Hello,
I am running reg-feat2anat and facing some problems.
First I ran the command in its default mode using FSL initialisation reg-feat2anat --feat featdir.feat --subject s. That gave me a bad registration. There is a warning coming up WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1
Next I tried the command using -spm option. The within-subject registration (anat2exf) looks good, but the registration to the standard does not look that good, although not as bad as with -fsl option.
The structural and the functional are using different conventions (structural is in radiological convention, whereas functional is neurological). I presume the determinants are associated with this and they have opposite signs. The orientations are also different. Additionally in both the log files (one with -fsl option and -spm option), I get another warning WARNING:: Flipping Left/Right orientation (as det < 0). Not sure whether this warning is something I should worry about.
Much appreciate your help.
Many thanks, Mariam.
The second warning you don't need to worry about. I should change that to not be a warning. reg-feat2anat is only registering the functional and anatomical. If the registration to mni152 does not look good, then that is an FSL issue doug
On 01/30/2014 11:06 AM, Mariam Sood wrote:
Hello,
I am running reg-feat2anat and facing some problems.
First I ran the command in its default mode using FSL initialisation /reg-feat2anat --feat featdir.feat --subject s. /That gave me a bad registration. There is a warning coming up ///WARNING: //initial G-W contrast is negative, but expecting positive./ / If the mov data has a T1 contrast, re-run with --T1/
Next I tried the command using -spm option. The within-subject registration (anat2exf) looks good, but the registration to the standard does not look that good, although not as bad as with -fsl option.
The structural and the functional are using different conventions (structural is in radiological convention, whereas functional is neurological). I presume the determinants are associated with this and they have opposite signs. The orientations are also different. Additionally in both the log files (one with -fsl option and -spm option), I get another warning /WARNING:: Flipping Left/Right orientation (as det < 0). /Not sure whether this warning is something I should worry about.
Much appreciate your help.
Many thanks, Mariam.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Doug, Thank you for your reply. I tried to investigate it further and would be grateful for your advice. While the reg-feat2anat registration (default FSL option) looks way off, the FEAT generated registration, both functional-anatomical and functional-standard look fine. I have used brainmask.nii as the anatomical in the registration tab of FEAT (with ‘bbr’ option selected for functional-standard registration and linear 12DOF for registration to standard). This is a partial FOV image and the determinant of functional & anatomical have opposite signs. Attached, please find my reg-feat2anat log file.
Also from your reply, what I understood is that exf2std.reg.dat is generated by FSL routines. Won’t exf2anat registration play any part in this?
I also have a T1-weighted alignment scan acquired with the same orientation and slice-block centre as the functional data. Is it possible to make use of this to get better registration should other methods fail?
Many thanks, Mariam.
On 30 Jan 2014, at 17:43, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The second warning you don't need to worry about. I should change that to not be a warning. reg-feat2anat is only registering the functional and anatomical. If the registration to mni152 does not look good, then that is an FSL issue doug
On 01/30/2014 11:06 AM, Mariam Sood wrote:
Hello,
I am running reg-feat2anat and facing some problems.
First I ran the command in its default mode using FSL initialisation /reg-feat2anat --feat featdir.feat --subject s. /That gave me a bad registration. There is a warning coming up ///WARNING: //initial G-W contrast is negative, but expecting positive./ / If the mov data has a T1 contrast, re-run with --T1/
Next I tried the command using -spm option. The within-subject registration (anat2exf) looks good, but the registration to the standard does not look that good, although not as bad as with -fsl option.
The structural and the functional are using different conventions (structural is in radiological convention, whereas functional is neurological). I presume the determinants are associated with this and they have opposite signs. The orientations are also different. Additionally in both the log files (one with -fsl option and -spm option), I get another warning /WARNING:: Flipping Left/Right orientation (as det < 0). /Not sure whether this warning is something I should worry about.
Much appreciate your help.
Many thanks, Mariam.
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/
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.
From the output it looks like the func-anat registration is off, probably because of the partial FoV is causing the FSL registration used to init BBR to be off (often happens with a partial FoV). Were the anatomical and functional acquired at the same time? If so, then you'll have to bypass reg-feat2anat to create the registration.
Unless you use --overwrite-exf2std, the exf2anat will not affect the exf2std
doug
On 02/02/2014 05:59 PM, Mariam Sood wrote:
Hello Doug, Thank you for your reply. I tried to investigate it further and would be grateful for your advice. While the reg-feat2anat registration (default FSL option) looks way off, the FEAT generated registration, both functional-anatomical and functional-standard look fine. I have used brainmask.nii as the anatomical in the registration tab of FEAT (with ‘bbr’ option selected for functional-standard registration and linear 12DOF for registration to standard). This is a partial FOV image and the determinant of functional & anatomical have opposite signs. Attached, please find my reg-feat2anat log file.
Also from your reply, what I understood is that exf2std.reg.dat is generated by FSL routines. Won’t exf2anat registration play any part in this?
I also have a T1-weighted alignment scan acquired with the same orientation and slice-block centre as the functional data. Is it possible to make use of this to get better registration should other methods fail?
Many thanks, Mariam.
On 30 Jan 2014, at 17:43, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The second warning you don't need to worry about. I should change that to not be a warning. reg-feat2anat is only registering the functional and anatomical. If the registration to mni152 does not look good, then that is an FSL issue doug
On 01/30/2014 11:06 AM, Mariam Sood wrote:
Hello,
I am running reg-feat2anat and facing some problems.
First I ran the command in its default mode using FSL initialisation /reg-feat2anat --feat featdir.feat --subject s. /That gave me a bad registration. There is a warning coming up ///WARNING: //initial G-W contrast is negative, but expecting positive./ / If the mov data has a T1 contrast, re-run with --T1/
Next I tried the command using -spm option. The within-subject registration (anat2exf) looks good, but the registration to the standard does not look that good, although not as bad as with -fsl option.
The structural and the functional are using different conventions (structural is in radiological convention, whereas functional is neurological). I presume the determinants are associated with this and they have opposite signs. The orientations are also different. Additionally in both the log files (one with -fsl option and -spm option), I get another warning /WARNING:: Flipping Left/Right orientation (as det < 0). /Not sure whether this warning is something I should worry about.
Much appreciate your help.
Many thanks, Mariam.
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/
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
Hello Doug, sorry for the delay. But thank you for going through the log and giving me helpful advice. The problems I was having with registration were down to the fact that the anatomical (brain mask) and functional were oriented differently and the flirt command line options (search angle in x,y,z:-90 to +90 degrees) used by reg-feat2anat were insufficient for correcting that. Changing those parameters (searchrx, searchry and searchrz to -180 to 180) fixed my problems and gave me good registration. Many thanks, Mariam.
On 4 Feb 2014, at 17:15, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
From the output it looks like the func-anat registration is off, probably because of the partial FoV is causing the FSL registration used to init BBR to be off (often happens with a partial FoV). Were the anatomical and functional acquired at the same time? If so, then you'll have to bypass reg-feat2anat to create the registration.
Unless you use --overwrite-exf2std, the exf2anat will not affect the exf2std
doug
On 02/02/2014 05:59 PM, Mariam Sood wrote:
Hello Doug, Thank you for your reply. I tried to investigate it further and would be grateful for your advice. While the reg-feat2anat registration (default FSL option) looks way off, the FEAT generated registration, both functional-anatomical and functional-standard look fine. I have used brainmask.nii as the anatomical in the registration tab of FEAT (with ‘bbr’ option selected for functional-standard registration and linear 12DOF for registration to standard). This is a partial FOV image and the determinant of functional & anatomical have opposite signs. Attached, please find my reg-feat2anat log file.
Also from your reply, what I understood is that exf2std.reg.dat is generated by FSL routines. Won’t exf2anat registration play any part in this?
I also have a T1-weighted alignment scan acquired with the same orientation and slice-block centre as the functional data. Is it possible to make use of this to get better registration should other methods fail?
Many thanks, Mariam.
On 30 Jan 2014, at 17:43, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The second warning you don't need to worry about. I should change that to not be a warning. reg-feat2anat is only registering the functional and anatomical. If the registration to mni152 does not look good, then that is an FSL issue doug
On 01/30/2014 11:06 AM, Mariam Sood wrote:
Hello,
I am running reg-feat2anat and facing some problems.
First I ran the command in its default mode using FSL initialisation /reg-feat2anat --feat featdir.feat --subject s. /That gave me a bad registration. There is a warning coming up ///WARNING: //initial G-W contrast is negative, but expecting positive./ / If the mov data has a T1 contrast, re-run with --T1/
Next I tried the command using -spm option. The within-subject registration (anat2exf) looks good, but the registration to the standard does not look that good, although not as bad as with -fsl option.
The structural and the functional are using different conventions (structural is in radiological convention, whereas functional is neurological). I presume the determinants are associated with this and they have opposite signs. The orientations are also different. Additionally in both the log files (one with -fsl option and -spm option), I get another warning /WARNING:: Flipping Left/Right orientation (as det < 0). /Not sure whether this warning is something I should worry about.
Much appreciate your help.
Many thanks, Mariam.
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/
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
-- 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Mariam Sood