Dear freesurfer experts,
Does adding an oblique angle during coronal or axial acquisitions of T1w images lead to topographical errors during mri_fix_topology process?
Thanks and regards,
Sampada
what do you mean by "adding" an oblique angle? If you mean acquiring the data obliquely you should be fine as long as the voxels are close to 1mm isotropic.
cheers Bruce On Sun, 20 Mar 2016, Dr Sampada Sinha wrote:
Dear freesurfer experts, Does adding an oblique angle during coronal or axial acquisitions of T1w images lead to topographical errors during mri_fix_topology process?
Thanks and regards,
Sampada
-- Sampada Sinha
Thanks Bruce for your reply. The acquisition was oblique and the voxel size doesn't conform to the 1mm cube isotropic. I am trying to work on it and figure out a solution. However, if I am not, hope its okay to send you the nifti image.
Thanks and regards,
Sampada
Rnday, March 20, 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what do you mean by "adding" an oblique angle? If you mean acquiring the data obliquely you should be fine as long as the voxels are close to 1mm isotropic.
cheers Bruce On Sun, 20 Mar 2016, Dr Sampada Sinha wrote:
Dear freesurfer experts, Does adding an oblique angle during coronal or axial acquisitions of T1w images lead to topographical errors during mri_fix_topology process?
Thanks and regards,
Sampada
-- Sampada Sinha
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; 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.
sure. Have you tried running it through recon-all? It may work fine.... On Tue, 22 Mar 2016, Dr Sampada Sinha wrote:
Thanks Bruce for your reply. The acquisition was oblique and the voxel size doesn't conform to the 1mm cube isotropic. I am trying to work on it and figure out a solution. However, if I am not, hope its okay to send you the nifti image. Thanks and regards,
Sampada
Rnday, March 20, 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: what do you mean by "adding" an oblique angle? If you mean acquiring the data obliquely you should be fine as long as the voxels are close to 1mm isotropic.
cheers Bruce On Sun, 20 Mar 2016, Dr Sampada Sinha wrote: > Dear freesurfer experts, > Does adding an oblique angle during coronal or axial acquisitions of T1w > images lead to topographical errors during mri_fix_topology process? > > Thanks and regards, > > Sampada > > > > -- > Sampada Sinha > > > > > > > > > > > > _______________________________________________ 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.-- Sampada Sinha
Thanks Bruce for your reply. I did run it thru' recon-all. It went for more than 2 days and then exited with XL defect error (convex hull was more than 14000 and vertex size about 54000). So today I started by running the recon-all in parts. I did not find anything wrong with brainmask files after running autorecon1. I am presently running the autorecon-2 process. Will get back with the surf files when this process is over.
Thank you again for your reply and support.
Kind regards,
Sampada
On Tuesday, March 22, 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
sure. Have you tried running it through recon-all? It may work fine.... On Tue, 22 Mar 2016, Dr Sampada Sinha wrote:
Thanks Bruce for your reply. The acquisition was oblique and the voxel
size doesn't
conform to the 1mm cube isotropic. I am trying to work on it and figure
out a
solution. However, if I am not, hope its okay to send you the nifti
image.
Thanks and regards,
Sampada
Rnday, March 20, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu
javascript:;> wrote:
what do you mean by "adding" an oblique angle? If you meanacquiring the
data obliquely you should be fine as long as the voxels are closeto 1mm
isotropic. cheers Bruce On Sun, 20 Mar 2016, Dr Sampada Sinha wrote: > Dear freesurfer experts, > Does adding an oblique angle during coronal or axialacquisitions of
T1w > images lead to topographical errors during mri_fix_topologyprocess?
> > Thanks and regards, > > Sampada > > > > -- > Sampada Sinha > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <javascript:;> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person towhom it
is addressed. If you believe this e-mail was sent to you in error andthe
e-mail contains patient information, please contact the PartnersCompliance
HelpLine at http://www.partners.org/complianceline . If the e-mail was sentto you in
error but does not contain patient information, please contact thesender and
properly dispose of the e-mail.-- Sampada Sinha
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I see
if you have defects that large you should look at the inflated.nofix surface to see what they are.
What is your voxel resolution?
cheers Bruce
On Tue, 22 Mar 2016, Dr Sampada Sinha wrote:
Thanks Bruce for your reply. I did run it thru' recon-all. It went for more than 2 days and then exited with XL defect error (convex hull was more than 14000 and vertex size about 54000). So today I started by running the recon-all in parts. I did not find anything wrong with brainmask files after running autorecon1. I am presently running the autorecon-2 process. Will get back with the surf files when this process is over. Thank you again for your reply and support.
Kind regards,
Sampada
On Tuesday, March 22, 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: sure. Have you tried running it through recon-all? It may work fine.... On Tue, 22 Mar 2016, Dr Sampada Sinha wrote:
> Thanks Bruce for your reply. The acquisition was oblique and the voxel size doesn't > conform to the 1mm cube isotropic. I am trying to work on it and figure out a > solution. However, if I am not, hope its okay to send you the nifti image. > Thanks and regards, > > Sampada > > > > Rnday, March 20, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > what do you mean by "adding" an oblique angle? If you mean acquiring the > data obliquely you should be fine as long as the voxels are close to 1mm > isotropic. > > cheers > Bruce > On Sun, 20 Mar 2016, Dr Sampada Sinha wrote: > > > Dear freesurfer experts, > > Does adding an oblique angle during coronal or axial acquisitions of > T1w > > images lead to topographical errors during mri_fix_topology process? > > > > Thanks and regards, > > > > Sampada > > > > > > > > -- > > Sampada Sinha > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > 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. > > > > -- > Sampada Sinha > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Sampada Sinha
Hello Bruce,
Thanks again for your prompt response. We have an official holiday here. Will send the info on Thursday.
Thanks and regards, Sampada Predoctoral student KGMU, Lko India
On haveay, March 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I see
if you have defects that large you should look at the inflated.nofix surface to see what they are.
What is your voxel resolution?
cheers Bruce
On Tue, 22 Mar 2016, Dr Sampada Sinha wrote:
Thanks Bruce for your reply. I did run it thru' recon-all. It went for
more than 2 days and then exited with XL defect error (convex hull was more than 14000 and vertex size about 54000). So today I started by running the recon-all in parts. I did not find anything wrong with brainmask files after running autorecon1. I am presently running the autorecon-2 process. Will get back with the surf files when this process is over. Thank you again for your reply and support.
Kind regards,
Sampada
On Tuesday, March 22, 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: sure. Have you tried running it through recon-all? It may work fine.... On Tue, 22 Mar 2016, Dr Sampada Sinha wrote:
> Thanks Bruce for your reply. The acquisition was oblique and thevoxel size doesn't > conform to the 1mm cube isotropic. I am trying to work on it and figure out a > solution. However, if I am not, hope its okay to send you the nifti image. > Thanks and regards, > > Sampada > > > > Rnday, March 20, 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: > what do you mean by "adding" an oblique angle? If you mean acquiring the > data obliquely you should be fine as long as the voxels are close to 1mm > isotropic. > > cheers > Bruce > On Sun, 20 Mar 2016, Dr Sampada Sinha wrote: > > > Dear freesurfer experts, > > Does adding an oblique angle during coronal or axial acquisitions of > T1w > > images lead to topographical errors during mri_fix_topology process? > > > > Thanks and regards, > > > > Sampada > > > > > > > > -- > > Sampada Sinha > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > 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. > > > > -- > Sampada Sinha > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Sampada Sinha
Hello Bruce,
The recon-all -autorecon2 process exited with the error. The lh inflated no fix image is attached with this email. I am also, attaching the mri_info and recon_all.log with this email. I am basically trying to calculate the lGI of the participants. I was having issues with lGI but, its sorted noe. Will appreciate if I can be guided by you about how to fix this. I found the same kind of surface in another participants.
With thanks and regards,
Sampada
On Tue, Mar 22, 2016 at 10:41 PM, Dr Sampada Sinha <drsampadasinha@gmail.com
wrote:
Hello Bruce,
Thanks again for your prompt response. We have an official holiday here. Will send the info on Thursday.
Thanks and regards, Sampada Predoctoral student KGMU, Lko India
On haveay, March 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I see
if you have defects that large you should look at the inflated.nofix surface to see what they are.
What is your voxel resolution?
cheers Bruce
On Tue, 22 Mar 2016, Dr Sampada Sinha wrote:
Thanks Bruce for your reply. I did run it thru' recon-all. It went for
more than 2 days and then exited with XL defect error (convex hull was more than 14000 and vertex size about 54000). So today I started by running the recon-all in parts. I did not find anything wrong with brainmask files after running autorecon1. I am presently running the autorecon-2 process. Will get back with the surf files when this process is over. Thank you again for your reply and support.
Kind regards,
Sampada
On Tuesday, March 22, 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: sure. Have you tried running it through recon-all? It may work fine.... On Tue, 22 Mar 2016, Dr Sampada Sinha wrote:
> Thanks Bruce for your reply. The acquisition was oblique and thevoxel size doesn't > conform to the 1mm cube isotropic. I am trying to work on it and figure out a > solution. However, if I am not, hope its okay to send you the nifti image. > Thanks and regards, > > Sampada > > > > Rnday, March 20, 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: > what do you mean by "adding" an oblique angle? If you mean acquiring the > data obliquely you should be fine as long as the voxels are close to 1mm > isotropic. > > cheers > Bruce > On Sun, 20 Mar 2016, Dr Sampada Sinha wrote: > > > Dear freesurfer experts, > > Does adding an oblique angle during coronal or axial acquisitions of > T1w > > images lead to topographical errors during mri_fix_topology process? > > > > Thanks and regards, > > > > Sampada > > > > > > > > -- > > Sampada Sinha > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > 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. > > > > -- > Sampada Sinha > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Sampada Sinha
-- Sampada Sinha
HI Sampada
wow, something went terribly wrong. Can you post an image of the actual volume and maybe of the wm segmentation?
cheers Bruce
On Thu, 24 Mar 2016, Dr Sampada Sinha wrote:
Hello Bruce,
The recon-all -autorecon2 process exited with the error. The lh inflated no fix image is attached with this email. I am also, attaching the mri_info and recon_all.log with this email. I am basically trying to calculate the lGI of the participants. I was having issues with lGI but, its sorted noe. Will appreciate if I can be guided by you about how to fix this. I found the same kind of surface in another participants.
With thanks and regards,
Sampada
On Tue, Mar 22, 2016 at 10:41 PM, Dr Sampada Sinha drsampadasinha@gmail.com wrote: Hello Bruce, Thanks again for your prompt response. We have an official holiday here. Will send the info on Thursday.
Thanks and regards, Sampada Predoctoral student KGMU, Lko India
On haveay, March 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: I see
if you have defects that large you should look at the inflated.nofix surface to see what they are. What is your voxel resolution? cheers Bruce On Tue, 22 Mar 2016, Dr Sampada Sinha wrote: Thanks Bruce for your reply. I did run it thru' recon-all. It went for more than 2 days and then exited with XL defect error (convex hull was more than 14000 and vertex size about 54000). So today I started by running the recon-all in parts. I did not find anything wrong with brainmask files after running autorecon1. I am presently running the autorecon-2 process. Will get back with the surf files when this process is over. Thank you again for your reply and support. Kind regards, Sampada On Tuesday, March 22, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: sure. Have you tried running it through recon-all? It may work fine.... On Tue, 22 Mar 2016, Dr Sampada Sinha wrote: > Thanks Bruce for your reply. The acquisition was oblique and the voxel size doesn't > conform to the 1mm cube isotropic. I am trying to work on it and figure out a > solution. However, if I am not, hope its okay to send you the nifti image. > Thanks and regards, > > Sampada > > > > Rnday, March 20, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > what do you mean by "adding" an oblique angle? If you mean acquiring the > data obliquely you should be fine as long as the voxels are close to 1mm > isotropic. > > cheers > Bruce > On Sun, 20 Mar 2016, Dr Sampada Sinha wrote: > > > Dear freesurfer experts, > > Does adding an oblique angle during coronal or axial acquisitions of > T1w > > images lead to topographical errors during mri_fix_topology process? > > > > Thanks and regards, > > > > Sampada > > > > > > > > -- > > Sampada Sinha > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > 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. > > > > -- > Sampada Sinha > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sampada Sinha-- Sampada Sinha
-- Sampada Sinha
Hello Bruce,
Please find enclosed snapshots of actual volume and wm_aseg.mgz (horizontal and coronal view). Also in case, if I need to send the image over will you please let me know where do I send it? Appreciate all your help.
Thanks and regards,
Sampada
On Thu, Mar 24, 2016 at 6:20 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
HI Sampada
wow, something went terribly wrong. Can you post an image of the actual volume and maybe of the wm segmentation?
cheers Bruce
On Thu, 24 Mar 2016, Dr Sampada Sinha wrote:
Hello Bruce,
The recon-all -autorecon2 process exited with the error. The lh inflated no fix image is attached with this email. I am also, attaching the mri_info and recon_all.log with this email. I am basically trying to calculate the lGI of the participants. I was having issues with lGI but, its sorted noe. Will appreciate if I can be guided by you about how to fix this. I found the same kind of surface in another participants.
With thanks and regards,
Sampada
On Tue, Mar 22, 2016 at 10:41 PM, Dr Sampada Sinha < drsampadasinha@gmail.com> wrote: Hello Bruce, Thanks again for your prompt response. We have an official holiday here. Will send the info on Thursday.
Thanks and regards, Sampada Predoctoral student KGMU, Lko India
On haveay, March 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: I see
if you have defects that large you should look at the inflated.nofix surface to see what they are. What is your voxel resolution? cheers Bruce On Tue, 22 Mar 2016, Dr Sampada Sinha wrote: Thanks Bruce for your reply. I did run it thru' recon-all. It went for more than 2 days and then exited with XL defect error (convex hull was more than 14000 and vertex size about 54000). So today I started by running the recon-all in parts. I did not find anything wrong with brainmask files after running autorecon1. I am presently running the autorecon-2 process. Will get back with the surf files when this process is over. Thank you again for your reply and support. Kind regards, Sampada On Tuesday, March 22, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: sure. Have you tried running it through recon-all? It may work fine.... On Tue, 22 Mar 2016, Dr Sampada Sinha wrote: > Thanks Bruce for your reply. The acquisition was oblique and the voxel size doesn't > conform to the 1mm cube isotropic. I am trying to work on it and figure out a > solution. However, if I am not, hope its okay to send you the nifti image. > Thanks and regards, > > Sampada > > > > Rnday, March 20, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > what do you mean by "adding" an oblique angle? If you mean acquiring the > data obliquely you should be fine as long as the voxels are close to 1mm > isotropic. > > cheers > Bruce > On Sun, 20 Mar 2016, Dr Sampada Sinha wrote: > > > Dear freesurfer experts, > > Does adding an oblique angle during coronal or axial acquisitions of > T1w > > images lead to topographical errors during mri_fix_topology process? > > > > Thanks and regards, > > > > Sampada > > > > > > > > -- > > Sampada Sinha > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > 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. > > > > -- > Sampada Sinha > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sampada Sinha-- Sampada Sinha
-- Sampada Sinha
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 Sampada
the problem isn't the oblique orientation it is the resolution (too low!) and contrast (not enough!). Can you give us the details of the scan? Resolution, type, etc....?
cheers Bruce On Fri, 25 Mar 2016, Dr Sampada Sinha wrote:
Hello Bruce,
Please find enclosed snapshots of actual volume and wm_aseg.mgz (horizontal and coronal view). Also in case, if I need to send the image over will you please let me know where do I send it? Appreciate all your help.
Thanks and regards,
Sampada
On Thu, Mar 24, 2016 at 6:20 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: HI Sampada
wow, something went terribly wrong. Can you post an image of the actual volume and maybe of the wm segmentation? cheers Bruce On Thu, 24 Mar 2016, Dr Sampada Sinha wrote: Hello Bruce, The recon-all -autorecon2 process exited with the error. The lh inflated no fix image is attached with this email. I am also, attaching the mri_info and recon_all.log with this email. I am basically trying to calculate the lGI of the participants. I was having issues with lGI but, its sorted noe. Will appreciate if I can be guided by you about how to fix this. I found the same kind of surface in another participants. With thanks and regards, Sampada On Tue, Mar 22, 2016 at 10:41 PM, Dr Sampada Sinha <drsampadasinha@gmail.com> wrote: Hello Bruce, Thanks again for your prompt response. We have an official holiday here. Will send the info on Thursday. Thanks and regards, Sampada Predoctoral student KGMU, Lko India On haveay, March 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: I see if you have defects that large you should look at the inflated.nofix surface to see what they are. What is your voxel resolution? cheers Bruce On Tue, 22 Mar 2016, Dr Sampada Sinha wrote: Thanks Bruce for your reply. I did run it thru' recon-all. It went for more than 2 days and then exited with XL defect error (convex hull was more than 14000 and vertex size about 54000). So today I started by running the recon-all in parts. I did not find anything wrong with brainmask files after running autorecon1. I am presently running the autorecon-2 process. Will get back with the surf files when this process is over. Thank you again for your reply and support. Kind regards, Sampada On Tuesday, March 22, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: sure. Have you tried running it through recon-all? It may work fine.... On Tue, 22 Mar 2016, Dr Sampada Sinha wrote: > Thanks Bruce for your reply. The acquisition was oblique and the voxel size doesn't > conform to the 1mm cube isotropic. I am trying to work on it and figure out a > solution. However, if I am not, hope its okay to send you the nifti image. > Thanks and regards, > > Sampada > > > > Rnday, March 20, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > what do you mean by "adding" an oblique angle? If you mean acquiring the > data obliquely you should be fine as long as the voxels are close to 1mm > isotropic. > > cheers > Bruce > On Sun, 20 Mar 2016, Dr Sampada Sinha wrote: > > > Dear freesurfer experts, > > Does adding an oblique angle during coronal or axial acquisitions of > T1w > > images lead to topographical errors during mri_fix_topology process? > > > > Thanks and regards, > > > > Sampada > > > > > > > > -- > > Sampada Sinha > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > 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. > > > > -- > Sampada Sinha > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sampada Sinha -- Sampada Sinha -- Sampada Sinha
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.
-- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India
Hello Bruce,
Thanks for following it up. Sorry for tardy response. I am at the mercy of power supply and Internet connectivity here. The details of scans are enclosed as a snapshots. Peculiar thing is that we have processed about 23-24 participants' sMRI having similar scanning parameters and their surface reconstruction is okay. One thing I would like to ask, if I may (?) is that: why am I seeing this problem in this particular participant and why not in other ones that have been processed? All participants so far pre-processed with recon-all have similar sMRI image protocol.
Appreciate all your help!
Thanks and kind regards,
Sampada
-- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India
Hi Sampada
could you include our previous corresponance in your emails so I can keep track of what we were talking about? If your slice thickness is really 6.5mm (or slice thickness + gap) then that is probably the source of your problems. You need something much closer to isotropic
cheers Bruce On Wed, 30 Mar 2016, Dr Sampada Sinha wrote:
Hello Bruce,
Thanks for following it up. Sorry for tardy response. I am at the mercy of power supply and Internet connectivity here. The details of scans are enclosed as a snapshots. Peculiar thing is that we have processed about 23-24 participants' sMRI having similar scanning parameters and their surface reconstruction is okay. One thing I would like to ask, if I may (?) is that: why am I seeing this problem in this particular participant and why not in other ones that have been processed? All participants so far pre-processed with recon-all have similar sMRI image protocol.
Appreciate all your help!
Thanks and kind regards,
Sampada
-- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India
Hello Bruce,
Thanks for your reply. Brief history of my problem so far is that: as you noticed before, my images have very low resolution and very less contrast. My images slice thickness is also about 5mm, voxel size: 0.46x0.46x6.5; dimension 512x512x20. I do run mri_convert to conform it to 1x1x1 mm voxel dimension. But I am getting huge topological defect and in 3-4 patients, and, brain areas are missing as well after running recon-all command. I tried to manually edit those missing brain voxels. But, apart from getting topological error, even after the process is complete, lGI stops running because of high Euler number.
I am trying not to discard those sMRI images. Want to glean at least some data out of it. Will greatly appreciate if I can be guided on this.
Thanks and regards,
Sampada
On Wed, Mar 30, 2016 at 6:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Sampada
could you include our previous corresponance in your emails so I can keep track of what we were talking about? If your slice thickness is really 6.5mm (or slice thickness + gap) then that is probably the source of your problems. You need something much closer to isotropic
cheers Bruce
On Wed, 30 Mar 2016, Dr Sampada Sinha wrote:
Hello Bruce,
Thanks for following it up. Sorry for tardy response. I am at the mercy of power supply and Internet connectivity here. The details of scans are enclosed as a snapshots. Peculiar thing is that we have processed about 23-24 participants' sMRI having similar scanning parameters and their surface reconstruction is okay. One thing I would like to ask, if I may (?) is that: why am I seeing this problem in this particular participant and why not in other ones that have been processed? All participants so far pre-processed with recon-all have similar sMRI image protocol.
Appreciate all your help!
Thanks and kind regards,
Sampada
-- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India
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 Sampada
I don't think it is possible to get reasonable surfaces out of 5 or 6.5mm slice data. You might get ok asegs.
sorry Bruce
On Fri, 8 Apr 2016, Dr Sampada Sinha wrote:
Hello Bruce,
Thanks for your reply. Brief history of my problem so far is that: as you noticed before, my images have very low resolution and very less contrast. My images slice thickness is also about 5mm, voxel size: 0.46x0.46x6.5; dimension 512x512x20. I do run mri_convert to conform it to 1x1x1 mm voxel dimension. But I am getting huge topological defect and in 3-4 patients, and, brain areas are missing as well after running recon-all command. I tried to manually edit those missing brain voxels. But, apart from getting topological error, even after the process is complete, lGI stops running because of high Euler number.
I am trying not to discard those sMRI images. Want to glean at least some data out of it. Will greatly appreciate if I can be guided on this.
Thanks and regards,
Sampada
On Wed, Mar 30, 2016 at 6:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Sampada
could you include our previous corresponance in your emails so I can keep track of what we were talking about? If your slice thickness is really 6.5mm (or slice thickness + gap) then that is probably the source of your problems. You need something much closer to isotropic cheers Bruce On Wed, 30 Mar 2016, Dr Sampada Sinha wrote: Hello Bruce, Thanks for following it up. Sorry for tardy response. I am at the mercy of power supply and Internet connectivity here. The details of scans are enclosed as a snapshots. Peculiar thing is that we have processed about 23-24 participants' sMRI having similar scanning parameters and their surface reconstruction is okay. One thing I would like to ask, if I may (?) is that: why am I seeing this problem in this particular participant and why not in other ones that have been processed? All participants so far pre-processed with recon-all have similar sMRI image protocol. Appreciate all your help! Thanks and kind regards, Sampada -- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India
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.
-- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India
Thanks Bruce. Appreciate all your help.
Kind regards,
Sampada
On Friday, April 8, 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Sampada
I don't think it is possible to get reasonable surfaces out of 5 or 6.5mm slice data. You might get ok asegs.
sorry Bruce
On Fri, 8 Apr 2016, Dr Sampada Sinha wrote:
Hello Bruce,
Thanks for your reply. Brief history of my problem so far is that: as you noticed before, my images have very low resolution and very less contrast. My images slice thickness is also about 5mm, voxel size: 0.46x0.46x6.5; dimension 512x512x20. I do run mri_convert to conform it to 1x1x1 mm voxel dimension. But I am getting huge topological defect and in 3-4 patients, and, brain areas are missing as well after running recon-all command. I tried to manually edit those missing brain voxels. But, apart from getting topological error, even after the process is complete, lGI stops running because of high Euler number.
I am trying not to discard those sMRI images. Want to glean at least some data out of it. Will greatly appreciate if I can be guided on this.
Thanks and regards,
Sampada
On Wed, Mar 30, 2016 at 6:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Sampada
could you include our previous corresponance in your emails so Ican keep track of what we were talking about? If your slice thickness is really 6.5mm (or slice thickness + gap) then that is probably the source of your problems. You need something much closer to isotropic
cheers Bruce On Wed, 30 Mar 2016, Dr Sampada Sinha wrote: Hello Bruce, Thanks for following it up. Sorry for tardy response. I amat the mercy of power supply and Internet connectivity here. The details of scans are enclosed as a snapshots. Peculiar thing is that we have processed about 23-24 participants' sMRI having similar scanning parameters and their surface reconstruction is okay. One thing I would like to ask, if I may (?) is that: why am I seeing this problem in this particular participant and why not in other ones that have been processed? All participants so far pre-processed with recon-all have similar sMRI image protocol.
Appreciate all your help! Thanks and kind regards, Sampada -- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India
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.
-- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India
sure. I wish I had a better answer for you On Fri, 8 Apr 2016, Dr Sampada Sinha wrote:
Thanks Bruce. Appreciate all your help. Kind regards,
Sampada
On Friday, April 8, 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Sampada
I don't think it is possible to get reasonable surfaces out of 5 or 6.5mm slice data. You might get ok asegs. sorry Bruce On Fri, 8 Apr 2016, Dr Sampada Sinha wrote: Hello Bruce, Thanks for your reply. Brief history of my problem so far is that: as you noticed before, my images have very low resolution and very less contrast. My images slice thickness is also about 5mm, voxel size: 0.46x0.46x6.5; dimension 512x512x20. I do run mri_convert to conform it to 1x1x1 mm voxel dimension. But I am getting huge topological defect and in 3-4 patients, and, brain areas are missing as well after running recon-all command. I tried to manually edit those missing brain voxels. But, apart from getting topological error, even after the process is complete, lGI stops running because of high Euler number. I am trying not to discard those sMRI images. Want to glean at least some data out of it. Will greatly appreciate if I can be guided on this. Thanks and regards, Sampada On Wed, Mar 30, 2016 at 6:53 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Sampada could you include our previous corresponance in your emails so I can keep track of what we were talking about? If your slice thickness is really 6.5mm (or slice thickness + gap) then that is probably the source of your problems. You need something much closer to isotropic cheers Bruce On Wed, 30 Mar 2016, Dr Sampada Sinha wrote: Hello Bruce, Thanks for following it up. Sorry for tardy response. I am at the mercy of power supply and Internet connectivity here. The details of scans are enclosed as a snapshots. Peculiar thing is that we have processed about 23-24 participants' sMRI having similar scanning parameters and their surface reconstruction is okay. One thing I would like to ask, if I may (?) is that: why am I seeing this problem in this particular participant and why not in other ones that have been processed? All participants so far pre-processed with recon-all have similar sMRI image protocol. Appreciate all your help! Thanks and kind regards, Sampada -- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India _______________________________________________ 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. -- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India-- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India
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