Re: [Freesurfer] Temporal lobe reconstruction problem
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 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 >> 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 >> 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. >> >> >> >> >> ___ 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.
Re: [Freesurfer] Temporal lobe reconstruction problem
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 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 > 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. >> >> > ___ 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.
Re: [Freesurfer] Temporal lobe reconstruction problem
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 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. > > ___ 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.
Re: [Freesurfer] Temporal lobe reconstruction problem
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.
