Hi Louis,
I would appreciate if I could get your feedback on this specific subject we are experiencing problems with.
Thanks James
On Tue, Jul 15, 2014 at 8:20 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi James
I did, and one of our RAs here is going to be looking into it. Louis (ccd) can give you more information
cheers Bruce
On Tue, 15 Jul 2014, james pardon wrote:
Hi Bruce,
I was wondering whether you have seen my email below?
Thanks so much
Cheers, James
On Sat, Jul 12, 2014 at 9:18 AM, james pardon james.pardon15@gmail.com wrote: Hi Bruce, I have sent the link for a problem subject via a private message. Please note since MS causes hypointense lesions in white matter I have used an algorithm that fills hypointense lesions in WM with median intensity of normal appearing WM.
Thanks James
On Fri, Jul 11, 2014 at 11:19 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi James
if you upload a problem subject we will take a look (the whole subject dir please) cheers Bruce On Fri, 11 Jul 2014, james pardon wrote: Hi all, On a few subjects with a specific pathology (MS) I cannot easily reconstruct temporal lobes. I think this issue comes up quite regularly on the mailing list, and I have tried to trouble shoot using control points, WM edits, even getting back to orig/001.mgz to correct areas that may seem the culprit for breaking surface reconstruction. Some subjects have gone through 7-8 runs of recon-all with different edits but still the problem persists in a few subjects in my study. I have also tried to use -mprage and -3T flags along the way to allow more liberal control point growing, despite an improvement in my results some of subjects still have very bad surface constructions. I have attached two snapshots to this email and I am happy to upload the complete subject folder if you need to take a look at them. As far as the SNR is concerned, I have designed my study based on recommended Freesurfer parameters a couple of years ago on 3T Siemens Trio with 32-channel receiver coil. A huge thank you for your previous helps, and thanks in advance for helping me with this new issue. James
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 James, With the wm edits in the temporal lobes, make sure that the wm painted in on the wm.mgz in the various gyri is connected to the main body of wm throughout each lobe. Even if there is a disconnection on only a couple slices, it tends to have an effect on nearby slices as well where the wm is completely connected. See snapshot attached for an example of a disconnection in the STG wm that should be filled in. -Louis
On Thu, 17 Jul 2014, james pardon wrote:
Hi Louis, I would appreciate if I could get your feedback on this specific subject we are experiencing problems with.
Thanks James
On Tue, Jul 15, 2014 at 8:20 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi James
I did, and one of our RAs here is going to be looking into it. Louis (ccd) can give you more information cheers Bruce On Tue, 15 Jul 2014, james pardon wrote: Hi Bruce, I was wondering whether you have seen my email below? Thanks so much Cheers, James On Sat, Jul 12, 2014 at 9:18 AM, james pardon <james.pardon15@gmail.com> wrote: Hi Bruce, I have sent the link for a problem subject via a private message. Please note since MS causes hypointense lesions in white matter I have used an algorithm that fills hypointense lesions in WM with median intensity of normal appearing WM. Thanks James On Fri, Jul 11, 2014 at 11:19 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi James if you upload a problem subject we will take a look (the whole subject dir please) cheers Bruce On Fri, 11 Jul 2014, james pardon wrote: Hi all, On a few subjects with a specific pathology (MS) I cannot easily reconstruct temporal lobes. I think this issue comes up quite regularly on the mailing list, and I have tried to trouble shoot using control points, WM edits, even getting back to orig/001.mgz to correct areas that may seem the culprit for breaking surface reconstruction. Some subjects have gone through 7-8 runs of recon-all with different edits but still the problem persists in a few subjects in my study. I have also tried to use -mprage and -3T flags along the way to allow more liberal control point growing, despite an improvement in my results some of subjects still have very bad surface constructions. I have attached two snapshots to this email and I am happy to upload the complete subject folder if you need to take a look at them. As far as the SNR is concerned, I have designed my study based on recommended Freesurfer parameters a couple of years ago on 3T Siemens Trio with 32-channel receiver coil. A huge thank you for your previous helps, and thanks in advance for helping me with this new issue. James _______________________________________________ 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.
I should add though that in some sections where there is a disconnection in the wm on the wm.gz that I would want to fill in, it's tough to tell where exactly the wm is since the intensities of the voxels on the brainmask.mgz in that gap look like uniform gm. Normally you can see at least a small relative difference in intensities, gm vs. wm.
Maybe it is pathology-related? -Louis
On Thu, 17 Jul 2014, Louis Nicholas Vinke wrote:
Hi James, With the wm edits in the temporal lobes, make sure that the wm painted in on the wm.mgz in the various gyri is connected to the main body of wm throughout each lobe. Even if there is a disconnection on only a couple slices, it tends to have an effect on nearby slices as well where the wm is completely connected. See snapshot attached for an example of a disconnection in the STG wm that should be filled in. -Louis
On Thu, 17 Jul 2014, james pardon wrote:
Hi Louis, I would appreciate if I could get your feedback on this specific subject we are experiencing problems with.
Thanks James
On Tue, Jul 15, 2014 at 8:20 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi James
I did, and one of our RAs here is going to be looking into it. Louis(ccd) can give you more information
cheers Bruce On Tue, 15 Jul 2014, james pardon wrote: Hi Bruce, I was wondering whether you have seen my email below? Thanks so much Cheers, James On Sat, Jul 12, 2014 at 9:18 AM, james pardon <james.pardon15@gmail.com> wrote: Hi Bruce, I have sent the link for a problem subject via a private message. Please note since MS causes hypointense lesions in white matter I have used an algorithm that fills hypointense lesions in WM with median intensity of normal appearing WM. Thanks James On Fri, Jul 11, 2014 at 11:19 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi James if you upload a problem subject we will take a look (the whole subject dir please) cheers Bruce On Fri, 11 Jul 2014, james pardon wrote: Hi all, On a few subjects with a specific pathology (MS) I cannot easily reconstruct temporal lobes. I think this issue comes up quite regularly on the mailing list, and I have tried to trouble shoot using control points, WM edits, even getting back to orig/001.mgz to correct areas that may seem the culprit for breaking surface reconstruction. Some subjects have gone through 7-8 runs of recon-all with different edits but still the problem persists in a few subjects in my study. I have also tried to use -mprage and -3T flags along the way to allow more liberal control point growing, despite an improvement in my results some of subjects still have very bad surface constructions. I have attached two snapshots to this email and I am happy to upload the complete subject folder if you need to take a look at them. As far as the SNR is concerned, I have designed my study based on recommended Freesurfer parameters a couple of years ago on 3T Siemens Trio with 32-channel receiver coil. A huge thank you for your previous helps, and thanks in advance for helping me with this new issue. James _______________________________________________ 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.
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Louis Nicholas Vinke