[Freesurfer] question about visualization of negative activation
Hello, I have a loaded a significance map using the tksurfer-sess command. I want to visualize only the negative activation on the surface. In the View -> Configure -> Overlay window, I check both the "truncate" and "inverse" buttons. So only the negative activation is shown however it is in Red-Orange-Yellow color scale. How can I get this negative activation to be represented by Dark and Light Blue color scale. Thanks in advance for the help! Balaji Goparaju ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] preproc-sess : Problem with spatial smoothing and brain masking
HI, I ran the preproc-sess command, but in the output for spatial smoothing, the fmcsm5 file is not created. It says [balaji-goparajus-computer:~/Desktop/subjectdata] balajigo% spatialsmooth-sess -i fmc -o fmcsm5 -fwhm 5 -fsd bold -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -update -noinorm /Users/balajigoparaju/Desktop/subjectdata/LD-functional Thu Jul 17 16:03:47 EDT 2008 ~/Desktop/subjectdata/LD-functional/bold ~/Desktop/subjectdata RunList 006 010 017 019 /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 006/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 11 10:15 006/fmc.nii Update not needed /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 010/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 08:26 010/fmc.nii Update not needed /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 017/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:03 017/fmc.nii Update not needed /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 019/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:07 019/fmc.nii Update not needed Started at Thu Jul 17 16:03:47 EDT 2008 Ended at Thu Jul 17 16:03:48 EDT 2008 spatiallysmooth-sess Done Thank you for your help! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Preproc-sess: Spatial smoothing and brain masking
Hi, I used the command preproc-sess -s LD-functional -fwhm 5 However, the command does not seem create the fmcsm5.nii file. The process completes motion correction successfully, but it does not complete the spatial smoothing and brain masking. I get a "Motion correction SUCCESSFULLY completed" message but I only get a "Spatial smoothing done" message. I have already asked this question in the mailing list. and i was asked to check the writing permissions of the directories. I have changed the "bold" directory and freesurfer directory to have read, write and execute permisions using the "chmod -R 777" command. I get the following output: -- preproc-sess logfile is log/preproc-sess.log -- instem f mc 1 f fmc stc 0 fmc sm 1 fmc fmcsm5 mask 1 brain LD-functional MC - Mon Jul 21 09:32:56 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata mc-sess -fstem f -fmcstem fmc -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -fsd bold -new -update -no-inorm Logfile is /Users/balajigoparaju/Desktop/subjectdata/log/mc-LD-functional-bold.log --- /Users/balajigoparaju/Desktop/subjectdata/LD-functional RunList: 006 010 017 019 Targ Stem is 006/f Update not needed -rwxrwxrwx 1 balajigo admin 41091424 Jul 11 10:15 006/fmc.nii -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 006/f.bhdr Update not needed -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 08:26 010/fmc.nii -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 010/f.bhdr Update not needed -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:03 017/fmc.nii -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 017/f.bhdr Update not needed -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:07 019/fmc.nii -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 019/f.bhdr Mon Jul 21 09:32:57 EDT 2008 mc-sess completed SUCCESSFULLY LD-functional Smooth Mon Jul 21 09:32:57 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata spatialsmooth-sess -i fmc -o fmcsm5 -fwhm 5 -fsd bold -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -update -noinorm /Users/balajigoparaju/Desktop/subjectdata/LD-functional Mon Jul 21 09:32:57 EDT 2008 ~/Desktop/subjectdata/LD-functional/bold ~/Desktop/subjectdata RunList 006 010 017 019 /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 006/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 11 10:15 006/fmc.nii Update not needed /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 010/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 08:26 010/fmc.nii Update not needed /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 017/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:03 017/fmc.nii Update not needed /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 019/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:07 019/fmc.nii Update not needed Started at Mon Jul 21 09:32:57 EDT 2008 Ended at Mon Jul 21 09:32:59 EDT 2008 spatiallysmooth-sess Done LD-functional Inorm Mon Jul 21 09:32:59 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata mkbrainmask-sess -maskstem brain -fsd bold -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -update /Users/balajigoparaju/Desktop/subjectdata/LD-functional Mon Jul 21 09:32:59 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: masks/brain.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 006/f.bhdr Update not needed Mon Jul 21 09:33:00 EDT 2008 mkbrainmask-sess done Started at Mon Jul 21 09:32:56 EDT 2008 Ended at Mon Jul 21 09:33:00 EDT 2008 preproc-sess done Any help is appreciated. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Preproc-sess: Spatial smoothing and brain masking
ok, Here is the output: I am still getting the same output. [comm726-0b01-dhcp9:~/Desktop/subjectdata] balajigo% spatialsmooth-sess -i fmc -o fmcsm5 -fwhm 5 -fsd bold -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -update -noinorm /Users/balajigoparaju/Desktop/subjectdata/LD-functional Mon Jul 21 12:40:18 EDT 2008 ~/Desktop/subjectdata/LD-functional/bold ~/Desktop/subjectdata RunList 006 010 017 019 /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 006/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 11 10:15 006/fmc.nii Update not needed /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 010/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 08:26 010/fmc.nii Update not needed /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 017/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:03 017/fmc.nii Update not needed /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 019/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:07 019/fmc.nii Update not needed Started at Mon Jul 21 12:40:18 EDT 2008 Ended at Mon Jul 21 12:40:20 EDT 2008 spatiallysmooth-sess Done [comm726-0b01-dhcp9:~/Desktop/subjectdata] balajigo% Thanks for the help ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Preproc-sess: Spatial smoothing and brain masking
Ok, here is the terminal output as an attachment On Mon, Jul 21, 2008 at 12:44 PM, Doug Greve <[EMAIL PROTECTED]> wrote: > Can you send the terminal output? The ls results are not informative. > > doug > > > Balaji Goparaju wrote: > > ok, Here is the output: I am still getting the same output. >> >> [comm726-0b01-dhcp9:~/Desktop/subjectdata] balajigo% spatialsmooth-sess -i >> fmc -o fmcsm5 -fwhm 5 -fsd bold -s LD-functional -d >> /Users/balajigoparaju/Desktop/subjectdata -update -noinorm >> >> >> /Users/balajigoparaju/Desktop/subjectdata/LD-functional >> Mon Jul 21 12:40:18 EDT 2008 >> ~/Desktop/subjectdata/LD-functional/bold ~/Desktop/subjectdata RunList 006 >> 010 017 019 >> /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold >> ls: 006/fmcsm5.nii: No such file or directory >> -rwxrwxrwx 1 balajigo admin 41091424 Jul 11 10:15 006/fmc.nii >> Update not needed >> /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold >> ls: 010/fmcsm5.nii: No such file or directory >> -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 08:26 010/fmc.nii >> Update not needed >> /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold >> ls: 017/fmcsm5.nii: No such file or directory >> -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:03 017/fmc.nii >> Update not needed >> /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold >> ls: 019/fmcsm5.nii: No such file or directory >> -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:07 019/fmc.nii >> Update not needed >> Started at Mon Jul 21 12:40:18 EDT 2008 >> Ended at Mon Jul 21 12:40:20 EDT 2008 >> spatiallysmooth-sess Done >> [comm726-0b01-dhcp9:~/Desktop/subjectdata] balajigo% >> Thanks for the help >> > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > spatialsmoothoutput Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Preproc-sess: Spatial smoothing and brain masking
after executing the command you suggested, /Users/balajigoparaju/Desktop/subjectdata contains some files which are enclosed as an attachment On Mon, Jul 21, 2008 at 12:55 PM, Balaji Goparaju <[EMAIL PROTECTED]> wrote: > Ok, here is the terminal output as an attachment > > > On Mon, Jul 21, 2008 at 12:44 PM, Doug Greve <[EMAIL PROTECTED]> > wrote: > >> Can you send the terminal output? The ls results are not informative. >> >> doug >> >> >> Balaji Goparaju wrote: >> >> ok, Here is the output: I am still getting the same output. >>> >>> [comm726-0b01-dhcp9:~/Desktop/subjectdata] balajigo% spatialsmooth-sess >>> -i fmc -o fmcsm5 -fwhm 5 -fsd bold -s LD-functional -d >>> /Users/balajigoparaju/Desktop/subjectdata -update -noinorm >>> >>> >>> /Users/balajigoparaju/Desktop/subjectdata/LD-functional >>> Mon Jul 21 12:40:18 EDT 2008 >>> ~/Desktop/subjectdata/LD-functional/bold ~/Desktop/subjectdata RunList >>> 006 010 017 019 >>> /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold >>> ls: 006/fmcsm5.nii: No such file or directory >>> -rwxrwxrwx 1 balajigo admin 41091424 Jul 11 10:15 006/fmc.nii >>> Update not needed >>> /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold >>> ls: 010/fmcsm5.nii: No such file or directory >>> -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 08:26 010/fmc.nii >>> Update not needed >>> /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold >>> ls: 017/fmcsm5.nii: No such file or directory >>> -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:03 017/fmc.nii >>> Update not needed >>> /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold >>> ls: 019/fmcsm5.nii: No such file or directory >>> -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:07 019/fmc.nii >>> Update not needed >>> Started at Mon Jul 21 12:40:18 EDT 2008 >>> Ended at Mon Jul 21 12:40:20 EDT 2008 >>> spatiallysmooth-sess Done >>> [comm726-0b01-dhcp9:~/Desktop/subjectdata] balajigo% >>> Thanks for the help >>> >> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> [EMAIL PROTECTED] >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> In order to help us help you, please follow the steps in: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> > list Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Preproc-sess: Spatial smoothing and brain masking
Hi,
I copied the new version of the programs
mktemplate-sess
surfsmooth-sess
stc-sess
mkbrainmask-sess
mc-sess
When i try to run preproc-sess -s LD-functional -fwhm 5 again, I get the
following error,
--
preproc-sess logfile is log/preproc-sess.log
--
instem f
mc 1 f fmc
stc 0 fmc
sm 1 fmc fmcsm5
mask 1 brain
LD-functional MC -
Tue Jul 22 09:25:08 EDT 2008
/Users/balajigoparaju/Desktop/subjectdata
mc-sess -fstem f -fmcstem fmc -s LD-functional -d
/Users/balajigoparaju/Desktop/subjectdata -fsd bold -new -update -no-inorm
/Applications/freesurfer/fsfast/bin/mc-sess: line 1:
{rtf1macansicpg1cocoartf824cocoasubrtf480: command not found
/Applications/freesurfer/fsfast/bin/mc-sess: line 2: syntax error near
unexpected token `}'
/Applications/freesurfer/fsfast/bin/mc-sess: line 2:
`{\fonttbl\f0\fswiss\fcharset77 Helvetica;}'
ERROR: mc-sess failed
And then i tried changing the mc-sess.backup file back to the mc-sess (Using
the older version of mc-sess), and then the mc-sess and spatialsmooth-sess
part of the preproc-sess program worked fine, but i get a similar error for
the brainmask-sess program.
Tue Jul 22 09:19:12 EDT 2008
/Users/balajigoparaju/Desktop/subjectdata
mkbrainmask-sess -maskstem brain -fsd bold -s LD-functional -d
/Users/balajigopa
raju/Desktop/subjectdata -update
/Applications/freesurfer/fsfast/bin/mkbrainmask-sess: line 1:
{rtf1macansicpg100
00cocoartf824cocoasubrtf480: command not found
/Applications/freesurfer/fsfast/bin/mkbrainmask-sess: line 2: syntax error
near
unexpected token `}'
/Applications/freesurfer/fsfast/bin/mkbrainmask-sess: line 2:
`{\fonttbl\f0\fswi
ss\fcharset77 Helvetica;}'
ERROR: mkbrainmask-sess failed
Thank you for any help.
___
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Re: [Freesurfer] Preproc-sess: Spatial smoothing and brain masking
Hi, Thank you for the help. I saved it as a plain text. and it did not give me that error again. However, even after I saved the new version of the mkbrainmask-sess, i get the same error. Tue Jul 22 14:32:30 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata mkbrainmask-sess -maskstem brain -fsd bold -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -update /Users/balajigoparaju/Desktop/subjectdata/LD-functional Tue Jul 22 14:32:30 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: masks/brain.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 006/f.bhdr Update not needed Tue Jul 22 14:32:32 EDT 2008 mkbrainmask-sess done Started at Tue Jul 22 14:32:26 EDT 2008 Ended at Tue Jul 22 14:32:32 EDT 2008 preproc-sess done Thank you for any help. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Compute individual statistics (selxavg3)
Hi Doug and all, There is another problem when i try the individual statistics, I use the command selxavg3-sess -analysis LD-analysis -s LD-functional and i am getting an error: ERROR: cannot find volume matching /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/mcextreg ERROR: loading nonpar reg /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/mcextreg -- ERROR: fast_selxavg3() failed\n so i was wondering if the problem was because the software is not creating the file, or if there was any other way i could make freesurfer create the file. Thank you for any help! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Preproc: Brainmasking
Hi Doug and all, I used the new version of mkbrainmask-sess. It looks like the file is getting created but it cannot find fslmaths for avmaths. Is this error something to do with the freesurfer software itself, or is there anything I can do about it? Thu Jul 24 09:15:51 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata mkbrainmask-sess -maskstem brain -fsd bold -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -update /Users/balajigoparaju/Desktop/subjectdata/LD-functional Thu Jul 24 09:15:52 EDT 2008 -- /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold mkbrainmask -i 006/f.bhdr -o masks/brain.nii -thresh 0.1 -ndil 1 -nerode 0 -- ERROR: cannot find either fslmaths for avwmaths ERROR: mkbrainmask failed ERROR: mkbrainmask-sess failed Thank you for any help! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] First Level analysis
Hi Doug and all, There is a problem when i try the individual statistics, I use the command selxavg3-sess -analysis LD-analysis -s LD-functional and i am getting an error: ERROR: cannot find volume matching /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/mcextreg ERROR: loading nonpar reg /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/mcextreg -- ERROR: fast_selxavg3() failed\n The error seems to be something to do with a file needed to use motion correction regressors so i was wondering if the problem was because the software is not creating the file, or if there was any other way i could make freesurfer create the file. Thank you for any help! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Compute individual Statistics
Hi Doug, When i run selxavg3-sess -analysis LD-analysis -s LD-functional i seem to get errors in some other files, The output is as follows: [balaji-goparajus-computer:~/Desktop/subjectdata] balajigo% selxavg3-sess -analysis LD-analysis -s LD-functional -- selxavg3-sess logfile is /Users/balajigoparaju/Desktop/subjectdata/log/selxavg3-sess-bold-LD-analysis-080728180123.log -- --- /Users/balajigoparaju/Desktop/subjectdata/LD-functional Mon Jul 28 18:01:23 EDT 2008 anadir = /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/LD-analysis -- --- matlab output Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2008 The MathWorks, Inc. Version 7.6.0.324 (R2008a) February 10, 2008 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2.2 2007/11/27 18:42:09 greve Exp $ outtop = /Users/balajigoparaju/Desktop/subjectdata Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 LD-contrast.mat Loaded /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/emotion.par as a par2 file. ERROR: empty nonpar matrix for mcextreg ??? Attempt to reference field of non-structure array. Error in ==> flac_taskregind at 37 nev = length(flac.ev); Error in ==> flac_customize at 267 flacnew.indtask = flac_taskregind(flacnew); Error in ==> fast_selxavg3 at 97 flac0 = flac_customize(flac0); >> -- ERROR: fast_selxavg3() failed\n Thank you for the help you have been providing! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Compute First Level Analysis
Hi Doug and all, When i run selxavg3-sess -analysis LD-analysis -s LD-functional i seem to get errors in some other files, The output is as follows: [balaji-goparajus-computer:~/Desktop/subjectdata] balajigo% selxavg3-sess -analysis LD-analysis -s LD-functional -- selxavg3-sess logfile is /Users/balajigoparaju/Desktop/subjectdata/log/selxavg3-sess-bold-LD-analysis-080728180123.log -- --- /Users/balajigoparaju/Desktop/subjectdata/LD-functional Mon Jul 28 18:01:23 EDT 2008 anadir = /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/LD-analysis -- --- matlab output Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2008 The MathWorks, Inc. Version 7.6.0.324 (R2008a) February 10, 2008 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2.2 2007/11/27 18:42:09 greve Exp $ outtop = /Users/balajigoparaju/Desktop/subjectdata Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 LD-contrast.mat Loaded /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/emotion.par as a par2 file. ERROR: empty nonpar matrix for mcextreg ??? Attempt to reference field of non-structure array. Error in ==> flac_taskregind at 37 nev = length(flac.ev); Error in ==> flac_customize at 267 flacnew.indtask = flac_taskregind(flacnew); Error in ==> fast_selxavg3 at 97 flac0 = flac_customize(flac0); >> -- ERROR: fast_selxavg3() failed\n Thank you for the help you have been providing! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Compute First level Analysis
Hi Doug and all, When i run selxavg3-sess -analysis LD-analysis -s LD-functional i seem to get errors in some other files, The output is as follows: [balaji-goparajus-computer:~/Desktop/subjectdata] balajigo% selxavg3-sess -analysis LD-analysis -s LD-functional -- selxavg3-sess logfile is /Users/balajigoparaju/Desktop/subjectdata/log/selxavg3-sess-bold-LD-analysis-080728180123.log -- --- /Users/balajigoparaju/Desktop/subjectdata/LD-functional Mon Jul 28 18:01:23 EDT 2008 anadir = /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/LD-analysis -- --- matlab output Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2008 The MathWorks, Inc. Version 7.6.0.324 (R2008a) February 10, 2008 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> 1.55.2.2 2007/11/27 18:42:09 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> greve Exp $ outtop = /Users/balajigoparaju/Desktop/subjectdata Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 LD-contrast.mat Loaded /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/emotion.par as a par2 file. ERROR: empty nonpar matrix for mcextreg ??? Attempt to reference field of non-structure array. Error in ==> flac_taskregind at 37 nev = length(flac.ev); Error in ==> flac_customize at 267 flacnew.indtask = flac_taskregind(flacnew); Error in ==> fast_selxavg3 at 97 flac0 = flac_customize(flac0); >> -- ERROR: fast_selxavg3() failed\n Thank you for the help you have been providing! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Resampling from MNI 152 to MNI 305 - Problem with orientation
Hello Freesurfers,
I have Brodmann Area binary masks in the ICBM MNI 152 space, that I acquired
using WFU_PickAtlas toolbox in SPM. These
masks are .nii files, and have a RAS orientation.
I am trying to resample these masks into the fsaverage MNI 305 space,
specifically with the dimensions matching the "mni305.cor.subfov2.mgz"
file found in the $FREESURFER_HOME/average file. This file is in the LIA
orientation.
However, the mni152.register.dat file seems to be transforming volumes from
the MNI 305 space to the MNI 152 Space in LAS orientation (MNI152_T1_2mm.nii
in FSL).
Should I transform my Brodmann Area masks from the RAS orientation to a LAS
orientation? If so, how can I achieve this? The RAS orientation is correct,
so I know using mri_convert --out_dimension is out of the question.
I have tried to use
*mri_label2vol --seg {BA_mask} --temp
{$FREESURFER_HOME/average/mni305.cor.subfov2.mgz} --o {output_file} --reg
mni152.register.dat --invertmtx*
Also, I have tried to use the inverted matrix from mni152.register.dat and
use it with
*mri_vol2vol -mov {BA_mask} --reg {inverted_mni152.register.dat} --o
{output_file} --tal --talres 2*
However, the output files had interchanged posterior (P) and anterior (A),
and superior (S) and interior (I) orientations.
What is the best way to achieve the resampling? Any guidance is really
appreciated!
Regards,
Balaji Goparaju
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Re: [Freesurfer] Resampling from MNI 152 to MNI 305 - Problem with orientation
Thanks for the response! I seem to be getting better results.
I was wondering if there was any way the same resampling can be achieved
using Freesurfer 4.5 since a
lot of analysis (including analysis with other tasks) has already been done
in it, or if it is okay to use JUST the reg.2mm.mni152.dat file from
Freesurfer 5.1 and keep the rest of the analysis the same as before?
Thank you once again for this help!
Regards,
Balaji Goparaju
On Tue, Jun 14, 2011 at 11:46 AM, Douglas N Greve wrote:
> To go from mni152 to the MNI305 2mm space, use
>
> mri_vol2vol --mov mni305.2mm.nii.gz \
> --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
> --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
> --inv --o output.mni305.2mm.nii.gz
>
> This will resample MNI152_T1_2mm.nii.gz (or anything in that space) to the
> mni305 2mm space.
>
> For your application, add --interp nearest, or use
>
> mri_label2vol --seg BA_mask.mni152.nii \
> --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
> --invertmtx --o outfile.nii
>
> doug
>
>
> Balaji Goparaju wrote:
>
>> Hello Freesurfers,
>>
>> I have Brodmann Area binary masks in the ICBM MNI 152 space, that I
>> acquired using WFU_PickAtlas toolbox in SPM. These
>> masks are .nii files, and have a RAS orientation.
>>
>> I am trying to resample these masks into the fsaverage MNI 305 space,
>> specifically with the dimensions matching the "mni305.cor.subfov2.mgz"
>> file found in the $FREESURFER_HOME/average file. This file is in the LIA
>> orientation.
>>
>> However, the mni152.register.dat file seems to be transforming volumes
>> from the MNI 305 space to the MNI 152 Space in LAS orientation
>> (MNI152_T1_2mm.nii in FSL).
>>
>> Should I transform my Brodmann Area masks from the RAS orientation to a
>> LAS orientation? If so, how can I achieve this? The RAS orientation is
>> correct, so I know using mri_convert --out_dimension is out of the question.
>>
>> I have tried to use
>> *mri_label2vol --seg {BA_mask} --temp
>> {$FREESURFER_HOME/average/mni305.cor.subfov2.mgz} --o {output_file} --reg
>> mni152.register.dat --invertmtx*
>>
>> Also, I have tried to use the inverted matrix from mni152.register.dat and
>> use it with
>> *mri_vol2vol -mov {BA_mask} --reg {inverted_mni152.register.dat} --o
>> {output_file} --tal --talres 2*
>> However, the output files had interchanged posterior (P) and anterior (A),
>> and superior (S) and interior (I) orientations.
>>
>> What is the best way to achieve the resampling? Any guidance is really
>> appreciated!
>>
>> Regards,
>>
>> Balaji Goparaju
>>
>>
>> ___
>> 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
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
> 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.
>
>
___
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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.
Re: [Freesurfer] Resampling from MNI 152 to MNI 305 - Problem with orientation
Thank you for the help!
On Tue, Jun 14, 2011 at 9:10 PM, Douglas Greve wrote:
> **
> You should be able to use the reg and mni305.2mm.nii.gz in 4.5
> doug
>
>
> On 6/14/11 12:25 PM, Balaji Goparaju wrote:
>
> Thanks for the response! I seem to be getting better results.
>
> I was wondering if there was any way the same resampling can be achieved
> using Freesurfer 4.5 since a
> lot of analysis (including analysis with other tasks) has already been done
> in it, or if it is okay to use JUST the reg.2mm.mni152.dat file from
> Freesurfer 5.1 and keep the rest of the analysis the same as before?
>
> Thank you once again for this help!
>
> Regards,
>
> Balaji Goparaju
>
>
>
> On Tue, Jun 14, 2011 at 11:46 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> To go from mni152 to the MNI305 2mm space, use
>>
>> mri_vol2vol --mov mni305.2mm.nii.gz \
>> --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
>> --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
>> --inv --o output.mni305.2mm.nii.gz
>>
>> This will resample MNI152_T1_2mm.nii.gz (or anything in that space) to the
>> mni305 2mm space.
>>
>> For your application, add --interp nearest, or use
>>
>> mri_label2vol --seg BA_mask.mni152.nii \
>> --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
>> --invertmtx --o outfile.nii
>>
>> doug
>>
>>
>> Balaji Goparaju wrote:
>>
>>> Hello Freesurfers,
>>>
>>> I have Brodmann Area binary masks in the ICBM MNI 152 space, that I
>>> acquired using WFU_PickAtlas toolbox in SPM. These
>>> masks are .nii files, and have a RAS orientation.
>>>
>>> I am trying to resample these masks into the fsaverage MNI 305 space,
>>> specifically with the dimensions matching the "mni305.cor.subfov2.mgz"
>>> file found in the $FREESURFER_HOME/average file. This file is in the LIA
>>> orientation.
>>>
>>> However, the mni152.register.dat file seems to be transforming volumes
>>> from the MNI 305 space to the MNI 152 Space in LAS orientation
>>> (MNI152_T1_2mm.nii in FSL).
>>>
>>> Should I transform my Brodmann Area masks from the RAS orientation to a
>>> LAS orientation? If so, how can I achieve this? The RAS orientation is
>>> correct, so I know using mri_convert --out_dimension is out of the question.
>>>
>>> I have tried to use
>>> *mri_label2vol --seg {BA_mask} --temp
>>> {$FREESURFER_HOME/average/mni305.cor.subfov2.mgz} --o {output_file} --reg
>>> mni152.register.dat --invertmtx*
>>>
>>> Also, I have tried to use the inverted matrix from mni152.register.dat
>>> and use it with
>>> *mri_vol2vol -mov {BA_mask} --reg {inverted_mni152.register.dat} --o
>>> {output_file} --tal --talres 2*
>>> However, the output files had interchanged posterior (P) and anterior
>>> (A), and superior (S) and interior (I) orientations.
>>>
>>> What is the best way to achieve the resampling? Any guidance is really
>>> appreciated!
>>>
>>> Regards,
>>>
>>> Balaji Goparaju
>>>
>>>
>>>
>>> ___
>>> 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
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358 Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>>
>>
>> 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
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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