Re: [Freesurfer] tkregister2 scripting- help with saving reg.dat
External Email - Use Caution I am using mri_vol2vol --mov L_AIP_mask.nii.gz --targ $FSLDIR/standard/MNI152_T1_1mm_brain.nii.gz --inv --reg $FREESURFER_HOME/average/mni152.mni305.subfov1.dat --o L_AIP_MNI152.nii.gz --interp nearest (I used mni152.mni305.subfov1.dat in my registration of T1.mgz into MNI152 space, at the time mni152.register.dat created weird flipping problems, so I am using it here as well) So when I check this in freeview it paints the whole brain and I see that the file is not binarized. I attached a picture, the brain under is the adjusted MNI152 T1 which I corrected manually. I also tried this: mri_label2vol --seg L_AIP_mask.nii.gz --reg $FREESURFER_HOME/average/mni152.mni305.subfov1.dat --invertmtx --o L_AIP_MNI152.nii.gz And it created a binarized volume just like I wanted, but registration was way off and not possible to correct manually because the unmasked volume is so small. I tried to feed a template volume inside this and it didn't create anything. Thank you for all the help! Best Idil [X] From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [dgr...@mgh.harvard.edu] Sent: Tuesday, July 24, 2018 5:09 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tkregister2 scripting- help with saving reg.dat no idea how to help with the vol2vol problem without a command line and more description of the problem On 7/24/18 6:52 AM, Yagmur Ozdemir 19 wrote: External Email - Use Caution By copying the matrix that comes up in the terminal, then readjusting it, if needed, in a different .dat file, I can fix the issue. But I would still appreciate any suggestions on how to use mri_vol2vol with a binarized mask, or what might be causing the system to fill the whole volume. Best Idil From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Yagmur Ozdemir 19 [yozdemi...@amherst.edu<mailto:yozdemi...@amherst.edu>] Sent: Tuesday, July 24, 2018 1:23 PM To: Freesurfer support list [freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>] Subject: [Freesurfer] tkregister2 scripting- help with saving reg.dat External Email - Use Caution Hello freesurfer experts, I am editing the registration matrix between two volumes (fsaverage's T1 to fit MNI152 from fsl) using tkregister2, and I cannot save the registration because I do not have permission to change the .dat file I originally opened with tkregister2. I cannot change the permissions. I do not want to lose all the editing I have done so far, so would really appreciate if someone could give me advice on how to save the registration as a seperate file either in GUI or from terminal. FYI, I know ideally I shouldn't need to edit the registration but for some reason I had weird flipping issues when using mri_vol2vol and mni152.register.dat with --inv option. Also the system for some reason does not recognize a binary volume with the --interp nearest option, so fills in the whole volume. I would appreciate any suggestions. Best Idil ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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.
Re: [Freesurfer] tkregister2 scripting- help with saving reg.dat
no idea how to help with the vol2vol problem without a command line and more description of the problem On 7/24/18 6:52 AM, Yagmur Ozdemir 19 wrote: External Email - Use Caution By copying the matrix that comes up in the terminal, then readjusting it, if needed, in a different .dat file, I can fix the issue. But I would still appreciate any suggestions on how to use mri_vol2vol with a binarized mask, or what might be causing the system to fill the whole volume. Best Idil *From:* freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yagmur Ozdemir 19 [yozdemi...@amherst.edu] *Sent:* Tuesday, July 24, 2018 1:23 PM *To:* Freesurfer support list [freesurfer@nmr.mgh.harvard.edu] *Subject:* [Freesurfer] tkregister2 scripting- help with saving reg.dat External Email - Use Caution Hello freesurfer experts, I am editing the registration matrix between two volumes (fsaverage's T1 to fit MNI152 from fsl) using tkregister2, and I cannot save the registration because I do not have permission to change the .dat file I originally opened with tkregister2. I cannot change the permissions. I do not want to lose all the editing I have done so far, so would really appreciate if someone could give me advice on how to save the registration as a seperate file either in GUI or from terminal. FYI, I know ideally I shouldn't need to edit the registration but for some reason I had weird flipping issues when using mri_vol2vol and mni152.register.dat with --inv option. Also the system for some reason does not recognize a binary volume with the --interp nearest option, so fills in the whole volume. I would appreciate any suggestions. Best Idil ___ 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.
Re: [Freesurfer] tkregister2 scripting- help with saving reg.dat
External Email - Use Caution By copying the matrix that comes up in the terminal, then readjusting it, if needed, in a different .dat file, I can fix the issue. But I would still appreciate any suggestions on how to use mri_vol2vol with a binarized mask, or what might be causing the system to fill the whole volume. Best Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yagmur Ozdemir 19 [yozdemi...@amherst.edu] Sent: Tuesday, July 24, 2018 1:23 PM To: Freesurfer support list [freesurfer@nmr.mgh.harvard.edu] Subject: [Freesurfer] tkregister2 scripting- help with saving reg.dat External Email - Use Caution Hello freesurfer experts, I am editing the registration matrix between two volumes (fsaverage's T1 to fit MNI152 from fsl) using tkregister2, and I cannot save the registration because I do not have permission to change the .dat file I originally opened with tkregister2. I cannot change the permissions. I do not want to lose all the editing I have done so far, so would really appreciate if someone could give me advice on how to save the registration as a seperate file either in GUI or from terminal. FYI, I know ideally I shouldn't need to edit the registration but for some reason I had weird flipping issues when using mri_vol2vol and mni152.register.dat with --inv option. Also the system for some reason does not recognize a binary volume with the --interp nearest option, so fills in the whole volume. I would appreciate any suggestions. Best Idil ___ 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.