External Email - Use Caution
Hello,
I am trying to overlay a .asc file in either freeview or tksurfer, but so far having no luck.
As practice and to determine the right format, I am simply using lh.thickness, which I've converted to .asc using the following command:
% mris_convert -c lh.thickness lh.white lh.thickness.asc
I am trying to overlay this onto lh.pial for one subject, however I cannot load the file and I get the following error message:
% mri_read(): couldn't determine type of file /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc surfer: couldn't load /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc. If you were trying to load a functional volume, make sure you selected the right registration method, and if necessary, that the registration file exists. If you were trying to load a volume-encoded value file, make sure it has the same number of values as this surface does vertices (128970). sclv_read_from_volume: error in FunD_New
Interestingly, I can load the file as a curvature file, but then can't play around with the threshold.
Do you have any idea what I'm doing wrong? Any help would be appreciated!
Thanks,
Amanda
Not sure. Can you use mris_convert to convert the asc back to a curv file?
On 10/15/2018 11:20 AM, Worker, Amanda wrote:
External Email - Use Caution
Hello,
I am trying to overlay a .asc file in either freeview or tksurfer, but so far having no luck.
As practice and to determine the right format, I am simply using lh.thickness, which I've converted to .asc using the following command:
% mris_convert -c lh.thickness lh.white lh.thickness.asc
I am trying to overlay this onto lh.pial for one subject, however I cannot load the file and I get the following error message:
% mri_read(): couldn't determine type of file /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc surfer: couldn't load /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc. If you were trying to load a functional volume, make sure you selected the right registration method, and if necessary, that the registration file exists. If you were trying to load a volume-encoded value file, make sure it has the same number of values as this surface does vertices (128970). sclv_read_from_volume: error in FunD_New
Interestingly, I can load the file as a curvature file, but then can't play around with the threshold.
Do you have any idea what I'm doing wrong? Any help would be appreciated!
Thanks,
Amanda
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
How would I do that? mris_convert doesn't seem to take .asc as an input?
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: 15 October 2018 16:25:51 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer
Not sure. Can you use mris_convert to convert the asc back to a curv file?
On 10/15/2018 11:20 AM, Worker, Amanda wrote:
External Email - Use CautionHello,
I am trying to overlay a .asc file in either freeview or tksurfer, but so far having no luck.
As practice and to determine the right format, I am simply using lh.thickness, which I've converted to .asc using the following command:
% mris_convert -c lh.thickness lh.white lh.thickness.asc
I am trying to overlay this onto lh.pial for one subject, however I cannot load the file and I get the following error message:
% mri_read(): couldn't determine type of file /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc surfer: couldn't load /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc. If you were trying to load a functional volume, make sure you selected the right registration method, and if necessary, that the registration file exists. If you were trying to load a volume-encoded value file, make sure it has the same number of values as this surface does vertices (128970). sclv_read_from_volume: error in FunD_New
Interestingly, I can load the file as a curvature file, but then can't play around with the threshold.
Do you have any idea what I'm doing wrong? Any help would be appreciated!
Thanks,
Amanda
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr....
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr....
Hi Amanda
mris_convert -c lh.thickness.asc lh.white lh.thickness.mgz
should do the trick cheers Bruce On Mon, 15 Oct 2018, Worker, Amanda wrote:
External Email - Use Caution
How would I do that? mris_convert doesn't seem to take .asc as an input?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: 15 October 2018 16:25:51 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer Not sure. Can you use mris_convert to convert the asc back to a curv file?
On 10/15/2018 11:20 AM, Worker, Amanda wrote:
External Email - Use Caution
Hello,
I am trying to overlay a .asc file in either freeview or tksurfer, but so far having no luck.
As practice and to determine the right format, I am simply using lh.thickness, which I've converted to .asc using the following command:
% mris_convert -c lh.thickness lh.white lh.thickness.asc
I am trying to overlay this onto lh.pial for one subject, however I cannot load the file and I get the following error message:
% mri_read(): couldn't determine type of file /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne
ss.asc
surfer: couldn't load /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne
ss.asc.
If you were trying to load a functional volume, make sure you selected the right registration method, and if necessary, that the registration file exists. If you were trying to load a volume-encoded value file, make sure it has the same number of values as this surface does vertices (128970). sclv_read_from_volume: error in FunD_New
Interestingly, I can load the file as a curvature file, but then can't play around with the threshold.
Do you have any idea what I'm doing wrong? Any help would be appreciated!
Thanks,
Amanda
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr....
an%2Flistinfo%2Ffreesurfer&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3ac3c35e85fb46f47e2c08d63 2b28e63%7C8370cf1416f34c16b83c724071654356%7C0&sdata=p6poNQ0vBOYwWAjR4Ujk5lfKTtIcbEDR6icoWCJ2mz 8%3D&reserved=0
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External Email - Use Caution
Thank you!
So the answer to the first question is that yes I can convert it back to a curvature file and that curvature file can be loaded as an overlay. So this must mean that the problem is with reading the .asc file rather than the file being corrupt?
Cheers,
Amanda
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 15 October 2018 17:06:26 To: Freesurfer support list Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer
Hi Amanda
mris_convert -c lh.thickness.asc lh.white lh.thickness.mgz
should do the trick cheers Bruce On Mon, 15 Oct 2018, Worker, Amanda wrote:
External Email - Use CautionHow would I do that? mris_convert doesn't seem to take .asc as an input?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: 15 October 2018 16:25:51 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer Not sure. Can you use mris_convert to convert the asc back to a curv file?
On 10/15/2018 11:20 AM, Worker, Amanda wrote:
External Email - Use CautionHello,
I am trying to overlay a .asc file in either freeview or tksurfer, but so far having no luck.
As practice and to determine the right format, I am simply using lh.thickness, which I've converted to .asc using the following command:
% mris_convert -c lh.thickness lh.white lh.thickness.asc
I am trying to overlay this onto lh.pial for one subject, however I cannot load the file and I get the following error message:
% mri_read(): couldn't determine type of file /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne
ss.asc
surfer: couldn't load /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne
ss.asc.
If you were trying to load a functional volume, make sure you selected the right registration method, and if necessary, that the registration file exists. If you were trying to load a volume-encoded value file, make sure it has the same number of values as this surface does vertices (128970). sclv_read_from_volume: error in FunD_New
Interestingly, I can load the file as a curvature file, but then can't play around with the threshold.
Do you have any idea what I'm doing wrong? Any help would be appreciated!
Thanks,
Amanda
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr....
an%2Flistinfo%2Ffreesurfer&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3ac3c35e85fb46f47e2c08d63 2b28e63%7C8370cf1416f34c16b83c724071654356%7C0&sdata=p6poNQ0vBOYwWAjR4Ujk5lfKTtIcbEDR6icoWCJ2mz 8%3D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.... an%2Flistinfo%2Ffreesurfer&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3ac3c35e85fb46f47e2c08d63 2b28e63%7C8370cf1416f34c16b83c724071654356%7C0&sdata=p6poNQ0vBOYwWAjR4Ujk5lfKTtIcbEDR6icoWCJ2mz 8%3D&reserved=0
Hi Amanda
can you try it in freeview? tksurfer has been deprecated for a while now
cheers Bruce On Tue, 16 Oct 2018, Worker, Amanda wrote:
External Email - Use Caution
Thank you!
So the answer to the first question is that yes I can convert it back to a curvature file and that curvature file can be loaded as an overlay. So this must mean that the problem is with reading the .asc file rather than the file being corrupt?
Cheers,
Amanda
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 15 October 2018 17:06:26 To: Freesurfer support list Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer Hi Amanda
mris_convert -c lh.thickness.asc lh.white lh.thickness.mgz
should do the trick cheers Bruce On Mon, 15 Oct 2018, Worker, Amanda wrote:
External Email - Use Caution
How would I do that? mris_convert doesn't seem to take .asc as an input?
From: freesurfer-bounces@nmr.mgh.harvard.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: 15 October 2018 16:25:51 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using a .asc file as overlay in
freeview/tksurfer
Not sure. Can you use mris_convert to convert the asc back to a curv file?
On 10/15/2018 11:20 AM, Worker, Amanda wrote:
External Email - Use Caution
Hello,
I am trying to overlay a .asc file in either freeview or tksurfer, but so far having no luck.
As practice and to determine the right format, I am simply using lh.thickness, which I've converted to .asc using the following command:
% mris_convert -c lh.thickness lh.white lh.thickness.asc
I am trying to overlay this onto lh.pial for one subject, however I cannot load the file and I get the following error message:
% mri_read(): couldn't determine type of file /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c70
62a631d19/surf/lh.thickne
ss.asc
surfer: couldn't load /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c70
62a631d19/surf/lh.thickne
ss.asc.
If you were trying to load a functional volume, make sure you selected the right registration method, and if necessary, that the registration file exists. If you were trying to load a volume-encoded value file, make sure it has the same number of values as this surface does vertices (128970). sclv_read_from_volume: error in FunD_New
Interestingly, I can load the file as a curvature file, but then can't play around with the threshold.
Do you have any idea what I'm doing wrong? Any help would be
appreciated!
Thanks,
Amanda
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nm
r.mgh.harvard.edu%2Fmailm
an%2Flistinfo%2Ffreesurfer&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3
ac3c35e85fb46f47e2c08d63
2b28e63%7C8370cf1416f34c16b83c724071654356%7C0&sdata=p6poNQ0vBOYwWAjR4U
jk5lfKTtIcbEDR6icoWCJ2mz
8%3D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr
.mgh.harvard.edu%2Fmailm
an%2Flistinfo%2Ffreesurfer&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3
ac3c35e85fb46f47e2c08d63
2b28e63%7C8370cf1416f34c16b83c724071654356%7C0&sdata=p6poNQ0vBOYwWAjR4U
jk5lfKTtIcbEDR6icoWCJ2mz
8%3D&reserved=0
External Email - Use Caution
Hi Bruce,
I have the same issue in freeview. The error is:
ERROR: could not determine type of /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc mri_read(): couldn't determine type of file /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc ERROR: could not determine type of /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc could not read overlay data from /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc mri_read(): couldn't determine type of file /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc
Thanks,
Amanda
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 16 October 2018 18:13:18 To: Freesurfer support list Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer
Hi Amanda
can you try it in freeview? tksurfer has been deprecated for a while now
cheers Bruce On Tue, 16 Oct 2018, Worker, Amanda wrote:
External Email - Use CautionThank you!
So the answer to the first question is that yes I can convert it back to a curvature file and that curvature file can be loaded as an overlay. So this must mean that the problem is with reading the .asc file rather than the file being corrupt?
Cheers,
Amanda
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 15 October 2018 17:06:26 To: Freesurfer support list Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer
Hi Amanda
mris_convert -c lh.thickness.asc lh.white lh.thickness.mgz
should do the trick cheers Bruce On Mon, 15 Oct 2018, Worker, Amanda wrote:
External Email - Use CautionHow would I do that? mris_convert doesn't seem to take .asc as an input?
From: freesurfer-bounces@nmr.mgh.harvard.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: 15 October 2018 16:25:51 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using a .asc file as overlay in
freeview/tksurfer
Not sure. Can you use mris_convert to convert the asc back to a curv file?
On 10/15/2018 11:20 AM, Worker, Amanda wrote:
External Email - Use CautionHello,
I am trying to overlay a .asc file in either freeview or tksurfer, but so far having no luck.
As practice and to determine the right format, I am simply using lh.thickness, which I've converted to .asc using the following command:
% mris_convert -c lh.thickness lh.white lh.thickness.asc
I am trying to overlay this onto lh.pial for one subject, however I cannot load the file and I get the following error message:
% mri_read(): couldn't determine type of file /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c70
62a631d19/surf/lh.thickne
ss.asc
surfer: couldn't load /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c70
62a631d19/surf/lh.thickne
ss.asc.
If you were trying to load a functional volume, make sure you selected the right registration method, and if necessary, that the registration file exists. If you were trying to load a volume-encoded value file, make sure it has the same number of values as this surface does vertices (128970). sclv_read_from_volume: error in FunD_New
Interestingly, I can load the file as a curvature file, but then can't play around with the threshold.
Do you have any idea what I'm doing wrong? Any help would be
appreciated!
Thanks,
Amanda
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nm
r.mgh.harvard.edu%2Fmailm
an%2Flistinfo%2Ffreesurfer&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3
ac3c35e85fb46f47e2c08d63
2b28e63%7C8370cf1416f34c16b83c724071654356%7C0&sdata=p6poNQ0vBOYwWAjR4U
jk5lfKTtIcbEDR6icoWCJ2mz
8%3D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr
.mgh.harvard.edu%2Fmailm
an%2Flistinfo%2Ffreesurfer&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3
ac3c35e85fb46f47e2c08d63
2b28e63%7C8370cf1416f34c16b83c724071654356%7C0&sdata=p6poNQ0vBOYwWAjR4U
jk5lfKTtIcbEDR6icoWCJ2mz
8%3D&reserved=0
Hi Amanda
what is your command line? And is there any reason you can't convert it back to binary and load it that way if ascii fails?
cheers Bruce On Wed, 17 Oct 2018, Worker, Amanda wrote:
External Email - Use Caution
Hi Bruce,
I have the same issue in freeview. The error is:
ERROR: could not determine type of/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne ss.asc mri_read(): couldn't determine type of file/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne ss.asc ERROR: could not determine type of/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne ss.asc could not read overlay data from/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne ss.asc mri_read(): couldn't determine type of file/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne ss.asc
Thanks,
Amanda
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 16 October 2018 18:13:18 To: Freesurfer support list Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer Hi Amanda
can you try it in freeview? tksurfer has been deprecated for a while now
cheers Bruce On Tue, 16 Oct 2018, Worker, Amanda wrote:
External Email - Use Caution
Thank you!
So the answer to the first question is that yes I can convert it back to a curvature file and that curvature file can be loaded as an overlay. So this must mean that the problem is with reading the .asc file rather than the file being corrupt?
Cheers,
Amanda
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 15 October 2018 17:06:26 To: Freesurfer support list Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer Hi Amanda
mris_convert -c lh.thickness.asc lh.white lh.thickness.mgz
should do the trick cheers Bruce On Mon, 15 Oct 2018, Worker, Amanda wrote:
External Email - Use Caution
How would I do that? mris_convert doesn't seem to take .asc as an input?
From: freesurfer-bounces@nmr.mgh.harvard.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: 15 October 2018 16:25:51 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using a .asc file as overlay in
freeview/tksurfer
Not sure. Can you use mris_convert to convert the asc back to a curv file?
On 10/15/2018 11:20 AM, Worker, Amanda wrote:
External Email - Use Caution
Hello,
I am trying to overlay a .asc file in either freeview or tksurfer, but so far having no luck.
As practice and to determine the right format, I am simply using lh.thickness, which I've converted to .asc using the following command:
% mris_convert -c lh.thickness lh.white lh.thickness.asc
I am trying to overlay this onto lh.pial for one subject, however I cannot load the file and I get the following error message:
% mri_read(): couldn't determine type of file /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c70
62a631d19/surf/lh.thickne
ss.asc
surfer: couldn't load /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c70
62a631d19/surf/lh.thickne
ss.asc.
If you were trying to load a functional volume, make sure you selected the right registration method, and if necessary, that the registration file exists. If you were trying to load a volume-encoded value file, make sure it has the same number of values as this surface does vertices (128970). sclv_read_from_volume: error in FunD_New
Interestingly, I can load the file as a curvature file, but then can't play around with the threshold.
Do you have any idea what I'm doing wrong? Any help would be
appreciated!
Thanks,
Amanda
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nm
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freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Greve, Douglas N.,Ph.D. -
Worker, Amanda