Hi Martin,

Thanks a lot. It had worked nicely. I got one question about this following cmd

tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fwhm15/osgm/sig.mgh

I got a red to yellow sig.mgh, does it mean I got a increased percent thickness change (pc1)? and the color bar showing 2 to 5 means?

Best, Jahanvi

On Sun, May 14, 2017 at 10:11 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu

wrote:

Hi Jahanvi,

1. yes, you need to create this table to then perform the stats
2. no, the format is as I described it below

fsid fsid-base tp1_subA templatesubA tp2_subA templatesubA tp1_subB templatesubB tp2_subB templatesubB

this is assuming that you called your base templatesubA and templatesubB for the two subjects. It will automatically look in the tp1_subA.long.templatesubA etc. directories.

Best, Martin

On 12 May 2017, at 16:55, jahanvi patel jahanvipatel.tw@gmail.com wrote:

Hi Martin,

Do you mean by creating this long.testretest.qdec file, one can then perform the stats for the longitudinal2StageModel?

So for a 2 timepoints analysis, eg. TP1 & TP2. the long.testretest.qdec will be looking like this ?

fsid fsid-base

tp1_subA.long.TemplatesubA tp2_subA.long.TemplatesubA tp1_subB.long.TemplatesubB tp2_subB.long.TemplatesubB tp1_subC.long.TemplatesubC tp2_subC.long.TemplatesubC

. . .

Thanks,

Jahanvi

tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1. fwhm15/osgm/sig.mgh

Hi Jahanvi,

...

long.testretest.qdec is a qdec table in the longitudional format (with the fsid-base as the second column).

For test-retest (e.g. same session with subject removal), you usually don't need a time column, that is why --generic-time is specified. the qdec table would just look like

fsid fsid-base

me me_test

me me_retest

you you_test

you you_retest

...

Best, Martin

On 05/08/2017 04:10 PM, jahanvi patel wrote: Hello list,

I have a simple question about the LongitudinalTwoStageModel tutorials on freesurfer website.

It is from this link https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel

long_mris_slopes --qdec long.testretest.qdec \ --meas thickness \ --hemi lh \ --sd $SUBJECTS_DIR \ --do-pc1 --do-label \ --generic-time \ --fwhm 15 \ --qcache fsaverage \ --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \ --isec-labels lh.testretest.fsaverage.cortex.label

My question is, what is the content of long.testretest.qdec ? I understood till 1st stage was done, we got only one file which is long.qdec.table.dat.

Could anyone help to clarify my question?

Thanks a lot Jahanvi

---

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---

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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.

Hi Martin,

Thanks a lot for the reply. Is there a way to display the bar in effect size? And is this sig.mgh already statistically corrected? (FDR?)

Best, Jahanvi

On Thu, May 18, 2017 at 1:55 AM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:

Hi Jahanvi,

I think red is positive (some people invert the colors, then red=hot=dangerous ). But I think default is blue negative, red positive, so there is an average increase in thickness. You should also look at the effect size (gamma). The p -values are in log 10 space, so 2 = 0.01 and 5 = 0.00001

Best, Martin

On 17 May 2017, at 22:17, jahanvi patel jahanvipatel.tw@gmail.com wrote:

Hi Martin,

Thanks a lot. It had worked nicely. I got one question about this following cmd

tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1. fwhm15/osgm/sig.mgh

I got a red to yellow sig.mgh, does it mean I got a increased percent thickness change (pc1)? and the color bar showing 2 to 5 means?

Best, Jahanvi

On Sun, May 14, 2017 at 10:11 PM, Martin Reuter < mreuter@nmr.mgh.harvard.edu> wrote:

...

Hi Jahanvi,

1. yes, you need to create this table to then perform the stats
2. no, the format is as I described it below

fsid fsid-base tp1_subA templatesubA tp2_subA templatesubA tp1_subB templatesubB tp2_subB templatesubB

this is assuming that you called your base templatesubA and templatesubB for the two subjects. It will automatically look in the tp1_subA.long.templatesubA etc. directories.

Best, Martin

On 12 May 2017, at 16:55, jahanvi patel jahanvipatel.tw@gmail.com wrote:

Hi Martin,

Do you mean by creating this long.testretest.qdec file, one can then perform the stats for the longitudinal2StageModel?

So for a 2 timepoints analysis, eg. TP1 & TP2. the long.testretest.qdec will be looking like this ?

fsid fsid-base

tp1_subA.long.TemplatesubA tp2_subA.long.TemplatesubA tp1_subB.long.TemplatesubB tp2_subB.long.TemplatesubB tp1_subC.long.TemplatesubC tp2_subC.long.TemplatesubC

. . .

Thanks,

Jahanvi

tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fw hm15/osgm/sig.mgh

Hi Jahanvi,

...

long.testretest.qdec is a qdec table in the longitudional format (with the fsid-base as the second column).

For test-retest (e.g. same session with subject removal), you usually don't need a time column, that is why --generic-time is specified. the qdec table would just look like

fsid fsid-base

me me_test

me me_retest

you you_test

you you_retest

...

Best, Martin

On 05/08/2017 04:10 PM, jahanvi patel wrote: Hello list,

I have a simple question about the LongitudinalTwoStageModel tutorials on freesurfer website.

It is from this link https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel

long_mris_slopes --qdec long.testretest.qdec \ --meas thickness \ --hemi lh \ --sd $SUBJECTS_DIR \ --do-pc1 --do-label \ --generic-time \ --fwhm 15 \ --qcache fsaverage \ --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \ --isec-labels lh.testretest.fsaverage.cortex.label

My question is, what is the content of long.testretest.qdec ? I understood till 1st stage was done, we got only one file which is long.qdec.table.dat.

Could anyone help to clarify my question?

Thanks a lot Jahanvi

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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

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.

Hi Martin,

Thanks a lot. So it is uncorrected. Can one use the following cmd to do multiple comparison correction?

mri_glmfit-sim \ --glmdir lh.testretest.thickness-pc1.fwhm15 \ --cache 4 neg \ --cwp 0.05\ --2spaces

I tried to run above cmd, it shows

ERROR: thresh = 4,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 done

Not sure if there is a bug or if my input is wrong.

Any suggestions is appreciated!

Best, Jahanvi

On Thu, May 18, 2017 at 9:46 AM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:

Hi Jahanvi,

there should be a way to display the bar, but I don’t know how (others will know)!

sig is not FDR corrected.

Best, Martin

On 18 May 2017, at 08:56, jahanvi patel jahanvipatel.tw@gmail.com wrote:

Hi Martin,

Thanks a lot for the reply. Is there a way to display the bar in effect size? And is this sig.mgh already statistically corrected? (FDR?)

Best, Jahanvi

On Thu, May 18, 2017 at 1:55 AM, Martin Reuter < mreuter@nmr.mgh.harvard.edu> wrote:

...

Hi Jahanvi,

I think red is positive (some people invert the colors, then red=hot=dangerous ). But I think default is blue negative, red positive, so there is an average increase in thickness. You should also look at the effect size (gamma). The p -values are in log 10 space, so 2 = 0.01 and 5 = 0.00001

Best, Martin

On 17 May 2017, at 22:17, jahanvi patel jahanvipatel.tw@gmail.com wrote:

Hi Martin,

Thanks a lot. It had worked nicely. I got one question about this following cmd

tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fw hm15/osgm/sig.mgh

I got a red to yellow sig.mgh, does it mean I got a increased percent thickness change (pc1)? and the color bar showing 2 to 5 means?

Best, Jahanvi

On Sun, May 14, 2017 at 10:11 PM, Martin Reuter < mreuter@nmr.mgh.harvard.edu> wrote:

...

Hi Jahanvi,

1. yes, you need to create this table to then perform the stats
2. no, the format is as I described it below

fsid fsid-base tp1_subA templatesubA tp2_subA templatesubA tp1_subB templatesubB tp2_subB templatesubB

this is assuming that you called your base templatesubA and templatesubB for the two subjects. It will automatically look in the tp1_subA.long.templatesubA etc. directories.

Best, Martin

On 12 May 2017, at 16:55, jahanvi patel jahanvipatel.tw@gmail.com wrote:

Hi Martin,

Do you mean by creating this long.testretest.qdec file, one can then perform the stats for the longitudinal2StageModel?

So for a 2 timepoints analysis, eg. TP1 & TP2. the long.testretest.qdec will be looking like this ?

fsid fsid-base

tp1_subA.long.TemplatesubA tp2_subA.long.TemplatesubA tp1_subB.long.TemplatesubB tp2_subB.long.TemplatesubB tp1_subC.long.TemplatesubC tp2_subC.long.TemplatesubC

. . .

Thanks,

Jahanvi

tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fw hm15/osgm/sig.mgh

Hi Jahanvi,

...

long.testretest.qdec is a qdec table in the longitudional format (with the fsid-base as the second column).

For test-retest (e.g. same session with subject removal), you usually don't need a time column, that is why --generic-time is specified. the qdec table would just look like

fsid fsid-base

me me_test

me me_retest

you you_test

you you_retest

...

Best, Martin

On 05/08/2017 04:10 PM, jahanvi patel wrote: Hello list,

I have a simple question about the LongitudinalTwoStageModel tutorials on freesurfer website.

It is from this link https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel

long_mris_slopes --qdec long.testretest.qdec \ --meas thickness \ --hemi lh \ --sd $SUBJECTS_DIR \ --do-pc1 --do-label \ --generic-time \ --fwhm 15 \ --qcache fsaverage \ --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \ --isec-labels lh.testretest.fsaverage.cortex.label

My question is, what is the content of long.testretest.qdec ? I understood till 1st stage was done, we got only one file which is long.qdec.table.dat.

Could anyone help to clarify my question?

Thanks a lot Jahanvi

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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

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.