what do you mean "flip" them?
On 11/5/2019 6:10 AM, Jose Graterol wrote:
External Email - Use Caution
I believe I found my problem. I was trying to run the analysis with xhemi.
Therefore it asked for 34 inputs (17subjects * 2 hemispheres). I was doing it
that way because I flipped the hemispheres of the right affected stroke
subjects. That was done with fscalc mul -1.
Now I have another question, would it still be possible to flip the hemispheres
with fscalc while doing a normal group analysis? Or is there another way to
flip them? I want to flip the hemispheres to have all the affected just in one
side (e. g. the left hemisphere).
Thanks in advance.
On Thu, Oct 31, 2019 at 7:10 PM Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote:
There are not any restrictions, just do the same as you would for a
non-paired analysis. In any event, you are creating a linear model
y = a +b1*x1 + b2*x2 ...
where y is the input (paired diff) and x1, x2, etc, are your factors.
You are the one who knows your data and what models would be appropriate
On 10/31/19 12:41 PM, Jose Graterol wrote:
>
> External Email - Use Caution
>
> My doubt is, if it is possible to use a FSGD file to add variables to
> a --paired-diff analysis. If it is, what would be the right way to
> format the FSGD file.
>
> Thanks in advance.
>
> On Wed, Oct 30, 2019 at 3:01 PM Greve, Douglas N.,Ph.D.
> <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
> <mailto:dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>> wrote:
>
> I don't understand. What per hemisphere variable?
>
> On 10/25/2019 3:15 AM, Jose Graterol wrote:
>>
>> External Email - Use Caution
>>
>> Thanks for your answer. A follow up question:
>> How should I then specify the variable's values per hemisphere
>> while making the FSGD file if I want to add covariates when
>> running mri_glmfit?
>>
>> Thanks in advance.
>>
>> On Fri, Oct 25, 2019 at 12:18 AM Greve, Douglas N.,Ph.D.
>> <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
>> <mailto:dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>> wrote:
>>
>> If you are trying to determine whether the hemispheres are
>> different,
>> then you need to do the subtraction between the hemis (ie, the
>> --paired-diff). If you want to look at the hemispheres
>> separately, then
>> don't combine them in a single file
>>
>> On 10/21/19 4:58 AM, Jose Graterol wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Thanks for your answer.
>> >
>> > I want to correlate TMS values in 17 stroke patients.
>> Following the
>> > instructions provided to Anders in this link
>> >
>>
>> https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+flipping+surface+data%22&o=newest&f=1
>>
>> > I created the --y file that joins the affected hemispheres
>> together
>> > and the unaffected hemispheres together. I omitted the
>> --paired-diff
>> > flag. When I run mri_glmfit with --fsgd it asks for 34
>> inputs. I am
>> > guessing those are for the 34 hemispheres of the patients
>> in the order
>> > mentioned in my first email. Would this be the right way to
>> correlate
>> > the variables?
>> >
>> > In short, I am trying to test if there is a difference in
>> cortical
>> > thickness, while adding covariates, between the affected and
>> > unaffected hemispheres in stroke patients.
>> >
>> > Thanks in advance
>> >
>> > On Fri, Oct 18, 2019 at 3:57 PM Greve, Douglas N.,Ph.D.
>> > <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
>> <mailto:dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>
>> <mailto:dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
>> <mailto:dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>>>
>> wrote:
>> >
>> > What are you trying to test? Usually you don't have lh
>> and rh in
>> > the same glm
>> >
>> > On 10/17/19 7:09 AM, Jose Graterol wrote:
>> >>
>> >> External Email - Use Caution
>> >>
>> >> Dear Freesurfer Community,
>> >>
>> >> I have a question regarding the formatting of the FSGD
>> file while
>> >> doing an analysis with Xhemi.
>> >> First the --y file was created as previously explained
>> in another
>> >> discussion
>> >>
>>
>> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63965.html).
>> >> That is, mris_preproc with --xhemi and no --fsgd flag.
>> >>
>> >> If I understood correctly, that would create a mgh
>> file with the
>> >> following order: sub01lh, sub01rh, sub02lh, sub02rh...
>> >> Then the FSGD file while running mri_glmfit would be:
>> >> GroupDescriptorFile 1
>> >> Title xxx
>> >> Class sub
>> >> Variables var1
>> >> Input sub01lh sub var1_lh_sub01
>> >> Input sub01rh sub var1_rh_sub01
>> >> Input sub02lh sub var1_lh_sub02
>> >> Input sub02rh sub var1_rh_sub02
>> >>
>> >> Would this be correct? If so, what would be the best
>> case for
>> >> specifying a variable like age? Just repeating the
>> value 2 times?
>> >>
>> >> As always, thanks in advance
>> >>
>> >> Kind Regards
>> >>
>> >> José
>> >>
>> >>
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