it needs to be:
mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
note the "4" which tells it how many echoes to read
On Thu, 9 May 2013, Jonathan Holt wrote:
I input:
mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
it returns:
detecting dura using 0 echos from memprage_echo%d.mgz
Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand.
On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote:
Thanks Bruce,
should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously?
Also, should the fact that after running mris_make_surfaces, it says "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly.
jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
Hi Jon
yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote:
Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon
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Oh, simple mistake!
However, now it spit's an error saying I need filled.mgz?
On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:
it needs to be:
mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
note the "4" which tells it how many echoes to read
On Thu, 9 May 2013, Jonathan Holt wrote:
I input:
mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
it returns:
detecting dura using 0 echos from memprage_echo%d.mgz
Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand.
On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote:
Thanks Bruce,
should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously?
Also, should the fact that after running mris_make_surfaces, it says "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly.
jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
Hi Jon
yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote:
Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon
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
is your SUBJECTS_DIR set properly? You need to put the memprage echoes in the subject's mri dir On Thu, 9 May 2013, Jonathan Holt wrote:
Oh, simple mistake!
However, now it spit's an error saying I need filled.mgz?
On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:
it needs to be:
mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
note the "4" which tells it how many echoes to read
On Thu, 9 May 2013, Jonathan Holt wrote:
I input:
mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
it returns:
detecting dura using 0 echos from memprage_echo%d.mgz
Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand.
On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote:
Thanks Bruce,
should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously?
Also, should the fact that after running mris_make_surfaces, it says "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly.
jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
Hi Jon
yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote:
> Hi all, > combed through the mail archives to figure out how to work with multi echo > mprage, found what I need but I wanted to confirm which of these two > commands is the appropriate > mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh > mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? > jon >
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That was my suspicion, I've got them in the wrong folder. None of them are 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and nothing else.
Also the exact error has it looking in /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz
as opposed to /example/directory/subjects/subjid/mri/filled.mgz
I can rename subject directory if need be.
On May 9, 2013, at 10:54 AM, Bruce Fischl wrote:
is your SUBJECTS_DIR set properly? You need to put the memprage echoes in the subject's mri dir On Thu, 9 May 2013, Jonathan Holt wrote:
Oh, simple mistake!
However, now it spit's an error saying I need filled.mgz?
On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:
it needs to be:
mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
note the "4" which tells it how many echoes to read
On Thu, 9 May 2013, Jonathan Holt wrote:
I input:
mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
it returns:
detecting dura using 0 echos from memprage_echo%d.mgz
Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand.
On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote:
Thanks Bruce,
should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously?
Also, should the fact that after running mris_make_surfaces, it says "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly.
jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
> Hi Jon > > yes, the subject and hemi need to be defined (they are required parameters) > Bruce > On Wed, 8 May 2013, Jonathan Holt wrote: > >> Hi all, >> combed through the mail archives to figure out how to work with multi echo >> mprage, found what I need but I wanted to confirm which of these two >> commands is the appropriate >> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? >> jon >> > > > 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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Did you run recon-all? It will create filled.mgz in the subject/mri dir
On May 9, 2013, at 11:00 AM, Jonathan Holt whatsdac@umich.edu wrote:
That was my suspicion, I've got them in the wrong folder. None of them are 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and nothing else.
Also the exact error has it looking in /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz
as opposed to /example/directory/subjects/subjid/mri/filled.mgz
I can rename subject directory if need be.
On May 9, 2013, at 10:54 AM, Bruce Fischl wrote:
is your SUBJECTS_DIR set properly? You need to put the memprage echoes in the subject's mri dir On Thu, 9 May 2013, Jonathan Holt wrote:
Oh, simple mistake!
However, now it spit's an error saying I need filled.mgz?
On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:
it needs to be:
mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
note the "4" which tells it how many echoes to read
On Thu, 9 May 2013, Jonathan Holt wrote:
I input:
mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
it returns:
detecting dura using 0 echos from memprage_echo%d.mgz
Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand.
On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote:
> Thanks Bruce, > > should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? > > Also, should the fact that after running mris_make_surfaces, it says "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. > > jon > On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: > >> Hi Jon >> >> yes, the subject and hemi need to be defined (they are required parameters) >> Bruce >> On Wed, 8 May 2013, Jonathan Holt wrote: >> >>> Hi all, >>> combed through the mail archives to figure out how to work with multi echo >>> mprage, found what I need but I wanted to confirm which of these two >>> commands is the appropriate >>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? >>> jon >>> >> >> >> 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 > > >
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No,
I believe my PI simply ran mri_convert on the 4 nii's,
Clearly there is a better approach?
jon On May 9, 2013, at 11:04 AM, Bruce Fischl wrote:
Did you run recon-all? It will create filled.mgz in the subject/mri dir
On May 9, 2013, at 11:00 AM, Jonathan Holt whatsdac@umich.edu wrote:
That was my suspicion, I've got them in the wrong folder. None of them are 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and nothing else.
Also the exact error has it looking in /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz
as opposed to /example/directory/subjects/subjid/mri/filled.mgz
I can rename subject directory if need be.
On May 9, 2013, at 10:54 AM, Bruce Fischl wrote:
is your SUBJECTS_DIR set properly? You need to put the memprage echoes in the subject's mri dir On Thu, 9 May 2013, Jonathan Holt wrote:
Oh, simple mistake!
However, now it spit's an error saying I need filled.mgz?
On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:
it needs to be:
mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
note the "4" which tells it how many echoes to read
On Thu, 9 May 2013, Jonathan Holt wrote:
I input:
mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
it returns:
detecting dura using 0 echos from memprage_echo%d.mgz
Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand.
On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
> can you send me the full command line? It should say 4 echoes, not 0 > On Thu, 9 May 2013, Jonathan Holt wrote: > >> Thanks Bruce, >> >> should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? >> >> Also, should the fact that after running mris_make_surfaces, it says "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. >> >> jon >> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >> >>> Hi Jon >>> >>> yes, the subject and hemi need to be defined (they are required parameters) >>> Bruce >>> On Wed, 8 May 2013, Jonathan Holt wrote: >>> >>>> Hi all, >>>> combed through the mail archives to figure out how to work with multi echo >>>> mprage, found what I need but I wanted to confirm which of these two >>>> commands is the appropriate >>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >>>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? >>>> jon >>>> >>> >>> >>> 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 >> >> >>
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Hi Jon
you need to run recon-all all the way through, then run the command I sent you with the echoes in the mri dir
cheers Bruce On Thu, 9 May 2013, Jonathan Holt wrote:
No,
I believe my PI simply ran mri_convert on the 4 nii's,
Clearly there is a better approach?
jon On May 9, 2013, at 11:04 AM, Bruce Fischl wrote:
Did you run recon-all? It will create filled.mgz in the subject/mri dir
On May 9, 2013, at 11:00 AM, Jonathan Holt whatsdac@umich.edu wrote:
That was my suspicion, I've got them in the wrong folder. None of them are 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and nothing else.
Also the exact error has it looking in /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz
as opposed to /example/directory/subjects/subjid/mri/filled.mgz
I can rename subject directory if need be.
On May 9, 2013, at 10:54 AM, Bruce Fischl wrote:
is your SUBJECTS_DIR set properly? You need to put the memprage echoes in the subject's mri dir On Thu, 9 May 2013, Jonathan Holt wrote:
Oh, simple mistake!
However, now it spit's an error saying I need filled.mgz?
On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:
it needs to be:
mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
note the "4" which tells it how many echoes to read
On Thu, 9 May 2013, Jonathan Holt wrote:
> I input: > > mris_make_surfaces -dura memprage_echo%d.mgz subjid lh > > it returns: > > detecting dura using 0 echos from memprage_echo%d.mgz > > > Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. > > > On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: > >> can you send me the full command line? It should say 4 echoes, not 0 >> On Thu, 9 May 2013, Jonathan Holt wrote: >> >>> Thanks Bruce, >>> >>> should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? >>> >>> Also, should the fact that after running mris_make_surfaces, it says "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. >>> >>> jon >>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >>> >>>> Hi Jon >>>> >>>> yes, the subject and hemi need to be defined (they are required parameters) >>>> Bruce >>>> On Wed, 8 May 2013, Jonathan Holt wrote: >>>> >>>>> Hi all, >>>>> combed through the mail archives to figure out how to work with multi echo >>>>> mprage, found what I need but I wanted to confirm which of these two >>>>> commands is the appropriate >>>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >>>>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? >>>>> jon >>>>> >>>> >>>> >>>> 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 >>> >>> >>> > > > >
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Jonathan Holt