Dear FreeSurfer,
Currently, we have only manual edited the BASE (the CROSS was left unedited) in an longitudinal data. However, some cortical areas (f.eks. such as the inferior temporal area) are difficult to edit accurately due to image quality. I then read through the release notes (stable v5.2.0) and found that a T2/FLAIR can be used to improve the pial surface.
Question: Is it possible to use a T2 and run either -autorecon3 and -T2pial on the [LONG] runs to get extra improvement of the final pial surfaces?
Best regards, Kasper Jessen
Hi Kasper,
I don't see why not, but we haven't done this yet I don't think, so there may be undiscovered bugs. Bruce On Fri, 13 May 2016, Kasper Jessen wrote:
Dear FreeSurfer, Currently, we have only manual edited the BASE (the CROSS was left unedited) in an longitudinal data. However, some cortical areas (f.eks. such as the inferior temporal area) are difficult to edit accurately due to image quality. I then read through the release notes (stable v5.2.0) and found that a T2/FLAIR can be used to improve the pial surface.
Question: Is it possible to use a T2 and run either -autorecon3 and -T2pial on the [LONG] runs to get extra improvement of the final pial surfaces?
Best regards, Kasper Jessen
Hi Kasper, It should work (I tried it a while ago with the dev version and it did not crash :-). Could not really tell if it helped much either. I don't remember if functionality is available in FS5.3 to include that in a long run. In dev, you would include the T2 for both the cross and long run. The long run then takes the T2 from the cross. Not sure if it works passing it directly into a longitudinal run.
Best, Martin
On 05/13/2016 08:43 AM, Bruce Fischl wrote:
Hi Kasper,
I don't see why not, but we haven't done this yet I don't think, so there may be undiscovered bugs. Bruce On Fri, 13 May 2016, Kasper Jessen wrote:
Dear FreeSurfer, Currently, we have only manual edited the BASE (the CROSS was left unedited) in an longitudinal data. However, some cortical areas (f.eks. such as the inferior temporal area) are difficult to edit accurately due to image quality. I then read through the release notes (stable v5.2.0) and found that a T2/FLAIR can be used to improve the pial surface.
Question: Is it possible to use a T2 and run either -autorecon3 and -T2pial on the [LONG] runs to get extra improvement of the final pial surfaces?
Best regards, Kasper Jessen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Unfortunately i do not think it works to pass it directly into a longitudinal run. I tried the following, which exited with errors:
recon-all -long d256a d256_base -FLAIR path/flair.nii.gz -autorecon3 -FLAIRpial
Any suggestions?
Best,
Kasper
2016-05-13 20:01 GMT+02:00 Martin Reuter mreuter@nmr.mgh.harvard.edu:
Hi Kasper, It should work (I tried it a while ago with the dev version and it did not crash :-). Could not really tell if it helped much either. I don't remember if functionality is available in FS5.3 to include that in a long run. In dev, you would include the T2 for both the cross and long run. The long run then takes the T2 from the cross. Not sure if it works passing it directly into a longitudinal run.
Best, Martin
On 05/13/2016 08:43 AM, Bruce Fischl wrote:
Hi Kasper,
I don't see why not, but we haven't done this yet I don't think, so there may be undiscovered bugs. Bruce On Fri, 13 May 2016, Kasper Jessen wrote:
Dear FreeSurfer, Currently, we have only manual edited the BASE (the CROSS was left unedited) in an longitudinal data. However, some cortical areas (f.eks. such as the inferior temporal area) are difficult to edit accurately due to image quality. I then read through the release notes (stable v5.2.0) and found that a T2/FLAIR can be used to improve the pial surface.
Question: Is it possible to use a T2 and run either -autorecon3 and -T2pial on the [LONG] runs to get extra improvement of the final pial surfaces?
Best regards, Kasper Jessen
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
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 Kasper
what is the error? Can you run it as a separate step at the end (without the -long flag)?
cheers Bruce On Tue, 17 May 2016, Kasper Jessen wrote:
Unfortunately i do not think it works to pass it directly into a longitudinal run. I tried the following, which exited with errors:
recon-all -long d256a d256_base -FLAIR path/flair.nii.gz -autorecon3 -FLAIRpial
Any suggestions?
Best,
Kasper
2016-05-13 20:01 GMT+02:00 Martin Reuter mreuter@nmr.mgh.harvard.edu: Hi Kasper, It should work (I tried it a while ago with the dev version and it did not crash :-). Could not really tell if it helped much either. I don't remember if functionality is available in FS5.3 to include that in a long run. In dev, you would include the T2 for both the cross and long run. The long run then takes the T2 from the cross. Not sure if it works passing it directly into a longitudinal run.
Best, Martin On 05/13/2016 08:43 AM, Bruce Fischl wrote: Hi Kasper, I don't see why not, but we haven't done this yet I don't think, so there may be undiscovered bugs. Bruce On Fri, 13 May 2016, Kasper Jessen wrote: Dear FreeSurfer, Currently, we have only manual edited the BASE (the CROSS was left unedited) in an longitudinal data. However, some cortical areas (f.eks. such as the inferior temporal area) are difficult to edit accurately due to image quality. I then read through the release notes (stable v5.2.0) and found that a T2/FLAIR can be used to improve the pial surface. Question: Is it possible to use a T2 and run either -autorecon3 and -T2pial on the [LONG] runs to get extra improvement of the final pial surfaces? Best regards, Kasper Jessen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Kasper,
if I remember correctly, you need to specify it in the cross and the long runs (see my email below). Also could be you need the dev version, I have never tested it in 5.3.
Best, Martin
On 05/17/2016 03:54 AM, Kasper Jessen wrote:
Unfortunately i do not think it works to pass it directly into a longitudinal run. I tried the following, which exited with errors:
recon-all -long d256a d256_base -FLAIR path/flair.nii.gz -autorecon3 -FLAIRpial
Any suggestions?
Best,
Kasper
2016-05-13 20:01 GMT+02:00 Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu>:
Hi Kasper, It should work (I tried it a while ago with the dev version and it did not crash :-). Could not really tell if it helped much either. I don't remember if functionality is available in FS5.3 to include that in a long run. In dev, you would include the T2 for both the cross and long run. The long run then takes the T2 from the cross. Not sure if it works passing it directly into a longitudinal run. Best, Martin On 05/13/2016 08:43 AM, Bruce Fischl wrote:Hi Kasper, I don't see why not, but we haven't done this yet I don't think, so there may be undiscovered bugs. Bruce On Fri, 13 May 2016, Kasper Jessen wrote:Dear FreeSurfer, Currently, we have only manual edited the BASE (the CROSS was left unedited) in an longitudinal data. However, some cortical areas (f.eks. such as the inferior temporal area) are difficult to edit accurately due to image quality. I then read through the release notes (stable v5.2.0) and found that a T2/FLAIR can be used to improve the pial surface. Question: Is it possible to use a T2 and run either -autorecon3 and -T2pial on the [LONG] runs to get extra improvement of the final pial surfaces? Best regards, Kasper Jessen_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> Web :http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.-- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j@cnsr.dk mailto:kasper_j@cnsr.dk eller kasper.jessen@regionh.dk mailto:kasper.jessen@regionh.dk
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Martin,
I am now trying to run it through the [CROSS] first, to see the effects. However, since our longitudinal data is already edited (i.e., in the base) i was interested to see if it was possible to pass the FLAIR in the longitudinal runs [LONG], which already have implemented the edited [BASE].
Best, Kasper
2016-05-17 14:59 GMT+02:00 Martin Reuter mreuter@nmr.mgh.harvard.edu:
Hi Kasper,
if I remember correctly, you need to specify it in the cross and the long runs (see my email below). Also could be you need the dev version, I have never tested it in 5.3.
Best, Martin
On 05/17/2016 03:54 AM, Kasper Jessen wrote:
Unfortunately i do not think it works to pass it directly into a longitudinal run. I tried the following, which exited with errors:
recon-all -long d256a d256_base -FLAIR path/flair.nii.gz -autorecon3 -FLAIRpial
Any suggestions?
Best,
Kasper
2016-05-13 20:01 GMT+02:00 Martin Reuter mreuter@nmr.mgh.harvard.edu:
Hi Kasper, It should work (I tried it a while ago with the dev version and it did not crash :-). Could not really tell if it helped much either. I don't remember if functionality is available in FS5.3 to include that in a long run. In dev, you would include the T2 for both the cross and long run. The long run then takes the T2 from the cross. Not sure if it works passing it directly into a longitudinal run.
Best, Martin
On 05/13/2016 08:43 AM, Bruce Fischl wrote:
Hi Kasper,
I don't see why not, but we haven't done this yet I don't think, so there may be undiscovered bugs. Bruce On Fri, 13 May 2016, Kasper Jessen wrote:
Dear FreeSurfer, Currently, we have only manual edited the BASE (the CROSS was left unedited) in an longitudinal data. However, some cortical areas (f.eks. such as the inferior temporal area) are difficult to edit accurately due to image quality. I then read through the release notes (stable v5.2.0) and found that a T2/FLAIR can be used to improve the pial surface.
Question: Is it possible to use a T2 and run either -autorecon3 and -T2pial on the [LONG] runs to get extra improvement of the final pial surfaces?
Best regards, Kasper Jessen
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
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.
-- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j@cnsr.dk eller kasper.jessen@regionh.dk
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
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
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