[Freesurfer] Assistance Request: Issue with Merging .mgh Files in Ubuntu18

External Email - Use Caution Dear Support Team, I'm reaching out for assistance with merging two .mgh files. As I try to generate a surface mapping for all subjects, I merged all volume files (.nii.gz) by mrcalc. So I get a volume file whose voxel value represents the number

[Freesurfer] Samseg (cross-sectional, longitudinal, MS lesions)

External Email - Use Caution Good morning, 1) For the Samseg protocol, are only T1 and FLAIR sequences required (no MPRAGE scans required)? 2) What does the numerical output of the Samseg calculation look like? Best regards, Krzysztof Barć __

Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

External Email - Use Caution Hi again and sorry for the very confusing questions... I now (without really knowing what I did) managed to get mris_convert --annot left.fsaverage_MY_PARC_2_164.label.gii fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii lh.MY_PARC_164

Re: [Freesurfer] Longitudinal Freesurfer in the presence of large tissue defects

If you construct the non-linear template within the current rigid (or affine) mid-space, then there are two things you can do. (1) You can just replace the base image and run the remainder of the base and longitudinal streams as is to transfer the results out to the TPs using the rigid (or affi

Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

All these filenames are too similar. You mentioned at least 3 different files. mris_info fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii (error) mris_info fs_R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii(ok) mris_

Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

External Email - Use Caution Hi again this gives ls -lt fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii -rw-rw-r-- 1 karin karin 4323015 feb 29 21:54 fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii best karin From:

Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

It seems to me that it failed to open the .gii file. Can you check if 'fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii' exists and you have the read permission? 'ls -lt fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii' From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Creating a custom registration template with FreeSurfer template

It looks like if you don't specify a subject (--target subject) as common space, it will default to 'fsaverage'. See https://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc The input to -surfreg <> is the surface registration to the common space. I think it should be a surface file not in .mgh

Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

External Email - Use Caution Hi I realized that the error occurs only with the Lh- file, that also gives this error mris_info fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii ** failed to open GIFTI XML file 'fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.sur

Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

The output from mris_info looks fine. Are you still having trouble creating .annot file from a label.gii file? The command looks like this: mris_convert --annot label/rh.aparc.annot.gii surf/rh.white.gii rh.aparc.annot You need to provide full path to your input files. Best, Yujing From: fre

Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

External Email - Use Caution Hi Thank you for your reply! mri_info mris_info fs_R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii returns the follwoing: == gifti_image struct version= 1 numDA = 2 gim->