Sorry, that was supposed to be a reply to this email

Damian Jenkins wrote:

We have been following the protocol in Han's paper to test repeatability and the following questions cropped up:

1. how many smoothing iterations were run to achieve a smoothing kernel size of 6mm?;
2. what was the reason for choosing this size?

Thanks, D

Doug Greve wrote:

Probably about 26. You can figure it out from this command:

mris_fwhm --fwhm 6 --niters-only --s fsaverage --hemi lh

dont know how they chose 6

doug

Martin Kavec wrote:

...

Hi,

is it possible to obtain LGI values of cortices, similarly as curvature indices in ?h.aparc.stats? Could this value possibly be included in the ?h.aparc.stats files? Thanks in advance,

Martin

Thanks for responce, Dough.

I've looked at recon-all as you suggested, and came up with the following commandline:

mris_anatomical_stats -mgz -f lh.lgi.stats -b -a ../label/lh.aparc.annot -c ../label/lgi.annot.ctab $SUBJECT lh pial_lgi

This, however yields segfault:

INFO: assuming MGZ format for volumes. computing statistics for each annotation in ../label/lh.aparc.annot. reading volume $SUBJECT/mri/wm.mgz... reading input surface $SUBJECT/surf/lh.pial_lgi... Segmentation fault

I'm wondering whether this could be related to the fact that mris_anatomical_stats, calculates mean and stdev on the per-vertex basis over the defined label, while here we want it to calculate LGI, which is not calculated in this manner.

Thanks,

Martin

On Thursday 08 May 2008 18:32:28 Doug Greve wrote:

use mris_anatomical_stats. Look in recon-all to see how to invoke it. You can create another stats file (can't add it to the one that is already there).

doug

Martin Kavec wrote:

...

Hi,

is it possible to obtain LGI values of cortices, similarly as curvature indices in ?h.aparc.stats? Could this value possibly be included in the ?h.aparc.stats files?

Thanks in advance,

Martin

Thanks a lot help, Marie.

Indeed the -t switch worked.

Now, the lh.aparc.stats (thickness) and my generated lh.lgi.stats (lGI) differ in the columns 4,5,6, which correspond to GrayVol, AverageThk, and StdevThk. Could you please help me to understand these values?

1. Why is the GM volume different in the two files (column 4)?

2. Is the average lGI in the column 5?

3. My impression is that the lGI is a property of an area, e.i. of the lateraloccipital cortex, so I would expect to get only a single value for the area.

Thanks a lot in advance,

Martin

On Friday 09 May 2008 10:53:13 Marie Schaer wrote:

Martin,

Try instead the option -t pial_lgi as follows:

...

mris_anatomical_stats -mgz -f lh.lgi.stats -b -a ../label/lh.aparc.annot -c ../label/ lgi.annot.ctab -t pial_lgi $SUBJECT lh

Otherwise it will read lh.pial_lgi as a surface file, whereas it is indeed a thickness / curv file

Have a nice day,

Marie

On 9 mai 08, at 10:29, Martin Kavec wrote:

...

Thanks for responce, Dough.

I've looked at recon-all as you suggested, and came up with the following commandline:

mris_anatomical_stats -mgz -f lh.lgi.stats -b -a ../label/lh.aparc.annot -c ../label/lgi.annot.ctab $SUBJECT lh pial_lgi

This, however yields segfault:

INFO: assuming MGZ format for volumes. computing statistics for each annotation in ../label/lh.aparc.annot. reading volume $SUBJECT/mri/wm.mgz... reading input surface $SUBJECT/surf/lh.pial_lgi... Segmentation fault

I'm wondering whether this could be related to the fact that mris_anatomical_stats, calculates mean and stdev on the per-vertex basis over the defined label, while here we want it to calculate LGI, which is not calculated in this manner.

Thanks,

Martin

On Thursday 08 May 2008 18:32:28 Doug Greve wrote:

...

use mris_anatomical_stats. Look in recon-all to see how to invoke it. You can create another stats file (can't add it to the one that is already there).

doug

Martin Kavec wrote:

...

Hi,

is it possible to obtain LGI values of cortices, similarly as curvature indices in ?h.aparc.stats? Could this value possibly be included in the ?h.aparc.stats files?

Thanks in advance,

Martin

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Thanks a lot for clarification, Marie.

On Friday 09 May 2008 14:37:46 Marie Schaer wrote:

Martin,

As lgi is read like a thickness file, the lgi values in your tabular output replaced the value where you had thickness before. So mean lgi is in column 4 (note that average lgi values per parcell are comprised between 1 and 5 if your lgi computation is ok). Standard deviation for lgi is in column 5. The other columns should not change if you run mris_anatomical_stats without the -t option (i.e on the thickness).

Well, the point is that the 3rd column (not counting the structure name) is changed as well. This corresponds to GM volume, which is (almost) systematically larger in the lh.lgi.stats. Should it really be the same? This is already off my questions, but I am just saying that as a feedback.

Thanks a lot,

Martin

Just a thought, but I suspect that the volume is calculated as some product of area * "thickness". Then, with the -t option, what FS is using as thickness is now really the lgi value. So, the "volume" value is really not appropriate in that case.

cheers, Mike H.

On Fri, 2008-05-09 at 15:28 +0200, Marie Schaer wrote:

On my understanding, the GM volume given by mris_anatomical_stats should be the same independently of the -t option (unless you reprocessed the surfaces in between), so that's surprising.

Doug, do you have any idea?

Marie

On 9 mai 08, at 15:12, Martin Kavec wrote:

...

Thanks a lot for clarification, Marie.

On Friday 09 May 2008 14:37:46 Marie Schaer wrote:

...

Martin,

As lgi is read like a thickness file, the lgi values in your tabular output replaced the value where you had thickness before. So mean lgi is in column 4 (note that average lgi values per parcell are comprised between 1 and 5 if your lgi computation is ok). Standard deviation for lgi is in column 5. The other columns should not change if you run mris_anatomical_stats without the -t option (i.e on the thickness).

Well, the point is that the 3rd column (not counting the structure name) is changed as well. This corresponds to GM volume, which is (almost) systematically larger in the lh.lgi.stats. Should it really be the same? This is already off my questions, but I am just saying that as a feedback.

Thanks a lot,

Martin

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