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_protocols.pdf";, not the ones I am using/planning to adjust.
Thanks, Jelmer ________________________________________ Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl [fis...@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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Kok, JG (neuro) > [j.g.ko...@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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Andre van der Kouwe > [an...@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_protocols.pdf": > > > > " > > 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-boun...@nmr.mgh.harvard.edu > > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl > [fis...@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
