[Freesurfer] smooth sulc on only part of the surface one more time

[Zhangyuanchao]

Hi, experts,
 
I am interested in only the positive sulc  and would like to make group 
analysis of the postive sulc values. Hence I would like to mask off the 
negative values (as the lh.sulc file has both positive and negative value). 
Before making group analysis, I have to resample and smooth the sulc value. How 
do I smooth the positive sulc in a way that the negative sulc values will not 
have an effect on the smoothing process? Example if I smooth the positive 
sulc directly with the negative values, it will have some effect on the 
positive values since gyri and sulci are alternating. 
 
you suggest me using mri_binarize and mri_fwhm to make a mask and smooth it 
with a mask.
As suggested, I have done so.
 
However, there is a problem I can not tackle.
 
Using mri_binarize --i lh.sulc --min 0 --o lh.such.mask.mgh
When I read the lh.such.mask.mgh into matlab so that I can see the data inside.
To my surprise, I saw a vector which contains nearly all 0's except some very 
small numbers like 1.401298464324817e-45, not binary file which contains only 
0's and 1's.
I further tried:
mri_binarize --i lh.sulc --min 0 --o lh.such.mask.mgh --binval 1
It has the same problem as above.
After launching:
mris_fwhm --i  sulc --subject Ad001 --surf white --mask lh.such.mask.mgh --hemi 
lh --fwhm 20 --o lh.sulc.mgh
I read lh.sulc.mgh into matlab, it contains all 0's.
 
I read the mgh file using Keith worsley's SurfStatReadData function.

I do not know where it is wrong.
 
Thank doug for your helpful suggestions!
 
Thank you very much!
 
yuanchao
 

 


  ___ 
  好玩贺卡等你发，邮箱贺卡全新上线！ 
http://card.mail.cn.yahoo.com/___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] smooth sulc on only part of the surface one more time

[Rudolph Pienaar]

Zhangyuanchao wrote:
I would like to mask off the 
negative values (as the lh.sulc file has both positive and negative 
value). 


Another way to filter the sulc is:

$mris_calc -o lh.sulc.pos lh.sulc gte 0

which filters 'lh.sulc' and only lets values that are greater than or 
equal to 0 through. All other values are set to zero. Results are saved 
to 'lh.sulc.pos'.


Similarly,

$mris_calc -o lh.sulc.neg lh.sulc lt 0

Will filter through all the values that are less than zero, setting all 
others to zero, and saving to 'lh.sulc.neg'.



Before making group analysis, I have to resample and smooth the 
sulc value. How do I smooth the positive sulc in a way that the negative 
sulc values will not have an effect on the smoothing process? 


If you just want to mitigate against the boundary effects of switching 
from positive to negative for your smoothing, having all the negative 
values set to 0 will probably go a long way to reducing the effect. You 
could replace all the  negative values in the original file with 
whatever arbitrary value you'd like:


$mris_calc -o lh.sulc.neg.bin lh.sulc.neg div lh.sulc.neg

which divides 'lh.sulc.neg' by itself, resulting in a file that is 
contains '1' for all the negative values, and '0' elsewhere. If you then do


$mris_calc -o lh.sulc.p1 lh.sulc.pos add lh.sulc.neg.bin

the result should be a file 'lh.sulc.p1' that has all the original 
positive values unchanged, and replaced all the original negative values 
with '1'. Of course, you can set the bin value in 'lh.sulc.neg.bin' to 
whatever you'd like by first multiplying it by the desired value:


$mris_calc -o lh.sulc.neg.bin.f lh.sulc.neg.bin mul 0.01

would create lh.sulc.neg.bin.f with values of 0 and 0.01...



--
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer