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 * greve@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 * greve@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 * greve@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 * greve@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 >>greve@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: ggonesc@upo.es >http://www.upo.es/neuroaging/es/
-- 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: 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: ggonesc@upo.es http://www.upo.es/neuroaging/es/
-- 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: 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: ggonesc@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: ggonesc@upo.es http://www.upo.es/neuroaging/es/
-- 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: 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: ggonesc@upo.es http://www.upo.es/neuroaging/es/
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Gabriel Gonzalez Escamilla