Hi doug
Thanks doug.
My mask and input mgh file are all fsaverage space.
I try the mri_segstats, and I cannot get what you mean clearly. So I read the help of mri_segstats, but neither do I get the information. Then I have to try to run this:
mri_segstats --i ./rh.36sb.10.mgh --mask ./cluster1.mgh --avgwf mytext --seg ../fsaverage/surf/rh.thickness
    But it aborted. I cannot find the problem, although I believe something is wrong. Also this command echo this error information:
======================================================
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --i ./rh.36sb.10.mgh --mask ./cluster1.mgh --avgwf mytext --seg ../fsaverage/surf/rh.thickness
sysname  Linux
hostname centos2
machine  x86_64
user     psylab16
UseRobust  0
Loading ../fsaverage/surf/rh.thickness
Loading ./rh.36sb.10.mgh
Loading ./cluster1.mgh
NOT INVERTING
There were 83 voxels in the orginal mask
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   2 segmentations
Computing statistics for each segmentation
  0     0                                     163759  163759.000
  1     2                                         83      83.000
 
Reporting on   2 segmentations
Computing spatial average of each frame
  0  1
Writing to mytext
*** glibc detected *** mri_segstats: malloc(): memory corruption: 0x2e6228f8 ***
======= Backtrace: =========
/lib/libc.so.6[0x9e11dd]
/lib/libc.so.6(__libc_malloc+0x67)[0x9e2d97]
/lib/libc.so.6[0x9cf4cf]
/lib/libc.so.6(fopen64+0x2c)[0x9d1a7c]
mri_segstats[0x80536cd]
/lib/libc.so.6(__libc_start_main+0xdc)[0x98ce9c]
mri_segstats(__gxx_personality_v0+0x1c9)[0x804f791]
======= Memory map: ========
00958000-00973000 r-xp 00000000 fd:00 60785448                           /lib/ld-2.5.so
00973000-00974000 r-xp 0001a000 fd:00 60785448                           /lib/ld-2.5.so
00974000-00975000 rwxp 0001b000 fd:00 60785448                           /lib/ld-2.5.so
00977000-00acb000 r-xp 00000000 fd:00 60784655                           /lib/libc-2.5.so
00acb000-00acc000 ---p 00154000 fd:00 60784655                           /lib/libc-2.5.so
00acc000-00ace000 r-xp 00154000 fd:00 60784655                           /lib/libc-2.5.so
00ace000-00acf000 rwxp 00156000 fd:00 60784655                           /lib/libc-2.5.so
00acf000-00ad2000 rwxp 00acf000 00:00 0
00ad4000-00add000 r-xp 00000000 fd:00 60784725                           /lib/libcrypt-2.5.so
00add000-00ade000 r-xp 00008000 fd:00 60784725                           /lib/libcrypt-2.5.so
00ade000-00adf000 rwxp 00009000 fd:00 60784725                           /lib/libcrypt-2.5.so
00adf000-00b06000 rwxp 00adf000 00:00 0
00b22000-00b2d000 r-xp 00000000 fd:00 60784686                           /lib/libgcc_s-4.1.2-20080825.so.1
00b2d000-00b2e000 rwxp 0000a000 fd:00 60784686                           /lib/libgcc_s-4.1.2-20080825.so.1
00c68000-00d48000 r-xp 00000000 fd:00 56176146                           /usr/lib/libstdc++.so.6.0.8
00d48000-00d4c000 r-xp 000df000 fd:00 56176146                           /usr/lib/libstdc++.so.6.0.8
00d4c000-00d4d000 rwxp 000e3000 fd:00 56176146                           /usr/lib/libstdc++.so.6.0.8
00d4d000-00d53000 rwxp 00d4d000 00:00 0
00d72000-00d84000 r-xp 00000000 fd:00 60784662                           /lib/libz.so.1.2.3
00d84000-00d85000 rwxp 00011000 fd:00 60784662                           /lib/libz.so.1.2.3
08048000-08817000 r-xp 08048000 00:00 0
08817000-2e63b000 rwxp 08817000 00:00 0                                  [heap]
f6300000-f6321000 rwxp f6300000 00:00 0
f6321000-f6400000 ---p f6321000 00:00 0
f6434000-f7cbb000 rwxp f6434000 00:00 0
f7d5c000-f7ea0000 rwxp f7d5c000 00:00 0
f7ea0000-f7ec7000 r-xp 00000000 fd:00 60784705                           /lib/libm-2.5.so
f7ec7000-f7ec8000 r-xp 00026000 fd:00 60784705                           /lib/libm-2.5.so
f7ec8000-f7ec9000 rwxp 00027000 fd:00 60784705                           /lib/libm-2.5.so
f7ec9000-f7ede000 r-xp 00000000 fd:00 60784716                           /lib/libpthread-2.5.so
f7ede000-f7edf000 ---p 00015000 fd:00 60784716                           /lib/libpthread-2.5.so
f7edf000-f7ee0000 r-xp 00015000 fd:00 60784716                           /lib/libpthread-2.5.so
f7ee0000-f7ee1000 rwxp 00016000 fd:00 60784716                           /lib/libpthread-2.5.so
f7ee1000-f7ee3000 rwxp f7ee1000 00:00 0
f7ee3000-f7ee6000 r-xp 00000000 fd:00 60784670                           /lib/libdl-2.5.so
f7ee6000-f7ee7000 r-xp 00002000 fd:00 60784670                           /lib/libdl-2.5.so
f7ee7000-f7ee8000 rwxp 00003000 fd:00 60784670                           /lib/libdl-2.5.so
f7ee8000-f7ee9000 rwxp f7ee8000 00:00 0
f7f0b000-f7f15000 r-xp 00000000 fd:00 60784678                           /lib/libnss_files-2.5.so
f7f15000-f7f16000 r-xp 00009000 fd:00 60784678                           /lib/libnss_files-2.5.so
f7f16000-f7f17000 rwxp 0000a000 fd:00 60784678                           /lib/libnss_files-2.5.so
f7f17000-f7f18000 rwxp f7f17000 00:00 0
ffcc0000-ffcd5000 rwxp 7ffffffe9000 00:00 0                              [stack]
ffffe000-fffff000 r-xp ffffe000 00:00 0
Aborted
================================================================
All the best
Rujing Zha
2014-05-13
charujing123
发件人：Douglas N Greve <greve@nmr.mgh.harvard.edu>
发送时间：2014-05-12 23:18
主题：Re: [Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask
收件人："freesurfer"<freesurfer@nmr.mgh.harvard.edu>
抄送：
 
 
For #2 you can get the average with mri_segstats passing the mask with  
the --seg command and using --id 1. If the mask is in fsaverage space,  
then just apply it to the y.mgh (i,e the input to mri_glmfit passed with  
--y). Use the --avgwf option to mri_segstats. This will give you the  
average for each subject in a single ascii file. For #1, I would not  
recommend using the data from the most significant voxel since this is  
not necessarily a stable measure 
 
doug 
 
 
On 05/09/2014 08:44 PM, charujing wrote: 
> Hi FS experts and users 
> I have done the each subjects' surface regestration on fsaverage  
> surface, and merge all of them into a *.mgh. Group analysis is also  
> completed. 
> Now I have two questions: 
> 1,I want to extract the VtxMax vertex number thickness for all  
> subjects. The VtxMax vertex number can be got in the  
> *.sig.cluster.summary file. And it represents the most significant  
> vertex in that cluster. I search my question in google and find these  
> scripts which maybe helpful for me: 
> for i in `seq 1 $numsubject` 
>        do 
>          mri_convert --frame $i y.mgh  
> $SUBJECTS_DIR/fsaverage/surf/lh.$i.mgh 
>          mris_convert -c $i.mgh  
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated lh.$i.asc 
>        done 
> I got the lh.*.asc file and open it. There are five columes in this  
> file. I guess that: first colume is vertex number, the 2nd-4th columes  
> represent MNI305 coordinates in surface, and the 5th colume is  
> thickness of this vertex. If I want to deal with my 1st question, all  
> I need to get the lh.*.asc file and search the specific vertex number  
> in this file. All of above, is there anything wrong? 
> 2, I created a surface mask, and want to extract the average thickness  
> value in this mask for every subject. How can I complete it? Can I  
> extract all vertex thickness in that mask, and average them in each  
> subject? If so, however, it will be a bot of inconvenience. I want to  
> some simple codes to deal with it. 
> Any reply will be highly appreaciated. 
> Thanks 
> All the best. 
> Rujing Zha 
> 2014-05-10 
> ------------------------------------------------------------------------ 
> charujing 
> 
> 
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--  
Douglas N. Greve, Ph.D. 
MGH-NMR Center 
greve@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 
 
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 
 
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