Re: [Freesurfer] IO with freesurfer files (.mgh in particular) from Python
Hi Krish, Thanks once again for providing that library. I came back to analyze the data and got some problems storing the results into MGH format. Before I try to figure out a fix (and send it back to you) I thought that may be you could share an uptodated snapshot of the library (may be the issue I am experiencing was already fixed). Thank you in advance! On Thu, 24 Apr 2008, Krish Subramaniam wrote: > Hi Yaroslav and Pádraig, > > Please follow the link pasted below to get an alpha version of pymgh. It > requires the latest Python and Numpy. > > https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/10224/1/2a5da2a125134fbdfc9e6850be1fcc09 > > (expires in 30 days ) > > Make sure PYTHONPATH has the directory which contains 'pymgh'. Found by > typing, -- Yaroslav Halchenko Research Assistant, Psychology Department, Rutgers-Newark Student Ph.D. @ CS Dept. NJIT Office: (973) 353-5440x263 | FWD: 82823 | Fax: (973) 353-1171 101 Warren Str, Smith Hall, Rm 4-105, Newark NJ 07102 WWW: http://www.linkedin.com/in/yarik ___ 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
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
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 ___ 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
Can you run: spatialsmooth-sess -i fmc -o fmcsm5 -fwhm 5 -fsd bold -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -update -noinorm capture the terminal output and send it to me? doug Balaji Goparaju wrote: 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help
[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
