2016-04-08 12:09 GMT-03:00 Gamaliel Huerta Urrea gamaliel.huerta@uv.cl:
Hello Freesurfers
I'm trying to do volumetric reconstruction, i already have done this but. i wanted to see if for the same subject, with different directions of slices i have the same result, and obviously i had different results of volumetric measures. i have used the sequence FSPGR T1 ponderation, with the same parameters for both data acquisition; with voxel 1 mm3, but the direction is changed in both studies axial and sagittal. Both studies are in *.dcm format, and i used the next command for convert dicom to .mgz and after to apply recon-all process:
mri_convert firstdicom.dcm 001.mgz
I would like to know why would i have this problem?
There is some specific slice direction for this kind of study which is suitable ?
I'm interested in cerebellum volumetric information. I attached my results for volumetry.
Cheers
-- *Gamaliel Huerta* *Ingeniero Civil Biomédico* *HealthCare Analytics* *Centro Interdisciplinario de Innovación en Salud* *Universidad de Valparaíso*
Hi Gamaliel
many things will change when you change the slice direction - amount of wrap, possibly your FOV, slab-selection profile if your protocol is slab-selective, and some types of distortion. These will all change the image which will change our results. Of course even if you don't change anything you won't get identical results if you scan twice, but our longitudinal stream is pretty reliable. Andre van der Kouwe has acquitisiton recommendations here:
http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...
cheers Bruce
On Fri, 8 Apr 2016, Gamaliel Huerta Urrea wrote:
2016-04-08 12:09 GMT-03:00 Gamaliel Huerta Urrea gamaliel.huerta@uv.cl: Hello Freesurfers I'm trying to do volumetric reconstruction, i already have done this but. i wanted to see if for the same subject, with different directions of slices i have the same result, and obviously i had different results of volumetric measures. i have used the sequence FSPGR T1 ponderation, with the same parameters for both data acquisition; with voxel 1 mm3, but the direction is changed in both studies axial and sagittal. Both studies are in *.dcm format, and i used the next command for convert dicom to .mgz and after to apply recon-all process:
mri_convert firstdicom.dcm 001.mgz
I would like to know why would i have this problem?
There is some specific slice direction for this kind of study which is suitable ?
I'm interested in cerebellum volumetric information. I attached my results for volumetry.
Cheers
-- Gamaliel Huerta Ingeniero Civil Biomédico HealthCare Analytics Centro Interdisciplinario de Innovación en Salud Universidad de Valparaíso
-- Gamaliel Huerta Ingeniero Civil Biomédico HealthCare Analytics Centro Interdisciplinario de Innovación en Salud Universidad de Valparaíso
I¹d add that SNR may also change if you don¹t acquire as much data axially as you did sagittally. Really it¹s better to acquire your 3D T1w/T2w/FLAIR scans sagittally as this is most efficient.
Peace,
Matt.
On 4/8/16, 10:23 AM, "Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Gamaliel
many things will change when you change the slice direction - amount of wrap, possibly your FOV, slab-selection profile if your protocol is slab-selective, and some types of distortion. These will all change the image which will change our results. Of course even if you don't change anything you won't get identical results if you scan twice, but our longitudinal stream is pretty reliable. Andre van der Kouwe has acquitisiton recommendations here:
http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_p rotocols.pdf
cheers Bruce
On Fri, 8 Apr 2016, Gamaliel Huerta Urrea wrote:
2016-04-08 12:09 GMT-03:00 Gamaliel Huerta Urrea gamaliel.huerta@uv.cl: Hello Freesurfers I'm trying to do volumetric reconstruction, i already have done this but. i wanted to see if for the same subject, with different directions of slices i have the same result, and obviously i had different results of volumetric measures. i have used the sequence FSPGR T1 ponderation, with the same parameters for both data acquisition; with voxel 1 mm3, but the direction is changed in both studies axial and sagittal. Both studies are in *.dcm format, and i used the next command for convert dicom to .mgz and after to apply recon-all process:
mri_convert firstdicom.dcm 001.mgz
I would like to know why would i have this problem?
There is some specific slice direction for this kind of study which is suitable ?
I'm interested in cerebellum volumetric information. I attached my results for volumetry.
Cheers
-- Gamaliel Huerta Ingeniero Civil Biomédico HealthCare Analytics Centro Interdisciplinario de Innovación en Salud Universidad de Valparaíso
-- Gamaliel Huerta Ingeniero Civil Biomédico HealthCare Analytics Centro Interdisciplinario de Innovación en Salud Universidad de Valparaíso
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.
thanks for the replies :)
2016-04-08 15:15 GMT-03:00 Matt Glasser matt@ma-tea.com:
I¹d add that SNR may also change if you don¹t acquire as much data axially as you did sagittally. Really it¹s better to acquire your 3D T1w/T2w/FLAIR scans sagittally as this is most efficient.
Peace,
Matt.
On 4/8/16, 10:23 AM, "Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Gamaliel
many things will change when you change the slice direction - amount of wrap, possibly your FOV, slab-selection profile if your protocol is slab-selective, and some types of distortion. These will all change the image which will change our results. Of course even if you don't change anything you won't get identical results if you scan twice, but our longitudinal stream is pretty reliable. Andre van der Kouwe has acquitisiton recommendations here:
http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_p
rotocols.pdf
cheers Bruce
On Fri, 8 Apr 2016, Gamaliel Huerta Urrea wrote:
2016-04-08 12:09 GMT-03:00 Gamaliel Huerta Urrea gamaliel.huerta@uv.cl: Hello Freesurfers I'm trying to do volumetric reconstruction, i already have done this but. i wanted to see if for the same subject, with different directions of slices i have the same result, and obviously i had different results of volumetric measures. i have used the sequence FSPGR T1 ponderation, with the same parameters for both data acquisition; with voxel 1 mm3, but the direction is changed in both studies axial and sagittal. Both studies are in *.dcm format, and i used the next command for convert dicom to .mgz and after to apply recon-all process:
mri_convert firstdicom.dcm 001.mgz
I would like to know why would i have this problem?
There is some specific slice direction for this kind of study which is suitable ?
I'm interested in cerebellum volumetric information. I attached my results for volumetry.
Cheers
-- Gamaliel Huerta Ingeniero Civil Biomédico HealthCare Analytics Centro Interdisciplinario de Innovación en Salud Universidad de Valparaíso
-- Gamaliel Huerta Ingeniero Civil Biomédico HealthCare Analytics Centro Interdisciplinario de Innovación en Salud Universidad de Valparaíso
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Gamaliel Huerta Urrea -
Matt Glasser