N Greve * <gr...@nmr.mgh.harvard.edu> escribió:
>> Unless you specifically need them for an individual, you should get them
>> from lh.lh-rh.thickness.mgh because that data is sampled onto the
>> symmetric template and so should be unbiased (ie, it will not
>> systematically favor lh or rh).
>> doug
>>
>>
>> On 03/26/2013 12:40 PM, Gabriel Gonzalez Escamilla wrote:
>> > Dear Doug,
>> >
>> > I meant of a given subject,
>> >
>> > But, As I'm thinking about this, I'm wondering if it has sense to have
>> > left and right cortical thickness of my every individual subjects, or
>> > if I should obtain the lh-rh thickness differences for the individuals?
>> >
>> > I suppose that I should read the lh.lh-rh.thickness.mgh created by
>> > mris_preproc to get the average differences in lh-rh hemispheres.
>> >
>> >
>> >
>> > Regards,
>> > Gabriel
>> >
>> >
>> >
>> >
>> > El 25/03/13, *Douglas N Greve * <gr...@nmr.mgh.harvard.edu> escribió:
>> >>
>> >> Do you mean you want the right hemi thicknesses on the left hemisphere
>> >> of a given subject or on the fsaverage_sym?
>> >> doug
>> >>
>> >>
>> >> On 03/25/2013 11:25 AM, Gabriel Gonzalez Escamilla wrote:
>> >> > Thank you, so I'm keeping the one I had.
>> >> >
>> >> > Sorry for my bad explanation. When I do a normal cortical thickness
>> >> > study, I know the average thickness for a label, e.g. cortex,
>> and the
>> >> > values at each vertex of each hemisphere are stored in
>> >> > $subject/surf/?l.thickness. I would like to know if it is
>> possible to
>> >> > obtain the same cortical thickness measure from the lh-rh registered
>> >> > hemispheres of each subject.
>> >> >
>> >> >
>> >> > Regards,
>> >> > Gabriel
>> >> >
>> >> >
>> >> > El 25/03/13, *Douglas N Greve * <gr...@nmr.mgh.harvard.edu>
>> escribió:
>> >> >>
>> >> >> On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote:
>> >> >> >Thanks a lot for your answer,
>> >> >> >
>> >> >> >I'm sending you attached the diff of the two mris_preproc.
>> >> >> Those differences are just added features and won't change your
>> >> results.
>> >> >> >
>> >> >> >When I wrote CT, I was meaning cortical thickness, as normally
>> this
>> >> >> values are in surf/?h.thickness, But how do I know the
>> >> >> Xhemi-registered thickness values of each subject for lh-rh, or
>> area
>> >> >> or any of those indices?
>> >> >> I'm not sure what you mean. When you run mris_preproc, you specify
>> >> >> whether you want thickness, etc.
>> >> >> doug
>> >> >> >
>> >> >> >Regards,
>> >> >> >Gabriel
>> >> >> >
>> >> >> >
>> >> >> >El 25/03/13, *Douglas N Greve * <gr...@nmr.mgh.harvard.edu>
>> escribió:
>> >> >> >>
>> >> >> >>On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote:
>> >> >> >>> Dear Doug,
>> >> >> >>>
>> >> >> >>> I've seen that you restore the files to download, for the Xhemi
>> >> >> >>> registration. While I'm checking for the statistical
>> process, I've
>> >> >> >>> seen that the one I have is: Date: 2012/12/06 16:06:52,
>> Revision:
>> >> >> >>> 1.59.2.4, and the one that is on your ftp server is Date:
>> >> 2012/12/06
>> >> >> >>> 16:06:17, Revision: 1.66, So mine is a lower version but
>> >> recent hour,
>> >> >> >>> and the actual is newer version but seems that was created
>> >> before the
>> >> >> >>> one I have. My question is, Which one should I keep?
>> >> >> >>Can you send me a diff of the two files?
>> >> >> >>>
>> >> >> >>> If I change the mris_precproc version. Shall I re-run this
>> step
>> >> >> >>> before statistical analyses, to create a new
>> >> >> lh.lh-rh.thickness.sm00.mgh?
>> >> >> >>>
>> >> >> >>> On the other hand I have some doubts about the statistical
>> >> procedure.
>> >> >> >>> It's supposed that if I apply the Xhemi registration, as
>> >> result the
>> >> >> >>> left and right hemispheres are equals to each other on every
>> >> >> subject, so:
>> >> >> >>>
>> >> >> >>> A) Where can I get the CT values after the Xhemi
>> registration to
>> >> >> >>> FSaverage_sym for the left and right hemispheres?
>> >> >> >>what are CT values?
>> >> >> >>>
>> >> >> >>>
>> >> >> >>> B) Given that I have two groups, Patients and Control, with two
>> >> >> levels
>> >> >> >>> each, i.e male-female (Gp1male Gp1female Gp2male Gp2female
>> >> >> >>> Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and
>> that
>> >> >> I can
>> >> >> >>> set the contrasts and fsgd files as with a normal CT
>> analisis, but
>> >> >> >>> only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to
>> >> >> contain the
>> >> >> >>> left-right differences across subjects, right?
>> >> >> >>>
>> >> >> >>> Wich would be the right interpretation? of:
>> >> >> >>The interpretation does not really change because it is a xhemi
>> >> >> analysis
>> >> >> >>>
>> >> >> >>> 1) 5 .5 -.5 -.5 0 0 0 0
>> >> >> >>Is the L-R difference between Grp1 and Grp2 different than 0
>> >> >> (regressing
>> >> >> >>out Var1 and gender)
>> >> >> >>>
>> >> >> >>> 2) 5 -.5 .5 -.5 0 0 0 0
>> >> >> >>Is the L-R difference between Males and Females different than 0
>> >> >> >>(regressing out Var1 and Group)
>> >> >> >>>
>> >> >> >>> 3) 0 0 0 0 .5 .5 -.5 -.5
>> >> >> >>Does the slope of the L-R difference with Var1 differ between
>> >> Grp1 and
>> >> >> >>Grp2(regressing out gender)
>> >> >> >>>
>> >> >> >>> 4) 0 0 0 0 5 -.5 .5 -.5
>> >> >> >>Does the slope of the L-R difference with Var1 differ between
>> >> Male and
>> >> >> >>Female(regressing out group)
>> >> >> >>>
>> >> >> >>
>> >> >> >>>
>> >> >> >>>
>> >> >> >>>
>> >> >> >>> Many thanks in advanced.
>> >> >> >>> Gabriel.
>> >> >> >>
>> >> >> >>--
>> >> >> >>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: 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
>> >> >> >>
>> >> >> >>
>> >> >> >>The information in this e-mail is intended only for the person to
>> >> >> whom it is
>> >> >> >>addressed. If you believe this e-mail was sent to you in
>> error and
>> >> >> the e-mail
>> >> >> >>contains patient information, please contact the Partners
>> >> >> Compliance HelpLine at
>> >> >> >>http://www.partners.org/complianceline . If the e-mail was
>> sent to
>> >> >> you in error
>> >> >> >>but does not contain patient information, please contact the
>> sender
>> >> >> and properly
>> >> >> >>dispose of the e-mail.
>> >> >> >>
>> >> >> >
>> >> >> >--
>> >> >> >--------------------------
>> >> >> >PhD. student Gabriel González-Escamilla
>> >> >> >Laboratory of Functional Neuroscience
>> >> >> >Department of Physiology, Anatomy, and Cell Biology
>> >> >> >University Pablo de Olavide
>> >> >> >Ctra. de Utrera, Km.1
>> >> >> >41013 - Seville
>> >> >> >- Spain -
>> >> >> >
>> >> >> >Email: ggon...@upo.es
>> >> >> >http://www.upo.es/neuroaging/es/
>> >> >>
>> >> >> --
>> >> >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> >> >> Outgoing:
>> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> >> >>
>> >> >
>> >> > --
>> >> > --------------------------
>> >> > PhD. student Gabriel González-Escamilla
>> >> > Laboratory of Functional Neuroscience
>> >> > Department of Physiology, Anatomy, and Cell Biology
>> >> > University Pablo de Olavide
>> >> > Ctra. de Utrera, Km.1
>> >> > 41013 - Seville
>> >> > - Spain -
>> >> >
>> >> > Email: ggon...@upo.es
>> >> > http://www.upo.es/neuroaging/es/
>> >>
>> >> --
>> >> 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: 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
>> >
>> > --
>> > --------------------------
>> > PhD. student Gabriel González-Escamilla
>> > Laboratory of Functional Neuroscience
>> > Department of Physiology, Anatomy, and Cell Biology
>> > University Pablo de Olavide
>> > Ctra. de Utrera, Km.1
>> > 41013 - Seville
>> > - Spain -
>> >
>> > Email: ggon...@upo.es
>> > http://www.upo.es/neuroaging/es/
>> >
>> >
>> > --
>> > --------------------------
>> > PhD. student Gabriel González-Escamilla
>> > Laboratory of Functional Neuroscience
>> > Department of Physiology, Anatomy, and Cell Biology
>> > University Pablo de Olavide
>> > Ctra. de Utrera, Km.1
>> > 41013 - Seville
>> > - Spain -
>> >
>> > Email: ggon...@upo.es
>> > http://www.upo.es/neuroaging/es/
>>
>> --
>> 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: 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
>
> --
> --------------------------
> PhD. student Gabriel González-Escamilla
> Laboratory of Functional Neuroscience
> Department of Physiology, Anatomy, and Cell Biology
> University Pablo de Olavide
> Ctra. de Utrera, Km.1
> 41013 - Seville
> - Spain -
>
> Email: ggon...@upo.es
> http://www.upo.es/neuroaging/es/
--
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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