RE: [Freesurfer] questions on check_subject
Below is the output from mris_euler_number: zion:/nfs/home/Subjects/ttt/surf> mris_euler_number rh.sphere.reg euler # = v-e+f = 2g-2: 134807 - 404415 + 269610 = 2 --> 0 holes F =2V-4: 269610 = 269614-4 (0) 2E=3F:808830 = 808830 (0) total defect index = 0 zion:/nfs/home/Subjects/ttt/surf> mris_euler_number rh.smoothwm euler # = v-e+f = 2g-2: 134807 - 404415 + 269610 = 2 --> 0 holes F =2V-4: 269610 = 269614-4 (0) 2E=3F:808830 = 808830 (0) total defect index = 0 zion:/nfs/home/Subjects/ttt/surf> mris_euler_number rh.orig euler # = v-e+f = 2g-2: 134807 - 404415 + 269610 = 2 --> 0 holes F =2V-4: 269610 = 269614-4 (0) 2E=3F:808830 = 808830 (0) total defect index = 0 Besides, there is no version # for mris_register (mris_register --version), but we are using the newest release (February 18th 2004). Thanks again for your help on this issue. Jia > -Original Message- > From: Bruce Fischl [mailto:[EMAIL PROTECTED] > Sent: Tuesday, May 31, 2005 8:16 PM > To: Jia Liu > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] questions on check_subject > > can you run mris_euler_number on them and send me the results? It may be > that you have a somewhat newer version of mris_register that embeds > geometry info into the surface file. > > On Tue, 31 May 2005, Jia Liu wrote: > > > No, I am using Linux (Fedora 1) but not Mac OS X, and yes, the problem > > exists in all my subjects (I happened to notice it when I ran > > check_subject). > > Best, > > jia > > > >> -Original Message- > >> From: Bruce Fischl [mailto:[EMAIL PROTECTED] > >> Sent: Tuesday, May 31, 2005 7:43 PM > >> To: Jia Liu > >> Cc: freesurfer@nmr.mgh.harvard.edu > >> Subject: RE: [Freesurfer] questions on check_subject > >> > >> is this only on Tiger? And does it happen with all your subjects now that > >> you have upgraded? > >> On Tue, 31 May 2005, Jia Liu wrote: > >> > >>> Hi, Bruce- > >>> > >>> Thanks for your reply. I re-did morph for the right hemisphere, and the > >>> problem persists. > >>> > >>> CHECKING SUBJECT ttt > >>> WARN: time for rh.orig is older than rh.qsphere > >>> WARN: file rh.sphere.reg is not equal in size to rh.smoothwm > >>> > >>> -rw-rw-r--1 jliu jliu 4853285 May 31 12:45 rh.sphere.reg > >>> -rwxrwxr-x1 jliu jliu 4853068 May 31 09:43 rh.smoothwm > >>> -rwxrwxr-x1 jliu jliu 4853068 May 31 09:43 rh.orig > >>> > >>> The log file is attached. What should I do to correct this problem? > > Thanks > >>> again for your help! > >>> > >>> Best, > >>> > >>> jia > >>> > >>>> -Original Message- > >>>> From: Bruce Fischl [mailto:[EMAIL PROTECTED] > >>>> Sent: Sunday, May 29, 2005 9:42 PM > >>>> To: Jia Liu > >>>> Cc: freesurfer@nmr.mgh.harvard.edu > >>>> Subject: RE: [Freesurfer] questions on check_subject > >>>> > >>>> you will need to rerun the morph. > >>>> On Sun, 29 May 2005, Jia Liu wrote: > >>>> > >>>>> Hi, Bruce- > >>>>> > >>>>> No, the ?h.sphere.reg files are slightly larger than the orig files. > >>> Below > >>>>> is the list of files in the surf directory. > >>>>> > >>>>> -rwxrwxrwx1 app app 4858504 Mar 8 2004 lh.inflated > >>>>> -rwxrwxrwx1 app app 4858504 Mar 8 2004 lh.orig > >>>>> -rwxrwxrwx1 app app 4858504 Mar 8 2004 lh.pial > >>>>> -rw-rw-r--1 app app 4858721 Mar 16 23:46 > > lh.rh.sphere.reg > >>>>> -rwxrwxrwx1 app app 4858504 Mar 8 2004 lh.smoothwm > >>>>> -rw-rw-r--1 app app 4858504 Mar 16 20:35 lh.sphere > >>>>> -rw-rw-r--1 app app 4858721 Mar 16 22:14 lh.sphere.reg > >>>>> -rwxrwxrwx1 app app 4858504 Mar 8 2004 lh.white > >>>>> -rwxrwxrwx1 app app 4853068 Mar 8 2004 rh.inflated > >>>>> -rw-rw-r--1 app app 4853285 Mar 16 18:54 > > rh.lh.sphere.reg > >>>>> -rwxrwxrwx1 app app 4853068 Mar 8 2004 rh.orig > >>>>> -rwxrwxrwx1 app app 4853068 Mar 8 2004 rh.pia
RE: [Freesurfer] questions on check_subject
No, I am using Linux (Fedora 1) but not Mac OS X, and yes, the problem exists in all my subjects (I happened to notice it when I ran check_subject). Best, jia > -Original Message- > From: Bruce Fischl [mailto:[EMAIL PROTECTED] > Sent: Tuesday, May 31, 2005 7:43 PM > To: Jia Liu > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] questions on check_subject > > is this only on Tiger? And does it happen with all your subjects now that > you have upgraded? > On Tue, 31 May 2005, Jia Liu wrote: > > > Hi, Bruce- > > > > Thanks for your reply. I re-did morph for the right hemisphere, and the > > problem persists. > > > > CHECKING SUBJECT ttt > > WARN: time for rh.orig is older than rh.qsphere > > WARN: file rh.sphere.reg is not equal in size to rh.smoothwm > > > > -rw-rw-r--1 jliu jliu 4853285 May 31 12:45 rh.sphere.reg > > -rwxrwxr-x1 jliu jliu 4853068 May 31 09:43 rh.smoothwm > > -rwxrwxr-x1 jliu jliu 4853068 May 31 09:43 rh.orig > > > > The log file is attached. What should I do to correct this problem? Thanks > > again for your help! > > > > Best, > > > > jia > > > >> -Original Message- > >> From: Bruce Fischl [mailto:[EMAIL PROTECTED] > >> Sent: Sunday, May 29, 2005 9:42 PM > >> To: Jia Liu > >> Cc: freesurfer@nmr.mgh.harvard.edu > >> Subject: RE: [Freesurfer] questions on check_subject > >> > >> you will need to rerun the morph. > >> On Sun, 29 May 2005, Jia Liu wrote: > >> > >>> Hi, Bruce- > >>> > >>> No, the ?h.sphere.reg files are slightly larger than the orig files. > > Below > >>> is the list of files in the surf directory. > >>> > >>> -rwxrwxrwx1 app app 4858504 Mar 8 2004 lh.inflated > >>> -rwxrwxrwx1 app app 4858504 Mar 8 2004 lh.orig > >>> -rwxrwxrwx1 app app 4858504 Mar 8 2004 lh.pial > >>> -rw-rw-r--1 app app 4858721 Mar 16 23:46 lh.rh.sphere.reg > >>> -rwxrwxrwx1 app app 4858504 Mar 8 2004 lh.smoothwm > >>> -rw-rw-r--1 app app 4858504 Mar 16 20:35 lh.sphere > >>> -rw-rw-r--1 app app 4858721 Mar 16 22:14 lh.sphere.reg > >>> -rwxrwxrwx1 app app 4858504 Mar 8 2004 lh.white > >>> -rwxrwxrwx1 app app 4853068 Mar 8 2004 rh.inflated > >>> -rw-rw-r--1 app app 4853285 Mar 16 18:54 rh.lh.sphere.reg > >>> -rwxrwxrwx1 app app 4853068 Mar 8 2004 rh.orig > >>> -rwxrwxrwx1 app app 4853068 Mar 8 2004 rh.pial > >>> -rwxrwxrwx1 app app 4853068 Mar 8 2004 rh.smoothwm > >>> -rw-rw-r--1 app app 4853068 Mar 16 15:17 rh.sphere > >>> -rw-rw-r--1 app app 4853285 Mar 16 16:59 rh.sphere.reg > >>> -rwxrwxrwx1 app app 4853068 Mar 8 2004 rh.white > >>> > >>> Will this affect the surface-based group analysis? > >>> > >>> Thanks again for your help! > >>> > >>> Best, > >>> > >>> jia > >>> > >>>> -Original Message- > >>>> From: Bruce Fischl [mailto:[EMAIL PROTECTED] > >>>> Sent: Friday, May 27, 2005 8:10 PM > >>>> To: Jia Liu > >>>> Cc: freesurfer@nmr.mgh.harvard.edu > >>>> Subject: Re: [Freesurfer] questions on check_subject > >>>> > >>>> not sure why the smoothwm would be different size. Is it the same size > > as > >>>> the orig? How about the rest of the surfaces for each hemis (sphere, > >>> white, > >>>> pial) > >>>> > >>>> On Fri, 27 May 2005, Jia > >>>> Liu wrote: > >>>> > >>>>> Hi, > >>>>> > >>>>> I used check_subject and found following error message on all my > >>> subjects: > >>>>> > >>>>> Zion:/nfs/home/Subjects> check_subject subKL > >>>>> CHECKING SUBJECT subKL > >>>>> WARN: file rh.sphere.reg is not equal in size to rh.smoothwm > >>>>> WARN: file lh.sphere.reg is not equal in size to lh.smoothwm > >>>>> WARN: file lh.rh.sphere.reg is not equal in size to lh.smoothwm > >>>>> Exit 3 > >>>>> > >>>>> However, I looked through recon-all log files and found no error > >>> messages. > >>>>> So what does the error message above mean? How to correct this > > problem? > >>> Is > >>>>> there any document on check_subject? Thanks a lot for your help! > >>>>> > >>>>> Best, > >>>>> > >>>>> Jia > >>>>> > >>>>> ___ > >>>>> 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 > >>> > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] questions on check_subject
Hi, Bruce- No, the ?h.sphere.reg files are slightly larger than the orig files. Below is the list of files in the surf directory. -rwxrwxrwx1 app app 4858504 Mar 8 2004 lh.inflated -rwxrwxrwx1 app app 4858504 Mar 8 2004 lh.orig -rwxrwxrwx1 app app 4858504 Mar 8 2004 lh.pial -rw-rw-r--1 app app 4858721 Mar 16 23:46 lh.rh.sphere.reg -rwxrwxrwx1 app app 4858504 Mar 8 2004 lh.smoothwm -rw-rw-r--1 app app 4858504 Mar 16 20:35 lh.sphere -rw-rw-r--1 app app 4858721 Mar 16 22:14 lh.sphere.reg -rwxrwxrwx1 app app 4858504 Mar 8 2004 lh.white -rwxrwxrwx1 app app 4853068 Mar 8 2004 rh.inflated -rw-rw-r--1 app app 4853285 Mar 16 18:54 rh.lh.sphere.reg -rwxrwxrwx1 app app 4853068 Mar 8 2004 rh.orig -rwxrwxrwx1 app app 4853068 Mar 8 2004 rh.pial -rwxrwxrwx1 app app 4853068 Mar 8 2004 rh.smoothwm -rw-rw-r--1 app app 4853068 Mar 16 15:17 rh.sphere -rw-rw-r--1 app app 4853285 Mar 16 16:59 rh.sphere.reg -rwxrwxrwx1 app app 4853068 Mar 8 2004 rh.white Will this affect the surface-based group analysis? Thanks again for your help! Best, jia > -Original Message- > From: Bruce Fischl [mailto:[EMAIL PROTECTED] > Sent: Friday, May 27, 2005 8:10 PM > To: Jia Liu > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] questions on check_subject > > not sure why the smoothwm would be different size. Is it the same size as > the orig? How about the rest of the surfaces for each hemis (sphere, white, > pial) > > On Fri, 27 May 2005, Jia > Liu wrote: > > > Hi, > > > > I used check_subject and found following error message on all my subjects: > > > > Zion:/nfs/home/Subjects> check_subject subKL > > CHECKING SUBJECT subKL > > WARN: file rh.sphere.reg is not equal in size to rh.smoothwm > > WARN: file lh.sphere.reg is not equal in size to lh.smoothwm > > WARN: file lh.rh.sphere.reg is not equal in size to lh.smoothwm > > Exit 3 > > > > However, I looked through recon-all log files and found no error messages. > > So what does the error message above mean? How to correct this problem? Is > > there any document on check_subject? Thanks a lot for your help! > > > > Best, > > > > Jia > > > > ___ > > 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
[Freesurfer] questions on check_subject
Hi, I used check_subject and found following error message on all my subjects: Zion:/nfs/home/Subjects> check_subject subKL CHECKING SUBJECT subKL WARN: file rh.sphere.reg is not equal in size to rh.smoothwm WARN: file lh.sphere.reg is not equal in size to lh.smoothwm WARN: file lh.rh.sphere.reg is not equal in size to lh.smoothwm Exit 3 However, I looked through recon-all log files and found no error messages. So what does the error message above mean? How to correct this problem? Is there any document on check_subject? Thanks a lot for your help! Best, Jia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mkbrainmask failed
Dear group- When I tried mkbrainmask-sess with my data, I encountered an error (see below), and the program aborted. Could any one tell me how to fix this problem? I am using the newest version available from FreeSurfer download site. Thanks, jia zion:/nfs/home/jliu/data/test/mystudy> mkbrainmask-sess -sf sessid_re001_2 -df sesspar /nfs/home/jliu/data/test/20040527rd Sun Mar 13 16:49:50 CST 2005 -- /nfs/home/jliu/data/test/20040527rd/bold mkbrainmask -i 005/f -o masks/brain -thresh 0.1 -umask 2 -- Scratch Dir is /tmp/mkbrainmask_22219 # -- Converting bvolume to .img -- # mri_convert 005/f_000.bshort /tmp/mkbrainmask_22219/f.img Reading 005/f_000.bshort ... Reading 005/f_001.bshort ... Reading 005/f_002.bshort ... Reading 005/f_003.bshort ... Reading 005/f_004.bshort ... Reading 005/f_005.bshort ... Reading 005/f_006.bshort ... Reading 005/f_007.bshort ... Reading 005/f_008.bshort ... Reading 005/f_009.bshort ... Reading 005/f_010.bshort ... Reading 005/f_011.bshort ... Reading 005/f_012.bshort ... Reading 005/f_013.bshort ... Reading 005/f_014.bshort ... Reading 005/f_015.bshort ... Reading 005/f_016.bshort ... Reading 005/f_017.bshort ... Reading 005/f_018.bshort ... Reading 005/f_019.bshort ... Reading 005/f_020.bshort ... reading from 005/f_000.bshort... INFO: bvolumeRead: min = 0, max = 1480 TR=1.50, TE=32.00, TI=32.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -0.990268, 0.139173) k_ras = (-0, 0.139173, 0.990268) writing to /tmp/mkbrainmask_22219/f.img... Analyze Output Matrix -3.125 0.000 -0.000 104.375; 0.000 -3.095 0.668 146.084; 0.000 0.435 4.753 -44.536; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to 3 # -- Using FSL's BET to Extract Brain-- # This program has not been compiled for this data type /nfs/home/jliu/data/test/20040527rd/bold bet /tmp/mkbrainmask_22219/f /tmp/mkbrainmask_22219/brain -m -f 0.1 ERROR: bet failed ERROR: mkbrainmask failed Exit 1 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] displaying group data on average7
Dear all- Today when I played average7, I found that labels (e.g. lh-avg_calcarine_sulcus.label) in the label folder of average7 were not properly displayed in the surface of average7 (e.g. the label for calcarine sulcus was put somewhere in the middle temporal cortex). Could anyone help me address this puzzle? I am using the newest version available from freesurfer download site. Thanks for your guidance! Best, Jia Liu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mkbrainmask-sess failed
Dear all, When I used mkbrainmask-sess, an error occurred shown below. I am using the latest FreeSurfer, and the bet command is included in the distribution. Could anyone tell me how to fix it? thanks, Jia ++begin of error message+ mkbrainmask-sess 20041007syhu $Id: mkbrainmask-sess,v 1.2 2003/10/01 21:54:43 greve Exp $ Linux zion 2.4.22-1.zion #5 SMP Sun Dec 21 12:35:17 CST 2003 i686 i686 i386 GNU/Linux Tue Nov 23 20:23:19 CST 2004 /nfs/home/jliu/data/scramface/mystudy -sf sessid_syhu -df sesspar ProjectDir /nfs/home/jliu/data/scramface/mystudy /nfs/home/jliu/data/scramface/20041007syhu Tue Nov 23 20:23:19 CST 2004 /nfs/home/jliu/data/scramface/20041007syhu/bold mkbrainmask -i 005/f -o masks/brain -thresh 0.1 -umask 2 Scratch Dir is /tmp/mkbrainmask_4734 # -- Converting bvolume to .img -- # mri_convert 005/f_000.bshort /tmp/mkbrainmask_4734/f.img Reading 005/f_000.bshort ... Reading 005/f_001.bshort ... Reading 005/f_002.bshort ... Reading 005/f_003.bshort ... Reading 005/f_004.bshort ... Reading 005/f_005.bshort ... Reading 005/f_006.bshort ... Reading 005/f_007.bshort ... Reading 005/f_008.bshort ... Reading 005/f_009.bshort ... Reading 005/f_010.bshort ... Reading 005/f_011.bshort ... Reading 005/f_012.bshort ... Reading 005/f_013.bshort ... Reading 005/f_014.bshort ... Reading 005/f_015.bshort ... reading from 005/f_000.bshort... INFO: bvolumeRead: min = 0, max = 885 TR=1.50, TE=30.00, TI=30.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -0.996195, 0.0871557) k_ras = (-0, 0.087156, 0.996195) writing to /tmp/mkbrainmask_4734/f.img... Analyze Output Matrix -3.125 0.000 -0.000 100.229; 0.000 -3.113 0.418 99.376; 0.000 0.272 4.782 -50.897; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to 3 # -- Using FSL's BET to Extract Brain-- # This program has not been compiled for this data type /nfs/home/jliu/data/scramface/20041007syhu/bold bet /tmp/mkbrainmask_4734/f /tmp/mkbrainmask_4734/brain -m -f 0.1 ERROR: bet failed ERROR: mkbrainmask failed +end of error message ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] questions on mkbrainmask-sess
Dear all- Today I tried mkbrainmask-sess (first time), and got the error message shown below: + zion:/nfs/home/jliu/VM/myProc> mkbrainmask-sess -sf sessid_S001 -df sesspar -funcstem fmcss /nfs/home/jliu/VM/S001 Mon Sep 20 21:20:40 CST 2004 -- /nfs/home/jliu/VM/S001/bold mkbrainmask -i 004/fmcss -o masks/brain -thresh 0.1 -umask 2 -- Scratch Dir is /tmp/mkbrainmask_23685 # -- Converting bvolume to .img -- # mri_convert 004/fmcss_000.bshort /tmp/mkbrainmask_23685/fmcss.img reading from 004/fmcss_000.bshort... INFO: bvolumeRead: min = 25, max = 1325 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0.995227, 0.0975827) k_ras = (-0, 0.097583, 0.995227) writing to /tmp/mkbrainmask_23685/fmcss.img... Analyze Output Matrix -1.406 0.000 -0.000 94.016; 0.000 -1.400 0.195 101.727; 0.000 0.137 1.990 -42.636; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to 3 # -- Using FSL's BET to Extract Brain-- # This program has not been compiled for this data type /nfs/home/jliu/VM/S001/bold bet /tmp/mkbrainmask_23685/fmcss /tmp/mkbrainmask_23685/brain -m -f 0.1 ERROR: bet failed ERROR: mkbrainmask failed Exit 1 +end+ The input data (fmcss) were motion-corrected, spatial-smoothed, and intensity-normalized using fsfast (the newest version released). Could anyone tell me how to fix this problem? Thanks for your help! jia ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
