Hi all,
Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface?
Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file.
Thanks, -Kayle
On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whatsdac@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
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
Hi Kayle
you would run recon-all on the RMS, then run the dura stuff posthoc.
cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote:
Hi all,
Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface?
Also, I'd like to make sure we are using dcmunpack properly. We take the
scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file.
Thanks, -Kayle
On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whatsdac@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
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 >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug
On 5/9/13 6:48 PM, Bruce Fischl wrote:
Hi Kayle
you would run recon-all on the RMS, then run the dura stuff posthoc.
cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote:
Hi all,
Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface?
Also, I'd like to make sure we are using dcmunpack properly. We take the
scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file.
Thanks, -Kayle
On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whatsdac@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
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 >>
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
I've gotten as far as running the mris_make_surfaces on the RMS, but after running for a bit it stopped with this error
mghRead (file/path/s_MEMPRAGE/mri/0010.mgz -1): coult not open file mris_make_surfaces: could not read 0th echo for dura localization from file/path/s_MEMPRAGE/mri/0010.mgz
for reference, the RMS file name is 001.mgz
jon On May 9, 2013, at 8:44 PM, Douglas Greve wrote:
the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug
On 5/9/13 6:48 PM, Bruce Fischl wrote:
Hi Kayle
you would run recon-all on the RMS, then run the dura stuff posthoc.
cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote:
Hi all,
Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface?
Also, I'd like to make sure we are using dcmunpack properly. We take the
scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file.
Thanks, -Kayle
On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whatsdac@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
can you send details about the steps you carried out including full command lines? On Fri, 10 May 2013, Jonathan Holt wrote:
I've gotten as far as running the mris_make_surfaces on the RMS, but after running for a bit it stopped with this error
mghRead (file/path/s_MEMPRAGE/mri/0010.mgz -1): coult not open file mris_make_surfaces: could not read 0th echo for dura localization from file/path/s_MEMPRAGE/mri/0010.mgz
for reference, the RMS file name is 001.mgz
jon On May 9, 2013, at 8:44 PM, Douglas Greve wrote:
the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug
On 5/9/13 6:48 PM, Bruce Fischl wrote:
Hi Kayle
you would run recon-all on the RMS, then run the dura stuff posthoc.
cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote:
Hi all,
Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface?
Also, I'd like to make sure we are using dcmunpack properly. We take the
scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file.
Thanks, -Kayle
On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whatsdac@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
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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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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Hi all,
I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509.
On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/
I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices
Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better!
Thanks, -Kayle
From: Douglas Greve greve@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu
the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug
On 5/9/13 6:48 PM, Bruce Fischl wrote:
Hi Kayle
you would run recon-all on the RMS, then run the dura stuff posthoc.
cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote:
Hi all,
Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface?
Also, I'd like to make sure we are using dcmunpack properly. We take the
scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file.
Thanks, -Kayle
On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whatsdac@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
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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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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.
Hi Kayle
it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look
cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote:
Hi all,
I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509.
On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/
I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices
Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better!
Thanks, -Kayle
From: Douglas Greve greve@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu
the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug
On 5/9/13 6:48 PM, Bruce Fischl wrote:
Hi Kayle
you would run recon-all on the RMS, then run the dura stuff posthoc.
cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote:
Hi all,
Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface?
Also, I'd like to make sure we are using dcmunpack properly. We take the
scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file.
Thanks, -Kayle
On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whatsdac@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
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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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.
Hi all,
last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly:
tkmedit <subjid> brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg
this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around.
best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote:
Hi Kayle
it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look
cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote:
Hi all,
I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509.
On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/
I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices
Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better!
Thanks, -Kayle
From: Douglas Greve greve@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu
the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug
On 5/9/13 6:48 PM, Bruce Fischl wrote:
Hi Kayle
you would run recon-all on the RMS, then run the dura stuff posthoc.
cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote:
Hi all,
Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface?
Also, I'd like to make sure we are using dcmunpack properly. We take the
scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file.
Thanks, -Kayle
On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whatsdac@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
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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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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Hi Jon
there shouldn't be more surfaces I don't think - the ?h.white and ?h.pial should still be the ones you look at Bruce
On Mon, 13 May 2013, Jonathan Holt wrote:
Hi all,
last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly:
tkmedit <subjid> brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg
this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around.
best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote:
Hi Kayle
it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look
cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote:
Hi all,
I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509.
On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/
I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices
Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better!
Thanks, -Kayle
From: Douglas Greve greve@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu
the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug
On 5/9/13 6:48 PM, Bruce Fischl wrote:
Hi Kayle
you would run recon-all on the RMS, then run the dura stuff posthoc.
cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote:
Hi all,
Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface?
Also, I'd like to make sure we are using dcmunpack properly. We take the
scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file.
Thanks, -Kayle
On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whatsdac@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
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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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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Bruce,
how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote:
Hi all,
last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly:
tkmedit <subjid> brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg
this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around.
best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote:
Hi Kayle
it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look
cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote:
Hi all,
I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509.
On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/
I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices
Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better!
Thanks, -Kayle
From: Douglas Greve greve@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu
the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug
On 5/9/13 6:48 PM, Bruce Fischl wrote:
Hi Kayle
you would run recon-all on the RMS, then run the dura stuff posthoc.
cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote:
Hi all,
Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface?
Also, I'd like to make sure we are using dcmunpack properly. We take the
scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file.
Thanks, -Kayle
On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whatsdac@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
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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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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you can use file->aux-surfaces->load aux main surface (or something like that). Or use freeview.
cheers Bruce On Mon, 13 May 2013, Jonathan Holt wrote:
Bruce,
how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote:
Hi all,
last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly:
tkmedit <subjid> brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg
this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around.
best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote:
Hi Kayle
it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look
cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote:
Hi all,
I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509.
On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/
I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices
Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better!
Thanks, -Kayle
From: Douglas Greve greve@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu
the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug
On 5/9/13 6:48 PM, Bruce Fischl wrote:
Hi Kayle
you would run recon-all on the RMS, then run the dura stuff posthoc.
cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote:
Hi all,
Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface?
Also, I'd like to make sure we are using dcmunpack properly. We take the
scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file.
Thanks, -Kayle
On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote: > Message: 35 > Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Working with MEMPRAGE > To: Jonathan Holt whatsdac@umich.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Message-ID: > alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu > Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII > > 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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p.s. make sure that the echoes are in float format, not uchar/int/short (you need to use -odt float in the mri_convert command line) On Mon, 13 May 2013, Bruce Fischl wrote:
you can use file->aux-surfaces->load aux main surface (or something like that). Or use freeview.
cheers Bruce On Mon, 13 May 2013, Jonathan Holt wrote:
Bruce,
how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote:
Hi all,
last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly:
tkmedit <subjid> brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg
this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around.
best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote:
Hi Kayle
it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look
cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote:
Hi all,
I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509.
On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/
I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices
Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better!
Thanks, -Kayle
From: Douglas Greve greve@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu
the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug
On 5/9/13 6:48 PM, Bruce Fischl wrote:
Hi Kayle
you would run recon-all on the RMS, then run the dura stuff posthoc.
cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote:
> Hi all, > > Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? > > Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. > Thanks, > -Kayle > > On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote: >> Message: 35 >> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >> From: Bruce Fischl fischl@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Working with MEMPRAGE >> To: Jonathan Holt whatsdac@umich.edu >> Cc: freesurfer@nmr.mgh.harvard.edu >> Message-ID: >> alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu >> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >> >> 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 >>>>>>> > > _______________________________________________ > 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
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I'll definitely do that next time...
although it didn't seem to pose any noticeable issues this time around?
jon On May 13, 2013, at 3:52 PM, Bruce Fischl wrote:
p.s. make sure that the echoes are in float format, not uchar/int/short (you need to use -odt float in the mri_convert command line) On Mon, 13 May 2013, Bruce Fischl wrote:
you can use file->aux-surfaces->load aux main surface (or something like that). Or use freeview.
cheers Bruce On Mon, 13 May 2013, Jonathan Holt wrote:
Bruce,
how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote:
Hi all,
last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly:
tkmedit <subjid> brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg
this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around.
best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote:
Hi Kayle
it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look
cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote:
Hi all,
I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509.
On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/
I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices
Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better!
Thanks, -Kayle
From: Douglas Greve greve@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu
the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug
On 5/9/13 6:48 PM, Bruce Fischl wrote: > Hi Kayle > > you would run recon-all on the RMS, then run the dura stuff posthoc. > > cheers > Bruce > On Thu, > 9 May 2013, Kayle Sawyer wrote: > >> Hi all, >> >> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? >> >> Also, I'd like to make sure we are using dcmunpack properly. We take the > scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run > number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz > file, and the RMS gets put into a separate mgz file. >> Thanks, >> -Kayle >> >> On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote: >>> Message: 35 >>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>> From: Bruce Fischl fischl@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>> To: Jonathan Holt whatsdac@umich.edu >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: >>> alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu >>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >>> >>> 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 >>>>>>>> >> >> _______________________________________________ >> 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 > >
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I'm surprised it would work well if they are not float. You'll lose a lot of precision On Mon, 13 May 2013, Jonathan Holt wrote:
I'll definitely do that next time...
although it didn't seem to pose any noticeable issues this time around?
jon On May 13, 2013, at 3:52 PM, Bruce Fischl wrote:
p.s. make sure that the echoes are in float format, not uchar/int/short (you need to use -odt float in the mri_convert command line) On Mon, 13 May 2013, Bruce Fischl wrote:
you can use file->aux-surfaces->load aux main surface (or something like that). Or use freeview.
cheers Bruce On Mon, 13 May 2013, Jonathan Holt wrote:
Bruce,
how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote:
Hi all,
last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly:
tkmedit <subjid> brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg
this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around.
best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote:
Hi Kayle
it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look
cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote:
> Hi all, > > I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. > > On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: > /space/ficus/6/users/SNEF_edits/OB01_orig/ > /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ > > I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? > 7 non-cortical segments detected > only using segment with 1900 vertices > > Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! > > Thanks, > -Kayle > > > > > From: Douglas Greve greve@nmr.mgh.harvard.edu > Date: Thu, May 9, 2013 at 8:44 PM > Subject: Re: [Freesurfer] Working with MEMPRAGE > To: freesurfer@nmr.mgh.harvard.edu > > > > the dcmunpack command is right. You should make sure to analyze only the > RMS in recon-all (ie , that is the only volume that goes into mri/orig > doug > > > On 5/9/13 6:48 PM, Bruce Fischl wrote: >> Hi Kayle >> >> you would run recon-all on the RMS, then run the dura stuff posthoc. >> >> cheers >> Bruce >> On Thu, >> 9 May 2013, Kayle Sawyer wrote: >> >>> Hi all, >>> >>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? >>> >>> Also, I'd like to make sure we are using dcmunpack properly. We take the >> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run >> number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz >> file, and the RMS gets put into a separate mgz file. >>> Thanks, >>> -Kayle >>> >>> On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote: >>>> Message: 35 >>>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>>> From: Bruce Fischl fischl@nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>> To: Jonathan Holt whatsdac@umich.edu >>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>> Message-ID: >>>> alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu >>>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >>>> >>>> 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 >>>>>>>>> >>> >>> _______________________________________________ >>> 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 > > > 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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I wont question it, but this is my first multi echo brain and it's the most beautiful i've ever seen. so crisp.
On May 13, 2013, at 3:55 PM, Bruce Fischl wrote:
I'm surprised it would work well if they are not float. You'll lose a lot of precision On Mon, 13 May 2013, Jonathan Holt wrote:
I'll definitely do that next time...
although it didn't seem to pose any noticeable issues this time around?
jon On May 13, 2013, at 3:52 PM, Bruce Fischl wrote:
p.s. make sure that the echoes are in float format, not uchar/int/short (you need to use -odt float in the mri_convert command line) On Mon, 13 May 2013, Bruce Fischl wrote:
you can use file->aux-surfaces->load aux main surface (or something like that). Or use freeview.
cheers Bruce On Mon, 13 May 2013, Jonathan Holt wrote:
Bruce,
how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote:
Hi all,
last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly:
tkmedit <subjid> brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg
this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around.
best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote:
> Hi Kayle > > it's been a long time since I wrote that code and we've only run it a few > times. If you upload your subject directory I'll take a look > > cheers > Bruce > On Sat, 11 May > 2013, Kayle Sawyer wrote: > >> Hi all, >> >> I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. >> >> On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: >> /space/ficus/6/users/SNEF_edits/OB01_orig/ >> /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ >> >> I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? >> 7 non-cortical segments detected >> only using segment with 1900 vertices >> >> Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! >> >> Thanks, >> -Kayle >> >> >> >> >> From: Douglas Greve greve@nmr.mgh.harvard.edu >> Date: Thu, May 9, 2013 at 8:44 PM >> Subject: Re: [Freesurfer] Working with MEMPRAGE >> To: freesurfer@nmr.mgh.harvard.edu >> >> >> >> the dcmunpack command is right. You should make sure to analyze only the >> RMS in recon-all (ie , that is the only volume that goes into mri/orig >> doug >> >> >> On 5/9/13 6:48 PM, Bruce Fischl wrote: >>> Hi Kayle >>> >>> you would run recon-all on the RMS, then run the dura stuff posthoc. >>> >>> cheers >>> Bruce >>> On Thu, >>> 9 May 2013, Kayle Sawyer wrote: >>> >>>> Hi all, >>>> >>>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? >>>> >>>> Also, I'd like to make sure we are using dcmunpack properly. We take the >>> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run >>> number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz >>> file, and the RMS gets put into a separate mgz file. >>>> Thanks, >>>> -Kayle >>>> >>>> On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote: >>>>> Message: 35 >>>>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>>>> From: Bruce Fischl fischl@nmr.mgh.harvard.edu >>>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>>> To: Jonathan Holt whatsdac@umich.edu >>>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>>> Message-ID: >>>>> alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu >>>>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >>>>> >>>>> 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 >>>>>>>>>> >>>> >>>> _______________________________________________ >>>> 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 >> >> >> 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Jonathan, FreeSurfer folks:
Did you have success in combining 4 echoes of MEMPRAGE images into one? I went through the archives and it appears to me that you would use: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh only after the scan has been through the recon all process. My question is did you use mri-concat to combine the 4 echoes into one?
thanks,
Alan
On Mon, May 13, 2013 at 11:26 AM, Jonathan Holt whatsdac@umich.edu wrote:
Bruce,
how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote:
Hi all,
last question promise. Successfully completed mris_make_surfaces for
both hemispheres. in my day-to-day editing I open tkmedit thusly:
tkmedit <subjid> brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz
-surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg
this works for mprage subjects. In evaluating and possibly editing
MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around.
best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote:
Hi Kayle
it's been a long time since I wrote that code and we've only run it a
few
times. If you upload your subject directory I'll take a look
cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote:
Hi all,
I tried to use the 4-echo MEMPRAGE dura detection for
mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509.
On the original recon, in the rh, there is a segment of dura marked as
grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here:
/space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/
I saw this output from mris_make_surfaces for the rh, so maybe -dura
did correct a different defect?
7 non-cortical segments detected only using segment with 1900 vertices
Any help would be appreciated, because we have over 130 brains and the
fewer manual corrections, the better!
Thanks, -Kayle
From: Douglas Greve greve@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu
the dcmunpack command is right. You should make sure to analyze only
the
RMS in recon-all (ie , that is the only volume that goes into mri/orig doug
On 5/9/13 6:48 PM, Bruce Fischl wrote:
Hi Kayle
you would run recon-all on the RMS, then run the dura stuff posthoc.
cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote:
Hi all,
Can the MEMPRAGE be specified in recon-all with the -i flag? We have
been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface?
Also, I'd like to make sure we are using dcmunpack properly. We take
the
scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso
run
number] 3danat mgz 001.mgz" so the multi echo scan gets put into one
mgz
file, and the RMS gets put into a separate mgz file.
Thanks, -Kayle
On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.eduwrote: > Message: 35 > Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Working with MEMPRAGE > To: Jonathan Holt whatsdac@umich.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Message-ID: > alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu > Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII > > 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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Hi Alan
to use the 4 echoes you want to compute the rms. I think something like
mri_average -noconform -sqr mprage_echo?.mgz mprage_rms.mgz
should do the trick (then use mprage_rms.mgz as the input to recon-all)
cheers Bruce
On Mon, 15 Jul 2013, Alan Francis wrote:
Hi Jonathan, FreeSurfer folks:
Did you have success in combining 4 echoes of MEMPRAGE images into one? I went through the archives and it appears to me that you would use: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh only after the scan has been through the recon all process. My question is did you use mri-concat to combine the 4 echoes into one?
thanks,
Alan
On Mon, May 13, 2013 at 11:26 AM, Jonathan Holt whatsdac@umich.edu wrote: Bruce,
how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: > Hi all, > > last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly: > > tkmedit <subjid> brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg > > this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. > > best, > jon > On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: > >> Hi Kayle >> >> it's been a long time since I wrote that code and we've only run it a few >> times. If you upload your subject directory I'll take a look >> >> cheers >> Bruce >> On Sat, 11 May >> 2013, Kayle Sawyer wrote: >> >>> Hi all, >>> >>> I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. >>> >>> On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: >>> /space/ficus/6/users/SNEF_edits/OB01_orig/ >>> /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ >>> >>> I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? >>> 7 non-cortical segments detected >>> only using segment with 1900 vertices >>> >>> Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! >>> >>> Thanks, >>> -Kayle >>> >>> >>> >>> >>> From: Douglas Greve <greve@nmr.mgh.harvard.edu> >>> Date: Thu, May 9, 2013 at 8:44 PM >>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>> To: freesurfer@nmr.mgh.harvard.edu >>> >>> >>> >>> the dcmunpack command is right. You should make sure to analyze only the >>> RMS in recon-all (ie , that is the only volume that goes into mri/orig >>> doug >>> >>> >>> On 5/9/13 6:48 PM, Bruce Fischl wrote: >>>> Hi Kayle >>>> >>>> you would run recon-all on the RMS, then run the dura stuff posthoc. >>>> >>>> cheers >>>> Bruce >>>> On Thu, >>>> 9 May 2013, Kayle Sawyer wrote: >>>> >>>>> Hi all, >>>>> >>>>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? >>>>> >>>>> Also, I'd like to make sure we are using dcmunpack properly. We take the >>>> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run >>>> number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz >>>> file, and the RMS gets put into a separate mgz file. >>>>> Thanks, >>>>> -Kayle >>>>> >>>>> On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote: >>>>>> Message: 35 >>>>>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>>>>> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu> >>>>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>>>> To: Jonathan Holt <whatsdac@umich.edu> >>>>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>>>> Message-ID: >>>>>> <alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu> >>>>>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >>>>>> >>>>>> 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 >>>>>>>>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>> >>> >>> 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 > > > _______________________________________________ > 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
Thanks Bruce.
On Mon, Jul 15, 2013 at 4:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Alan
to use the 4 echoes you want to compute the rms. I think something like
mri_average -noconform -sqr mprage_echo?.mgz mprage_rms.mgz
should do the trick (then use mprage_rms.mgz as the input to recon-all)
cheers Bruce
On Mon, 15 Jul 2013, Alan Francis wrote:
Hi Jonathan, FreeSurfer folks:
Did you have success in combining 4 echoes of MEMPRAGE images into one? I went through the archives and it appears to me that you would use: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh only after the scan has been through the recon all process. My question is did you use mri-concat to combine the 4 echoes into one?
thanks,
Alan
On Mon, May 13, 2013 at 11:26 AM, Jonathan Holt whatsdac@umich.edu wrote: Bruce,
how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: > Hi all, > > last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly: > > tkmedit <subjid> brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.**mgz -surface $SUBJECTS_DIR/subjid/surf/lh.**white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.**white -aparc+aseg > > this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. > > best, > jon > On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: > >> Hi Kayle >> >> it's been a long time since I wrote that code and we've only run it a few >> times. If you upload your subject directory I'll take a look >> >> cheers >> Bruce >> On Sat, 11 May >> 2013, Kayle Sawyer wrote: >> >>> Hi all, >>> >>> I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_**64-stable-v5.3.0-BETA-**20130509. >>> >>> On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: >>> /space/ficus/6/users/SNEF_**edits/OB01_orig/ >>> /space/ficus/6/users/SNEF_**edits/OB01_orig_dura/ >>> >>> I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? >>> 7 non-cortical segments detected >>> only using segment with 1900 vertices >>> >>> Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! >>> >>> Thanks, >>> -Kayle >>> >>> >>> >>> >>> From: Douglas Greve <greve@nmr.mgh.harvard.edu> >>> Date: Thu, May 9, 2013 at 8:44 PM >>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>> To: freesurfer@nmr.mgh.harvard.edu >>> >>> >>> >>> the dcmunpack command is right. You should make sure to analyze only the >>> RMS in recon-all (ie , that is the only volume that goes into mri/orig >>> doug >>> >>> >>> On 5/9/13 6:48 PM, Bruce Fischl wrote: >>>> Hi Kayle >>>> >>>> you would run recon-all on the RMS, then run the dura stuff posthoc. >>>> >>>> cheers >>>> Bruce >>>> On Thu, >>>> 9 May 2013, Kayle Sawyer wrote: >>>> >>>>> Hi all, >>>>> >>>>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? >>>>> >>>>> Also, I'd like to make sure we are using dcmunpack properly. We take the >>>> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run >>>> number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz >>>> file, and the RMS gets put into a separate mgz file. >>>>> Thanks, >>>>> -Kayle >>>>> >>>>> On May 9, 2013, at 12:00 PM, freesurfer-request@nmr.mgh.**harvard.edu<freesurfer-request@nmr.mgh.harvard.edu>wrote: >>>>>> Message: 35 >>>>>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>>>>> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu> >>>>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>>>> To: Jonathan Holt <whatsdac@umich.edu> >>>>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>>>> Message-ID: >>>>>> <alpine.LRH.2.02.**1305091043500.13418@gate.nmr.**mgh.harvard.edu<alpine.LRH.2.02.1305091043500.13418@gate.nmr.mgh.harvard.edu>>>>>>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >>>>>> >>>>>> 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 >>>>>>>>>>> >>>>> >>>>> ______________________________**_________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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 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. 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Jonathan Holt -
Kayle Sawyer