What was the error message?
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of John Anderson j.anderson@publicist.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Sunday, June 11, 2017 at 9:06 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] difference in T1 and T2 resolution
Dear Freesurfer experts, I have T1 and T2 images were unfortunately acquired with different resolution (i.e the voxel sizes is not the same) T1 is 280X280X208 T2 is 270X270X200
I tried to run "recon-all" but it failed to process the data. The command that I used is : pbsubmit -c " recon-all -subjid subj1 -T2 PATH_TO_/T2.nii.gz -qcache -T2pial -all"
How can I analyze these images? Is it a correct procedure to conform the voxels using "mri_convert". Is this procedure correct? does it hurt the anatomy of the images?
I highly appreciate your help John _______________________________________________ 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.
can you send the log file?
On 6/11/17 10:08 PM, John Anderson wrote:
In the log file the error was: ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 1, 1, 1 size(0) = 0.7, 0.7, 0.8 MultiRegistration::loadMovables: voxel size is different /recons/subj1/mri/orig/002.mgz. Jon *Sent:* Sunday, June 11, 2017 at 2:12 PM *From:* "Matt Glasser" matt@ma-tea.com *To:* "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] difference in T1 and T2 resolution What was the error message? Peace, Matt. From: <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Anderson <j.anderson@publicist.com mailto:j.anderson@publicist.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Sunday, June 11, 2017 at 9:06 AM To: <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] difference in T1 and T2 resolution Dear Freesurfer experts, I have T1 and T2 images were unfortunately acquired with different resolution (i.e the voxel sizes is not the same) T1 is 280X280X208 T2 is 270X270X200
I tried to run "recon-all" but it failed to process the data. The command that I used is : pbsubmit -c " recon-all -subjid subj1 -T2 PATH_TO_/T2.nii.gz -qcache -T2pial -all" How can I analyze these images? Is it a correct procedure to conform the voxels using "mri_convert". Is this procedure correct? does it hurt the anatomy of the images? I highly appreciate your help John _______________________________________________ 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 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
This is not due to a difference between T1 and T2 resolution. The problem is that the two T1 volumes (001.mgz and 002.mgz) are difference sizes. It is probably not a good idea to try to combine them, but if you really want to, I can supply you with a solution.
On 6/14/17 1:12 PM, John Anderson wrote:
Thank you for your response. The log file is attached *Sent:* Tuesday, June 13, 2017 at 2:02 AM *From:* "Douglas Greve" greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] difference in T1 and T2 resolution
can you send the log file?
On 6/11/17 10:08 PM, John Anderson wrote:
In the log file the error was: ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 1, 1, 1 size(0) = 0.7, 0.7, 0.8 MultiRegistration::loadMovables: voxel size is different /recons/subj1/mri/orig/002.mgz. Jon *Sent:* Sunday, June 11, 2017 at 2:12 PM *From:* "Matt Glasser" <matt@ma-tea.com> *To:* "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] difference in T1 and T2 resolution What was the error message? Peace, Matt. From: <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of John Anderson <j.anderson@publicist.com <mailto:j.anderson@publicist.com>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Sunday, June 11, 2017 at 9:06 AM To: <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] difference in T1 and T2 resolution Dear Freesurfer experts, I have T1 and T2 images were unfortunately acquired with different resolution (i.e the voxel sizes is not the same) T1 is 280X280X208 T2 is 270X270X200 I tried to run "recon-all" but it failed to process the data. The command that I used is : pbsubmit -c " recon-all -subjid subj1 -T2 PATH_TO_/T2.nii.gz -qcache -T2pial -all" How can I analyze these images? Is it a correct procedure to conform the voxels using "mri_convert". Is this procedure correct? does it hurt the anatomy of the images? I highly appreciate your help John _______________________________________________ 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 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 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
It looks like at least the number of voxels is different between the two (not sure about the voxel size). You may or may not want to average the two images together. If they are different sizes, it is probably the case that they have different acquisition parameters and so different contrasts. If you want to analyze both, then you'll need to resample one into the other, eg,
mv 002.mgz orig.002.mgz
mri_vol2vol --mov orig.002.mgz --targ 001.mgz --regheader --o 002.mgz
but this is probably not a good idea
On 6/14/17 4:20 PM, John Anderson wrote:
Thank Doug for the response. This is very interesting!! I never thought about that! I was thinking that the two images (i.e. T1 and T2) must have the same resolution. I understand that when we talk about differnce in the size of the files that means either the thickness of the slices is different or the number of images is differnt correct? Kindly could you please shed more light on this issue and how we can handle it. Also is it matter if the resolution of the two images is different? How can I analyse such images correctly? Many thanks! John *Sent:* Wednesday, June 14, 2017 at 10:02 AM *From:* "Douglas Greve" greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] difference in T1 and T2 resolution
This is not due to a difference between T1 and T2 resolution. The problem is that the two T1 volumes (001.mgz and 002.mgz) are difference sizes. It is probably not a good idea to try to combine them, but if you really want to, I can supply you with a solution.
On 6/14/17 1:12 PM, John Anderson wrote:
Thank you for your response. The log file is attached *Sent:* Tuesday, June 13, 2017 at 2:02 AM *From:* "Douglas Greve" <greve@nmr.mgh.harvard.edu> *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] difference in T1 and T2 resolution can you send the log file? On 6/11/17 10:08 PM, John Anderson wrote: In the log file the error was: ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 1, 1, 1 size(0) = 0.7, 0.7, 0.8 MultiRegistration::loadMovables: voxel size is different /recons/subj1/mri/orig/002.mgz. Jon *Sent:* Sunday, June 11, 2017 at 2:12 PM *From:* "Matt Glasser" <matt@ma-tea.com> *To:* "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] difference in T1 and T2 resolution What was the error message? Peace, Matt. From: <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of John Anderson <j.anderson@publicist.com <mailto:j.anderson@publicist.com>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Sunday, June 11, 2017 at 9:06 AM To: <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] difference in T1 and T2 resolution Dear Freesurfer experts, I have T1 and T2 images were unfortunately acquired with different resolution (i.e the voxel sizes is not the same) T1 is 280X280X208 T2 is 270X270X200 I tried to run "recon-all" but it failed to process the data. The command that I used is : pbsubmit -c " recon-all -subjid subj1 -T2 PATH_TO_/T2.nii.gz -qcache -T2pial -all" How can I analyze these images? Is it a correct procedure to conform the voxels using "mri_convert". Is this procedure correct? does it hurt the anatomy of the images? I highly appreciate your help John _______________________________________________ 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 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 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 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
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Douglas Greve -
John Anderson -
Matt Glasser