Dear Freesurfer experts,
I uploaded a .nii.gz file (which can be downloaded from 'http://gate.nmr.mgh.harvard.edu/filedrop2/?p=7pbsgklemux'). I hope you would be willing to comment on the quality of this scan for use with Freesurfer (you can find some parameters below; the scan was acquired on a 3T Philips scanner). Running it through recon-all seems to give nice results, but then again, I am in a phase of running pilots before the start of a new study, and I do not have much experience with Freesurfer results yet.
coil: 32 channel Sequence: T1w_TFE_3D TFE factor: 256 Acquisition time: 10:14 FoV FH256xAP256xRL160 mm 160 sagittal slices fold-over direction AP fat shift direction F scan mode 3D
acquisition matrix 256 x 256 acquisition voxel size 1.00/1.00/1.00 reconstructed voxel size 1.00/1.00/1.00 TR shortest (=7.6ms) TE shortest (=3.5ms) RF: flip angle 8 degrees Acceleration: no SENSE inversion-prepared, inversion delay time: shortest
Cheers,
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.
Hi Jelmer
the scan looks quite nice to me. Have you run it through recon-all? That is the best way to get an idea of how well it will work.
cheers Bruce On Fri, 18 Apr 2014, Kok, JG (neuro) wrote:
Dear Freesurfer experts,
I uploaded a .nii.gz file (which can be downloaded from 'http://gate.nmr.mgh.harvard.edu/filedrop2/?p=7pbsgklemux'). I hope you would be willing to comment on the quality of this scan for use with Freesurfer (you can find some parameters below; the scan was acquired on a 3T Philips scanner). Running it through recon-all seems to give nice results, but then again, I am in a phase of running pilots before the start of a new study, and I do not have much experience with Freesurfer results yet.
coil: 32 channel Sequence: T1w_TFE_3D TFE factor: 256 Acquisition time: 10:14 FoV FH256xAP256xRL160 mm 160 sagittal slices fold-over direction AP fat shift direction F scan mode 3D acquisition matrix 256 x 256 acquisition voxel size 1.00/1.00/1.00 reconstructed voxel size 1.00/1.00/1.00 TR shortest (=7.6ms) TE shortest (=3.5ms) RF: flip angle 8 degrees Acceleration: no SENSE inversion-prepared, inversion delay time: shortest
Cheers,
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.
Hi Bruce,
Many thanks for your reply.
I did run it through recon-all and it seems to give nice results. Still, as I am just a beginner using Freesurfer, I would greatly appreciate it when you would have a look at the output which can be downloaded from 'http://gate.nmr.mgh.harvard.edu/filedrop2/?p=69915f8pefn'.
Cheers,
Jelmer
________________________________________
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: vrijdag 18 april 2014 15:45 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 for new study
Hi Jelmer
the scan looks quite nice to me. Have you run it through recon-all? That is the best way to get an idea of how well it will work.
cheers Bruce On Fri, 18 Apr 2014, Kok, JG (neuro) wrote:
Dear Freesurfer experts,
I uploaded a .nii.gz file (which can be downloaded from 'http://gate.nmr.mgh.harvard.edu/filedrop2/?p=7pbsgklemux'). I hope you would be willing to comment on the quality of this scan for use with Freesurfer (you can find some parameters below; the scan was acquired on a 3T Philips scanner). Running it through recon-all seems to give nice results, but then again, I am in a phase of running pilots before the start of a new study, and I do not have much experience with Freesurfer results yet.
coil: 32 channel Sequence: T1w_TFE_3D TFE factor: 256 Acquisition time: 10:14 FoV FH256xAP256xRL160 mm 160 sagittal slices fold-over direction AP fat shift direction F scan mode 3D
acquisition matrix 256 x 256 acquisition voxel size 1.00/1.00/1.00 reconstructed voxel size 1.00/1.00/1.00 TR shortest (=7.6ms) TE shortest (=3.5ms) RF: flip angle 8 degrees Acceleration: no SENSE inversion-prepared, inversion delay time: shortest
Cheers,
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.
________________________________ 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
-
Bruce Fischl -
Kok, JG (neuro)