Hi
I would like to analyse local gyrification data for a number of brains in Matlab. I have ran the command
mris_compute_lgi -i lh.pial
which results in a file called lh.pial_lgi. However, I was expecting an output of the form lh.pial_lgi.mat which could be immediately read into Matlab. Do you know how I can convert the file I have into a .mat file?
Thanks in advance, Jonathan
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Hi, B1 field correction was collected during the scan. My question is how it can be used in the surface reconstruction? Thanks, Xiaomin Yue
Hi Xiaomin
can you be more specific? What kind of B1 field map did you collect? Do you mean B1 transmit or receive?
cheers Bruce On Mon, 24 Mar 2014, Xiaomin Yue wrote:
Hi,
B1 field correction was collected during the scan. My question is how it can be used in the surface reconstruction?
Thanks,
Xiaomin Yue
Hi Bruce, Thanks for your response. It is B0 normalization scan. What it does is to get an homogeneity image, which could be used to normalize the MRRAGE image by dividing it. Is there an build in function in freesurfer to do this operation? Thanks,Xiaomin
Date: Mon, 24 Mar 2014 12:42:52 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] B1 correction
Hi Xiaomin
can you be more specific? What kind of B1 field map did you collect? Do you mean B1 transmit or receive?
cheers Bruce On Mon, 24 Mar 2014, Xiaomin Yue wrote:
Hi,
B1 field correction was collected during the scan. My question is how it can be used in the surface reconstruction?
Thanks,
Xiaomin Yue
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Hi, The analysis necessary to my study is to run some analysis on the raw time course data. Before working on the raw time course data, it is necessary to remove linear drifting, mean, and head motion. Can I just specify those parameters without having conditions in the steps of generating design matrix? If so, what command should be used? Thanks,Xiaomin Yue
Sorry, I don't follow what you are asking. FSFAST does not do any drift removal from the raw data, all of that is in the design matrix doug
On 03/26/2014 10:45 AM, Xiaomin Yue wrote:
Hi,
The analysis necessary to my study is to run some analysis on the raw time course data. Before working on the raw time course data, it is necessary to remove linear drifting, mean, and head motion. Can I just specify those parameters without having conditions in the steps of generating design matrix? If so, what command should be used?
Thanks, Xiaomin Yue
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I like to regress out the linear drift, mean, and head motion generated by the motion correction step of fsfast from the raw time course only. Is it possible using fsfast? Xiaomin
Date: Wed, 26 Mar 2014 11:28:57 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fsfast question
Sorry, I don't follow what you are asking. FSFAST does not do any drift removal from the raw data, all of that is in the design matrix doug
On 03/26/2014 10:45 AM, Xiaomin Yue wrote:
Hi,
The analysis necessary to my study is to run some analysis on the raw time course data. Before working on the raw time course data, it is necessary to remove linear drifting, mean, and head motion. Can I just specify those parameters without having conditions in the steps of generating design matrix? If so, what command should be used?
Thanks, Xiaomin Yue
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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No, sorry On 03/26/2014 01:54 PM, Xiaomin Yue wrote:
I like to regress out the linear drift, mean, and head motion generated by the motion correction step of fsfast from the raw time course only. Is it possible using fsfast?
Xiaomin
Date: Wed, 26 Mar 2014 11:28:57 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fsfast question
Sorry, I don't follow what you are asking. FSFAST does not do any drift removal from the raw data, all of that is in the design matrix doug
On 03/26/2014 10:45 AM, Xiaomin Yue wrote:
Hi,
The analysis necessary to my study is to run some analysis on the raw time course data. Before working on the raw time course data, it is necessary to remove linear drifting, mean, and head motion. Can I just specify those parameters without having conditions in the steps of generating design matrix? If so, what command should be used?
Thanks, Xiaomin Yue
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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you could try to run mkanalysis-sess with -notask and your nuisance regressors specified as -nuisreg, then run selxavg3-sess with -no-con-ok and -svres to save the residuals. maybe that solves your problem? caspar
2014-03-26 14:38 GMT-04:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
No, sorry On 03/26/2014 01:54 PM, Xiaomin Yue wrote:
I like to regress out the linear drift, mean, and head motion generated by the motion correction step of fsfast from the raw time course only. Is it possible using fsfast?
Xiaomin
Date: Wed, 26 Mar 2014 11:28:57 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fsfast question
Sorry, I don't follow what you are asking. FSFAST does not do any drift removal from the raw data, all of that is in the design matrix doug
On 03/26/2014 10:45 AM, Xiaomin Yue wrote:
Hi,
The analysis necessary to my study is to run some analysis on the raw time course data. Before working on the raw time course data, it is necessary to remove linear drifting, mean, and head motion. Can I just specify those parameters without having conditions in the steps of generating design matrix? If so, what command should be used?
Thanks, Xiaomin Yue
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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that might work. You'd have to make sure that you specified native space in mkanalysis-sess doug
On 03/26/2014 02:56 PM, Caspar M. Schwiedrzik wrote:
you could try to run mkanalysis-sess with -notask and your nuisance regressors specified as -nuisreg, then run selxavg3-sess with -no-con-ok and -svres to save the residuals. maybe that solves your problem? caspar
2014-03-26 14:38 GMT-04:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
No, sorry On 03/26/2014 01:54 PM, Xiaomin Yue wrote: > I like to regress out the linear drift, mean, and head motion > generated by the motion correction step of fsfast from the raw time > course only. Is it possible using fsfast? > > Xiaomin > > > Date: Wed, 26 Mar 2014 11:28:57 -0400 > > From: greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] fsfast question > > > > > > Sorry, I don't follow what you are asking. FSFAST does not do any drift > > removal from the raw data, all of that is in the design matrix > > doug > > > > On 03/26/2014 10:45 AM, Xiaomin Yue wrote: > > > Hi, > > > > > > The analysis necessary to my study is to run some analysis on the raw > > > time course data. Before working on the raw time course data, it is > > > necessary to remove linear drifting, mean, and head motion. Can I > > > just specify those parameters without having conditions in the steps > > > of generating design matrix? If so, what command should be used? > > > > > > Thanks, > > > Xiaomin Yue > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks very much, i will try it. Xiaomin From: cschwiedrz@mail.rockefeller.edu Date: Wed, 26 Mar 2014 14:56:26 -0400 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fsfast question
you could try to run mkanalysis-sess with -notask and your nuisance regressors specified as -nuisreg, then run selxavg3-sess with -no-con-ok and -svres to save the residuals. maybe that solves your problem?
caspar
2014-03-26 14:38 GMT-04:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
No, sorry
On 03/26/2014 01:54 PM, Xiaomin Yue wrote:
I like to regress out the linear drift, mean, and head motion
generated by the motion correction step of fsfast from the raw time
course only. Is it possible using fsfast?
Xiaomin
Date: Wed, 26 Mar 2014 11:28:57 -0400
From: greve@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fsfast question
Sorry, I don't follow what you are asking. FSFAST does not do any drift
removal from the raw data, all of that is in the design matrix
doug
On 03/26/2014 10:45 AM, Xiaomin Yue wrote:
Hi,
The analysis necessary to my study is to run some analysis on the raw
time course data. Before working on the raw time course data, it is
necessary to remove linear drifting, mean, and head motion. Can I
just specify those parameters without having conditions in the steps
of generating design matrix? If so, what command should be used?
Thanks,
Xiaomin Yue
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list
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HelpLine at
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Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
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Hi, I got this error while running recon: 'imgreg_4dfp /opt/freesurfer-530/average/711-2C_as_mni_average_305 /opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254ERROR: mpr2mni305 execution aborted Xiaomin From: yuexm@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] fsfast question Date: Wed, 26 Mar 2014 17:03:48 -0400
Thanks very much, i will try it. Xiaomin From: cschwiedrz@mail.rockefeller.edu Date: Wed, 26 Mar 2014 14:56:26 -0400 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fsfast question
you could try to run mkanalysis-sess with -notask and your nuisance regressors specified as -nuisreg, then run selxavg3-sess with -no-con-ok and -svres to save the residuals. maybe that solves your problem?
caspar
2014-03-26 14:38 GMT-04:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
No, sorry
On 03/26/2014 01:54 PM, Xiaomin Yue wrote:
I like to regress out the linear drift, mean, and head motion
generated by the motion correction step of fsfast from the raw time
course only. Is it possible using fsfast?
Xiaomin
Date: Wed, 26 Mar 2014 11:28:57 -0400
From: greve@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fsfast question
Sorry, I don't follow what you are asking. FSFAST does not do any drift
removal from the raw data, all of that is in the design matrix
doug
On 03/26/2014 10:45 AM, Xiaomin Yue wrote:
Hi,
The analysis necessary to my study is to run some analysis on the raw
time course data. Before working on the raw time course data, it is
necessary to remove linear drifting, mean, and head motion. Can I
just specify those parameters without having conditions in the steps
of generating design matrix? If so, what command should be used?
Thanks,
Xiaomin Yue
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
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the e-mail
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HelpLine at
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Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
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Hi, I got this error while running recon-all : 'imgreg_4dfp /opt/freesurfer-530/average/711-2C_as_mni_average_305 /opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254ERROR: mpr2mni305 execution aborted Any idea what could be the cause? Thanks,Xiaomin Yue
Hi Xiaomin
do you mean dividing by the Jacobian of the B0 unwarping field? Are you sure it's not B1? That is by far the more common intensity normalization for an mprage. The B0 effects are small due to the high bandwidth of the mprage.
I think Rudolph and/or Doug have tools for multiplying or dividing images, but I'm not sure what they are called.
cheers Bruce
On Wed, 26 Mar 2014, Xiaomin Yue wrote:
Hi Bruce, Thanks for your response. It is B0 normalization scan. What it does is to get an homogeneity image, which could be used to normalize the MRRAGE image by dividing it. Is there an build in function in freesurfer to do this operation?
Thanks, Xiaomin
Date: Mon, 24 Mar 2014 12:42:52 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] B1 correction
Hi Xiaomin
can you be more specific? What kind of B1 field map did you collect? Do you mean B1 transmit or receive?
cheers Bruce On Mon, 24 Mar 2014, Xiaomin Yue wrote:
Hi,
B1 field correction was collected during the scan. My question is how it
can be used in the surface reconstruction?
Thanks,
Xiaomin Yue
_______________________________________________ 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.
You can use fscalc, something like
fscalc file1.mgz div file2.mgz -o file1-div-file2.nii
On 03/26/2014 11:54 AM, Bruce Fischl wrote:
Hi Xiaomin
do you mean dividing by the Jacobian of the B0 unwarping field? Are you sure it's not B1? That is by far the more common intensity normalization for an mprage. The B0 effects are small due to the high bandwidth of the mprage.
I think Rudolph and/or Doug have tools for multiplying or dividing images, but I'm not sure what they are called.
cheers Bruce
On Wed, 26 Mar 2014, Xiaomin Yue wrote:
Hi Bruce, Thanks for your response. It is B0 normalization scan. What it does is to get an homogeneity image, which could be used to normalize the MRRAGE image by dividing it. Is there an build in function in freesurfer to do this operation?
Thanks, Xiaomin
Date: Mon, 24 Mar 2014 12:42:52 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] B1 correction
Hi Xiaomin
can you be more specific? What kind of B1 field map did you collect? Do you mean B1 transmit or receive?
cheers Bruce On Mon, 24 Mar 2014, Xiaomin Yue wrote:
Hi,
B1 field correction was collected during the scan. My question
is how it can be used in the surface reconstruction?
Thanks, Xiaomin Yue
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thanks. Xiaomin Yue
Date: Wed, 26 Mar 2014 11:54:58 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] B1 correction
Hi Xiaomin
do you mean dividing by the Jacobian of the B0 unwarping field? Are you sure it's not B1? That is by far the more common intensity normalization for an mprage. The B0 effects are small due to the high bandwidth of the mprage.
I think Rudolph and/or Doug have tools for multiplying or dividing images, but I'm not sure what they are called.
cheers Bruce
On Wed, 26 Mar 2014, Xiaomin Yue wrote:
Hi Bruce, Thanks for your response. It is B0 normalization scan. What it does is to get an homogeneity image, which could be used to normalize the MRRAGE image by dividing it. Is there an build in function in freesurfer to do this operation?
Thanks, Xiaomin
Date: Mon, 24 Mar 2014 12:42:52 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] B1 correction
Hi Xiaomin
can you be more specific? What kind of B1 field map did you collect? Do you mean B1 transmit or receive?
cheers Bruce On Mon, 24 Mar 2014, Xiaomin Yue wrote:
Hi,
B1 field correction was collected during the scan. My question is how it
can be used in the surface reconstruction?
Thanks,
Xiaomin Yue
_______________________________________________ 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
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.
Hi Bruce, You are correct that it is B1. How could I incorporate this data into the reconstruction stream? Thanks,Xiaomin
From: yuexm@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] B1 correction Date: Wed, 26 Mar 2014 13:54:37 -0400
thanks. Xiaomin Yue
Date: Wed, 26 Mar 2014 11:54:58 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] B1 correction
Hi Xiaomin
do you mean dividing by the Jacobian of the B0 unwarping field? Are you sure it's not B1? That is by far the more common intensity normalization for an mprage. The B0 effects are small due to the high bandwidth of the mprage.
I think Rudolph and/or Doug have tools for multiplying or dividing images, but I'm not sure what they are called.
cheers Bruce
On Wed, 26 Mar 2014, Xiaomin Yue wrote:
Hi Bruce, Thanks for your response. It is B0 normalization scan. What it does is to get an homogeneity image, which could be used to normalize the MRRAGE image by dividing it. Is there an build in function in freesurfer to do this operation?
Thanks, Xiaomin
Date: Mon, 24 Mar 2014 12:42:52 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] B1 correction
Hi Xiaomin
can you be more specific? What kind of B1 field map did you collect? Do you mean B1 transmit or receive?
cheers Bruce On Mon, 24 Mar 2014, Xiaomin Yue wrote:
Hi,
B1 field correction was collected during the scan. My question is how it
can be used in the surface reconstruction?
Thanks,
Xiaomin Yue
_______________________________________________ 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
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.
you should probably apply it before giving the data to recon-all
cheers Bruce On Wed, 26 Mar 2014, Xiaomin Yue wrote:
Hi Bruce, You are correct that it is B1. How could I incorporate this data into the reconstruction stream?
Thanks, Xiaomin
From: yuexm@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] B1 correction Date: Wed, 26 Mar 2014 13:54:37 -0400
thanks. Xiaomin Yue
Date: Wed, 26 Mar 2014 11:54:58 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] B1 correction
Hi Xiaomin
do you mean dividing by the Jacobian of the B0 unwarping field? Are you sure it's not B1? That is by far the more common intensity normalization for an mprage. The B0 effects are small due to the high bandwidth of the mprage.
I think Rudolph and/or Doug have tools for multiplying or dividing images, but I'm not sure what they are called.
cheers Bruce
On Wed, 26 Mar 2014, Xiaomin Yue wrote:
Hi Bruce, Thanks for your response. It is B0 normalization scan. What it does is t
o
get an homogeneity image, which could be used to normalize the MRRAGE imag
e
by dividing it. Is there an build in function in freesurfer to do this operation?
Thanks, Xiaomin
Date: Mon, 24 Mar 2014 12:42:52 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] B1 correction
Hi Xiaomin
can you be more specific? What kind of B1 field map did you collect? Do you mean B1 transmit or receive?
cheers Bruce On Mon, 24 Mar 2014, Xiaomin Yue wrote:
Hi,
B1 field correction was collected during the scan. My question is how i
t
can be used in the surface reconstruction?
Thanks,
Xiaomin Yue
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati
on
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 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@nmr.mgh.harvard.edu
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Bruce Fischl -
Caspar M. Schwiedrzik -
Crofts, Jonathan -
Douglas N Greve -
Xiaomin Yue