problems about extracting specific vertex thickness value and getting a average thickness for a specific mask
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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 greve@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.
There are a lot of things that I don't understand about your command line. Why are you passing the thickness as the segmentation? The mask only limits the computations to be inside the mask. What precisely are you trying to do?
On 05/13/2014 11:27 AM, charujing123 wrote:
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
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 greve@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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi doug, I read your last e-mail again. After changed my command, it worked. Thanks doug. Rujing Zha
2014-05-14
charujing123
发件人：Douglas N Greve greve@nmr.mgh.harvard.edu 发送时间：2014-05-14 03:14 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：
There are a lot of things that I don't understand about your command line. Why are you passing the thickness as the segmentation? The mask only limits the computations to be inside the mask. What precisely are you trying to do?
On 05/13/2014 11:27 AM, charujing123 wrote:
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
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/
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Douglas N Greve