Hello,
I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 6.0. I have a whole brain T1-weighted image as well as a high-resolution T2-weighted image of the hippocampus. The T2 weighted image covers the entire hippocampus, but not the whole brain.
My understanding (and please correct me if I'm wrong) is that I should first run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag, but that I must first make sure that the two scans are roughly aligned.
I was able to successfully register the T1-weighted scan to the T2-weighted scan using mri_robust_register using the following commands:
mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta wholebrain_to_hippocampus.lta -satit --noinit --nosym
mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz
My plan was then to run recon-all on the newly upsampled, registered wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the resampled whole brain T1-weighted image now has only a partial FOV.
Is there a way that I can preserve the full field of view in the T1-weighted scan? I've experimented with mri_coreg and flirt and am at a loss.
Many thanks in advance, Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
Dear Lara, Two things: 1. You don't need to recon the T2 scan. The recon-all stream only works for T1 data anyway. 2. The registration between the T1 and T2 scans happens internally (with a mri_register command similar to the one you wrote) during the hippocampal subfield segmentation. You only need to coarsely align the T1 and T2 scans manually if the initial alignment between the two is terrible. What happens when you open them both in Freeview? 3. If the alignment is decent, just run recon-all once, with both the -all and the -hippocampal-subfields-T1T2 flags. Feel free to send me the T1 and T2 scans if you are not sure whether they are sufficiently well aligned or not. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Lara Foland-Ross" lfoland@stanford.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, April 5, 2016 11:14:39 PM Subject: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Hello,
I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 6.0. I have a whole brain T1-weighted image as well as a high-resolution T2-weighted image of the hippocampus. The T2 weighted image covers the entire hippocampus, but not the whole brain.
My understanding (and please correct me if I'm wrong) is that I should first run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag, but that I must first make sure that the two scans are roughly aligned.
I was able to successfully register the T1-weighted scan to the T2-weighted scan using mri_robust_register using the following commands:
mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta wholebrain_to_hippocampus.lta -satit --noinit --nosym
mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz
My plan was then to run recon-all on the newly upsampled, registered wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the resampled whole brain T1-weighted image now has only a partial FOV.
Is there a way that I can preserve the full field of view in the T1-weighted scan? I've experimented with mri_coreg and flirt and am at a loss.
Many thanks in advance, Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
_______________________________________________ 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 Eugenio,
Thank you so much for the quick and helpful reply. I checked the images in Freeview and they actually line up quite nicely!
Can you provide further guidance on how to run recon-all once with both the -all and the hippocampal-subfields-T1T2 flags?
For example, in my rawdata directory, I have two folders: subj1_T1 and subj1_hipp. I cd'd into the rawdata folder and ran the following with no success:
recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 subj1_hipp T2hipp
Is this directory setup correct? And can you please point out the errors in the above recon-all command?
Many thanks again for your help! Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.iglesias@bcbl.eu Sent: Tuesday, April 5, 2016 2:32 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Dear Lara, Two things: 1. You don't need to recon the T2 scan. The recon-all stream only works for T1 data anyway. 2. The registration between the T1 and T2 scans happens internally (with a mri_register command similar to the one you wrote) during the hippocampal subfield segmentation. You only need to coarsely align the T1 and T2 scans manually if the initial alignment between the two is terrible. What happens when you open them both in Freeview? 3. If the alignment is decent, just run recon-all once, with both the -all and the -hippocampal-subfields-T1T2 flags. Feel free to send me the T1 and T2 scans if you are not sure whether they are sufficiently well aligned or not. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Lara Foland-Ross" lfoland@stanford.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, April 5, 2016 11:14:39 PM Subject: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Hello,
I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 6.0. I have a whole brain T1-weighted image as well as a high-resolution T2-weighted image of the hippocampus. The T2 weighted image covers the entire hippocampus, but not the whole brain.
My understanding (and please correct me if I'm wrong) is that I should first run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag, but that I must first make sure that the two scans are roughly aligned.
I was able to successfully register the T1-weighted scan to the T2-weighted scan using mri_robust_register using the following commands:
mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta wholebrain_to_hippocampus.lta -satit --noinit --nosym
mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz
My plan was then to run recon-all on the newly upsampled, registered wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the resampled whole brain T1-weighted image now has only a partial FOV.
Is there a way that I can preserve the full field of view in the T1-weighted scan? I've experimented with mri_coreg and flirt and am at a loss.
Many thanks in advance, Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
_______________________________________________ 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
Almost correct! recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 subj1_hipp/I0001.dcm T2hipp Also, this is assuming that you have defined the environment variable SUBJECTS_DIR. Otherwise, you'd need to add the flag -sd <subjectsDirectory>. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Lara Foland-Ross" lfoland@stanford.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 6, 2016 12:29:09 AM Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Hi Eugenio,
Thank you so much for the quick and helpful reply. I checked the images in Freeview and they actually line up quite nicely!
Can you provide further guidance on how to run recon-all once with both the -all and the hippocampal-subfields-T1T2 flags?
For example, in my rawdata directory, I have two folders: subj1_T1 and subj1_hipp. I cd'd into the rawdata folder and ran the following with no success:
recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 subj1_hipp T2hipp
Is this directory setup correct? And can you please point out the errors in the above recon-all command?
Many thanks again for your help! Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.iglesias@bcbl.eu Sent: Tuesday, April 5, 2016 2:32 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Dear Lara, Two things: 1. You don't need to recon the T2 scan. The recon-all stream only works for T1 data anyway. 2. The registration between the T1 and T2 scans happens internally (with a mri_register command similar to the one you wrote) during the hippocampal subfield segmentation. You only need to coarsely align the T1 and T2 scans manually if the initial alignment between the two is terrible. What happens when you open them both in Freeview? 3. If the alignment is decent, just run recon-all once, with both the -all and the -hippocampal-subfields-T1T2 flags. Feel free to send me the T1 and T2 scans if you are not sure whether they are sufficiently well aligned or not. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Lara Foland-Ross" lfoland@stanford.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, April 5, 2016 11:14:39 PM Subject: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Hello,
I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 6.0. I have a whole brain T1-weighted image as well as a high-resolution T2-weighted image of the hippocampus. The T2 weighted image covers the entire hippocampus, but not the whole brain.
My understanding (and please correct me if I'm wrong) is that I should first run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag, but that I must first make sure that the two scans are roughly aligned.
I was able to successfully register the T1-weighted scan to the T2-weighted scan using mri_robust_register using the following commands:
mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta wholebrain_to_hippocampus.lta -satit --noinit --nosym
mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz
My plan was then to run recon-all on the newly upsampled, registered wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the resampled whole brain T1-weighted image now has only a partial FOV.
Is there a way that I can preserve the full field of view in the T1-weighted scan? I've experimented with mri_coreg and flirt and am at a loss.
Many thanks in advance, Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
_______________________________________________ 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
Thank you Eugenio! This worked like a charm.
Wondering now if you could help me troubleshoot running this command on 2 scans from a single subject (time 1 and time 2) that were processed using the longitudinal pipeline in version 5.3.
I ran the following:
recon-all -all -s 18512_T1_v5.3_hipp_v6.0 -hippocampal-subfields-T2 18512_hipp/MR.1.2.840.113619.2.283.4120.7575399.16012.1376585566.598.dcm T2hipp
and got the error that Freesurfer could not find mri/orig file... It is indeed not there, presumably because it isn't produced after the creation and editing of the long.base timepoints. I read elsewhere on the list that the hippocampal subfield analysis could be run on the individual longitudinal timepoints but can't seem to get this to work. Can you advise?
Many thanks in advance for your continued help! Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.iglesias@bcbl.eu Sent: Tuesday, April 5, 2016 3:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Almost correct! recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 subj1_hipp/I0001.dcm T2hipp Also, this is assuming that you have defined the environment variable SUBJECTS_DIR. Otherwise, you'd need to add the flag -sd <subjectsDirectory>. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Lara Foland-Ross" lfoland@stanford.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 6, 2016 12:29:09 AM Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Hi Eugenio,
Thank you so much for the quick and helpful reply. I checked the images in Freeview and they actually line up quite nicely!
Can you provide further guidance on how to run recon-all once with both the -all and the hippocampal-subfields-T1T2 flags?
For example, in my rawdata directory, I have two folders: subj1_T1 and subj1_hipp. I cd'd into the rawdata folder and ran the following with no success:
recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 subj1_hipp T2hipp
Is this directory setup correct? And can you please point out the errors in the above recon-all command?
Many thanks again for your help! Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.iglesias@bcbl.eu Sent: Tuesday, April 5, 2016 2:32 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Dear Lara, Two things: 1. You don't need to recon the T2 scan. The recon-all stream only works for T1 data anyway. 2. The registration between the T1 and T2 scans happens internally (with a mri_register command similar to the one you wrote) during the hippocampal subfield segmentation. You only need to coarsely align the T1 and T2 scans manually if the initial alignment between the two is terrible. What happens when you open them both in Freeview? 3. If the alignment is decent, just run recon-all once, with both the -all and the -hippocampal-subfields-T1T2 flags. Feel free to send me the T1 and T2 scans if you are not sure whether they are sufficiently well aligned or not. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Lara Foland-Ross" lfoland@stanford.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, April 5, 2016 11:14:39 PM Subject: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Hello,
I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 6.0. I have a whole brain T1-weighted image as well as a high-resolution T2-weighted image of the hippocampus. The T2 weighted image covers the entire hippocampus, but not the whole brain.
My understanding (and please correct me if I'm wrong) is that I should first run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag, but that I must first make sure that the two scans are roughly aligned.
I was able to successfully register the T1-weighted scan to the T2-weighted scan using mri_robust_register using the following commands:
mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta wholebrain_to_hippocampus.lta -satit --noinit --nosym
mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz
My plan was then to run recon-all on the newly upsampled, registered wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the resampled whole brain T1-weighted image now has only a partial FOV.
Is there a way that I can preserve the full field of view in the T1-weighted scan? I've experimented with mri_coreg and flirt and am at a loss.
Many thanks in advance, Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
_______________________________________________ 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Lara,
mri/orig.mgz should be there also in the longitudinal directories. If it is missing, more might be wrong. I would recommend rerunning those long runs from scratch.
Best, Martin
On 04/25/2016 07:07 PM, Lara Foland-Ross wrote:
Thank you Eugenio! This worked like a charm.
Wondering now if you could help me troubleshoot running this command on 2 scans from a single subject (time 1 and time 2) that were processed using the longitudinal pipeline in version 5.3.
I ran the following:
recon-all -all -s 18512_T1_v5.3_hipp_v6.0 -hippocampal-subfields-T2 18512_hipp/MR.1.2.840.113619.2.283.4120.7575399.16012.1376585566.598.dcm T2hipp
and got the error that Freesurfer could not find mri/orig file... It is indeed not there, presumably because it isn't produced after the creation and editing of the long.base timepoints. I read elsewhere on the list that the hippocampal subfield analysis could be run on the individual longitudinal timepoints but can't seem to get this to work. Can you advise?
Many thanks in advance for your continued help! Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.iglesias@bcbl.eu Sent: Tuesday, April 5, 2016 3:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Almost correct! recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 subj1_hipp/I0001.dcm T2hipp Also, this is assuming that you have defined the environment variable SUBJECTS_DIR. Otherwise, you'd need to add the flag -sd <subjectsDirectory>. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Lara Foland-Ross" lfoland@stanford.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 6, 2016 12:29:09 AM Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Hi Eugenio,
Thank you so much for the quick and helpful reply. I checked the images in Freeview and they actually line up quite nicely!
Can you provide further guidance on how to run recon-all once with both the -all and the hippocampal-subfields-T1T2 flags?
For example, in my rawdata directory, I have two folders: subj1_T1 and subj1_hipp. I cd'd into the rawdata folder and ran the following with no success:
recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 subj1_hipp T2hipp
Is this directory setup correct? And can you please point out the errors in the above recon-all command?
Many thanks again for your help! Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.iglesias@bcbl.eu Sent: Tuesday, April 5, 2016 2:32 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Dear Lara, Two things:
- You don't need to recon the T2 scan. The recon-all stream only works for T1 data anyway.
- The registration between the T1 and T2 scans happens internally (with a mri_register command similar to the one you wrote) during the hippocampal subfield segmentation. You only need to coarsely align the T1 and T2 scans manually if the initial alignment between the two is terrible. What happens when you open them both in Freeview?
- If the alignment is decent, just run recon-all once, with both the -all and the -hippocampal-subfields-T1T2 flags.
Feel free to send me the T1 and T2 scans if you are not sure whether they are sufficiently well aligned or not. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Lara Foland-Ross" lfoland@stanford.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, April 5, 2016 11:14:39 PM Subject: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Hello,
I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 6.0. I have a whole brain T1-weighted image as well as a high-resolution T2-weighted image of the hippocampus. The T2 weighted image covers the entire hippocampus, but not the whole brain.
My understanding (and please correct me if I'm wrong) is that I should first run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag, but that I must first make sure that the two scans are roughly aligned.
I was able to successfully register the T1-weighted scan to the T2-weighted scan using mri_robust_register using the following commands:
mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta wholebrain_to_hippocampus.lta -satit --noinit --nosym
mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz
My plan was then to run recon-all on the newly upsampled, registered wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the resampled whole brain T1-weighted image now has only a partial FOV.
Is there a way that I can preserve the full field of view in the T1-weighted scan? I've experimented with mri_coreg and flirt and am at a loss.
Many thanks in advance, Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
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
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My apologies - there was a typo in my last message. The error reads that the program could not find mri/001.mgz:
cibsr-i27-410:inProgress6.0b kel32$ pwd /Volumes/Xspace/Freesurfer/inProgress6.0b cibsr-i27-410:inProgress6.0b kel32$ ls 18512_T1_v5.3_hipp_v6.0 18512_hipp fsaverage cibsr-i27-410:inProgress6.0b kel32$ recon-all -all -s 18512_T1_v5.3_hipp_v6.0 -hippocampal-subfields-T2 /Volumes/Xspace/Freesurfer/Liraglutide6.0b/rawdata/18512_hipp/MR.1.2.840.113619.2.283.4120.7575399.16012.1376585566.598.dcm T2hipp_in_long INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-OSX-dev-20160326 INFO: SUBJECTS_DIR is /Volumes/Xspace/Freesurfer/inProgress6.0b Actual FREESURFER_HOME /Volumes/ToolsMac/freesurfer6.0b -rw-rw-r-- 1 kel32 staff 1368492 Apr 26 08:33 /Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/scripts/recon-all.log Darwin cibsr-i27-410.stanford.edu 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Volumes/ToolsMac/freesurfer6.0b Previous: /Volumes/ToolsMac/freesurfer5.3 #-------------------------------------------- #@# MotionCor Tue Apr 26 08:41:07 PDT 2016 ERROR: no run data found in /Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/mri. Make sure to have a volume called 001.mgz in /Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Darwin cibsr-i27-410.stanford.edu 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64
recon-all -s 18512_T1_v5.3_hipp_v6.0 exited with ERRORS at Tue Apr 26 08:41:08 PDT 2016
For more details, see the log file /Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Can you please advise on how best to proceed?
May thanks! Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Martin Reuter mreuter@nmr.mgh.harvard.edu Sent: Tuesday, April 26, 2016 6:06 AM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Hi Lara,
mri/orig.mgz should be there also in the longitudinal directories. If it is missing, more might be wrong. I would recommend rerunning those long runs from scratch.
Best, Martin
On 04/25/2016 07:07 PM, Lara Foland-Ross wrote:
Thank you Eugenio! This worked like a charm.
Wondering now if you could help me troubleshoot running this command on 2 scans from a single subject (time 1 and time 2) that were processed using the longitudinal pipeline in version 5.3.
I ran the following:
recon-all -all -s 18512_T1_v5.3_hipp_v6.0 -hippocampal-subfields-T2 18512_hipp/MR.1.2.840.113619.2.283.4120.7575399.16012.1376585566.598.dcm T2hipp
and got the error that Freesurfer could not find mri/orig file... It is indeed not there, presumably because it isn't produced after the creation and editing of the long.base timepoints. I read elsewhere on the list that the hippocampal subfield analysis could be run on the individual longitudinal timepoints but can't seem to get this to work. Can you advise?
Many thanks in advance for your continued help! Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.iglesias@bcbl.eu Sent: Tuesday, April 5, 2016 3:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Almost correct! recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 subj1_hipp/I0001.dcm T2hipp Also, this is assuming that you have defined the environment variable SUBJECTS_DIR. Otherwise, you'd need to add the flag -sd <subjectsDirectory>. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Lara Foland-Ross" lfoland@stanford.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 6, 2016 12:29:09 AM Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Hi Eugenio,
Thank you so much for the quick and helpful reply. I checked the images in Freeview and they actually line up quite nicely!
Can you provide further guidance on how to run recon-all once with both the -all and the hippocampal-subfields-T1T2 flags?
For example, in my rawdata directory, I have two folders: subj1_T1 and subj1_hipp. I cd'd into the rawdata folder and ran the following with no success:
recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 subj1_hipp T2hipp
Is this directory setup correct? And can you please point out the errors in the above recon-all command?
Many thanks again for your help! Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.iglesias@bcbl.eu Sent: Tuesday, April 5, 2016 2:32 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Dear Lara, Two things:
- You don't need to recon the T2 scan. The recon-all stream only works for T1 data anyway.
- The registration between the T1 and T2 scans happens internally (with a mri_register command similar to the one you wrote) during the hippocampal subfield segmentation. You only need to coarsely align the T1 and T2 scans manually if the initial alignment between the two is terrible. What happens when you open them both in Freeview?
- If the alignment is decent, just run recon-all once, with both the -all and the -hippocampal-subfields-T1T2 flags.
Feel free to send me the T1 and T2 scans if you are not sure whether they are sufficiently well aligned or not. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Lara Foland-Ross" lfoland@stanford.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, April 5, 2016 11:14:39 PM Subject: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Hello,
I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 6.0. I have a whole brain T1-weighted image as well as a high-resolution T2-weighted image of the hippocampus. The T2 weighted image covers the entire hippocampus, but not the whole brain.
My understanding (and please correct me if I'm wrong) is that I should first run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag, but that I must first make sure that the two scans are roughly aligned.
I was able to successfully register the T1-weighted scan to the T2-weighted scan using mri_robust_register using the following commands:
mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta wholebrain_to_hippocampus.lta -satit --noinit --nosym
mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz
My plan was then to run recon-all on the newly upsampled, registered wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the resampled whole brain T1-weighted image now has only a partial FOV.
Is there a way that I can preserve the full field of view in the T1-weighted scan? I've experimented with mri_coreg and flirt and am at a loss.
Many thanks in advance, Lara
Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795
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
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-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
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