Re: [Freesurfer] group analysis all measures same results

2016-03-19 Thread Kaiming Yin 
Title AD_HV_GroupAnalysis
>> Class AD
>> Class HV
>> InputAD_003AD
>> InputAD_005AD
>> ...
>> InputHV_ABHV
>> InputHV_AEHV
>>
>>
>> group_diff.mtx
>>
>> 1 -1
>>
>>
>> right thickness
>>
>> mris_preproc --fsgd ad_hv.fsgd --cache-in
>> thickness.fwhm10.fsaverage --target fsaverage
>> --hemi rh
>> --out rh.ad_hv.thick.10.mgh
>>
>> mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd
>> ad_hv.fsgd dods
>> --C group_diff.mtx --surf fsaverage rh
>> --cortex --glmdir
>> rh.ad_hv.thick.glmdir
>>
>> mri_glmfit-sim --glmdir rh.ad_hv.thick.glmdir
>> --cache 4 neg
>> --cwp 0.05 --2spaces
>>
>>
>> right white surface
>>
>> mris_preproc --fsgd ad_hv.fsgd --cache-in
>> area.fwhm10.fsaverage --target fsaverage
>> --hemi rh --out
>> rh.ad_hv.area.10.mgh
>>
>> mri_glmfit --y rh.ad_hv.area.10.mgh --fsgd
>> ad_hv.fsgd dods
>> --C group_diff.mtx --surf fsaverage rh
>> --cortex --glmdir
>> rh.ad_hv.area.glmdir
>>
>>             mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir
>> --cache 4 neg
>> --cwp 0.05 --2spaces
>>
>>
>> Their results were all the same.
>>
>> Thanks,
>> Kaiming
>>
>>
>> -- Forwarded message --
>> From: Douglas N Greve
>> <gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>
>> <mailto:gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>>>
>> To: freesurfer@nmr.mgh.harvard.edu
>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>> <mailto:freesurfer@nmr.mgh.harvard.edu
>> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Cc:
>> Date: Mon, 7 Mar 2016 18:47:11 -0500
>> Subject: Re: [Freesurfer] group analysis all
>> measures same
>> results
>> what are your command lines?
>>
>>
>> On 5 March 2016 at 02:01, Kaiming Yin
>> <yinkaiming6...@gmail.com
>> <mailto:yinkaiming6...@gmail.com>
>> <mailto:yinkaiming6...@gmail.com
>>
>> <mailto:yinkaiming6...@gmail.com>>>
>>
>> wrote:
>>
>> Dear guys,
>>
>> I was doing group analysis (command-line)
>> on two groups
>> (patients and control, no age or other
>> information). The
>> data has been "qcached", and after
>> following the three
>> steps as "mris_preproc, mri_glmfit and
>> mri_glmfit-sim"
>> shown in the tutorial on the Freesurfer
>> website, I
>> obtained the difference on thickness in
>> both left and
>> right hemispheres, which seems great.
>> However, when I
>> repeated the above steps on other
>> measures, e.g. area,
>> area.pial, volume (also replaced the parts of
>> "thickness" in the command lines), the
>> results seemed to
>> be exactly the same again as those in the
>> thickness
>>

Re: [Freesurfer] group analysis all measures same results

2016-03-15 Thread Kaiming Yin 
ess.fwhm10.fsaverage --target fsaverage
>> --hemi rh
>> --out rh.ad_hv.thick.10.mgh
>>
>> mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd
>> ad_hv.fsgd dods
>> --C group_diff.mtx --surf fsaverage rh
>> --cortex --glmdir
>> rh.ad_hv.thick.glmdir
>>
>> mri_glmfit-sim --glmdir rh.ad_hv.thick.glmdir
>> --cache 4 neg
>> --cwp 0.05 --2spaces
>>
>>
>> right white surface
>>
>> mris_preproc --fsgd ad_hv.fsgd --cache-in
>> area.fwhm10.fsaverage --target fsaverage
>> --hemi rh --out
>> rh.ad_hv.area.10.mgh
>>
>> mri_glmfit --y rh.ad_hv.area.10.mgh --fsgd
>> ad_hv.fsgd dods
>> --C group_diff.mtx --surf fsaverage rh
>> --cortex --glmdir
>> rh.ad_hv.area.glmdir
>>
>>     mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir
>>     --cache 4 neg
>>     --cwp 0.05 --2spaces
>>
>>
>> Their results were all the same.
>>
>> Thanks,
>> Kaiming
>>
>>
>> -- Forwarded message --
>> From: Douglas N Greve
>> <gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>
>> <mailto:gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>>>
>> To: freesurfer@nmr.mgh.harvard.edu
>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>> <mailto:freesurfer@nmr.mgh.harvard.edu
>> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Cc:
>> Date: Mon, 7 Mar 2016 18:47:11 -0500
>> Subject: Re: [Freesurfer] group analysis all
>> measures same
>> results
>> what are your command lines?
>>
>>
>> On 5 March 2016 at 02:01, Kaiming Yin
>> <yinkaiming6...@gmail.com
>> <mailto:yinkaiming6...@gmail.com>
>> <mailto:yinkaiming6...@gmail.com
>>
>> <mailto:yinkaiming6...@gmail.com>>>
>>
>> wrote:
>>
>> Dear guys,
>>
>> I was doing group analysis (command-line)
>> on two groups
>> (patients and control, no age or other
>> information). The
>> data has been "qcached", and after
>> following the three
>> steps as "mris_preproc, mri_glmfit and
>> mri_glmfit-sim"
>> shown in the tutorial on the Freesurfer
>> website, I
>> obtained the difference on thickness in
>> both left and
>> right hemispheres, which seems great.
>> However, when I
>> repeated the above steps on other
>> measures, e.g. area,
>> area.pial, volume (also replaced the parts of
>> "thickness" in the command lines), the
>> results seemed to
>> be exactly the same again as those in the
>> thickness
>> comparison, even the p-value numbers in
>> the file
>> "cache.th40.neg.sig.cluster.summary" were
>> the same. I
>> was using Freesurfer v6.0-beta, and I
>> performed the
>> individual data analysis on a linux
>> cluster and I
>> copied/downloaded the whole "qcached"
>> subject directory
>> to

Re: [Freesurfer] group analysis all measures same results

2016-03-15 Thread Douglas N Greve 
  rh.ad_hv.area.10.mgh
>
> mri_glmfit --y rh.ad_hv.area.10.mgh --fsgd
> ad_hv.fsgd dods
> --C group_diff.mtx --surf fsaverage rh
> --cortex --glmdir
> rh.ad_hv.area.glmdir
>
> mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir
> --cache 4 neg
> --cwp 0.05 --2spaces
>
>
> Their results were all the same.
>
> Thanks,
> Kaiming
>
>
> -- Forwarded message --
> From: Douglas N Greve
> <gr...@nmr.mgh.harvard.edu
>         <mailto:gr...@nmr.mgh.harvard.edu>
>     <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>>
> To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Cc:
> Date: Mon, 7 Mar 2016 18:47:11 -0500
> Subject: Re: [Freesurfer] group analysis all
> measures same
> results
> what are your command lines?
>
>
> On 5 March 2016 at 02:01, Kaiming Yin
> <yinkaiming6...@gmail.com
> <mailto:yinkaiming6...@gmail.com>
> <mailto:yinkaiming6...@gmail.com
> <mailto:yinkaiming6...@gmail.com>>>
>
> wrote:
>
> Dear guys,
>
> I was doing group analysis (command-line)
> on two groups
> (patients and control, no age or other
> information). The
> data has been "qcached", and after
> following the three
> steps as "mris_preproc, mri_glmfit and
> mri_glmfit-sim"
> shown in the tutorial on the Freesurfer
> website, I
> obtained the difference on thickness in
> both left and
> right hemispheres, which seems great.
> However, when I
> repeated the above steps on other
> measures, e.g. area,
> area.pial, volume (also replaced the parts of
> "thickness" in the command lines), the
> results seemed to
> be exactly the same again as those in the
> thickness
> comparison, even the p-value numbers in
> the file
> "cache.th40.neg.sig.cluster.summary" were
> the same. I
> was using Freesurfer v6.0-beta, and I
> performed the
> individual data analysis on a linux
> cluster and I
> copied/downloaded the whole "qcached"
> subject directory
> to my linux laptop to perform the group
> comparison, both
> using the same version of Freesurfer, does
> it matter? Or
> do you know why it happened like this?
>
> Thanks,
> Kaiming
>
>
>
> 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.
>
>
>
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mail

Re: [Freesurfer] group analysis all measures same results

2016-03-14 Thread Douglas Greve 
I don't know what happened. I cannot replicate it here. Can you re-run 
the recon-all -s -qcache command and verify that the files are still the 
same?


On 3/14/16 11:11 AM, Kaiming Yin wrote:

Dear Douglas,

Yes, both of the two pairs of files are the same. i.e.

mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh

diffcount 0


mri_diff rh.thickness.fwhm10.fsaverage.mgh rh.area.fwhm10.fsaverage.mgh

diffcount 0


Does this mean I run the "-qcache" wrongly? I just run "recon-all -s 
XX -qcache" on each subject.


Thanks,
Kaiming


On 14 March 2016 at 14:58, Douglas Greve <gr...@nmr.mgh.harvard.edu 
<mailto:gr...@nmr.mgh.harvard.edu>> wrote:


Check whether rh.ad_hv.thick.10.mgh and rh.ad_hv.area.10.mgh are
the same, ie,
mri_diff  rh.ad_hv.thick.10.mgh  rh.ad_hv.area.10.mgh

If those are the same, then check whether
thickness.fwhm10.fsaverage and area.fwhm10.fsaverage  are the same
in each subject


On 3/14/16 10:53 AM, Kaiming Yin wrote:

Dear Douglas,

My command lines were, e.g. right thickness and right white
surface (using the same ad_hv.fsgd and group_diff.mtx files in
the command lines):


ad_hv.fsgd

GroupDescriptorFile 1
Title AD_HV_GroupAnalysis
Class AD
Class HV
InputAD_003AD
InputAD_005AD
...
InputHV_ABHV
InputHV_AEHV


group_diff.mtx

1 -1


right thickness

mris_preproc --fsgd ad_hv.fsgd --cache-in
thickness.fwhm10.fsaverage --target fsaverage --hemi rh --out
rh.ad_hv.thick.10.mgh

mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd ad_hv.fsgd dods --C
group_diff.mtx --surf fsaverage rh --cortex --glmdir
rh.ad_hv.thick.glmdir

mri_glmfit-sim --glmdir rh.ad_hv.thick.glmdir --cache 4 neg --cwp
0.05 --2spaces


right white surface

mris_preproc --fsgd ad_hv.fsgd --cache-in area.fwhm10.fsaverage
--target fsaverage --hemi rh --out rh.ad_hv.area.10.mgh

mri_glmfit --y rh.ad_hv.area.10.mgh --fsgd ad_hv.fsgd dods --C
group_diff.mtx --surf fsaverage rh --cortex --glmdir
rh.ad_hv.area.glmdir

mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir --cache 4 neg --cwp
0.05 --2spaces


Their results were all the same.

Thanks,
Kaiming


-- Forwarded message --
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc:
Date: Mon, 7 Mar 2016 18:47:11 -0500
Subject: Re: [Freesurfer] group analysis all measures same results
what are your command lines?


On 5 March 2016 at 02:01, Kaiming Yin <yinkaiming6...@gmail.com
<mailto:yinkaiming6...@gmail.com>> wrote:

Dear guys,

I was doing group analysis (command-line) on two groups
(patients and control, no age or other information). The data
has been "qcached", and after following the three steps as
"mris_preproc, mri_glmfit and mri_glmfit-sim" shown in the
tutorial on the Freesurfer website, I obtained the difference
on thickness in both left and right hemispheres, which seems
great. However, when I repeated the above steps on other
measures, e.g. area, area.pial, volume (also replaced the
parts of "thickness" in the command lines), the results
seemed to be exactly the same again as those in the thickness
comparison, even the p-value numbers in the file
"cache.th40.neg.sig.cluster.summary" were the same. I was
using Freesurfer v6.0-beta, and I performed the individual
data analysis on a linux cluster and I copied/downloaded the
whole "qcached" subject directory to my linux laptop to
perform the group comparison, both using the same version of
Freesurfer, does it matter? Or do you know why it happened
like this?

Thanks,
Kaiming




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
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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
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dispose of the e-mail.

Re: [Freesurfer] group analysis all measures same results

2016-03-14 Thread Kaiming Yin 
Dear Douglas,

Yes, both of the two pairs of files are the same. i.e.

mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh

diffcount 0


mri_diff rh.thickness.fwhm10.fsaverage.mgh rh.area.fwhm10.fsaverage.mgh

diffcount 0


Does this mean I run the "-qcache" wrongly? I just run "recon-all -s XX
-qcache" on each subject.

Thanks,
Kaiming


On 14 March 2016 at 14:58, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote:

> Check whether rh.ad_hv.thick.10.mgh and rh.ad_hv.area.10.mgh are the same,
> ie,
> mri_diff  rh.ad_hv.thick.10.mgh  rh.ad_hv.area.10.mgh
>
> If those are the same, then check whether thickness.fwhm10.fsaverage and
> area.fwhm10.fsaverage  are the same in each subject
>
>
> On 3/14/16 10:53 AM, Kaiming Yin wrote:
>
> Dear Douglas,
>
> My command lines were, e.g. right thickness and right white surface (using
> the same ad_hv.fsgd and group_diff.mtx files in the command lines):
>
>
> ad_hv.fsgd
>
> GroupDescriptorFile 1
> Title AD_HV_GroupAnalysis
> Class AD
> Class HV
> Input AD_003 AD
> Input AD_005 AD
> ...
> Input HV_AB HV
> Input HV_AE HV
>
>
> group_diff.mtx
>
> 1 -1
>
>
> right thickness
>
> mris_preproc --fsgd ad_hv.fsgd --cache-in thickness.fwhm10.fsaverage
> --target fsaverage --hemi rh --out rh.ad_hv.thick.10.mgh
>
> mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd ad_hv.fsgd dods --C
> group_diff.mtx --surf fsaverage rh --cortex --glmdir rh.ad_hv.thick.glmdir
>
> mri_glmfit-sim --glmdir rh.ad_hv.thick.glmdir --cache 4 neg --cwp 0.05
> --2spaces
>
>
> right white surface
>
> mris_preproc --fsgd ad_hv.fsgd --cache-in area.fwhm10.fsaverage --target
> fsaverage --hemi rh --out rh.ad_hv.area.10.mgh
>
> mri_glmfit --y rh.ad_hv.area.10.mgh --fsgd ad_hv.fsgd dods --C
> group_diff.mtx --surf fsaverage rh --cortex --glmdir rh.ad_hv.area.glmdir
>
> mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir --cache 4 neg --cwp 0.05
> --2spaces
>
>
> Their results were all the same.
>
> Thanks,
> Kaiming
>
>
> -- Forwarded message --
> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
> To: freesurfer@nmr.mgh.harvard.edu
> Cc:
> Date: Mon, 7 Mar 2016 18:47:11 -0500
> Subject: Re: [Freesurfer] group analysis all measures same results
> what are your command lines?
>
>
> On 5 March 2016 at 02:01, Kaiming Yin <yinkaiming6...@gmail.com> wrote:
>
>> Dear guys,
>>
>> I was doing group analysis (command-line) on two groups (patients and
>> control, no age or other information). The data has been "qcached", and
>> after following the three steps as "mris_preproc, mri_glmfit and
>> mri_glmfit-sim" shown in the tutorial on the Freesurfer website, I obtained
>> the difference on thickness in both left and right hemispheres, which seems
>> great. However, when I repeated the above steps on other measures, e.g.
>> area, area.pial, volume (also replaced the parts of "thickness" in the
>> command lines), the results seemed to be exactly the same again as those in
>> the thickness comparison, even the p-value numbers in the file
>> "cache.th40.neg.sig.cluster.summary" were the same. I was using Freesurfer
>> v6.0-beta, and I performed the individual data analysis on a linux cluster
>> and I copied/downloaded the whole "qcached" subject directory to my linux
>> laptop to perform the group comparison, both using the same version of
>> Freesurfer, does it matter? Or do you know why it happened like this?
>>
>> Thanks,
>> Kaiming
>>
>
>
> 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.
>
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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.

Re: [Freesurfer] group analysis all measures same results

2016-03-14 Thread Douglas Greve 
Check whether rh.ad_hv.thick.10.mgh and rh.ad_hv.area.10.mgh are the 
same, ie,

mri_diff  rh.ad_hv.thick.10.mgh  rh.ad_hv.area.10.mgh

If those are the same, then check whether thickness.fwhm10.fsaverage and 
area.fwhm10.fsaverage  are the same in each subject


On 3/14/16 10:53 AM, Kaiming Yin wrote:

Dear Douglas,

My command lines were, e.g. right thickness and right white surface 
(using the same ad_hv.fsgd and group_diff.mtx files in the command lines):



ad_hv.fsgd

GroupDescriptorFile 1
Title AD_HV_GroupAnalysis
Class AD
Class HV
InputAD_003AD
InputAD_005AD
...
InputHV_ABHV
InputHV_AEHV


group_diff.mtx

1 -1


right thickness

mris_preproc --fsgd ad_hv.fsgd --cache-in thickness.fwhm10.fsaverage 
--target fsaverage --hemi rh --out rh.ad_hv.thick.10.mgh


mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd ad_hv.fsgd dods --C 
group_diff.mtx --surf fsaverage rh --cortex --glmdir rh.ad_hv.thick.glmdir


mri_glmfit-sim --glmdir rh.ad_hv.thick.glmdir --cache 4 neg --cwp 0.05 
--2spaces



right white surface

mris_preproc --fsgd ad_hv.fsgd --cache-in area.fwhm10.fsaverage 
--target fsaverage --hemi rh --out rh.ad_hv.area.10.mgh


mri_glmfit --y rh.ad_hv.area.10.mgh --fsgd ad_hv.fsgd dods --C 
group_diff.mtx --surf fsaverage rh --cortex --glmdir rh.ad_hv.area.glmdir


mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir --cache 4 neg --cwp 0.05 
--2spaces



Their results were all the same.

Thanks,
Kaiming


-- Forwarded message --
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu 
<mailto:gr...@nmr.mgh.harvard.edu>>

To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
Cc:
Date: Mon, 7 Mar 2016 18:47:11 -0500
Subject: Re: [Freesurfer] group analysis all measures same results
what are your command lines?


On 5 March 2016 at 02:01, Kaiming Yin <yinkaiming6...@gmail.com 
<mailto:yinkaiming6...@gmail.com>> wrote:


Dear guys,

I was doing group analysis (command-line) on two groups (patients
and control, no age or other information). The data has been
"qcached", and after following the three steps as "mris_preproc,
mri_glmfit and mri_glmfit-sim" shown in the tutorial on the
Freesurfer website, I obtained the difference on thickness in both
left and right hemispheres, which seems great. However, when I
repeated the above steps on other measures, e.g. area, area.pial,
volume (also replaced the parts of "thickness" in the command
lines), the results seemed to be exactly the same again as those
in the thickness comparison, even the p-value numbers in the file
"cache.th40.neg.sig.cluster.summary" were the same. I was using
Freesurfer v6.0-beta, and I performed the individual data analysis
on a linux cluster and I copied/downloaded the whole "qcached"
subject directory to my linux laptop to perform the group
comparison, both using the same version of Freesurfer, does it
matter? Or do you know why it happened like this?

Thanks,
Kaiming




___
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.

Re: [Freesurfer] group analysis all measures same results

2016-03-14 Thread Kaiming Yin 
Dear Douglas,

My command lines were, e.g. right thickness and right white surface (using
the same ad_hv.fsgd and group_diff.mtx files in the command lines):


ad_hv.fsgd

GroupDescriptorFile 1
Title AD_HV_GroupAnalysis
Class AD
Class HV
Input AD_003 AD
Input AD_005 AD
...
Input HV_AB HV
Input HV_AE HV


group_diff.mtx

1 -1


right thickness

mris_preproc --fsgd ad_hv.fsgd --cache-in thickness.fwhm10.fsaverage
--target fsaverage --hemi rh --out rh.ad_hv.thick.10.mgh

mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd ad_hv.fsgd dods --C
group_diff.mtx --surf fsaverage rh --cortex --glmdir rh.ad_hv.thick.glmdir

mri_glmfit-sim --glmdir rh.ad_hv.thick.glmdir --cache 4 neg --cwp 0.05
--2spaces


right white surface

mris_preproc --fsgd ad_hv.fsgd --cache-in area.fwhm10.fsaverage --target
fsaverage --hemi rh --out rh.ad_hv.area.10.mgh

mri_glmfit --y rh.ad_hv.area.10.mgh --fsgd ad_hv.fsgd dods --C
group_diff.mtx --surf fsaverage rh --cortex --glmdir rh.ad_hv.area.glmdir

mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir --cache 4 neg --cwp 0.05
--2spaces


Their results were all the same.

Thanks,
Kaiming


-- Forwarded message --
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Cc:
Date: Mon, 7 Mar 2016 18:47:11 -0500
Subject: Re: [Freesurfer] group analysis all measures same results
what are your command lines?


On 5 March 2016 at 02:01, Kaiming Yin <yinkaiming6...@gmail.com> wrote:

> Dear guys,
>
> I was doing group analysis (command-line) on two groups (patients and
> control, no age or other information). The data has been "qcached", and
> after following the three steps as "mris_preproc, mri_glmfit and
> mri_glmfit-sim" shown in the tutorial on the Freesurfer website, I obtained
> the difference on thickness in both left and right hemispheres, which seems
> great. However, when I repeated the above steps on other measures, e.g.
> area, area.pial, volume (also replaced the parts of "thickness" in the
> command lines), the results seemed to be exactly the same again as those in
> the thickness comparison, even the p-value numbers in the file
> "cache.th40.neg.sig.cluster.summary" were the same. I was using Freesurfer
> v6.0-beta, and I performed the individual data analysis on a linux cluster
> and I copied/downloaded the whole "qcached" subject directory to my linux
> laptop to perform the group comparison, both using the same version of
> Freesurfer, does it matter? Or do you know why it happened like this?
>
> Thanks,
> Kaiming
>
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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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
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Re: [Freesurfer] group analysis all measures same results

2016-03-08 Thread Kaiming Yin 
Dear Douglas,

Sorry for this, but could I ask how to include the previous correspondence?
I just saw your responses from Freesurfer Digest, Vol 145, Issue 19, and I
don't know how to do that. I use gmail.

Best,
Kaiming


On Tue, Mar 8, 2016 at 10:50 PM, Douglas N Greve 
wrote:

> Kaiming, can you include my previous correspondence with your email?
>
>
> On 03/08/2016 05:48 PM, Kaiming Yin wrote:
>
>> Dear Douglas,
>>
>> My command lines were, e.g. right thickness and right white surface
>> (using the same ad_hv.fsgd and group_diff.mtx files in the command lines):
>>
>>
>> ad_hv.fsgd
>>
>> GroupDescriptorFile 1
>> Title AD_HV_GroupAnalysis
>> Class AD
>> Class HV
>> InputAD_003AD
>> InputAD_005AD
>> ...
>> InputHV_ABHV
>> InputHV_AEHV
>>
>>
>> group_diff.mtx
>>
>> 1 -1
>>
>>
>> right thickness
>>
>> mris_preproc --fsgd ad_hv.fsgd --cache-in thickness.fwhm10.fsaverage
>> --target fsaverage --hemi rh --out rh.ad_hv.thick.10.mgh
>>
>> mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd ad_hv.fsgd dods --C
>> group_diff.mtx --surf fsaverage rh --cortex --glmdir rh.ad_hv.thick.glmdir
>>
>> mri_glmfit-sim --glmdir rh.ad_hv.thick.glmdir --cache 4 neg --cwp 0.05
>> --2spaces
>>
>>
>> right white surface
>>
>> mris_preproc --fsgd ad_hv.fsgd --cache-in area.fwhm10.fsaverage --target
>> fsaverage --hemi rh --out rh.ad_hv.area.10.mgh
>>
>> mri_glmfit --y rh.ad_hv.area.10.mgh --fsgd ad_hv.fsgd dods --C
>> group_diff.mtx --surf fsaverage rh --cortex --glmdir rh.ad_hv.area.glmdir
>>
>> mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir --cache 4 neg --cwp 0.05
>> --2spaces
>>
>>
>> Their results were all the same.
>>
>> Thanks,
>> Kaiming
>>
>>
>> On Sat, Mar 5, 2016 at 2:01 AM, Kaiming Yin > > wrote:
>>
>> Dear guys,
>>
>> I was doing group analysis (command-line) on two groups (patients
>> and control, no age or other information). The data has been
>> "qcached", and after following the three steps as "mris_preproc,
>> mri_glmfit and mri_glmfit-sim" shown in the tutorial on the
>> Freesurfer website, I obtained the difference on thickness in both
>> left and right hemispheres, which seems great. However, when I
>> repeated the above steps on other measures, e.g. area, area.pial,
>> volume (also replaced the parts of "thickness" in the command
>> lines), the results seemed to be exactly the same again as those
>> in the thickness comparison, even the p-value numbers in the file
>> "cache.th40.neg.sig.cluster.summary" were the same. I was using
>> Freesurfer v6.0-beta, and I performed the individual data analysis
>> on a linux cluster and I copied/downloaded the whole "qcached"
>> subject directory to my linux laptop to perform the group
>> comparison, both using the same version of Freesurfer, does it
>> matter? Or do you know why it happened like this?
>>
>> Thanks,
>> Kaiming
>>
>>
>>
> --
> 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: 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/
>
>
>
> 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.
>
___
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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.

Re: [Freesurfer] group analysis all measures same results

2016-03-08 Thread Kaiming Yin 
Dear Douglas,

My command lines were, e.g. right thickness and right white surface (using
the same ad_hv.fsgd and group_diff.mtx files in the command lines):


ad_hv.fsgd

GroupDescriptorFile 1
Title AD_HV_GroupAnalysis
Class AD
Class HV
Input AD_003 AD
Input AD_005 AD
...
Input HV_AB HV
Input HV_AE HV


group_diff.mtx

1 -1


right thickness

mris_preproc --fsgd ad_hv.fsgd --cache-in thickness.fwhm10.fsaverage
--target fsaverage --hemi rh --out rh.ad_hv.thick.10.mgh

mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd ad_hv.fsgd dods --C
group_diff.mtx --surf fsaverage rh --cortex --glmdir rh.ad_hv.thick.glmdir

mri_glmfit-sim --glmdir rh.ad_hv.thick.glmdir --cache 4 neg --cwp 0.05
--2spaces


right white surface

mris_preproc --fsgd ad_hv.fsgd --cache-in area.fwhm10.fsaverage --target
fsaverage --hemi rh --out rh.ad_hv.area.10.mgh

mri_glmfit --y rh.ad_hv.area.10.mgh --fsgd ad_hv.fsgd dods --C
group_diff.mtx --surf fsaverage rh --cortex --glmdir rh.ad_hv.area.glmdir

mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir --cache 4 neg --cwp 0.05
--2spaces


Their results were all the same.

Thanks,
Kaiming


On Sat, Mar 5, 2016 at 2:01 AM, Kaiming Yin 
wrote:

> Dear guys,
>
> I was doing group analysis (command-line) on two groups (patients and
> control, no age or other information). The data has been "qcached", and
> after following the three steps as "mris_preproc, mri_glmfit and
> mri_glmfit-sim" shown in the tutorial on the Freesurfer website, I obtained
> the difference on thickness in both left and right hemispheres, which seems
> great. However, when I repeated the above steps on other measures, e.g.
> area, area.pial, volume (also replaced the parts of "thickness" in the
> command lines), the results seemed to be exactly the same again as those in
> the thickness comparison, even the p-value numbers in the file
> "cache.th40.neg.sig.cluster.summary" were the same. I was using Freesurfer
> v6.0-beta, and I performed the individual data analysis on a linux cluster
> and I copied/downloaded the whole "qcached" subject directory to my linux
> laptop to perform the group comparison, both using the same version of
> Freesurfer, does it matter? Or do you know why it happened like this?
>
> Thanks,
> Kaiming
>
___
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.

Re: [Freesurfer] group analysis all measures same results

2016-03-07 Thread Douglas N Greve 
what are your command lines?

On 03/04/2016 09:01 PM, Kaiming Yin wrote:
> Dear guys,
>
> I was doing group analysis (command-line) on two groups (patients and 
> control, no age or other information). The data has been "qcached", 
> and after following the three steps as "mris_preproc, mri_glmfit and 
> mri_glmfit-sim" shown in the tutorial on the Freesurfer website, I 
> obtained the difference on thickness in both left and right 
> hemispheres, which seems great. However, when I repeated the above 
> steps on other measures, e.g. area, area.pial, volume (also replaced 
> the parts of "thickness" in the command lines), the results seemed to 
> be exactly the same again as those in the thickness comparison, even 
> the p-value numbers in the file "cache.th40.neg.sig.cluster.summary" 
> were the same. I was using Freesurfer v6.0-beta, and I performed the 
> individual data analysis on a linux cluster and I copied/downloaded 
> the whole "qcached" subject directory to my linux laptop to perform 
> the group comparison, both using the same version of Freesurfer, does 
> it matter? Or do you know why it happened like this?
>
> Thanks,
> Kaiming
>
>
> ___
> 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
gr...@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


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.