Dear all, I need to compute the geodesic distance (i.,e. the distance on the cortical surface) between a series of vertices. Specifically, I want to compute the distance between all the vertices in the right hemisphere (>100000) and a series of vertices of interest (around 20000), always located in the right hemisphere. Ideally, my output should be a matrix right_verticesXvertices_of_interest where in each entry there is the geodesic distance between the pair of vertices. And I need to do this for hundreds of subjects! I tried to use mris_pmake: for i = right_vertices; for j=vertices_of_interest; command1 = ['/Applications/freesurfer_v5.3/bin/mris_pmake --subject 001 --hemi rh --surface0 white --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:' num2str(i) ',' 'endVertex:' num2str(j)] T(i)=evalc('system([command1])') end end But the problem is that it is way too much time consuming and it is difficult to store the results in a matrix. Is there a way to adapt this command for such high computations? I Are there other ways to obtain the geodesic distance between vertices, either than mris_pmake (for example a matlab function)? Thank you in advance,Marica
Hi Bruce, I have done the recon-all (fs5.3) with the data collected from a 7T scanner using MP2Rage. The recon went well without problem. But the the temporal reconstruction looks clearly not correct (see attached). I tried to push the pial surface outside by editing the white matter evidenced in the attached figures, but has no effect to genera correct pial surface. I do realize that the contrast is low in the anterior temporal lobes. However, I am wondering if there are expert parameters I can use to push the pial surface into the right place. If that isn't a option, can I use some other images collected during the MP2rage scan to help the segmentation in the anterior temporal lobe? Those extract scans are: inv1_nd, inv1_phs_nd, , t1, inv2_nd, invs_phas_nd, thanks very much. Xiaomin
Hi Xiaomin
it's really hard to say without seeing more detail in your images. Do you have contrast in the temporal lobe? Frequently it goes away at 7T due to dielectric effects. I'll cc Jon Polimeni who is our 7T (among other things!) expert.
cheers Bruce
On Fri, 15 Apr 2016, Xiaomin Yue wrote:
Hi Bruce, I have done the recon-all (fs5.3) with the data collected from a 7T scanner using MP2Rage. The recon went well without problem. But the the temporal reconstruction looks clearly not correct (see attached). I tried to push the pial surface outside by editing the white matter evidenced in the attached figures, but has no effect to genera correct pial surface. I do realize that the contrast is low in the anterior temporal lobes. However, I am wondering if there are expert parameters I can use to push the pial surface into the right place. If that isn't a option, can I use some other images collected during the MP2rage scan to help the segmentation in the anterior temporal lobe? Those extract scans are: inv1_nd, inv1_phs_nd, , t1, inv2_nd, invs_phas_nd,
thanks very much.
Xiaomin
Thanks for your response. I do have contrast at the temporal lobe. I can upload the images to your file drop site if you want.
Xiaomin
On Fri, Apr 15, 2016 at 9:08 AM -0700, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Xiaomin
it's really hard to say without seeing more detail in your images. Do you have contrast in the temporal lobe? Frequently it goes away at 7T due to dielectric effects. I'll cc Jon Polimeni who is our 7T (among other things!) expert.
cheers Bruce
On Fri, 15 Apr 2016, Xiaomin Yue wrote:
Hi Bruce, I have done the recon-all (fs5.3) with the data collected from a 7T scanner using MP2Rage. The recon went well without problem. But the the temporal reconstruction looks clearly not correct (see attached). I tried to push the pial surface outside by editing the white matter evidenced in the attached figures, but has no effect to genera correct pial surface. I do realize that the contrast is low in the anterior temporal lobes. However, I am wondering if there are expert parameters I can use to push the pial surface into the right place. If that isn't a option, can I use some other images collected during the MP2rage scan to help the segmentation in the anterior temporal lobe? Those extract scans are: inv1_nd, inv1_phs_nd, , t1, inv2_nd, invs_phas_nd,
thanks very much.
Xiaomin
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Hi Jon Polimeni, Do you have any suggestions on the following questions? Thanks,Xiaomin
Date: Fri, 15 Apr 2016 12:07:48 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: macara.p@libero.it; jonp@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] temporal lobe pial surface problem
Hi Xiaomin
it's really hard to say without seeing more detail in your images. Do you have contrast in the temporal lobe? Frequently it goes away at 7T due to dielectric effects. I'll cc Jon Polimeni who is our 7T (among other things!) expert.
cheers Bruce
On Fri, 15 Apr 2016, Xiaomin Yue wrote:
Hi Bruce, I have done the recon-all (fs5.3) with the data collected from a 7T scanner using MP2Rage. The recon went well without problem. But the the temporal reconstruction looks clearly not correct (see attached). I tried to push the pial surface outside by editing the white matter evidenced in the attached figures, but has no effect to genera correct pial surface. I do realize that the contrast is low in the anterior temporal lobes. However, I am wondering if there are expert parameters I can use to push the pial surface into the right place. If that isn't a option, can I use some other images collected during the MP2rage scan to help the segmentation in the anterior temporal lobe? Those extract scans are: inv1_nd, inv1_phs_nd, , t1, inv2_nd, invs_phas_nd,
thanks very much.
Xiaomin
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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 Xiaomin,
it is tough to say what might be causing the problem since a lot can go wrong in the anterior temporal lobes at 7T. you say that your contrast is low there? it is possible to have OK gray-white contrast but low overall signal levels (so poor gray-CSF contrast) due to dielectric effects as bruce mentioned, which can make the MP2RAGE ratio images noisy in that region. also some adiabatic inversion pulses break down around the temporal poles due to the B0 inhomogeneity around the ear canals. if you could send a screenshot we'd have a better chance at diagnosing the problem.
-jon
On Mon, 18 Apr 2016, Xiaomin Yue wrote:
Hi Jon Polimeni, Do you have any suggestions on the following questions? Thanks,Xiaomin
Date: Fri, 15 Apr 2016 12:07:48 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: macara.p@libero.it; jonp@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] temporal lobe pial surface problem
Hi Xiaomin
it's really hard to say without seeing more detail in your images. Do you have contrast in the temporal lobe? Frequently it goes away at 7T due to dielectric effects. I'll cc Jon Polimeni who is our 7T (among other things!) expert.
cheers Bruce
On Fri, 15 Apr 2016, Xiaomin Yue wrote:
Hi Bruce, I have done the recon-all (fs5.3) with the data collected from a 7T scanner using MP2Rage. The recon went well without problem. But the the temporal reconstruction looks clearly not correct (see attached). I tried to push the pial surface outside by editing the white matter evidenced in the attached figures, but has no effect to genera correct pial surface. I do realize that the contrast is low in the anterior temporal lobes. However, I am wondering if there are expert parameters I can use to push the pial surface into the right place. If that isn't a option, can I use some other images collected during the MP2rage scan to help the segmentation in the anterior temporal lobe? Those extract scans are: inv1_nd, inv1_phs_nd, , t1, inv2_nd, invs_phas_nd,
thanks very much.
Xiaomin
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 Jon, Thanks for your answers. There is gray-white contrast in the temporal lobe, but same as you said that the gray-csf is low. Attached is a screenshot. let's me know if you need more information. Xiaomin
Date: Mon, 18 Apr 2016 17:43:47 -0400 From: jonp@nmr.mgh.harvard.edu To: yuexm@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; macara.p@libero.it Subject: Re: [Freesurfer] temporal lobe pial surface problem
hi Xiaomin,
it is tough to say what might be causing the problem since a lot can go wrong in the anterior temporal lobes at 7T. you say that your contrast is low there? it is possible to have OK gray-white contrast but low overall signal levels (so poor gray-CSF contrast) due to dielectric effects as bruce mentioned, which can make the MP2RAGE ratio images noisy in that region. also some adiabatic inversion pulses break down around the temporal poles due to the B0 inhomogeneity around the ear canals. if you could send a screenshot we'd have a better chance at diagnosing the problem.
-jon
On Mon, 18 Apr 2016, Xiaomin Yue wrote:
Hi Jon Polimeni, Do you have any suggestions on the following questions? Thanks,Xiaomin
Date: Fri, 15 Apr 2016 12:07:48 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: macara.p@libero.it; jonp@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] temporal lobe pial surface problem
Hi Xiaomin
it's really hard to say without seeing more detail in your images. Do you have contrast in the temporal lobe? Frequently it goes away at 7T due to dielectric effects. I'll cc Jon Polimeni who is our 7T (among other things!) expert.
cheers Bruce
On Fri, 15 Apr 2016, Xiaomin Yue wrote:
Hi Bruce, I have done the recon-all (fs5.3) with the data collected from a 7T scanner using MP2Rage. The recon went well without problem. But the the temporal reconstruction looks clearly not correct (see attached). I tried to push the pial surface outside by editing the white matter evidenced in the attached figures, but has no effect to genera correct pial surface. I do realize that the contrast is low in the anterior temporal lobes. However, I am wondering if there are expert parameters I can use to push the pial surface into the right place. If that isn't a option, can I use some other images collected during the MP2rage scan to help the segmentation in the anterior temporal lobe? Those extract scans are: inv1_nd, inv1_phs_nd, , t1, inv2_nd, invs_phas_nd,
thanks very much.
Xiaomin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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It's tough to make out much from the snapshots, if you upload the entire subject dir to our ftp site I'll take a look Cheers Bruce
On Apr 18, 2016, at 7:13 PM, Xiaomin Yue yuexm@hotmail.com wrote:
Hi Jon,
Thanks for your answers. There is gray-white contrast in the temporal lobe, but same as you said that the gray-csf is low. Attached is a screenshot. let's me know if you need more information.
Xiaomin
Date: Mon, 18 Apr 2016 17:43:47 -0400 From: jonp@nmr.mgh.harvard.edu To: yuexm@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; macara.p@libero.it Subject: Re: [Freesurfer] temporal lobe pial surface problem
hi Xiaomin,
it is tough to say what might be causing the problem since a lot can go wrong in the anterior temporal lobes at 7T. you say that your contrast is low there? it is possible to have OK gray-white contrast but low overall signal levels (so poor gray-CSF contrast) due to dielectric effects as bruce mentioned, which can make the MP2RAGE ratio images noisy in that region. also some adiabatic inversion pulses break down around the temporal poles due to the B0 inhomogeneity around the ear canals. if you could send a screenshot we'd have a better chance at diagnosing the problem.
-jon
On Mon, 18 Apr 2016, Xiaomin Yue wrote:
Hi Jon Polimeni, Do you have any suggestions on the following questions? Thanks,Xiaomin
Date: Fri, 15 Apr 2016 12:07:48 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: macara.p@libero.it; jonp@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] temporal lobe pial surface problem
Hi Xiaomin
it's really hard to say without seeing more detail in your images. Do you have contrast in the temporal lobe? Frequently it goes away at 7T due to dielectric effects. I'll cc Jon Polimeni who is our 7T (among other things!) expert.
cheers Bruce
On Fri, 15 Apr 2016, Xiaomin Yue wrote:
Hi Bruce, I have done the recon-all (fs5.3) with the data collected from a 7T scanner using MP2Rage. The recon went well without problem. But the the temporal reconstruction looks clearly not correct (see attached). I tried to push the pial surface outside by editing the white matter evidenced in the attached figures, but has no effect to genera correct pial surface. I do realize that the contrast is low in the anterior temporal lobes. However, I am wondering if there are expert parameters I can use to push the pial surface into the right place. If that isn't a option, can I use some other images collected during the MP2rage scan to help the segmentation in the anterior temporal lobe? Those extract scans are: inv1_nd, inv1_phs_nd, , t1, inv2_nd, invs_phas_nd,
thanks very much.
Xiaomin
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
<temporalLoba-small.tif> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce, the data was uploaded to the ftp site. The file name is xyueSubj.mgz. thanks,Xiaomin
From: fischl@nmr.mgh.harvard.edu Date: Mon, 18 Apr 2016 22:58:30 -0400 To: freesurfer@nmr.mgh.harvard.edu CC: macara.p@libero.it Subject: Re: [Freesurfer] temporal lobe pial surface problem
It's tough to make out much from the snapshots, if you upload the entire subject dir to our ftp site I'll take a lookCheersBruce On Apr 18, 2016, at 7:13 PM, Xiaomin Yue yuexm@hotmail.com wrote:
Hi Jon, Thanks for your answers. There is gray-white contrast in the temporal lobe, but same as you said that the gray-csf is low. Attached is a screenshot. let's me know if you need more information. Xiaomin
Date: Mon, 18 Apr 2016 17:43:47 -0400 From: jonp@nmr.mgh.harvard.edu To: yuexm@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; macara.p@libero.it Subject: Re: [Freesurfer] temporal lobe pial surface problem
hi Xiaomin,
it is tough to say what might be causing the problem since a lot can go wrong in the anterior temporal lobes at 7T. you say that your contrast is low there? it is possible to have OK gray-white contrast but low overall signal levels (so poor gray-CSF contrast) due to dielectric effects as bruce mentioned, which can make the MP2RAGE ratio images noisy in that region. also some adiabatic inversion pulses break down around the temporal poles due to the B0 inhomogeneity around the ear canals. if you could send a screenshot we'd have a better chance at diagnosing the problem.
-jon
On Mon, 18 Apr 2016, Xiaomin Yue wrote:
Hi Jon Polimeni, Do you have any suggestions on the following questions? Thanks,Xiaomin
Date: Fri, 15 Apr 2016 12:07:48 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: macara.p@libero.it; jonp@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] temporal lobe pial surface problem
Hi Xiaomin
it's really hard to say without seeing more detail in your images. Do you have contrast in the temporal lobe? Frequently it goes away at 7T due to dielectric effects. I'll cc Jon Polimeni who is our 7T (among other things!) expert.
cheers Bruce
On Fri, 15 Apr 2016, Xiaomin Yue wrote:
Hi Bruce, I have done the recon-all (fs5.3) with the data collected from a 7T scanner using MP2Rage. The recon went well without problem. But the the temporal reconstruction looks clearly not correct (see attached). I tried to push the pial surface outside by editing the white matter evidenced in the attached figures, but has no effect to genera correct pial surface. I do realize that the contrast is low in the anterior temporal lobes. However, I am wondering if there are expert parameters I can use to push the pial surface into the right place. If that isn't a option, can I use some other images collected during the MP2rage scan to help the segmentation in the anterior temporal lobe? Those extract scans are: inv1_nd, inv1_phs_nd, , t1, inv2_nd, invs_phas_nd,
thanks very much.
Xiaomin
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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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<temporalLoba-small.tif>_______________________________________________ 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.
Hi Xiaomin,
currently I don't have access to my notes, however, if I remember correctly, you can specify thresholds in mris_make_surfaces for consideration in the surface placement. This obviously works well only if the contrast between WM/GM/CSF is high enough.
If you are interested and nobody jumps in giving you the according flags, let me know.
Best, Falk
________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Xiaomin Yue [yuexm@hotmail.com] Gesendet: Dienstag, 19. April 2016 01:13 An: Freesurfer support list Cc: macara.p@libero.it Betreff: Re: [Freesurfer] temporal lobe pial surface problem
Hi Jon,
Thanks for your answers. There is gray-white contrast in the temporal lobe, but same as you said that the gray-csf is low. Attached is a screenshot. let's me know if you need more information.
Xiaomin
Date: Mon, 18 Apr 2016 17:43:47 -0400 From: jonp@nmr.mgh.harvard.edu To: yuexm@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; macara.p@libero.it Subject: Re: [Freesurfer] temporal lobe pial surface problem
hi Xiaomin,
it is tough to say what might be causing the problem since a lot can go wrong in the anterior temporal lobes at 7T. you say that your contrast is low there? it is possible to have OK gray-white contrast but low overall signal levels (so poor gray-CSF contrast) due to dielectric effects as bruce mentioned, which can make the MP2RAGE ratio images noisy in that region. also some adiabatic inversion pulses break down around the temporal poles due to the B0 inhomogeneity around the ear canals. if you could send a screenshot we'd have a better chance at diagnosing the problem.
-jon
On Mon, 18 Apr 2016, Xiaomin Yue wrote:
Hi Jon Polimeni, Do you have any suggestions on the following questions? Thanks,Xiaomin
Date: Fri, 15 Apr 2016 12:07:48 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: macara.p@libero.it; jonp@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] temporal lobe pial surface problem
Hi Xiaomin
it's really hard to say without seeing more detail in your images. Do you have contrast in the temporal lobe? Frequently it goes away at 7T due to dielectric effects. I'll cc Jon Polimeni who is our 7T (among other things!) expert.
cheers Bruce
On Fri, 15 Apr 2016, Xiaomin Yue wrote:
Hi Bruce, I have done the recon-all (fs5.3) with the data collected from a 7T scanner using MP2Rage. The recon went well without problem. But the the temporal reconstruction looks clearly not correct (see attached). I tried to push the pial surface outside by editing the white matter evidenced in the attached figures, but has no effect to genera correct pial surface. I do realize that the contrast is low in the anterior temporal lobes. However, I am wondering if there are expert parameters I can use to push the pial surface into the right place. If that isn't a option, can I use some other images collected during the MP2rage scan to help the segmentation in the anterior temporal lobe? Those extract scans are: inv1_nd, inv1_phs_nd, , t1, inv2_nd, invs_phas_nd,
thanks very much.
Xiaomin
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yes, you can do that for both mris_make_surfaces and mri_segment, but that will only help if you've removed the majority of the bias field. Is anterior temporal white matter near 110? If so, what is the gray matter at? On Tue, 19 Apr 2016, Falk Lüsebrink wrote:
Hi Xiaomin, currently I don't have access to my notes, however, if I remember correctly, you can specify thresholds in mris_make_surfaces for consideration in the surface placement. This obviously works well only if the contrast between WM/GM/CSF is high enough.
If you are interested and nobody jumps in giving you the according flags, let me know.
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Xiaomin Yue [yuexm@hotmail.com] Gesendet: Dienstag, 19. April 2016 01:13 An: Freesurfer support list Cc: macara.p@libero.it Betreff: Re: [Freesurfer] temporal lobe pial surface problem
Hi Jon, Thanks for your answers. There is gray-white contrast in the temporal lobe, but same as you said that the gray-csf is low. Attached is a screenshot. let's me know if you need more information.
Xiaomin
Date: Mon, 18 Apr 2016 17:43:47 -0400 From: jonp@nmr.mgh.harvard.edu To: yuexm@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; macara.p@libero.it Subject: Re: [Freesurfer] temporal lobe pial surface problem
hi Xiaomin,
it is tough to say what might be causing the problem since a lot can go wrong in the anterior temporal lobes at 7T. you say that your contrast is low there? it is possible to have OK gray-white contrast but low overall signal levels (so poor gray-CSF contrast) due to dielectric effects as bruce mentioned, which can make the MP2RAGE ratio images noisy in that region. also some adiabatic inversion pulses break down around the temporal poles due to the B0 inhomogeneity around the ear canals. if you could send a screenshot we'd have a better chance at diagnosing the problem.
-jon
On Mon, 18 Apr 2016, Xiaomin Yue wrote:
Hi Jon Polimeni, Do you have any suggestions on the following questions? Thanks,Xiaomin
Date: Fri, 15 Apr 2016 12:07:48 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: macara.p@libero.it; jonp@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] temporal lobe pial surface problem
Hi Xiaomin
it's really hard to say without seeing more detail in your images. Do
you
have contrast in the temporal lobe? Frequently it goes away at 7T due to dielectric effects. I'll cc Jon Polimeni who is our 7T (among other things!) expert.
cheers Bruce
On Fri, 15 Apr 2016, Xiaomin Yue wrote:
Hi Bruce, I have done the recon-all (fs5.3) with the data collected from a 7T
scanner
using MP2Rage. The recon went well without problem. But the the
temporal
reconstruction looks clearly not correct (see attached). I tried to
push
the pial surface outside by editing the white matter evidenced in the attached figures, but has no effect to genera correct pial surface. I
do
realize that the contrast is low in the anterior temporal lobes.
However, I
am wondering if there are expert parameters I can use to push the pial surface into the right place. If that isn't a option, can I use some
other
images collected during the MP2rage scan to help the segmentation in
the
anterior temporal lobe? Those extract scans are: inv1_nd, inv1_phs_nd,
,
t1, inv2_nd, invs_phas_nd,
thanks very much.
Xiaomin
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
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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The white matter in the anterior temporal lobe is around 70, the gray matter is about 30. The number is read from brain.finalsurfs.mgz. Xiaomin
Date: Tue, 19 Apr 2016 09:29:50 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: macara.p@libero.it; yuexm@hotmail.com Subject: Re: [Freesurfer] temporal lobe pial surface problem
yes, you can do that for both mris_make_surfaces and mri_segment, but that will only help if you've removed the majority of the bias field. Is anterior temporal white matter near 110? If so, what is the gray matter at? On Tue, 19 Apr 2016, Falk Lüsebrink wrote:
Hi Xiaomin, currently I don't have access to my notes, however, if I remember correctly, you can specify thresholds in mris_make_surfaces for consideration in the surface placement. This obviously works well only if the contrast between WM/GM/CSF is high enough.
If you are interested and nobody jumps in giving you the according flags, let me know.
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Xiaomin Yue [yuexm@hotmail.com] Gesendet: Dienstag, 19. April 2016 01:13 An: Freesurfer support list Cc: macara.p@libero.it Betreff: Re: [Freesurfer] temporal lobe pial surface problem
Hi Jon, Thanks for your answers. There is gray-white contrast in the temporal lobe, but same as you said that the gray-csf is low. Attached is a screenshot. let's me know if you need more information.
Xiaomin
Date: Mon, 18 Apr 2016 17:43:47 -0400 From: jonp@nmr.mgh.harvard.edu To: yuexm@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; macara.p@libero.it Subject: Re: [Freesurfer] temporal lobe pial surface problem
hi Xiaomin,
it is tough to say what might be causing the problem since a lot can go wrong in the anterior temporal lobes at 7T. you say that your contrast is low there? it is possible to have OK gray-white contrast but low overall signal levels (so poor gray-CSF contrast) due to dielectric effects as bruce mentioned, which can make the MP2RAGE ratio images noisy in that region. also some adiabatic inversion pulses break down around the temporal poles due to the B0 inhomogeneity around the ear canals. if you could send a screenshot we'd have a better chance at diagnosing the problem.
-jon
On Mon, 18 Apr 2016, Xiaomin Yue wrote:
Hi Jon Polimeni, Do you have any suggestions on the following questions? Thanks,Xiaomin
Date: Fri, 15 Apr 2016 12:07:48 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: macara.p@libero.it; jonp@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] temporal lobe pial surface problem
Hi Xiaomin
it's really hard to say without seeing more detail in your images. Do
you
have contrast in the temporal lobe? Frequently it goes away at 7T due to dielectric effects. I'll cc Jon Polimeni who is our 7T (among other things!) expert.
cheers Bruce
On Fri, 15 Apr 2016, Xiaomin Yue wrote:
Hi Bruce, I have done the recon-all (fs5.3) with the data collected from a 7T
scanner
using MP2Rage. The recon went well without problem. But the the
temporal
reconstruction looks clearly not correct (see attached). I tried to
push
the pial surface outside by editing the white matter evidenced in the attached figures, but has no effect to genera correct pial surface. I
do
realize that the contrast is low in the anterior temporal lobes.
However, I
am wondering if there are expert parameters I can use to push the pial surface into the right place. If that isn't a option, can I use some
other
images collected during the MP2rage scan to help the segmentation in
the
anterior temporal lobe? Those extract scans are: inv1_nd, inv1_phs_nd,
,
t1, inv2_nd, invs_phas_nd,
thanks very much.
Xiaomin
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then you need to put some control points in the white matter. 70 is way too low On Tue, 19 Apr 2016, Xiaomin Yue wrote:
The white matter in the anterior temporal lobe is around 70, the gray matter is about 30. The number is read from brain.finalsurfs.mgz. Xiaomin
Date: Tue, 19 Apr 2016 09:29:50 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: macara.p@libero.it; yuexm@hotmail.com Subject: Re: [Freesurfer] temporal lobe pial surface problem
yes, you can do that for both mris_make_surfaces and mri_segment, but that will only help if you've removed the majority of the bias field. Is anterior temporal white matter near 110? If so, what is the gray matter at? On Tue, 19 Apr 2016, Falk Lüsebrink wrote:
Hi Xiaomin, currently I don't have access to my notes, however, if I remember
correctly,
you can specify thresholds in mris_make_surfaces for consideration in
the
surface placement. This obviously works well only if the contrast
between
WM/GM/CSF is high enough.
If you are interested and nobody jumps in giving you the according
flags,
let me know.
Best, Falk
_
Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Xiaomin Yue [yuexm@hotmail.com] Gesendet: Dienstag, 19. April 2016 01:13 An: Freesurfer support list Cc: macara.p@libero.it Betreff: Re: [Freesurfer] temporal lobe pial surface problem
Hi Jon, Thanks for your answers. There is gray-white contrast in the temporal lobe, but same as you said that the gray-csf is low. Attached is a screenshot. let's me know if you need more information.
Xiaomin
Date: Mon, 18 Apr 2016 17:43:47 -0400 From: jonp@nmr.mgh.harvard.edu To: yuexm@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; macara.p@libero.it Subject: Re: [Freesurfer] temporal lobe pial surface problem
hi Xiaomin,
it is tough to say what might be causing the problem since a lot can
go
wrong in the anterior temporal lobes at 7T. you say that your contrast
is
low there? it is possible to have OK gray-white contrast but low
overall
signal levels (so poor gray-CSF contrast) due to dielectric effects as bruce mentioned, which can make the MP2RAGE ratio images noisy in that region. also some adiabatic inversion pulses break down around the temporal poles due to the B0 inhomogeneity around the ear canals. if
you
could send a screenshot we'd have a better chance at diagnosing the problem.
-jon
On Mon, 18 Apr 2016, Xiaomin Yue wrote:
Hi Jon Polimeni, Do you have any suggestions on the following questions? Thanks,Xiaomin
Date: Fri, 15 Apr 2016 12:07:48 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: macara.p@libero.it; jonp@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] temporal lobe pial surface problem
Hi Xiaomin
it's really hard to say without seeing more detail in your images.
Do
you
have contrast in the temporal lobe? Frequently it goes away at 7T
due to
dielectric effects. I'll cc Jon Polimeni who is our 7T (among other things!) expert.
cheers Bruce
On Fri, 15 Apr 2016, Xiaomin Yue wrote:
Hi Bruce, I have done the recon-all (fs5.3) with the data collected from a
7T
scanner
using MP2Rage. The recon went well without problem. But the the
temporal
reconstruction looks clearly not correct (see attached). I tried
to
push
the pial surface outside by editing the white matter evidenced in
the
attached figures, but has no effect to genera correct pial
surface. I
do
realize that the contrast is low in the anterior temporal lobes.
However, I
am wondering if there are expert parameters I can use to push the
pial
surface into the right place. If that isn't a option, can I use
some
other
images collected during the MP2rage scan to help the segmentation
in
the
anterior temporal lobe? Those extract scans are: inv1_nd,
inv1_phs_nd,
,
t1, inv2_nd, invs_phas_nd,
thanks very much.
Xiaomin
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
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
OK. I will do it. Xiaomin
Date: Tue, 19 Apr 2016 10:56:15 -0400 From: fischl@nmr.mgh.harvard.edu To: yuexm@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; macara.p@libero.it Subject: Re: [Freesurfer] temporal lobe pial surface problem
then you need to put some control points in the white matter. 70 is way too low On Tue, 19 Apr 2016, Xiaomin Yue wrote:
The white matter in the anterior temporal lobe is around 70, the gray matter is about 30. The number is read from brain.finalsurfs.mgz. Xiaomin
Date: Tue, 19 Apr 2016 09:29:50 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: macara.p@libero.it; yuexm@hotmail.com Subject: Re: [Freesurfer] temporal lobe pial surface problem
yes, you can do that for both mris_make_surfaces and mri_segment, but that will only help if you've removed the majority of the bias field. Is anterior temporal white matter near 110? If so, what is the gray matter at? On Tue, 19 Apr 2016, Falk Lüsebrink wrote:
Hi Xiaomin, currently I don't have access to my notes, however, if I remember
correctly,
you can specify thresholds in mris_make_surfaces for consideration in
the
surface placement. This obviously works well only if the contrast
between
WM/GM/CSF is high enough.
If you are interested and nobody jumps in giving you the according
flags,
let me know.
Best, Falk
_
Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Xiaomin Yue [yuexm@hotmail.com] Gesendet: Dienstag, 19. April 2016 01:13 An: Freesurfer support list Cc: macara.p@libero.it Betreff: Re: [Freesurfer] temporal lobe pial surface problem
Hi Jon, Thanks for your answers. There is gray-white contrast in the temporal lobe, but same as you said that the gray-csf is low. Attached is a screenshot. let's me know if you need more information.
Xiaomin
Date: Mon, 18 Apr 2016 17:43:47 -0400 From: jonp@nmr.mgh.harvard.edu To: yuexm@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; macara.p@libero.it Subject: Re: [Freesurfer] temporal lobe pial surface problem
hi Xiaomin,
it is tough to say what might be causing the problem since a lot can
go
wrong in the anterior temporal lobes at 7T. you say that your contrast
is
low there? it is possible to have OK gray-white contrast but low
overall
signal levels (so poor gray-CSF contrast) due to dielectric effects as bruce mentioned, which can make the MP2RAGE ratio images noisy in that region. also some adiabatic inversion pulses break down around the temporal poles due to the B0 inhomogeneity around the ear canals. if
you
could send a screenshot we'd have a better chance at diagnosing the problem.
-jon
On Mon, 18 Apr 2016, Xiaomin Yue wrote:
Hi Jon Polimeni, Do you have any suggestions on the following questions? Thanks,Xiaomin
Date: Fri, 15 Apr 2016 12:07:48 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: macara.p@libero.it; jonp@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] temporal lobe pial surface problem
Hi Xiaomin
it's really hard to say without seeing more detail in your images.
Do
you
have contrast in the temporal lobe? Frequently it goes away at 7T
due to
dielectric effects. I'll cc Jon Polimeni who is our 7T (among other things!) expert.
cheers Bruce
On Fri, 15 Apr 2016, Xiaomin Yue wrote:
Hi Bruce, I have done the recon-all (fs5.3) with the data collected from a
7T
scanner
using MP2Rage. The recon went well without problem. But the the
temporal
reconstruction looks clearly not correct (see attached). I tried
to
push
the pial surface outside by editing the white matter evidenced in
the
attached figures, but has no effect to genera correct pial
surface. I
do
realize that the contrast is low in the anterior temporal lobes.
However, I
am wondering if there are expert parameters I can use to push the
pial
surface into the right place. If that isn't a option, can I use
some
other
images collected during the MP2rage scan to help the segmentation
in
the
anterior temporal lobe? Those extract scans are: inv1_nd,
inv1_phs_nd,
,
t1, inv2_nd, invs_phas_nd,
thanks very much.
Xiaomin
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
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
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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Falk Lüsebrink -
Jonathan Polimeni -
macara.p＠libero.it -
Xiaomin Yue