No, I think that's a reasonable protocol to use and good to use SENSE to speed it up.
-------- Original message -------- From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date:04/01/2014 2:28 PM (GMT+02:00) To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Andre van der Kouwe andre@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] quality T1 scans for new study
looks pretty reasonable. Andre: any comments/suggestions?
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Hi Bruce,
Thanks for your fast reply.
Hereby I attach the parameter files of both scans (although I suspect looking at the parameters of "scan1" may be sufficient). Checking it with the information on Philips at "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...":
" Sequence: T1W_3D_TFE_SENSE Acquisition time: 5:13 Voxel size: 1.0 x 1.0 x 1.0 mm3 Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness 1 mm, (3D encoding) Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth 191.5 Hz/px RF: flip angle 7° Acceleration: 2x SENSE "
suggests that parameters in "scan1_parameter_file.txt" are already pretty similar to those I guess. (Is it the SENSE that is missing in our protocol that is the most important difference?)
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 14:09 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Jelmer
if you give us the specific acquisition details we can help more (receive coil, acceleration, voxel size, sequence type, TR/TE/TI/flip angle/bandwidth, etc....). We also have recommended morphometry sequences on our website.
10 min is a pretty long structural scan for a modern MRI scanner.
cheers Bruce
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Freesurfer experts, We are planning to start a new MRI study which will include T1 scans. As we are in a testing phase now, I was wondering whether you could comment on the attached screenshots. Clearly, "scan1" has a better white matter/grey matter contrast than "scan2". Do you think going for "scan1" would be the sensible thing to do when we later wish to use Freesurfer with these scans? Or perhaps is neither of the examples I attached good enough?
By the way, these scans were acquired on a Philips 3T scanner, both taking around 10 minutes.
It you need any more information, please let me know. Many thanks in advance for your advice.
Jelmer Kok
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
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.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
Hi Bruce and Andre,
Many thanks for your comments!
Cheers,
Jelmer ________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Andre van der Kouwe [andre@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 15:37 Aan: Bruce Fischl; Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
No, I think that's a reasonable protocol to use and good to use SENSE to speed it up.
-------- Original message -------- From: Bruce Fischl Date:04/01/2014 2:28 PM (GMT+02:00) To: Freesurfer support list Cc: Andre van der Kouwe Subject: Re: [Freesurfer] quality T1 scans for new study
looks pretty reasonable. Andre: any comments/suggestions?
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Hi Bruce,
Thanks for your fast reply.
Hereby I attach the parameter files of both scans (although I suspect looking at the parameters of "scan1" may be sufficient). Checking it with the information on Philips at "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...":
" Sequence: T1W_3D_TFE_SENSE Acquisition time: 5:13 Voxel size: 1.0 x 1.0 x 1.0 mm3 Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness 1 mm, (3D encoding) Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth 191.5 Hz/px RF: flip angle 7° Acceleration: 2x SENSE "
suggests that parameters in "scan1_parameter_file.txt" are already pretty similar to those I guess. (Is it the SENSE that is missing in our protocol that is the most important difference?)
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 14:09 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Jelmer
if you give us the specific acquisition details we can help more (receive coil, acceleration, voxel size, sequence type, TR/TE/TI/flip angle/bandwidth, etc....). We also have recommended morphometry sequences on our website.
10 min is a pretty long structural scan for a modern MRI scanner.
cheers Bruce
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Freesurfer experts, We are planning to start a new MRI study which will include T1 scans. As we are in a testing phase now, I was wondering whether you could comment on the attached screenshots. Clearly, "scan1" has a better white matter/grey matter contrast than "scan2". Do you think going for "scan1" would be the sensible thing to do when we later wish to use Freesurfer with these scans? Or perhaps is neither of the examples I attached good enough?
By the way, these scans were acquired on a Philips 3T scanner, both taking around 10 minutes.
It you need any more information, please let me know. Many thanks in advance for your advice.
Jelmer Kok
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
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.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
Dear Bruce and Andre,
PS I am sorry, but may I assume you have only looked at the parameters in "scan1_parameter_file.txt" and not in "scan2_parameter_file.txt"? That would be fine, but I would just like to check we are talking about the same scan parameters that seem to be fine...
Thanks,
Jelmer ________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Kok, JG (neuro) [j.g.kok02@umcg.nl] Verzonden: dinsdag 1 april 2014 16:45 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Bruce and Andre,
Many thanks for your comments!
Cheers,
Jelmer ________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Andre van der Kouwe [andre@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 15:37 Aan: Bruce Fischl; Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
No, I think that's a reasonable protocol to use and good to use SENSE to speed it up.
-------- Original message -------- From: Bruce Fischl Date:04/01/2014 2:28 PM (GMT+02:00) To: Freesurfer support list Cc: Andre van der Kouwe Subject: Re: [Freesurfer] quality T1 scans for new study
looks pretty reasonable. Andre: any comments/suggestions?
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Hi Bruce,
Thanks for your fast reply.
Hereby I attach the parameter files of both scans (although I suspect looking at the parameters of "scan1" may be sufficient). Checking it with the information on Philips at "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...":
" Sequence: T1W_3D_TFE_SENSE Acquisition time: 5:13 Voxel size: 1.0 x 1.0 x 1.0 mm3 Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness 1 mm, (3D encoding) Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth 191.5 Hz/px RF: flip angle 7° Acceleration: 2x SENSE "
suggests that parameters in "scan1_parameter_file.txt" are already pretty similar to those I guess. (Is it the SENSE that is missing in our protocol that is the most important difference?)
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 14:09 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Jelmer
if you give us the specific acquisition details we can help more (receive coil, acceleration, voxel size, sequence type, TR/TE/TI/flip angle/bandwidth, etc....). We also have recommended morphometry sequences on our website.
10 min is a pretty long structural scan for a modern MRI scanner.
cheers Bruce
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Freesurfer experts, We are planning to start a new MRI study which will include T1 scans. As we are in a testing phase now, I was wondering whether you could comment on the attached screenshots. Clearly, "scan1" has a better white matter/grey matter contrast than "scan2". Do you think going for "scan1" would be the sensible thing to do when we later wish to use Freesurfer with these scans? Or perhaps is neither of the examples I attached good enough?
By the way, these scans were acquired on a Philips 3T scanner, both taking around 10 minutes.
It you need any more information, please let me know. Many thanks in advance for your advice.
Jelmer Kok
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
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.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
no, I just looked at the ones in the body of your email On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Bruce and Andre,
PS I am sorry, but may I assume you have only looked at the parameters in "scan1_parameter_file.txt" and not in "scan2_parameter_file.txt"? That would be fine, but I would just like to check we are talking about the same scan parameters that seem to be fine...
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Kok, JG (neuro) [j.g.kok02@umcg.nl] Verzonden: dinsdag 1 april 2014 16:45 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Bruce and Andre,
Many thanks for your comments!
Cheers,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Andre van der Kouwe [andre@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 15:37 Aan: Bruce Fischl; Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
No, I think that's a reasonable protocol to use and good to use SENSE to speed it up.
-------- Original message -------- From: Bruce Fischl Date:04/01/2014 2:28 PM (GMT+02:00) To: Freesurfer support list Cc: Andre van der Kouwe Subject: Re: [Freesurfer] quality T1 scans for new study
looks pretty reasonable. Andre: any comments/suggestions?
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Hi Bruce,
Thanks for your fast reply.
Hereby I attach the parameter files of both scans (although I suspect looking at the parameters of "scan1" may be sufficient).
Checking it with the information on Philips at "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...":
" Sequence: T1W_3D_TFE_SENSE Acquisition time: 5:13 Voxel size: 1.0 x 1.0 x 1.0 mm3 Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness 1 mm, (3D encoding) Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth 191.5 Hz/px RF: flip angle 7° Acceleration: 2x SENSE "
suggests that parameters in "scan1_parameter_file.txt" are already pretty similar to those I guess. (Is it the SENSE that is
missing in our protocol that is the most important difference?)
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl
[fischl@nmr.mgh.harvard.edu]
Verzonden: dinsdag 1 april 2014 14:09 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Jelmer
if you give us the specific acquisition details we can help more (receive coil, acceleration, voxel size, sequence type, TR/TE/TI/flip angle/bandwidth, etc....). We also have recommended morphometry sequences on our website.
10 min is a pretty long structural scan for a modern MRI scanner.
cheers Bruce
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Freesurfer experts, We are planning to start a new MRI study which will include T1 scans. As we are in a testing phase now, I was wondering whether you could comment on the attached screenshots. Clearly, "scan1" has a better white matter/grey matter contrast than "scan2". Do you think going for "scan1" would be the sensible thing to do when we later wish to use Freesurfer with these scans? Or perhaps is neither of the examples I attached good enough?
By the way, these scans were acquired on a Philips 3T scanner, both taking around 10 minutes.
It you need any more information, please let me know. Many thanks in advance for your advice.
Jelmer Kok
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
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.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen
geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s)
are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
Hi Andre,
I hope you looked at the attached "scan1_parameter_file.txt" when you mentioned that you think it seemed to be a reasonable protocol: the parameters in the body of the email Bruce is referring to were the suggested parameters in "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...", not the ones I am using/planning to adjust.
Thanks,
Jelmer
________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 18:10 Aan: Freesurfer support list CC: Andre van der Kouwe Onderwerp: Re: [Freesurfer] quality T1 scans for new study
no, I just looked at the ones in the body of your email On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Bruce and Andre,
PS I am sorry, but may I assume you have only looked at the parameters in "scan1_parameter_file.txt" and not in "scan2_parameter_file.txt"? That would be fine, but I would just like to check we are talking about the same scan parameters that seem to be fine...
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Kok, JG (neuro) [j.g.kok02@umcg.nl] Verzonden: dinsdag 1 april 2014 16:45 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Bruce and Andre,
Many thanks for your comments!
Cheers,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Andre van der Kouwe [andre@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 15:37 Aan: Bruce Fischl; Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
No, I think that's a reasonable protocol to use and good to use SENSE to speed it up.
-------- Original message -------- From: Bruce Fischl Date:04/01/2014 2:28 PM (GMT+02:00) To: Freesurfer support list Cc: Andre van der Kouwe Subject: Re: [Freesurfer] quality T1 scans for new study
looks pretty reasonable. Andre: any comments/suggestions?
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Hi Bruce,
Thanks for your fast reply.
Hereby I attach the parameter files of both scans (although I suspect looking at the parameters of "scan1" may be sufficient).
Checking it with the information on Philips at "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...":
" Sequence: T1W_3D_TFE_SENSE Acquisition time: 5:13 Voxel size: 1.0 x 1.0 x 1.0 mm3 Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness 1 mm, (3D encoding) Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth 191.5 Hz/px RF: flip angle 7° Acceleration: 2x SENSE "
suggests that parameters in "scan1_parameter_file.txt" are already pretty similar to those I guess. (Is it the SENSE that is
missing in our protocol that is the most important difference?)
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl
[fischl@nmr.mgh.harvard.edu]
Verzonden: dinsdag 1 april 2014 14:09 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Jelmer
if you give us the specific acquisition details we can help more (receive coil, acceleration, voxel size, sequence type, TR/TE/TI/flip angle/bandwidth, etc....). We also have recommended morphometry sequences on our website.
10 min is a pretty long structural scan for a modern MRI scanner.
cheers Bruce
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Freesurfer experts, We are planning to start a new MRI study which will include T1 scans. As we are in a testing phase now, I was wondering whether you could comment on the attached screenshots. Clearly, "scan1" has a better white matter/grey matter contrast than "scan2". Do you think going for "scan1" would be the sensible thing to do when we later wish to use Freesurfer with these scans? Or perhaps is neither of the examples I attached good enough?
By the way, these scans were acquired on a Philips 3T scanner, both taking around 10 minutes.
It you need any more information, please let me know. Many thanks in advance for your advice.
Jelmer Kok
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
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.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen
geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s)
are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
Dear Bruce, Andre, someone else,
I think I caused some misunderstanding yesterday for which I am sorry. Now I do not know on what parameters Andre commented. So to hopefully make things clear I am once more attaching the parameter file which was used to create a T1 image (see attached screenshots) that may be of good quality. I hope you are willing to have a look and see if these parameters would result in good quaity T1 images.
Thanks,
Jelmer
________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Kok, JG (neuro) [j.g.kok02@umcg.nl] Verzonden: dinsdag 1 april 2014 18:17 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Andre,
I hope you looked at the attached "scan1_parameter_file.txt" when you mentioned that you think it seemed to be a reasonable protocol: the parameters in the body of the email Bruce is referring to were the suggested parameters in "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...", not the ones I am using/planning to adjust.
Thanks,
Jelmer
________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 18:10 Aan: Freesurfer support list CC: Andre van der Kouwe Onderwerp: Re: [Freesurfer] quality T1 scans for new study
no, I just looked at the ones in the body of your email On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Bruce and Andre,
PS I am sorry, but may I assume you have only looked at the parameters in "scan1_parameter_file.txt" and not in "scan2_parameter_file.txt"? That would be fine, but I would just like to check we are talking about the same scan parameters that seem to be fine...
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Kok, JG (neuro) [j.g.kok02@umcg.nl] Verzonden: dinsdag 1 april 2014 16:45 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Bruce and Andre,
Many thanks for your comments!
Cheers,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Andre van der Kouwe [andre@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 15:37 Aan: Bruce Fischl; Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
No, I think that's a reasonable protocol to use and good to use SENSE to speed it up.
-------- Original message -------- From: Bruce Fischl Date:04/01/2014 2:28 PM (GMT+02:00) To: Freesurfer support list Cc: Andre van der Kouwe Subject: Re: [Freesurfer] quality T1 scans for new study
looks pretty reasonable. Andre: any comments/suggestions?
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Hi Bruce,
Thanks for your fast reply.
Hereby I attach the parameter files of both scans (although I suspect looking at the parameters of "scan1" may be sufficient).
Checking it with the information on Philips at "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...":
" Sequence: T1W_3D_TFE_SENSE Acquisition time: 5:13 Voxel size: 1.0 x 1.0 x 1.0 mm3 Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness 1 mm, (3D encoding) Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth 191.5 Hz/px RF: flip angle 7° Acceleration: 2x SENSE "
suggests that parameters in "scan1_parameter_file.txt" are already pretty similar to those I guess. (Is it the SENSE that is
missing in our protocol that is the most important difference?)
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl
[fischl@nmr.mgh.harvard.edu]
Verzonden: dinsdag 1 april 2014 14:09 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Jelmer
if you give us the specific acquisition details we can help more (receive coil, acceleration, voxel size, sequence type, TR/TE/TI/flip angle/bandwidth, etc....). We also have recommended morphometry sequences on our website.
10 min is a pretty long structural scan for a modern MRI scanner.
cheers Bruce
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Freesurfer experts, We are planning to start a new MRI study which will include T1 scans. As we are in a testing phase now, I was wondering whether you could comment on the attached screenshots. Clearly, "scan1" has a better white matter/grey matter contrast than "scan2". Do you think going for "scan1" would be the sensible thing to do when we later wish to use Freesurfer with these scans? Or perhaps is neither of the examples I attached good enough?
By the way, these scans were acquired on a Philips 3T scanner, both taking around 10 minutes.
It you need any more information, please let me know. Many thanks in advance for your advice.
Jelmer Kok
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
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.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen
geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s)
are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
Hi Jelmer
I took a quick look, but it is a lot easier for us if you extract the relevant parameters, as we are not that familiar with Philips in general. Is this inversion-prepared? I didn't see a TI. Generally inversion-preparation improves T1 CNR/unit-time. Also, your wrap direction looks like it is A/P.You might try making it L/R instead which is a shorter dimension. What coil are you using? Are you using sense?
cheers Bruce
On Wed, 2 Apr 2014, Kok, JG (neuro) wrote:
Dear Bruce, Andre, someone else,
I think I caused some misunderstanding yesterday for which I am sorry. Now I do not know on what parameters Andre commented. So to hopefully make things clear I am once more attaching the parameter file which was used to create a T1 image (see attached screenshots) that may be of good quality. I hope you are willing to have a look and see if these parameters would result in good quaity T1 images.
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Kok, JG (neuro) [j.g.kok02@umcg.nl] Verzonden: dinsdag 1 april 2014 18:17 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Andre,
I hope you looked at the attached "scan1_parameter_file.txt" when you mentioned that you think it seemed to be a reasonable protocol: the parameters in the body of the email Bruce is referring to were the suggested parameters in "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...", not the ones I am using/planning to adjust.
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 18:10 Aan: Freesurfer support list CC: Andre van der Kouwe Onderwerp: Re: [Freesurfer] quality T1 scans for new study
no, I just looked at the ones in the body of your email On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Bruce and Andre,
PS I am sorry, but may I assume you have only looked at the parameters in "scan1_parameter_file.txt" and not in "scan2_parameter_file.txt"? That would be fine, but I would just like to check we are talking about the same scan parameters that seem to be fine...
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Kok, JG (neuro) [j.g.kok02@umcg.nl] Verzonden: dinsdag 1 april 2014 16:45 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Bruce and Andre,
Many thanks for your comments!
Cheers,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Andre van der Kouwe [andre@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 15:37 Aan: Bruce Fischl; Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
No, I think that's a reasonable protocol to use and good to use SENSE to speed it up.
-------- Original message -------- From: Bruce Fischl Date:04/01/2014 2:28 PM (GMT+02:00) To: Freesurfer support list Cc: Andre van der Kouwe Subject: Re: [Freesurfer] quality T1 scans for new study
looks pretty reasonable. Andre: any comments/suggestions?
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Hi Bruce,
Thanks for your fast reply.
Hereby I attach the parameter files of both scans (although I suspect looking at the parameters of "scan1" may be sufficient).
Checking it with the information on Philips at "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...":
" Sequence: T1W_3D_TFE_SENSE Acquisition time: 5:13 Voxel size: 1.0 x 1.0 x 1.0 mm3 Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness 1 mm, (3D encoding) Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth 191.5 Hz/px RF: flip angle 7° Acceleration: 2x SENSE "
suggests that parameters in "scan1_parameter_file.txt" are already pretty similar to those I guess. (Is it the SENSE that is
missing in our protocol that is the most important difference?)
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl
[fischl@nmr.mgh.harvard.edu]
Verzonden: dinsdag 1 april 2014 14:09 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Jelmer
if you give us the specific acquisition details we can help more (receive coil, acceleration, voxel size, sequence type, TR/TE/TI/flip angle/bandwidth, etc....). We also have recommended morphometry sequences on our website.
10 min is a pretty long structural scan for a modern MRI scanner.
cheers Bruce
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Freesurfer experts, We are planning to start a new MRI study which will include T1 scans. As we are in a testing phase now, I was wondering whether you could comment on the attached screenshots. Clearly, "scan1" has a better white matter/grey matter contrast than "scan2". Do you think going for "scan1" would be the sensible thing to do when we later wish to use Freesurfer with these scans? Or perhaps is neither of the examples I attached good enough?
By the way, these scans were acquired on a Philips 3T scanner, both taking around 10 minutes.
It you need any more information, please let me know. Many thanks in advance for your advice.
Jelmer Kok
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
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.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen
geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s)
are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
Hi Bruce,
Thank you very much for your time. I was just talking to our physicist on this subject, and he said, as you judge the quality of a sequence by its parameters, it may make more sense to run a scan using the parameters as proposed by Freesurfer for Philips (as in the body of the email yesterday) than to ask you to comment on our parameters.
As I agree that may be more sensible, we will try that first. Thank you very much for your considerations (so far)!
Cheers,
Jelmer
________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: woensdag 2 april 2014 14:30 Aan: Freesurfer support list CC: Andre van der Kouwe Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Jelmer
I took a quick look, but it is a lot easier for us if you extract the relevant parameters, as we are not that familiar with Philips in general. Is this inversion-prepared? I didn't see a TI. Generally inversion-preparation improves T1 CNR/unit-time. Also, your wrap direction looks like it is A/P.You might try making it L/R instead which is a shorter dimension. What coil are you using? Are you using sense?
cheers Bruce
On Wed, 2 Apr 2014, Kok, JG (neuro) wrote:
Dear Bruce, Andre, someone else,
I think I caused some misunderstanding yesterday for which I am sorry. Now I do not know on what parameters Andre commented. So to hopefully make things clear I am once more attaching the parameter file which was used to create a T1 image (see attached screenshots) that may be of good quality. I hope you are willing to have a look and see if these parameters would result in good quaity T1 images.
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Kok, JG (neuro) [j.g.kok02@umcg.nl] Verzonden: dinsdag 1 april 2014 18:17 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Andre,
I hope you looked at the attached "scan1_parameter_file.txt" when you mentioned that you think it seemed to be a reasonable protocol: the parameters in the body of the email Bruce is referring to were the suggested parameters in "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...", not the ones I am using/planning to adjust.
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 18:10 Aan: Freesurfer support list CC: Andre van der Kouwe Onderwerp: Re: [Freesurfer] quality T1 scans for new study
no, I just looked at the ones in the body of your email On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Bruce and Andre,
PS I am sorry, but may I assume you have only looked at the parameters in "scan1_parameter_file.txt" and not in "scan2_parameter_file.txt"? That would be fine, but I would just like to check we are talking about the same scan parameters that seem to be fine...
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Kok, JG (neuro) [j.g.kok02@umcg.nl] Verzonden: dinsdag 1 april 2014 16:45 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Bruce and Andre,
Many thanks for your comments!
Cheers,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Andre van der Kouwe [andre@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 15:37 Aan: Bruce Fischl; Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
No, I think that's a reasonable protocol to use and good to use SENSE to speed it up.
-------- Original message -------- From: Bruce Fischl Date:04/01/2014 2:28 PM (GMT+02:00) To: Freesurfer support list Cc: Andre van der Kouwe Subject: Re: [Freesurfer] quality T1 scans for new study
looks pretty reasonable. Andre: any comments/suggestions?
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Hi Bruce,
Thanks for your fast reply.
Hereby I attach the parameter files of both scans (although I suspect looking at the parameters of "scan1" may be sufficient).
Checking it with the information on Philips at "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...":
" Sequence: T1W_3D_TFE_SENSE Acquisition time: 5:13 Voxel size: 1.0 x 1.0 x 1.0 mm3 Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness 1 mm, (3D encoding) Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth 191.5 Hz/px RF: flip angle 7° Acceleration: 2x SENSE "
suggests that parameters in "scan1_parameter_file.txt" are already pretty similar to those I guess. (Is it the SENSE that is
missing in our protocol that is the most important difference?)
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl
[fischl@nmr.mgh.harvard.edu]
Verzonden: dinsdag 1 april 2014 14:09 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Jelmer
if you give us the specific acquisition details we can help more (receive coil, acceleration, voxel size, sequence type, TR/TE/TI/flip angle/bandwidth, etc....). We also have recommended morphometry sequences on our website.
10 min is a pretty long structural scan for a modern MRI scanner.
cheers Bruce
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Freesurfer experts, We are planning to start a new MRI study which will include T1 scans. As we are in a testing phase now, I was wondering whether you could comment on the attached screenshots. Clearly, "scan1" has a better white matter/grey matter contrast than "scan2". Do you think going for "scan1" would be the sensible thing to do when we later wish to use Freesurfer with these scans? Or perhaps is neither of the examples I attached good enough?
By the way, these scans were acquired on a Philips 3T scanner, both taking around 10 minutes.
It you need any more information, please let me know. Many thanks in advance for your advice.
Jelmer Kok
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
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.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen
geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s)
are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
sure, that would be fine. Upload teh whole dataset and we will take a look Bruce On Wed, 2 Apr 2014, Kok, JG (neuro) wrote:
Hi Bruce,
Thank you very much for your time. I was just talking to our physicist on this subject, and he said, as you judge the quality of a sequence by its parameters, it may make more sense to run a scan using the parameters as proposed by Freesurfer for Philips (as in the body of the email yesterday) than to ask you to comment on our parameters.
As I agree that may be more sensible, we will try that first. Thank you very much for your considerations (so far)!
Cheers,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: woensdag 2 april 2014 14:30 Aan: Freesurfer support list CC: Andre van der Kouwe Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Jelmer
I took a quick look, but it is a lot easier for us if you extract the relevant parameters, as we are not that familiar with Philips in general. Is this inversion-prepared? I didn't see a TI. Generally inversion-preparation improves T1 CNR/unit-time. Also, your wrap direction looks like it is A/P.You might try making it L/R instead which is a shorter dimension. What coil are you using? Are you using sense?
cheers Bruce
On Wed, 2 Apr 2014, Kok, JG (neuro) wrote:
Dear Bruce, Andre, someone else,
I think I caused some misunderstanding yesterday for which I am sorry. Now I do not know on what parameters Andre commented. So to hopefully make things clear I am once more attaching the parameter file which was used to create a T1 image (see attached screenshots) that may be of good quality. I hope you are willing to have a look and see if these parameters would result in good quaity T1 images.
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Kok, JG (neuro) [j.g.kok02@umcg.nl] Verzonden: dinsdag 1 april 2014 18:17 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Andre,
I hope you looked at the attached "scan1_parameter_file.txt" when you mentioned that you think it seemed to be a reasonable protocol: the parameters in the body of the email Bruce is referring to were the suggested parameters in "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...", not the ones I am using/planning to adjust.
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 18:10 Aan: Freesurfer support list CC: Andre van der Kouwe Onderwerp: Re: [Freesurfer] quality T1 scans for new study
no, I just looked at the ones in the body of your email On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Bruce and Andre,
PS I am sorry, but may I assume you have only looked at the parameters in "scan1_parameter_file.txt" and not in "scan2_parameter_file.txt"? That would be fine, but I would just like to check we are talking about the same scan parameters that seem to be fine...
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Kok, JG (neuro) [j.g.kok02@umcg.nl] Verzonden: dinsdag 1 april 2014 16:45 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Bruce and Andre,
Many thanks for your comments!
Cheers,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Andre van der Kouwe [andre@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 15:37 Aan: Bruce Fischl; Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
No, I think that's a reasonable protocol to use and good to use SENSE to speed it up.
-------- Original message -------- From: Bruce Fischl Date:04/01/2014 2:28 PM (GMT+02:00) To: Freesurfer support list Cc: Andre van der Kouwe Subject: Re: [Freesurfer] quality T1 scans for new study
looks pretty reasonable. Andre: any comments/suggestions?
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Hi Bruce,
Thanks for your fast reply.
Hereby I attach the parameter files of both scans (although I suspect looking at the parameters of "scan1" may be sufficient).
Checking it with the information on Philips at "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...":
" Sequence: T1W_3D_TFE_SENSE Acquisition time: 5:13 Voxel size: 1.0 x 1.0 x 1.0 mm3 Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness 1 mm, (3D encoding) Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth 191.5 Hz/px RF: flip angle 7° Acceleration: 2x SENSE "
suggests that parameters in "scan1_parameter_file.txt" are already pretty similar to those I guess. (Is it the SENSE that is
missing in our protocol that is the most important difference?)
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl
[fischl@nmr.mgh.harvard.edu]
Verzonden: dinsdag 1 april 2014 14:09 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Jelmer
if you give us the specific acquisition details we can help more (receive coil, acceleration, voxel size, sequence type, TR/TE/TI/flip angle/bandwidth, etc....). We also have recommended morphometry sequences on our website.
10 min is a pretty long structural scan for a modern MRI scanner.
cheers Bruce
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Freesurfer experts, We are planning to start a new MRI study which will include T1 scans. As we are in a testing phase now, I was wondering whether you could comment on the attached screenshots. Clearly, "scan1" has a better white matter/grey matter contrast than "scan2". Do you think going for "scan1" would be the sensible thing to do when we later wish to use Freesurfer with these scans? Or perhaps is neither of the examples I attached good enough?
By the way, these scans were acquired on a Philips 3T scanner, both taking around 10 minutes.
It you need any more information, please let me know. Many thanks in advance for your advice.
Jelmer Kok
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
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.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen
geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s)
are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Great, thanks again!
________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: woensdag 2 april 2014 18:22 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
sure, that would be fine. Upload teh whole dataset and we will take a look Bruce On Wed, 2 Apr 2014, Kok, JG (neuro) wrote:
Hi Bruce,
Thank you very much for your time. I was just talking to our physicist on this subject, and he said, as you judge the quality of a sequence by its parameters, it may make more sense to run a scan using the parameters as proposed by Freesurfer for Philips (as in the body of the email yesterday) than to ask you to comment on our parameters.
As I agree that may be more sensible, we will try that first. Thank you very much for your considerations (so far)!
Cheers,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: woensdag 2 april 2014 14:30 Aan: Freesurfer support list CC: Andre van der Kouwe Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Jelmer
I took a quick look, but it is a lot easier for us if you extract the relevant parameters, as we are not that familiar with Philips in general. Is this inversion-prepared? I didn't see a TI. Generally inversion-preparation improves T1 CNR/unit-time. Also, your wrap direction looks like it is A/P.You might try making it L/R instead which is a shorter dimension. What coil are you using? Are you using sense?
cheers Bruce
On Wed, 2 Apr 2014, Kok, JG (neuro) wrote:
Dear Bruce, Andre, someone else,
I think I caused some misunderstanding yesterday for which I am sorry. Now I do not know on what parameters Andre commented. So to hopefully make things clear I am once more attaching the parameter file which was used to create a T1 image (see attached screenshots) that may be of good quality. I hope you are willing to have a look and see if these parameters would result in good quaity T1 images.
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Kok, JG (neuro) [j.g.kok02@umcg.nl] Verzonden: dinsdag 1 april 2014 18:17 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Andre,
I hope you looked at the attached "scan1_parameter_file.txt" when you mentioned that you think it seemed to be a reasonable protocol: the parameters in the body of the email Bruce is referring to were the suggested parameters in "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...", not the ones I am using/planning to adjust.
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 18:10 Aan: Freesurfer support list CC: Andre van der Kouwe Onderwerp: Re: [Freesurfer] quality T1 scans for new study
no, I just looked at the ones in the body of your email On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Bruce and Andre,
PS I am sorry, but may I assume you have only looked at the parameters in "scan1_parameter_file.txt" and not in "scan2_parameter_file.txt"? That would be fine, but I would just like to check we are talking about the same scan parameters that seem to be fine...
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Kok, JG (neuro) [j.g.kok02@umcg.nl] Verzonden: dinsdag 1 april 2014 16:45 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Bruce and Andre,
Many thanks for your comments!
Cheers,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Andre van der Kouwe [andre@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 15:37 Aan: Bruce Fischl; Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
No, I think that's a reasonable protocol to use and good to use SENSE to speed it up.
-------- Original message -------- From: Bruce Fischl Date:04/01/2014 2:28 PM (GMT+02:00) To: Freesurfer support list Cc: Andre van der Kouwe Subject: Re: [Freesurfer] quality T1 scans for new study
looks pretty reasonable. Andre: any comments/suggestions?
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Hi Bruce,
Thanks for your fast reply.
Hereby I attach the parameter files of both scans (although I suspect looking at the parameters of "scan1" may be sufficient).
Checking it with the information on Philips at "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...":
" Sequence: T1W_3D_TFE_SENSE Acquisition time: 5:13 Voxel size: 1.0 x 1.0 x 1.0 mm3 Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness 1 mm, (3D encoding) Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth 191.5 Hz/px RF: flip angle 7° Acceleration: 2x SENSE "
suggests that parameters in "scan1_parameter_file.txt" are already pretty similar to those I guess. (Is it the SENSE that is
missing in our protocol that is the most important difference?)
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl
[fischl@nmr.mgh.harvard.edu]
Verzonden: dinsdag 1 april 2014 14:09 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Jelmer
if you give us the specific acquisition details we can help more (receive coil, acceleration, voxel size, sequence type, TR/TE/TI/flip angle/bandwidth, etc....). We also have recommended morphometry sequences on our website.
10 min is a pretty long structural scan for a modern MRI scanner.
cheers Bruce
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Freesurfer experts, We are planning to start a new MRI study which will include T1 scans. As we are in a testing phase now, I was wondering whether you could comment on the attached screenshots. Clearly, "scan1" has a better white matter/grey matter contrast than "scan2". Do you think going for "scan1" would be the sensible thing to do when we later wish to use Freesurfer with these scans? Or perhaps is neither of the examples I attached good enough?
By the way, these scans were acquired on a Philips 3T scanner, both taking around 10 minutes.
It you need any more information, please let me know. Many thanks in advance for your advice.
Jelmer Kok
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
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.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen
geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s)
are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
freesurfer@nmr.mgh.harvard.edu
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Andre van der Kouwe -
Bruce Fischl -
Kok, JG (neuro)