Dear freesurfers,
I wondered is it okay to analyze isotropic data which was converted to the anisotropic one.
The original data has (0.390625, 0.390625, 1.5) mm size and (512, 512, 104) voxels. It obtained from 3T scanner.
I know the Freesurfer recommend isotropic data (1,1,1)mm. Does it have any problem to use the data I just transformed?
To do this, I rescaled the images and did bilinear interpolation to create an isotropic 8-bit version of images.
Thanks for any help.
EK
Hi EK
it's an empirical question. That is *very* anisotropic, so I suspect that there will be unavoidable biases in things like thickness maps which will be more accurate in regions in which the folds happen to place the cortex in the high resolution plane. That said, if the CNR is good enough it will probably generate reasonable surfaces.
cheers Bruce On Fri, 4 May 2012, EK Kim wrote:
Dear freesurfers, I wondered is it okay to analyze isotropic data which was converted to the anisotropic one. The original data has (0.390625, 0.390625, 1.5) mm size and (512, 512, 104) voxels. It obtained from 3T scanner. I know the Freesurfer recommend isotropic data (1,1,1)mm. Does it have any problem to use the data I just transformed? To do this, I rescaled the images and did bilinear interpolation to create an isotropic 8-bit version of images. Thanks for any help. EK
Thank you for the answer. But I still confuse to convert the data. Does this mean is it 'not okay' to convert the anisotropic data to the isotropic? Then should I analyze the original one?
2012년 5월 4일 금요일에 Bruce Fischlfischl@nmr.mgh.harvard.edu님이 작성:
Hi EK
it's an empirical question. That is *very* anisotropic, so I suspect that
there will be unavoidable biases in things like thickness maps which will be more accurate in regions in which the folds happen to place the cortex in the high resolution plane. That said, if the CNR is good enough it will probably generate reasonable surfaces.
cheers Bruce On Fri, 4 May 2012, EK Kim wrote:
Dear freesurfers,
I wondered is it okay to analyze isotropic data which was converted to
the
anisotropic one.
The original data has (0.390625, 0.390625, 1.5) mm size and (512, 512,
104)
voxels. It obtained from 3T scanner.
I know the Freesurfer recommend isotropic data (1,1,1)mm. Does it have any problem to use the data I just transformed?
To do this, I rescaled the images and did bilinear interpolation to
create
an isotropic 8-bit version of images.
Thanks for any help.
EK
The information in this e-mail is intended only for the person to whom it
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if you give it to recon-all it will convert it internally, so you don't need to convert it yourself On Fri, 4 May 2012, EK Kim wrote:
Thank you for the answer. But I still confuse to convert the data. Does this mean is it 'not okay' to convert the anisotropic data to the isotropic? Then should I analyze the original one?
2012? 5?4?????Bruce Fischlfischl@nmr.mgh.harvard.edu?? ??:
Hi EK
it's an empirical question. That is *very* anisotropic, so I suspect that
there will be unavoidable biases in things like thickness maps which will be more accurate in regions in which the folds happen to place the cortex in the high resolution plane. That said, if the CNR is good enough it will probably generate reasonable surfaces.
cheers Bruce On Fri, 4 May 2012, EK Kim wrote:
Dear freesurfers, I wondered is it okay to analyze isotropic data which was converted to
the
anisotropic one. The original data has (0.390625, 0.390625, 1.5) mm size and (512, 512,
voxels. It obtained from 3T scanner. I know the Freesurfer recommend isotropic data (1,1,1)mm. Does it have any problem to use the data I just transformed? To do this, I rescaled the images and did bilinear interpolation to
create
an isotropic 8-bit version of images. Thanks for any help. EK
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
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.
Thank you, but again I think that there might be no internal convert in my data from the recon-all log files.
The other data set I used had records about internal convert in their recon-all log file representing as (1 1 1)mm but this data was not.
So I worry about whether correct internal convert was preprocessed or not. How can I confirm the processes?
Sorry for bothering you. Thank you in advance.
2012년 5월 4일 금요일에 Bruce Fischlfischl@nmr.mgh.harvard.edu님이 작성:
if you give it to recon-all it will convert it internally, so you don't
need to convert it yourself
On Fri, 4 May 2012, EK Kim wrote:
Thank you for the answer. But I still confuse to convert the data. Does this mean is it 'not okay' to convert the anisotropic data to the isotropic? Then should I analyze the original one?
2012? 5?4?????Bruce Fischlfischl@nmr.mgh.harvard.edu?? ??:
Hi EK
it's an empirical question. That is *very* anisotropic, so I suspect
that
there will be unavoidable biases in things like thickness maps which
will be
more accurate in regions in which the folds happen to place the cortex in the high resolution plane. That said, if the CNR is good enough it will probably generate reasonable surfaces.
cheers Bruce On Fri, 4 May 2012, EK Kim wrote:
Dear freesurfers,
I wondered is it okay to analyze isotropic data which was converted to
the
anisotropic one.
The original data has (0.390625, 0.390625, 1.5) mm size and (512, 512,
voxels. It obtained from 3T scanner.
I know the Freesurfer recommend isotropic data (1,1,1)mm. Does it have any problem to use the data I just transformed?
To do this, I rescaled the images and did bilinear interpolation to
create
an isotropic 8-bit version of images.
Thanks for any help.
EK
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
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.
You could run mri_info on the orig.mgz to verify the dimensions.
On Fri, 4 May 2012, EK Kim wrote:
Thank you, but again I think that there might be no internal convert in my data from the recon-all log files.
The other data set I used had records about internal convert in their recon-all log file representing as (1 1 1)mm but this data was not.
So I worry about whether correct internal convert was preprocessed or not. How can I confirm the processes?
Sorry for bothering you. Thank you in advance.
2012³â 5¿ù 4ÀÏ ±Ý¿äÀÏ¿¡ Bruce Fischlfischl@nmr.mgh.harvard.edu´ÔÀÌ ÀÛ¼º:
if you give it to recon-all it will convert it internally, so you don't
need to convert it yourself
On Fri, 4 May 2012, EK Kim wrote:
Thank you for the answer. But I still confuse to convert the data. Does this mean is it 'not okay' to convert the anisotropic data to the isotropic? Then should I analyze the original one?
2012? 5?4?????Bruce Fischlfischl@nmr.mgh.harvard.edu?? ??:
Hi EK
it's an empirical question. That is *very* anisotropic, so I suspect
that
there will be unavoidable biases in things like thickness maps which
will be
more accurate in regions in which the folds happen to place the cortex in the high resolution plane. That said, if the CNR is good enough it will probably generate reasonable surfaces.
cheers Bruce On Fri, 4 May 2012, EK Kim wrote:
Dear freesurfers,
I wondered is it okay to analyze isotropic data which was converted to
the
anisotropic one.
The original data has (0.390625, 0.390625, 1.5) mm size and (512, 512,
voxels. It obtained from 3T scanner.
I know the Freesurfer recommend isotropic data (1,1,1)mm. Does it have any problem to use the data I just transformed?
To do this, I rescaled the images and did bilinear interpolation to
create
an isotropic 8-bit version of images.
Thanks for any help.
EK
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
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.
run:
mri_info $SUBJECTS_DIR/$subject/mri/orig.mgz
and you should see that it is 1mm isotropic
cheers Bruce On Fri, 4 May 2012, EK Kim wrote:
Thank you, but again I think that there might be no internal convert in my data from the recon-all log files.
The other data set I used had records about internal convert in their recon-all log file representing as (1 1 1)mm but this data was not.
So I worry about whether correct internal convert was preprocessed or not. How can I confirm the processes?
Sorry for bothering you. Thank you in advance.
2012? 5?4?????Bruce Fischlfischl@nmr.mgh.harvard.edu?? ??:
if you give it to recon-all it will convert it internally, so you don't
need to convert it yourself
On Fri, 4 May 2012, EK Kim wrote:
Thank you for the answer. But I still confuse to convert the data. Does this mean is it 'not okay' to convert the anisotropic data to the isotropic? Then should I analyze the original one?
2012? 5?4?????Bruce Fischlfischl@nmr.mgh.harvard.edu?? ??:
Hi EK
it's an empirical question. That is *very* anisotropic, so I suspect
that
there will be unavoidable biases in things like thickness maps which will
be
more accurate in regions in which the folds happen to place the cortex in the high resolution plane. That said, if the CNR is good enough it will probably generate reasonable surfaces.
cheers Bruce On Fri, 4 May 2012, EK Kim wrote:
Dear freesurfers, I wondered is it okay to analyze isotropic data which was converted to
the
anisotropic one. The original data has (0.390625, 0.390625, 1.5) mm size and (512, 512,
voxels. It obtained from 3T scanner. I know the Freesurfer recommend isotropic data (1,1,1)mm. Does it have any problem to use the data I just transformed? To do this, I rescaled the images and did bilinear interpolation to
create
an isotropic 8-bit version of images. Thanks for any help. EK
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
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.
Yes I found it :) Thank you for your help!
Sincerely,
EK.
2012/5/4 Bruce Fischl fischl@nmr.mgh.harvard.edu
run:
mri_info $SUBJECTS_DIR/$subject/mri/**orig.mgz
and you should see that it is 1mm isotropic
cheers Bruce On Fri, 4 May 2012, EK Kim wrote:
Thank you, but again I think that there might be no internal convert in
my data from the recon-all log files.
The other data set I used had records about internal convert in their recon-all log file representing as (1 1 1)mm but this data was not.
So I worry about whether correct internal convert was preprocessed or not. How can I confirm the processes?
Sorry for bothering you. Thank you in advance.
2012? 5?4?????Bruce Fischl<fischl@nmr.mgh.harvard.**edufischl@nmr.mgh.harvard.edu>?? ??:
if you give it to recon-all it will convert it internally, so you don't
need to convert it yourself
On Fri, 4 May 2012, EK Kim wrote:
Thank you for the answer. But I still confuse to convert the data. Does this mean is it 'not okay' to convert the anisotropic data to the isotropic? Then should I analyze the original one?
2012? 5?4?????Bruce Fischl<fischl@nmr.mgh.harvard.**edufischl@nmr.mgh.harvard.edu>??
??:
Hi EK
it's an empirical question. That is *very* anisotropic, so I suspect
that
there will be unavoidable biases in things like thickness maps which
will be
more accurate in regions in which the folds happen to place the cortex
in
the high resolution plane. That said, if the CNR is good enough it will probably generate reasonable surfaces.
cheers Bruce On Fri, 4 May 2012, EK Kim wrote:
Dear freesurfers,
I wondered is it okay to analyze isotropic data which was converted
to
the
anisotropic one.
The original data has (0.390625, 0.390625, 1.5) mm size and (512,
512,
voxels. It obtained from 3T scanner.
I know the Freesurfer recommend isotropic data (1,1,1)mm. Does it have any problem to use the data I just transformed?
To do this, I rescaled the images and did bilinear interpolation to
create
an isotropic 8-bit version of images.
Thanks for any help.
EK
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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/**compliancelinehttp://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@nmr.mgh.harvard.edu
-
Bruce Fischl -
EK Kim -
Louis Nicholas Vinke