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. < jiglesiasgonza...@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 <amirhussei...@gmail.com> > *Date: *Tuesday, October 20, 2020 at 02:40 > *To: *"Iglesias Gonzalez, Juan E." <jiglesiasgonza...@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. < > jiglesiasgonza...@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 <amirhussei...@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.igles...@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. >
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