Dear FreeSurfer Experts, I want to compute some intensity information (e.g., mean and std) of each Hippocampal subfields (similar to aseg.stats file). I think one option could be mri_segstats command, but I am not sure. If it works, what are the inputs of this command?
Thank you in advance for any help. Alireza
The basic command is
mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz
where seg is the hippo sub field seg and input is the input where you want to get the intensities from (probably norm.mgz). Note that you need to use the hipp sub field output that is 1mm (not the high res one)
On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote:
Dear FreeSurfer Experts, I want to compute some intensity information (e.g., mean and std) of each Hippocampal subfields (similar to aseg.stats file). I think one option could be mri_segstats command, but I am not sure. If it works, what are the inputs of this command?
Thank you in advance for any help. Alireza
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you so much Dr. Doug! I just have one more question: Now I want to compute the same information for our second modality (i.e., mean and std intensity of different HP_subfields for our additional scan, e,g., T2 or FLAIR).My question is that how could I use <analysisID>.FSspace.mgz (in mri folder) and T1_to_<analysisID>.v10.Ita (in transform folder) files in mri_segstats command? Thank you in advance for any help.Best regards,Alireza
On Friday, February 24, 2017 10:51 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The basic command is
mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz
where seg is the hippo sub field seg and input is the input where you want to get the intensities from (probably norm.mgz). Note that you need to use the hipp sub field output that is 1mm (not the high res one)
On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote:
Dear FreeSurfer Experts, I want to compute some intensity information (e.g., mean and std) of each Hippocampal subfields (similar to aseg.stats file). I think one option could be mri_segstats command, but I am not sure. If it works, what are the inputs of this command?
Thank you in advance for any help. Alireza
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you so much Dr. Doug! I just have one more question:
Now I want to compute the same information for our second modality (i.e., mean and std intensity of different HP_subfields for our additional scan, e,g., T2 or FLAIR). My question is that how could I use <analysisID>.FSspace.mgz (in mri folder) and T1_to_<analysisID>.v10.Ita (in transform folder) files in mri_segstats command?
Thank you in advance for any help. Best regards, Alireza
On Feb 24, 2017, at 10:51 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The basic command is
mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz
where seg is the hippo sub field seg and input is the input where you want to get the intensities from (probably norm.mgz). Note that you need to use the hipp sub field output that is 1mm (not the high res one)
On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote: Dear FreeSurfer Experts, I want to compute some intensity information (e.g., mean and std) of each Hippocampal subfields (similar to aseg.stats file). I think one option could be mri_segstats command, but I am not sure. If it works, what are the inputs of this command?
Thank you in advance for any help. Alireza
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.
There is usually a T2.norm.mgz file in the mri folder. If that is there, then you should use that rather than the raw data that is not bias field corrected
On 02/27/2017 12:30 PM, ali reza mohammadi nejad wrote:
Thank you so much Dr. Doug! I just have one more question:
Now I want to compute the same information for our second modality (i.e., mean and std intensity of different HP_subfields for our additional scan, e,g., T2 or FLAIR). My question is that how could I use <analysisID>.FSspace.mgz (in mri folder) and T1_to_<analysisID>.v10.Ita (in transform folder) files in mri_segstats command?
Thank you in advance for any help. Best regards, Alireza
On Feb 24, 2017, at 10:51 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The basic command is
mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz
where seg is the hippo sub field seg and input is the input where you want to get the intensities from (probably norm.mgz). Note that you need to use the hipp sub field output that is 1mm (not the high res one)
On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote: Dear FreeSurfer Experts, I want to compute some intensity information (e.g., mean and std) of each Hippocampal subfields (similar to aseg.stats file). I think one option could be mri_segstats command, but I am not sure. If it works, what are the inputs of this command?
Thank you in advance for any help. Alireza
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
I processed the T1-weighted data without T2. Therefore, we do not have T2.norm.mgz in the mri folder of each subject. Only for the HP-subfields segmentation, we added additional high-resolution T2-weighted data to increase the accuracy of HP-subfields segmentation.
Thanks! Alireza
On Feb 27, 2017, at 12:53 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
There is usually a T2.norm.mgz file in the mri folder. If that is there, then you should use that rather than the raw data that is not bias field corrected
On 02/27/2017 12:30 PM, ali reza mohammadi nejad wrote: Thank you so much Dr. Doug! I just have one more question:
Now I want to compute the same information for our second modality (i.e., mean and std intensity of different HP_subfields for our additional scan, e,g., T2 or FLAIR). My question is that how could I use <analysisID>.FSspace.mgz (in mri folder) and T1_to_<analysisID>.v10.Ita (in transform folder) files in mri_segstats command?
Thank you in advance for any help. Best regards, Alireza
On Feb 24, 2017, at 10:51 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The basic command is
mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz
where seg is the hippo sub field seg and input is the input where you want to get the intensities from (probably norm.mgz). Note that you need to use the hipp sub field output that is 1mm (not the high res one)
On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote: Dear FreeSurfer Experts, I want to compute some intensity information (e.g., mean and std) of each Hippocampal subfields (similar to aseg.stats file). I think one option could be mri_segstats command, but I am not sure. If it works, what are the inputs of this command?
Thank you in advance for any help. Alireza
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
Is there a T2.prenorm.mgz in the mri folder? If not, you can run
bbregister --mov T2.nativespace.mgz --t2 --s subject --reg t2.reg.lta
mri_vol2vol --mov T2.nativespace.mgz --reg t2.reg.lta --targ orig.mgz --o T2.prenorm.mgz
Then run something like
mri_normalize \ -sigma 0.5 -nonmax_suppress 0 -min_dist 1 \ -aseg $mdir/aseg.presurf.mgz \ -surface $sdir/rh.white identity.nofile \ -surface $sdir/lh.white identity.nofile \ $mdir/${t2flair}.prenorm.mgz \ $mdir/${t2flair}.norm.mgz
On 02/27/2017 01:28 PM, ali reza mohammadi nejad wrote:
I processed the T1-weighted data without T2. Therefore, we do not have T2.norm.mgz in the mri folder of each subject. Only for the HP-subfields segmentation, we added additional high-resolution T2-weighted data to increase the accuracy of HP-subfields segmentation.
Thanks! Alireza
On Feb 27, 2017, at 12:53 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
There is usually a T2.norm.mgz file in the mri folder. If that is there, then you should use that rather than the raw data that is not bias field corrected
On 02/27/2017 12:30 PM, ali reza mohammadi nejad wrote: Thank you so much Dr. Doug! I just have one more question:
Now I want to compute the same information for our second modality (i.e., mean and std intensity of different HP_subfields for our additional scan, e,g., T2 or FLAIR). My question is that how could I use <analysisID>.FSspace.mgz (in mri folder) and T1_to_<analysisID>.v10.Ita (in transform folder) files in mri_segstats command?
Thank you in advance for any help. Best regards, Alireza
On Feb 24, 2017, at 10:51 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The basic command is
mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz
where seg is the hippo sub field seg and input is the input where you want to get the intensities from (probably norm.mgz). Note that you need to use the hipp sub field output that is 1mm (not the high res one)
On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote: Dear FreeSurfer Experts, I want to compute some intensity information (e.g., mean and std) of each Hippocampal subfields (similar to aseg.stats file). I think one option could be mri_segstats command, but I am not sure. If it works, what are the inputs of this command?
Thank you in advance for any help. Alireza
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 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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