[Freesurfer] Samseg pallidum issue
Hello FreeSurfer Developers, I ran longitudinal samseg on a group of subjects with MS (each with 5 MRI timepoints over 2 years) and found that the average volume of the pallidum increased over time, while other subcortical volumes (caudate, putamen, thalamus) decreased. I also tried longitudinal samseg using the --pallidum-separate flag and had similar results. As the putamen gets smaller it looks like the pallidum volume grows to fill in the space. Have you encountered this issue before? I am using enhanced T1 images (made from T1, FLAIR, and FA data) as the input for run_samseg_long (FreeSurfer v7). Thank you, Andrew Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531 ___ 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 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] FA map registration to T1
We don't have B0 fieldmap data, would I still be able to perform this correction? For preprocessing we ran eddy_openmp and dtifit. The helpdesk has added klawms to your sudo groups for access to the data. Please let me know if you need any more information. Thanks so much for your help, Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Sunday, April 25, 2021 10:39 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FA map registration to T1 Everything looks ok in the log file. Did you do an B0 distortion correction? Can you give me access to that data? On 4/20/2021 10:34 AM, Russo, Andrew William wrote: Log file is attached. Thank you, Andrew Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531 From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <mailto:dgr...@mgh.harvard.edu> Sent: Tuesday, April 20, 2021 10:09 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FA map registration to T1 can you send the bbr log file? On 4/19/2021 2:29 PM, Russo, Andrew William wrote: Hello FreeSurfer Developers, I am registering FA maps to T1 for a group of subjects with MS and in many cases the registration is poor for the anterior corpus callosum (attached), cerebellum, pons, and temporal lobe. I am using the following commands (FreeSurfer version 6.0): bbregister \ --dti \ --reg diff2T1_reg.dat \ --mov eddy_corrected_b0.nii.gz \ --s subject_temp mri_vol2vol \ --mov dtifit_FA.nii.gz \ --targ orig.mgz \ --o FA2T1.nii.gz \ --reg diff2T1_reg.dat Do you have any suggestions for improving this registration? Thank you, Andrew Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531 ___ 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<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 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] FA map registration to T1
Log file is attached. Thank you, Andrew Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Tuesday, April 20, 2021 10:09 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FA map registration to T1 can you send the bbr log file? On 4/19/2021 2:29 PM, Russo, Andrew William wrote: Hello FreeSurfer Developers, I am registering FA maps to T1 for a group of subjects with MS and in many cases the registration is poor for the anterior corpus callosum (attached), cerebellum, pons, and temporal lobe. I am using the following commands (FreeSurfer version 6.0): bbregister \ --dti \ --reg diff2T1_reg.dat \ --mov eddy_corrected_b0.nii.gz \ --s subject_temp mri_vol2vol \ --mov dtifit_FA.nii.gz \ --targ orig.mgz \ --o FA2T1.nii.gz \ --reg diff2T1_reg.dat Do you have any suggestions for improving this registration? Thank you, Andrew Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer diff2T1_reg.dat.log Description: diff2T1_reg.dat.log ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_vol2surf resolution warning
Hello, I am moving a 6mm volume from MNI152 to fsaverage for group analysis and I get the following warning: mri_vol2surf --src MNI_6mm.nii.gz --out surf_sm4_lh.mgh --mni152reg --hemi lh --interp nearest --surf-fwhm 4 WARNING: the voxel resolution in the source volume (6,6,6) differs from that listed in the registration file (1,1,1) Do you know if this needs to be corrected or if there is a better method? Thanks for the help, Andrew Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] samseg permissions error
Hello Freesurfer Developers, I am trying to use the "samseg" function in /usr/local/freesurfer/dev but do not have permission to access the directory /usr/local/freesurfer/dev/subjects/fsaverage. Is this a restricted directory? ValueError: file /usr/local/freesurfer/dev/subjects/fsaverage/mri/orig.mgz does not exist ERROR: fs_time run_samseg I did not find any related issues with samseg on the archive and I have had it work in the past. Before running samseg I sourced the freesurfer environment: export FREESURFER_HOME=/usr/local/freesurfer/dev source $FREESURFER_HOME/SetUpFreeSurfer.sh (Using Freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) Thank you in advance, Andrew Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
