External Email - Use Caution
Hi,
I am trying to run segmentHA pipeline on HCP data. To do so, I have downloaded FS processed-extended structural data, manually made "scripts", "trash", and "stats" folders in each subject's folder [HCP output does not have these folders]. A few notes and questions:
1. segmentHA_T1 runs smoothly. However, I do not know which T1 does segmentHA use, since there are also a few "_hires" (high resolution) files resulting from HCP's structural analysis pipeline ( https://github.com/Washington-University/HCPpipelines).
2. segmentHA_T2 also runs smoothly. However, I didn't know which T2 file is the most suitable to be given to this command. I did give T2w_hires.nii.gz (Voxelsize = 0.7 mm isotropic) in the /mri folder of each subject.
3. I statistically checked the correlation between HCP FS generated values of whole hippocampus/amygdala, and segmentHA generated ones. Of note, they were highly correlated (all p-values < 0.001, all r ~ 0.9).
I will be glad to know whether the pipeline I used to analyze HCP data is correct or any further steps are required.
Bests, Amir
Dear Amir,
1. By default, FS will use norm.mgz, aseg.mgz, etc. You will have to eg rename norm.mgz to norm.1mm.mgz and copy / symlink / rename the _hires equivalents to get FS to use the highres T1s. 2. That sounds appropriate! 3. That sounds about right 😉 Cheers, /Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: AmirHussein Abdolalizadeh amirhussein.a@gmail.com Date: Sunday, October 18, 2020 at 02:48 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Cc: "Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk Subject: segmentHA on Human Connectome Project
Hi,
I am trying to run segmentHA pipeline on HCP data. To do so, I have downloaded FS processed-extended structural data, manually made "scripts", "trash", and "stats" folders in each subject's folder [HCP output does not have these folders]. A few notes and questions:
1. segmentHA_T1 runs smoothly. However, I do not know which T1 does segmentHA use, since there are also a few "_hires" (high resolution) files resulting from HCP's structural analysis pipeline (https://github.com/Washington-University/HCPpipelines).
2. segmentHA_T2 also runs smoothly. However, I didn't know which T2 file is the most suitable to be given to this command. I did give T2w_hires.nii.gz (Voxelsize = 0.7 mm isotropic) in the /mri folder of each subject.
3. I statistically checked the correlation between HCP FS generated values of whole hippocampus/amygdala, and segmentHA generated ones. Of note, they were highly correlated (all p-values < 0.001, all r ~ 0.9).
I will be glad to know whether the pipeline I used to analyze HCP data is correct or any further steps are required.
Bests, Amir
External Email - Use Caution
Thanks for your reply Eugenio. I renamed a few files in the /mri folder:
aseg.mgz → aseg.1mm.mgz
aseg.hires.mgz → aseg.mgz
brain.mgz → brain.1mm.mgz
brain.hires.mgz → brain.mgz
filled.mgz → filled.1mm.mgz
filled.hires.mgz → filled.mgz
norm.mgz → norm.1mm.mgz
T1w_hires.masked.norm.mgz → norm.mgz
T1.mgz → T1.1mm.mgz
T1w_hires.norm.mgz → T1.mgz
wm.mgz → wm.1mm.mgz
wm.hires.mgz → wm.mgz
However, it exits with this error: Error in segmentSubjectT1_autoEstimateAlveusML (line 822) MATLAB:sizeDimensionsMustMatch
It seems there was a file that I did not have to rename or a file that I have forgotten to rename, and two files in the process are based on different resolutions causing mismatch. Any ideas?
Bests, Amir
p.s. The pipeline works fine with the same subject in which I haven't applied any changes to filenames.
On Sun, Oct 18, 2020 at 6:43 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Dear Amir,
- By default, FS will use norm.mgz, aseg.mgz, etc. You will have to
eg rename norm.mgz to norm.1mm.mgz and copy / symlink / rename the _hires equivalents to get FS to use the highres T1s. 2. That sounds appropriate! 3. That sounds about right 😉
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
*From: *AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Date: *Sunday, October 18, 2020 at 02:48 *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Cc: *"Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk *Subject: *segmentHA on Human Connectome Project
Hi,
I am trying to run segmentHA pipeline on HCP data. To do so, I have downloaded FS processed-extended structural data, manually made "scripts", "trash", and "stats" folders in each subject's folder [HCP output does not have these folders]. A few notes and questions:
- segmentHA_T1 runs smoothly. However, I do not know which T1 does
segmentHA use, since there are also a few "_hires" (high resolution) files resulting from HCP's structural analysis pipeline ( https://github.com/Washington-University/HCPpipelines).
- segmentHA_T2 also runs smoothly. However, I didn't know which T2 file
is the most suitable to be given to this command. I did give T2w_hires.nii.gz (Voxelsize = 0.7 mm isotropic) in the /mri folder of each subject.
- I statistically checked the correlation between HCP FS generated values
of whole hippocampus/amygdala, and segmentHA generated ones. Of note, they were highly correlated (all p-values < 0.001, all r ~ 0.9).
I will be glad to know whether the pipeline I used to analyze HCP data is correct or any further steps are required.
Bests,
Amir 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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.
This is most likely a problema with wmparc.mgz which is still at 1mm. Can you please try these commands from the mri directory of a subject and rerunning? The first one renames wmparc to wmparc.1mm and the second upscales it to the resolution of the other high resolution volumes using aseg.mgz as a references (you could also use any other high res volume like norm.mgz, etc). mv wmparc.mgz wmparc.1mm.mgz mri_convert wmparc.1mm.mgz wmparc.mgz -rl aseg.mgz -odt float -rt nearest
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: AmirHussein Abdolalizadeh amirhussein.a@gmail.com Date: Tuesday, October 20, 2020 at 02:40 To: "Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: segmentHA on Human Connectome Project
External Email - Use Caution Thanks for your reply Eugenio. I renamed a few files in the /mri folder:
aseg.mgz → aseg.1mm.mgz
aseg.hires.mgz → aseg.mgz
brain.mgz → brain.1mm.mgz
brain.hires.mgz → brain.mgz
filled.mgz → filled.1mm.mgz
filled.hires.mgz → filled.mgz
norm.mgz → norm.1mm.mgz
T1w_hires.masked.norm.mgz → norm.mgz
T1.mgz → T1.1mm.mgz
T1w_hires.norm.mgz → T1.mgz
wm.mgz → wm.1mm.mgz
wm.hires.mgz → wm.mgz
However, it exits with this error: Error in segmentSubjectT1_autoEstimateAlveusML (line 822) MATLAB:sizeDimensionsMustMatch
It seems there was a file that I did not have to rename or a file that I have forgotten to rename, and two files in the process are based on different resolutions causing mismatch. Any ideas?
Bests, Amir
p.s. The pipeline works fine with the same subject in which I haven't applied any changes to filenames.
On Sun, Oct 18, 2020 at 6:43 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: Dear Amir,
1. By default, FS will use norm.mgz, aseg.mgz, etc. You will have to eg rename norm.mgz to norm.1mm.mgz and copy / symlink / rename the _hires equivalents to get FS to use the highres T1s. 2. That sounds appropriate! 3. That sounds about right 😉 Cheers, /Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: AmirHussein Abdolalizadeh <amirhussein.a@gmail.commailto:amirhussein.a@gmail.com> Date: Sunday, October 18, 2020 at 02:48 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> Subject: segmentHA on Human Connectome Project
Hi,
I am trying to run segmentHA pipeline on HCP data. To do so, I have downloaded FS processed-extended structural data, manually made "scripts", "trash", and "stats" folders in each subject's folder [HCP output does not have these folders]. A few notes and questions:
1. segmentHA_T1 runs smoothly. However, I do not know which T1 does segmentHA use, since there are also a few "_hires" (high resolution) files resulting from HCP's structural analysis pipeline (https://github.com/Washington-University/HCPpipelines).
2. segmentHA_T2 also runs smoothly. However, I didn't know which T2 file is the most suitable to be given to this command. I did give T2w_hires.nii.gz (Voxelsize = 0.7 mm isotropic) in the /mri folder of each subject.
3. I statistically checked the correlation between HCP FS generated values of whole hippocampus/amygdala, and segmentHA generated ones. Of note, they were highly correlated (all p-values < 0.001, all r ~ 0.9).
I will be glad to know whether the pipeline I used to analyze HCP data is correct or any further steps are required.
Bests, Amir 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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.
External Email - Use Caution
I applied the change you suggested. It took me a while to run both segmentHA_T1 and segmentHA_T2 on all my subjects (n = 145), to see whether I'll encounter any kind of errors, which I didn't. Thanks a lot!
Bests, Amir
On Tue, Oct 20, 2020 at 5:35 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
This is most likely a problema with wmparc.mgz which is still at 1mm.
Can you please try these commands from the mri directory of a subject and rerunning? The first one renames wmparc to wmparc.1mm and the second upscales it to the resolution of the other high resolution volumes using aseg.mgz as a references (you could also use any other high res volume like norm.mgz, etc).
mv wmparc.mgz wmparc.1mm.mgz
mri_convert wmparc.1mm.mgz wmparc.mgz -rl aseg.mgz -odt float -rt nearest
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
*From: *AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Date: *Tuesday, October 20, 2020 at 02:40 *To: *"Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu *Cc: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: segmentHA on Human Connectome Project
External Email - Use Caution *Thanks for your reply Eugenio. I renamed a few files in the /mri folder:
aseg.mgz → aseg.1mm.mgz
aseg.hires.mgz → aseg.mgz
brain.mgz → brain.1mm.mgz
brain.hires.mgz → brain.mgz
filled.mgz → filled.1mm.mgz
filled.hires.mgz → filled.mgz
norm.mgz → norm.1mm.mgz
T1w_hires.masked.norm.mgz → norm.mgz
T1.mgz → T1.1mm.mgz
T1w_hires.norm.mgz → T1.mgz
wm.mgz → wm.1mm.mgz
wm.hires.mgz → wm.mgz
However, it exits with this error:
Error in segmentSubjectT1_autoEstimateAlveusML (line 822)
MATLAB:sizeDimensionsMustMatch
It seems there was a file that I did not have to rename or a file that I have forgotten to rename, and two files in the process are based on different resolutions causing mismatch. Any ideas?
Bests,
Amir
p.s. The pipeline works fine with the same subject in which I haven't applied any changes to filenames.
On Sun, Oct 18, 2020 at 6:43 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Dear Amir,
- By default, FS will use norm.mgz, aseg.mgz, etc. You will have to
eg rename norm.mgz to norm.1mm.mgz and copy / symlink / rename the _hires equivalents to get FS to use the highres T1s. 2. That sounds appropriate! 3. That sounds about right 😉
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
*From: *AmirHussein Abdolalizadeh amirhussein.a@gmail.com *Date: *Sunday, October 18, 2020 at 02:48 *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Cc: *"Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk *Subject: *segmentHA on Human Connectome Project
Hi,
I am trying to run segmentHA pipeline on HCP data. To do so, I have downloaded FS processed-extended structural data, manually made "scripts", "trash", and "stats" folders in each subject's folder [HCP output does not have these folders]. A few notes and questions:
- segmentHA_T1 runs smoothly. However, I do not know which T1 does
segmentHA use, since there are also a few "_hires" (high resolution) files resulting from HCP's structural analysis pipeline ( https://github.com/Washington-University/HCPpipelines).
- segmentHA_T2 also runs smoothly. However, I didn't know which T2 file
is the most suitable to be given to this command. I did give T2w_hires.nii.gz (Voxelsize = 0.7 mm isotropic) in the /mri folder of each subject.
- I statistically checked the correlation between HCP FS generated values
of whole hippocampus/amygdala, and segmentHA generated ones. Of note, they were highly correlated (all p-values < 0.001, all r ~ 0.9).
I will be glad to know whether the pipeline I used to analyze HCP data is correct or any further steps are required.
Bests,
Amir
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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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.
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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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.
Glad to hear; thanks for sharing! It’s nice to see success stories here and there among all the questions 😊
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: AmirHussein Abdolalizadeh amirhussein.a@gmail.com Date: Sunday, October 25, 2020 at 06:33 To: "Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: segmentHA on Human Connectome Project
External Email - Use Caution I applied the change you suggested. It took me a while to run both segmentHA_T1 and segmentHA_T2 on all my subjects (n = 145), to see whether I'll encounter any kind of errors, which I didn't. Thanks a lot!
Bests, Amir
On Tue, Oct 20, 2020 at 5:35 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: This is most likely a problema with wmparc.mgz which is still at 1mm. Can you please try these commands from the mri directory of a subject and rerunning? The first one renames wmparc to wmparc.1mm and the second upscales it to the resolution of the other high resolution volumes using aseg.mgz as a references (you could also use any other high res volume like norm.mgz, etc). mv wmparc.mgz wmparc.1mm.mgz mri_convert wmparc.1mm.mgz wmparc.mgz -rl aseg.mgz -odt float -rt nearest
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: AmirHussein Abdolalizadeh <amirhussein.a@gmail.commailto:amirhussein.a@gmail.com> Date: Tuesday, October 20, 2020 at 02:40 To: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> Cc: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: segmentHA on Human Connectome Project
External Email - Use Caution Thanks for your reply Eugenio. I renamed a few files in the /mri folder:
aseg.mgz → aseg.1mm.mgz
aseg.hires.mgz → aseg.mgz
brain.mgz → brain.1mm.mgz
brain.hires.mgz → brain.mgz
filled.mgz → filled.1mm.mgz
filled.hires.mgz → filled.mgz
norm.mgz → norm.1mm.mgz
T1w_hires.masked.norm.mgz → norm.mgz
T1.mgz → T1.1mm.mgz
T1w_hires.norm.mgz → T1.mgz
wm.mgz → wm.1mm.mgz
wm.hires.mgz → wm.mgz
However, it exits with this error: Error in segmentSubjectT1_autoEstimateAlveusML (line 822) MATLAB:sizeDimensionsMustMatch
It seems there was a file that I did not have to rename or a file that I have forgotten to rename, and two files in the process are based on different resolutions causing mismatch. Any ideas?
Bests, Amir
p.s. The pipeline works fine with the same subject in which I haven't applied any changes to filenames.
On Sun, Oct 18, 2020 at 6:43 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: Dear Amir,
1. By default, FS will use norm.mgz, aseg.mgz, etc. You will have to eg rename norm.mgz to norm.1mm.mgz and copy / symlink / rename the _hires equivalents to get FS to use the highres T1s. 2. That sounds appropriate! 3. That sounds about right 😉 Cheers, /Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: AmirHussein Abdolalizadeh <amirhussein.a@gmail.commailto:amirhussein.a@gmail.com> Date: Sunday, October 18, 2020 at 02:48 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> Subject: segmentHA on Human Connectome Project
Hi,
I am trying to run segmentHA pipeline on HCP data. To do so, I have downloaded FS processed-extended structural data, manually made "scripts", "trash", and "stats" folders in each subject's folder [HCP output does not have these folders]. A few notes and questions:
1. segmentHA_T1 runs smoothly. However, I do not know which T1 does segmentHA use, since there are also a few "_hires" (high resolution) files resulting from HCP's structural analysis pipeline (https://github.com/Washington-University/HCPpipelines).
2. segmentHA_T2 also runs smoothly. However, I didn't know which T2 file is the most suitable to be given to this command. I did give T2w_hires.nii.gz (Voxelsize = 0.7 mm isotropic) in the /mri folder of each subject.
3. I statistically checked the correlation between HCP FS generated values of whole hippocampus/amygdala, and segmentHA generated ones. Of note, they were highly correlated (all p-values < 0.001, all r ~ 0.9).
I will be glad to know whether the pipeline I used to analyze HCP data is correct or any further steps are required.
Bests, Amir 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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
-
AmirHussein Abdolalizadeh -
Iglesias Gonzalez, Juan E.