Hi, so, instead of converting the files, i unpacked them into bshort and it gave me, i think, the right amount of files. then i used the command preproc-sess --sf sessid --df sesspar --fwhm 6. it ran for a while, gave me the sections converting input to afni, motion correcting, and matlab file. after it opens matlab it has the errors saying the mc-sess failed. i am running this from /space/troy. it does create the file fmc.mcdat and it looks like its complete. it just stops after that and doesn't make the actual motion corrected files. thanks for your help. margaret
SPM stores each *frame* in a separate file, but all slices for a given frame in the same file. Thus, the number of files will equal the number of frames. bshort/bfloat stores each *slice* in a separate file, but all frames for a given slice in the same file. Thus the number of files will equal the number of slices. Does this resolve the difference?
It sounds like your bshorts are not being converted to AFNI properly. Can you send me your preproc-sess command-line and the location you are running it from?
doug
Margaret Duff wrote:
Hi, I have 12 runs of functional data I am trying to convert to
FSFast
formats and then preprocess. I have been using mri_convert to make
my
.img files into bshorts. However mri_convert makes only 30 files
when my
folders originally contained 37 or 73 files. Is this what it is
supposed
to do? I am also then trying to run preproc-sess on these files but
i
keep getting an error during the motion correction of the first
run. it
says can't register a 1 brick dataset to itself, and ERROR: 3dvolreg existed with status 1. I am using the command "preproc-sess -sf
sessid
-df sesspar -fwhm 6" for preprocessing and "mri_convert 028/f001.img 028/f_001.bshort" for file conversion. Does anyone know why my steps aren't working or knows of a better way to do these steps? Thank
you so
much, Margaret Duff
Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Margaret,
is the input volume bshort or bfloat? I've never been able to get the AFNI 3dvolreg to work with floats. Could be my bfloat-AFNI converter.
doug
Margaret Duff wrote:
Hi, so, instead of converting the files, i unpacked them into bshort and it gave me, i think, the right amount of files. then i used the command preproc-sess --sf sessid --df sesspar --fwhm 6. it ran for a while, gave me the sections converting input to afni, motion correcting, and matlab file. after it opens matlab it has the errors saying the mc-sess failed. i am running this from /space/troy. it does create the file fmc.mcdat and it looks like its complete. it just stops after that and doesn't make the actual motion corrected files. thanks for your help. margaret
SPM stores each *frame* in a separate file, but all slices for a given frame in the same file. Thus, the number of files will equal the number of frames. bshort/bfloat stores each *slice* in a separate file, but all frames for a given slice in the same file. Thus the number of files will equal the number of slices. Does this resolve the difference?
It sounds like your bshorts are not being converted to AFNI properly. Can you send me your preproc-sess command-line and the location you are running it from?
doug
Margaret Duff wrote:
Hi, I have 12 runs of functional data I am trying to convert to
FSFast
formats and then preprocess. I have been using mri_convert to make
my
.img files into bshorts. However mri_convert makes only 30 files
when my
folders originally contained 37 or 73 files. Is this what it is
supposed
to do? I am also then trying to run preproc-sess on these files but
i
keep getting an error during the motion correction of the first
run. it
says can't register a 1 brick dataset to itself, and ERROR: 3dvolreg existed with status 1. I am using the command "preproc-sess -sf
sessid
-df sesspar -fwhm 6" for preprocessing and "mri_convert 028/f001.img 028/f_001.bshort" for file conversion. Does anyone know why my steps aren't working or knows of a better way to do these steps? Thank
you so
much, Margaret Duff
Freesurfer mailing list [EMAIL PROTECTED] 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 _______________________________________________ Freesurfer mailing list [EMAIL PROTECTED] 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
hi, i am using bshort files. should i try bfloat? thanks, margaret
On Thu, 4 Nov 2004, Doug Greve wrote:
Hi Margaret,
is the input volume bshort or bfloat? I've never been able to get the AFNI 3dvolreg to work with floats. Could be my bfloat-AFNI converter.
doug
Margaret Duff wrote:
Hi, so, instead of converting the files, i unpacked them into bshort and it gave me, i think, the right amount of files. then i used the command preproc-sess --sf sessid --df sesspar --fwhm 6. it ran for a while, gave me the sections converting input to afni, motion correcting, and matlab file. after it opens matlab it has the errors saying the mc-sess failed. i am running this from /space/troy. it does create the file fmc.mcdat and it looks like its complete. it just stops after that and doesn't make the actual motion corrected files. thanks for your help. margaret
SPM stores each *frame* in a separate file, but all slices for a given frame in the same file. Thus, the number of files will equal the number of frames. bshort/bfloat stores each *slice* in a separate file, but all frames for a given slice in the same file. Thus the number of files will equal the number of slices. Does this resolve the difference?
It sounds like your bshorts are not being converted to AFNI properly. Can you send me your preproc-sess command-line and the location you are running it from?
doug
Margaret Duff wrote:
Hi, I have 12 runs of functional data I am trying to convert to
FSFast
formats and then preprocess. I have been using mri_convert to make
my
.img files into bshorts. However mri_convert makes only 30 files
when my
folders originally contained 37 or 73 files. Is this what it is
supposed
to do? I am also then trying to run preproc-sess on these files but
i
keep getting an error during the motion correction of the first
run. it
says can't register a 1 brick dataset to itself, and ERROR: 3dvolreg existed with status 1. I am using the command "preproc-sess -sf
sessid
-df sesspar -fwhm 6" for preprocessing and "mri_convert 028/f001.img 028/f_001.bshort" for file conversion. Does anyone know why my steps aren't working or knows of a better way to do these steps? Thank
you so
much, Margaret Duff
Freesurfer mailing list [EMAIL PROTECTED] 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 _______________________________________________ Freesurfer mailing list [EMAIL PROTECTED] 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
No, bshort should work fine. Can you be more specific as to where the data are? There are lots of possibilities under /space/troy ...
doug
Margaret Duff wrote:
hi, i am using bshort files. should i try bfloat? thanks, margaret
On Thu, 4 Nov 2004, Doug Greve wrote:
Hi Margaret,
is the input volume bshort or bfloat? I've never been able to get the AFNI 3dvolreg to work with floats. Could be my bfloat-AFNI converter.
doug
Margaret Duff wrote:
Hi, so, instead of converting the files, i unpacked them into bshort and it gave me, i think, the right amount of files. then i used the command preproc-sess --sf sessid --df sesspar --fwhm 6. it ran for a while, gave me the sections converting input to afni, motion correcting, and matlab file. after it opens matlab it has the errors saying the mc-sess failed. i am running this from /space/troy. it does create the file fmc.mcdat and it looks like its complete. it just stops after that and doesn't make the actual motion corrected files. thanks for your help. margaret
SPM stores each *frame* in a separate file, but all slices for a given frame in the same file. Thus, the number of files will equal the number of frames. bshort/bfloat stores each *slice* in a separate file, but all frames for a given slice in the same file. Thus the number of files will equal the number of slices. Does this resolve the difference?
It sounds like your bshorts are not being converted to AFNI properly. Can you send me your preproc-sess command-line and the location you are running it from?
doug
Margaret Duff wrote:
Hi, I have 12 runs of functional data I am trying to convert to
FSFast
formats and then preprocess. I have been using mri_convert to make
my
.img files into bshorts. However mri_convert makes only 30 files
when my
folders originally contained 37 or 73 files. Is this what it is
supposed
to do? I am also then trying to run preproc-sess on these files but
i
keep getting an error during the motion correction of the first
run. it
says can't register a 1 brick dataset to itself, and ERROR: 3dvolreg existed with status 1. I am using the command "preproc-sess -sf
sessid
-df sesspar -fwhm 6" for preprocessing and "mri_convert 028/f001.img 028/f_001.bshort" for file conversion. Does anyone know why my steps aren't working or knows of a better way to do these steps? Thank
you so
much, Margaret Duff
Freesurfer mailing list [EMAIL PROTECTED] 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 _______________________________________________ Freesurfer mailing list [EMAIL PROTECTED] 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
oh sorry, /space/troy/1/users/FREESURFER/SM2S1_fsfast/func/SM2S1 and i was trying to run it on the bold folder. could it have to do with my matlab startup? i thought i modified it correctly when i started using the program. but as i look back through my command window i see a warning that my startup.m file might be wrong. can you tell me everything that needs to be included in that file? thanks so much, margaret
On Mon, 8 Nov 2004, Doug Greve wrote:
No, bshort should work fine. Can you be more specific as to where the data are? There are lots of possibilities under /space/troy ...
doug
Margaret Duff wrote:
hi, i am using bshort files. should i try bfloat? thanks, margaret
On Thu, 4 Nov 2004, Doug Greve wrote:
Hi Margaret,
is the input volume bshort or bfloat? I've never been able to get the AFNI 3dvolreg to work with floats. Could be my bfloat-AFNI converter.
doug
Margaret Duff wrote:
Hi, so, instead of converting the files, i unpacked them into bshort and it gave me, i think, the right amount of files. then i used the command preproc-sess --sf sessid --df sesspar --fwhm 6. it ran for a while, gave me the sections converting input to afni, motion correcting, and matlab file. after it opens matlab it has the errors saying the mc-sess failed. i am running this from /space/troy. it does create the file fmc.mcdat and it looks like its complete. it just stops after that and doesn't make the actual motion corrected files. thanks for your help. margaret
SPM stores each *frame* in a separate file, but all slices for a given frame in the same file. Thus, the number of files will equal the number of frames. bshort/bfloat stores each *slice* in a separate file, but all frames for a given slice in the same file. Thus the number of files will equal the number of slices. Does this resolve the difference?
It sounds like your bshorts are not being converted to AFNI properly. Can you send me your preproc-sess command-line and the location you are running it from?
doug
Margaret Duff wrote:
Hi, I have 12 runs of functional data I am trying to convert to
FSFast
formats and then preprocess. I have been using mri_convert to make
my
.img files into bshorts. However mri_convert makes only 30 files
when my
folders originally contained 37 or 73 files. Is this what it is
supposed
to do? I am also then trying to run preproc-sess on these files but
i
keep getting an error during the motion correction of the first
run. it
says can't register a 1 brick dataset to itself, and ERROR: 3dvolreg existed with status 1. I am using the command "preproc-sess -sf
sessid
-df sesspar -fwhm 6" for preprocessing and "mri_convert 028/f001.img 028/f_001.bshort" for file conversion. Does anyone know why my steps aren't working or knows of a better way to do these steps? Thank
you so
much, Margaret Duff
Freesurfer mailing list [EMAIL PROTECTED] 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 _______________________________________________ Freesurfer mailing list [EMAIL PROTECTED] 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@nmr.mgh.harvard.edu
-
Doug Greve -
Margaret Duff