Re: [caret-users] Myelin Mapping: different number of nodes
Hi Eileen, This version of myelin mapping is no longer supported. Please use the HCP Structural Pipelines to create your myelin maps: https://github.com/Washington-University/Pipelines Thanks, Matt. From: Eileen Moore Reply-To: "Caret, SureFit, and SuMS software users" Date: Thursday, December 18, 2014 at 5:50 PM To: Subject: [caret-users] Myelin Mapping: different number of nodes Hi - I'm trying to run myelin mapping. I've processed my data with FreeSurfer v5.3, applied freesurfer_to_fs_LR.sh, downloaded the Conte69 atlas, and followed all the steps outlined on Caret:Operations/MyelinMapping. I obtained the L.MyelinMapping.metric, R.MyelinMapping.metric, T1wDividedByT2w.nii.gz, and T1wDividedByT2w_ribbon.nii.gz files for a single subject. I'm running into problems when trying to view the myelin map using caret5. I generated a spec file using caret_command -spec-file-create subj1039 both Individual -add-files-in-directory But when I tried to load the MyelinMapping metrics I got an error indicating that the MyelinMapping.metrics have a different number of nodes. I've tried overlaying the myelin map on several surfaces, but I keep getting the different number of nodes error. I'm a new caret user and am at a loss for how to troubleshoot this. I'd appreciate any suggestions. Thanks! ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
[caret-users] Myelin Mapping: different number of nodes
Hi - I'm trying to run myelin mapping. I've processed my data with FreeSurfer v5.3, applied freesurfer_to_fs_LR.sh, downloaded the Conte69 atlas, and followed all the steps outlined on Caret:Operations/MyelinMapping. I obtained the L.MyelinMapping.metric, R.MyelinMapping.metric, T1wDividedByT2w.nii.gz, and T1wDividedByT2w_ribbon.nii.gz files for a single subject. I'm running into problems when trying to view the myelin map using caret5. I generated a spec file using caret_command -spec-file-create subj1039 both Individual -add-files-in-directory But when I tried to load the MyelinMapping metrics I got an error indicating that the MyelinMapping.metrics have a different number of nodes. I've tried overlaying the myelin map on several surfaces, but I keep getting the different number of nodes error. I'm a new caret user and am at a loss for how to troubleshoot this. I'd appreciate any suggestions. Thanks! ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Myelin Mapping
;>> slice_code 0 >>> slice_start0 >>> slice_end 0 >>> slice_duration 0.00 >>> time_offset0.00 >>> intent Unknown >>> intent_code0 >>> intent_name >>> intent_p1 0.00 >>> intent_p2 0.00 >>> intent_p3 0.00 >>> qform_name Scanner Anat >>> qform_code 1 >>> qto_xyz:1 -1.00 -0.00 -0.00 123.848427 >>> qto_xyz:2 -0.00 -0.00 1.00 -86.819458 >>> qto_xyz:3 0.00 -1.00 0.00 136.943146 >>> qto_xyz:4 0.00 0.00 0.00 1.00 >>> qform_xorient Right-to-Left >>> qform_yorient Superior-to-Inferior >>> qform_zorient Posterior-to-Anterior >>> sform_name Scanner Anat >>> sform_code 1 >>> sto_xyz:1 -1.00 -0.00 0.00 123.848427 >>> sto_xyz:2 0.00 -0.00 1.00 -86.819458 >>> sto_xyz:3 -0.00 -1.00 0.00 136.943146 >>> sto_xyz:4 0.00 0.00 0.00 1.00 >>> sform_xorient Right-to-Left >>> sform_yorient Superior-to-Inferior >>> sform_zorient Posterior-to-Anterior >>> file_type NIFTI-1+ >>> file_code 1 >>> descripFSL5.0 >>> aux_file >>> >>> >>> For T1: >>> >>> filename OrigT1.nii.gz >>> >>> sizeof_hdr 348 >>> data_type UINT8 >>> dim0 3 >>> dim1 256 >>> dim2 256 >>> dim3 256 >>> dim4 1 >>> dim5 1 >>> dim6 1 >>> dim7 1 >>> vox_units mm >>> time_units s >>> datatype 2 >>> nbyper 1 >>> bitpix 8 >>> pixdim00.00 >>> pixdim11.00 >>> pixdim21.00 >>> pixdim31.00 >>> pixdim42.529714 >>> pixdim51.00 >>> pixdim61.00 >>> pixdim71.00 >>> vox_offset 352 >>> cal_max0. >>> cal_min0. >>> scl_slope 0.00 >>> scl_inter 0.00 >>> phase_dim 0 >>> freq_dim 0 >>> slice_dim 0 >>> slice_name Unknown >>> slice_code 0 >>> slice_start0 >>> slice_end 0 >>> slice_duration 0.00 >>> time_offset0.00 >>> intent Unknown >>> intent_code0 >>> intent_name >>> intent_p1 0.00 >>> intent_p2 0.00 >>> intent_p3 0.00 >>> qform_name Scanner Anat >>> qform_code 1 >>> qto_xyz:1 -1.00 -0.00 -0.00 123.848427 >>> qto_xyz:2 -0.00 -0.00 1.00 -86.819458 >>> qto_xyz:3 0.00 -1.00 0.00 136.943146 >>> qto_xyz:4 0.00 0.00 0.00 1.00 >>> qform_xorient Right-to-Left >>> qform_yorient Superior-to-Inferior >>> qform_zorient Posterior-to-Anterior >>> sform_name Scanner Anat >>> sform_code 1 >>> sto_xyz:1 -1.00 -0.00 0.00 123.848427 >>> sto_xyz:2 0.00 -0.00 1.00 -86.819458 >>> sto_xyz:3 -0.00 -1.00 0.00 136.943146 >>> sto_xyz:4 0.00 0.00 0.00 1.00 >>> sform_xorient Right-to-Left >>> sform_yorient Superior-to-Inferior >>> sform_zorient Posterior-to-Anterior >>> file_type NIFTI-1+ >>> file_code 1 >>> descripFreeSurfer May 14 2013 >>> aux_file >>> >>> >>> > Please paste the output of fslhd on both files. >>> > >>> > Peace, >>> > >>> > Matt. >>> > >>> > From: SHAHIN NASR >>> > Reply-To: "Caret, SureFit, and SuMS software users" >>> > >>> > Date: Thursday, July 31, 2014 at 11:18 AM >>> > To: "Caret, SureFit, and SuMS software users" >>> > >>> > Subject: [caret-users] Myelin Mapping >>> > >>> > Hi, >>> >I am trying to do myelin mapping. I am following your instructions >>> on >>> > this website: >>> > >>> > >>> http://brainvis.wustl.edu/wiki/index.php/Caret:O
Re: [caret-users] Myelin Mapping
z >> >> sizeof_hdr 348 >> data_type UINT8 >> dim0 3 >> dim1 256 >> dim2 256 >> dim3 256 >> dim4 1 >> dim5 1 >> dim6 1 >> dim7 1 >> vox_units mm >> time_units s >> datatype 2 >> nbyper 1 >> bitpix 8 >> pixdim00.00 >> pixdim11.00 >> pixdim21.00 >> pixdim31.00 >> pixdim42.529714 >> pixdim51.00 >> pixdim61.00 >> pixdim71.00 >> vox_offset 352 >> cal_max0. >> cal_min0. >> scl_slope 0.00 >> scl_inter 0.00 >> phase_dim 0 >> freq_dim 0 >> slice_dim 0 >> slice_name Unknown >> slice_code 0 >> slice_start0 >> slice_end 0 >> slice_duration 0.00 >> time_offset0.00 >> intent Unknown >> intent_code0 >> intent_name >> intent_p1 0.00 >> intent_p2 0.00 >> intent_p3 0.00 >> qform_name Scanner Anat >> qform_code 1 >> qto_xyz:1 -1.00 -0.00 -0.00 123.848427 >> qto_xyz:2 -0.00 -0.00 1.00 -86.819458 >> qto_xyz:3 0.00 -1.00 0.00 136.943146 >> qto_xyz:4 0.00 0.00 0.00 1.00 >> qform_xorient Right-to-Left >> qform_yorient Superior-to-Inferior >> qform_zorient Posterior-to-Anterior >> sform_name Scanner Anat >> sform_code 1 >> sto_xyz:1 -1.00 -0.00 0.00 123.848427 >> sto_xyz:2 0.00 -0.00 1.00 -86.819458 >> sto_xyz:3 -0.00 -1.00 0.00 136.943146 >> sto_xyz:4 0.00 0.00 0.00 1.00 >> sform_xorient Right-to-Left >> sform_yorient Superior-to-Inferior >> sform_zorient Posterior-to-Anterior >> file_type NIFTI-1+ >> file_code 1 >> descripFreeSurfer May 14 2013 >> aux_file >> >> >> > Please paste the output of fslhd on both files. >> > >> > Peace, >> > >> > Matt. >> > >> > From: SHAHIN NASR >> > Reply-To: "Caret, SureFit, and SuMS software users" >> > >> > Date: Thursday, July 31, 2014 at 11:18 AM >> > To: "Caret, SureFit, and SuMS software users" >> > >> > Subject: [caret-users] Myelin Mapping >> > >> > Hi, >> >I am trying to do myelin mapping. I am following your instructions >> on >> > this website: >> > >> > http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MyelinMapping >> > >> >and I don't get any error till the last command which says: >> > >> > MYELIN MAPPING ERROR: t1 Dimensions do not match t2 dimensions >> > >> >But when I check the my T1 and T2 files (using mri_info), I do not >> see >> > any difference: >> > >> > For T1: >> > type: nii >> > dimensions: 256 x 256 x 256 >> >voxel sizes: 1., 1., 1. >> > type: UCHAR (0) >> >fov: 256.000 >> >dof: 0 >> > xstart: -128.0, xend: 128.0 >> > ystart: -128.0, yend: 128.0 >> > zstart: -128.0, zend: 128.0 >> > >> > >> > >> > For T2: >> > type: nii >> > dimensions: 256 x 256 x 256 >> >voxel sizes: 1., 1., 1. >> > type: FLOAT (3) >> >fov: 256.000 >> >dof: 0 >> > xstart: -128.0, xend: 128.0 >> > ystart: -128.0, yend: 128.0 >> > zstart: -128.0, zend: 128.0 >> > >> > Would you tell me what is the problem. >> > >> > P.S.: I have already checked the Registration and it looks very OK. >> > >> > Regards >> > - >> > Shahin Nasr >> > >> > PhD in Cognitive Neuroscience >> > Martinos Imaging Center, MGH >> > Harvard Medical School >> > >> > ___ caret-users mailing list >> > caret-users@brainvis.wustl.edu >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > >> > ___ >> > caret-users mailing list >> > caret-users@brainvis.wustl.edu >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > >> >> >> >> 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. >> >> >> ___ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Myelin Mapping
A quick look at the source shows that the same error text is used when the mask volume doesn't have the same dimensions as the cortical ribbon volume, please check that file also. Tim On Thu, Jul 31, 2014 at 1:31 PM, wrote: > Matt, >The output of fslhd when i apply it to my T1 and T2 files are as below: > > For T2: > > filename T2w.nii.gz > > > sizeof_hdr 348 > data_type INT16 > dim0 3 > dim1 256 > dim2 256 > dim3 256 > dim4 1 > dim5 1 > dim6 1 > dim7 1 > vox_units mm > time_units s > datatype 4 > nbyper 2 > bitpix 16 > pixdim00.00 > pixdim11.00 > pixdim21.00 > pixdim31.00 > pixdim43.200477 > pixdim50.00 > pixdim60.00 > pixdim70.00 > vox_offset 352 > cal_max0. > cal_min0. > scl_slope 1.00 > scl_inter 0.00 > phase_dim 0 > freq_dim 0 > slice_dim 0 > slice_name Unknown > slice_code 0 > slice_start0 > slice_end 0 > slice_duration 0.00 > time_offset0.00 > intent Unknown > intent_code0 > intent_name > intent_p1 0.00 > intent_p2 0.00 > intent_p3 0.00 > qform_name Scanner Anat > qform_code 1 > qto_xyz:1 -1.00 -0.00 -0.00 123.848427 > qto_xyz:2 -0.00 -0.00 1.00 -86.819458 > qto_xyz:3 0.00 -1.00 0.00 136.943146 > qto_xyz:4 0.00 0.00 0.00 1.00 > qform_xorient Right-to-Left > qform_yorient Superior-to-Inferior > qform_zorient Posterior-to-Anterior > sform_name Scanner Anat > sform_code 1 > sto_xyz:1 -1.00 -0.00 0.00 123.848427 > sto_xyz:2 0.00 -0.00 1.00 -86.819458 > sto_xyz:3 -0.00 -1.00 0.00 136.943146 > sto_xyz:4 0.00 0.00 0.00 1.00 > sform_xorient Right-to-Left > sform_yorient Superior-to-Inferior > sform_zorient Posterior-to-Anterior > file_type NIFTI-1+ > file_code 1 > descripFSL5.0 > aux_file > > > For T1: > > filename OrigT1.nii.gz > > sizeof_hdr 348 > data_type UINT8 > dim0 3 > dim1 256 > dim2 256 > dim3 256 > dim4 1 > dim5 1 > dim6 1 > dim7 1 > vox_units mm > time_units s > datatype 2 > nbyper 1 > bitpix 8 > pixdim00.00 > pixdim11.00 > pixdim21.00 > pixdim31.00 > pixdim42.529714 > pixdim51.00 > pixdim61.00 > pixdim71.00 > vox_offset 352 > cal_max0. > cal_min0. > scl_slope 0.00 > scl_inter 0.00 > phase_dim 0 > freq_dim 0 > slice_dim 0 > slice_name Unknown > slice_code 0 > slice_start0 > slice_end 0 > slice_duration 0.00 > time_offset0.00 > intent Unknown > intent_code0 > intent_name > intent_p1 0.00 > intent_p2 0.00 > intent_p3 0.00 > qform_name Scanner Anat > qform_code 1 > qto_xyz:1 -1.00 -0.00 -0.00 123.848427 > qto_xyz:2 -0.00 -0.00 1.00 -86.819458 > qto_xyz:3 0.00 -1.00 0.00 136.943146 > qto_xyz:4 0.00 0.00 0.00 1.00 > qform_xorient Right-to-Left > qform_yorient Superior-to-Inferior > qform_zorient Posterior-to-Anterior > sform_name Scanner Anat > sform_code 1 > sto_xyz:1 -1.00 -0.00 0.00 123.848427 > sto_xyz:2 0.00 -0.00 1.00 -86.819458 > sto_xyz:3 -0.00 -1.00 0.00 136.943146 > sto_xyz:4 0.00 0.00 0.00 1.00 > sform_xorient Right-to-Left > sform_yorient Superior-to-Inferior > sform_zorient Posterior-to-Anterior > file_type NIFTI-1+ > file_code 1 > descripFreeSurfer May 14 2013 > aux_file > > > > Please paste the output of fslhd on both files. > > > > Peace, > > > > Matt. > > > > From: SHAHIN NASR > > Reply-To: "Caret, SureFit, and SuMS software users" > > > > Date: Thursday, July 31, 2014 at 11:18 AM > > To: "Caret, SureFit, and SuMS software users" > > > > Subject: [caret-users] Myelin Mapping &
Re: [caret-users] Myelin Mapping
It may not be capable of working with images that are not LPI or RPI. I¹d also note that hopefully within the next week or two the HCP pipelines will be released and this code will become unsupported (since the HCP pipelines make myelin maps much better). Peace, Matt. On 7/31/14, 1:31 PM, "sha...@nmr.mgh.harvard.edu" wrote: >Matt, > The output of fslhd when i apply it to my T1 and T2 files are as below: > >For T2: > >filename T2w.nii.gz > > >sizeof_hdr 348 >data_type INT16 >dim0 3 >dim1 256 >dim2 256 >dim3 256 >dim4 1 >dim5 1 >dim6 1 >dim7 1 >vox_units mm >time_units s >datatype 4 >nbyper 2 >bitpix 16 >pixdim00.00 >pixdim11.00 >pixdim21.00 >pixdim31.00 >pixdim43.200477 >pixdim50.00 >pixdim60.00 >pixdim70.00 >vox_offset 352 >cal_max0. >cal_min0. >scl_slope 1.00 >scl_inter 0.00 >phase_dim 0 >freq_dim 0 >slice_dim 0 >slice_name Unknown >slice_code 0 >slice_start0 >slice_end 0 >slice_duration 0.00 >time_offset0.00 >intent Unknown >intent_code0 >intent_name >intent_p1 0.00 >intent_p2 0.00 >intent_p3 0.00 >qform_name Scanner Anat >qform_code 1 >qto_xyz:1 -1.00 -0.00 -0.00 123.848427 >qto_xyz:2 -0.00 -0.00 1.00 -86.819458 >qto_xyz:3 0.00 -1.00 0.00 136.943146 >qto_xyz:4 0.00 0.00 0.00 1.00 >qform_xorient Right-to-Left >qform_yorient Superior-to-Inferior >qform_zorient Posterior-to-Anterior >sform_name Scanner Anat >sform_code 1 >sto_xyz:1 -1.00 -0.00 0.00 123.848427 >sto_xyz:2 0.00 -0.00 1.00 -86.819458 >sto_xyz:3 -0.00 -1.00 0.00 136.943146 >sto_xyz:4 0.00 0.00 0.00 1.00 >sform_xorient Right-to-Left >sform_yorient Superior-to-Inferior >sform_zorient Posterior-to-Anterior >file_type NIFTI-1+ >file_code 1 >descripFSL5.0 >aux_file > > >For T1: > >filename OrigT1.nii.gz > >sizeof_hdr 348 >data_type UINT8 >dim0 3 >dim1 256 >dim2 256 >dim3 256 >dim4 1 >dim5 1 >dim6 1 >dim7 1 >vox_units mm >time_units s >datatype 2 >nbyper 1 >bitpix 8 >pixdim00.00 >pixdim11.00 >pixdim21.00 >pixdim31.00 >pixdim42.529714 >pixdim51.00 >pixdim61.00 >pixdim71.00 >vox_offset 352 >cal_max0. >cal_min0. >scl_slope 0.00 >scl_inter 0.00 >phase_dim 0 >freq_dim 0 >slice_dim 0 >slice_name Unknown >slice_code 0 >slice_start0 >slice_end 0 >slice_duration 0.00 >time_offset0.00 >intent Unknown >intent_code0 >intent_name >intent_p1 0.00 >intent_p2 0.00 >intent_p3 0.00 >qform_name Scanner Anat >qform_code 1 >qto_xyz:1 -1.00 -0.00 -0.00 123.848427 >qto_xyz:2 -0.00 -0.00 1.00 -86.819458 >qto_xyz:3 0.00 -1.00 0.00 136.943146 >qto_xyz:4 0.00 0.00 0.00 1.00 >qform_xorient Right-to-Left >qform_yorient Superior-to-Inferior >qform_zorient Posterior-to-Anterior >sform_name Scanner Anat >sform_code 1 >sto_xyz:1 -1.00 -0.00 0.00 123.848427 >sto_xyz:2 0.00 -0.00 1.00 -86.819458 >sto_xyz:3 -0.00 -1.00 0.00 136.943146 >sto_xyz:4 0.00 0.00 0.00 1.00 >sform_xorient Right-to-Left >sform_yorient Superior-to-Inferior >sform_zorient Posterior-to-Anterior >file_type NIFTI-1+ >file_code 1 >descripFreeSurfer May 14 2013 >aux_file > > >> Please paste the output of fslhd on both files. >> >> Peace, >> >> Matt. >> >> From: SHAHIN NASR >> Reply-To: "Caret, SureFit, and SuMS software users" >> >> Date: Thursday, July 31, 2014 at 11:18 AM >> To: "Caret, SureFit, and SuMS software users" >> >> Subject: [caret-users] Myelin Mapping >> >> Hi, >>I am trying
Re: [caret-users] Myelin Mapping
Matt, The output of fslhd when i apply it to my T1 and T2 files are as below: For T2: filename T2w.nii.gz sizeof_hdr 348 data_type INT16 dim0 3 dim1 256 dim2 256 dim3 256 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units s datatype 4 nbyper 2 bitpix 16 pixdim00.00 pixdim11.00 pixdim21.00 pixdim31.00 pixdim43.200477 pixdim50.00 pixdim60.00 pixdim70.00 vox_offset 352 cal_max0. cal_min0. scl_slope 1.00 scl_inter 0.00 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start0 slice_end 0 slice_duration 0.00 time_offset0.00 intent Unknown intent_code0 intent_name intent_p1 0.00 intent_p2 0.00 intent_p3 0.00 qform_name Scanner Anat qform_code 1 qto_xyz:1 -1.00 -0.00 -0.00 123.848427 qto_xyz:2 -0.00 -0.00 1.00 -86.819458 qto_xyz:3 0.00 -1.00 0.00 136.943146 qto_xyz:4 0.00 0.00 0.00 1.00 qform_xorient Right-to-Left qform_yorient Superior-to-Inferior qform_zorient Posterior-to-Anterior sform_name Scanner Anat sform_code 1 sto_xyz:1 -1.00 -0.00 0.00 123.848427 sto_xyz:2 0.00 -0.00 1.00 -86.819458 sto_xyz:3 -0.00 -1.00 0.00 136.943146 sto_xyz:4 0.00 0.00 0.00 1.00 sform_xorient Right-to-Left sform_yorient Superior-to-Inferior sform_zorient Posterior-to-Anterior file_type NIFTI-1+ file_code 1 descripFSL5.0 aux_file For T1: filename OrigT1.nii.gz sizeof_hdr 348 data_type UINT8 dim0 3 dim1 256 dim2 256 dim3 256 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units s datatype 2 nbyper 1 bitpix 8 pixdim00.00 pixdim11.00 pixdim21.00 pixdim31.00 pixdim42.529714 pixdim51.00 pixdim61.00 pixdim71.00 vox_offset 352 cal_max0. cal_min0. scl_slope 0.00 scl_inter 0.00 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start0 slice_end 0 slice_duration 0.00 time_offset0.00 intent Unknown intent_code0 intent_name intent_p1 0.00 intent_p2 0.00 intent_p3 0.00 qform_name Scanner Anat qform_code 1 qto_xyz:1 -1.00 -0.00 -0.00 123.848427 qto_xyz:2 -0.00 -0.00 1.00 -86.819458 qto_xyz:3 0.00 -1.00 0.00 136.943146 qto_xyz:4 0.00 0.00 0.00 1.00 qform_xorient Right-to-Left qform_yorient Superior-to-Inferior qform_zorient Posterior-to-Anterior sform_name Scanner Anat sform_code 1 sto_xyz:1 -1.00 -0.00 0.00 123.848427 sto_xyz:2 0.00 -0.00 1.00 -86.819458 sto_xyz:3 -0.00 -1.00 0.00 136.943146 sto_xyz:4 0.00 0.00 0.00 1.00 sform_xorient Right-to-Left sform_yorient Superior-to-Inferior sform_zorient Posterior-to-Anterior file_type NIFTI-1+ file_code 1 descripFreeSurfer May 14 2013 aux_file > Please paste the output of fslhd on both files. > > Peace, > > Matt. > > From: SHAHIN NASR > Reply-To: "Caret, SureFit, and SuMS software users" > > Date: Thursday, July 31, 2014 at 11:18 AM > To: "Caret, SureFit, and SuMS software users" > > Subject: [caret-users] Myelin Mapping > > Hi, >I am trying to do myelin mapping. I am following your instructions on > this website: > > http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MyelinMapping > >and I don't get any error till the last command which says: > > MYELIN MAPPING ERROR: t1 Dimensions do not match t2 dimensions > >But when I check the my T1 and T2 files (using mri_info), I do not see > any difference: > > For T1: > type: nii > dimensions: 256 x 256 x 256 >voxel sizes: 1., 1., 1. > type: UCHAR (0) >fov: 256.000 >dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -128.0, zend: 128.0 > > > > For T2: > type: nii > dimensions: 256 x 256 x 256 >voxel sizes: 1., 1., 1. > type: FLOAT (3) >fov: 256.000 >dof: 0 > xstart: -128.0,
Re: [caret-users] Myelin Mapping
Please paste the output of fslhd on both files. Peace, Matt. From: SHAHIN NASR Reply-To: "Caret, SureFit, and SuMS software users" Date: Thursday, July 31, 2014 at 11:18 AM To: "Caret, SureFit, and SuMS software users" Subject: [caret-users] Myelin Mapping Hi, I am trying to do myelin mapping. I am following your instructions on this website: http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MyelinMapping and I don't get any error till the last command which says: MYELIN MAPPING ERROR: t1 Dimensions do not match t2 dimensions But when I check the my T1 and T2 files (using mri_info), I do not see any difference: For T1: type: nii dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 For T2: type: nii dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 Would you tell me what is the problem. P.S.: I have already checked the Registration and it looks very OK. Regards - Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
[caret-users] Myelin Mapping
Hi, I am trying to do myelin mapping. I am following your instructions on this website: http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MyelinMapping and I don't get any error till the last command which says: MYELIN MAPPING ERROR: t1 Dimensions do not match t2 dimensions But when I check the my T1 and T2 files (using mri_info), I do not see any difference: For T1: type: nii dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 For T2: type: nii dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 Would you tell me what is the problem. P.S.: I have already checked the Registration and it looks very OK. Regards - Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Myelin mapping
It's possible it is trying to write something to the current directory and you don't have permission to write there. Peace, Matt. On 3/9/14 2:02 PM, "Righart, Ruthger" wrote: >Dear Caret experts, > >I would like to perform myelin mapping following the descriptions on >the Caret website. All the pre-processing operations seem to work fine >until the point that I use caret_command -myelin mapping. >Here the error that I get is: MYELIN MAPPING ERROR: ERROR >DEBUG.L.METRIC: OPEN FOR WRITING, PERMISSION DENIED. > >Initially I thought that this might be related to access permissions to >the files, and therefore checked this with chmod 777 -R for both Caret >and Freesurfer files, but changing the access rights does not resolve >this problem. > >I would be glad to hear from you what this error may mean and any >suggestions to resolve this would be welcome. I am working on a Linux >machine. > >All the best, >Ruthger Righart >___ >caret-users mailing list >caret-users@brainvis.wustl.edu >http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
[caret-users] Myelin mapping
Dear Caret experts, I would like to perform myelin mapping following the descriptions on the Caret website. All the pre-processing operations seem to work fine until the point that I use caret_command -myelin mapping. Here the error that I get is: MYELIN MAPPING ERROR: ERROR DEBUG.L.METRIC: OPEN FOR WRITING, PERMISSION DENIED. Initially I thought that this might be related to access permissions to the files, and therefore checked this with chmod 777 -R for both Caret and Freesurfer files, but changing the access rights does not resolve this problem. I would be glad to hear from you what this error may mean and any suggestions to resolve this would be welcome. I am working on a Linux machine. All the best, Ruthger Righart ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] myelin mapping
lh.curv and rh.curv are made by mris_make_surfaces normally. You might as well use caret to remake the curvature files: caret_command -surface-curvature and then use mean curvature. You will want to make sure that the thickness matches your volumes, because it is used as a part of the mapping. If you have 1mm volumes in Caret, then it is fine. If you have 0.25mm volumes, you should divide the thickness by 4. Peace, Matt. _ From: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Colin Reveley Sent: Sunday, July 01, 2012 4:13 PM To: caret-users@brainvis.wustl.edu Subject: [caret-users] myelin mapping Hi - I had a data accident a while ago. I lost a freesurfer dir. But, since I was importing to caret I have lh and rh white and pial from freesurfer, and I have the thickness files for each. And I have the appropriate MRIs. These files took a LONG time to get right, and then it took quite a while to register them to F99 in a way I found acceptable. So I'm not sure about doing it again, for this animal anyway. I can get a ribbon volume using mri_ribbon. It's one file for each hemisphere. I presume I can just merge them, and call it ribbon,mgz what I'm missinng, for myelin mapping, are the rh.curv and lh.curv. there are two programs: mris_curvature mris_curvature_stats the former outputs a mean and gaussian curvature file (I think these files are an intermediate in making "rh.curv"; mris_make_surfaces does generate them I think anyway) then the other program makes this stuff rh.smoothwm.K.crv rh.smoothwm.H.crv rh.smoothwm.k1.crv rh.smoothwm.k2.crv rh.smoothwm.S.crv rh.smoothwm.C.crv rh.smoothwm.BE.crv can I make the curv file that you want for myelin mapping from any of the above files? maybe just renaming the mean curvature file or gaussian curvature file to "rh.curv" would be fine? Also, my voxels are 1mm in freesurfer, but 0.25 in reality. is that going to be a problem for this (curvature, thickness)? Probably not. but making sure. cheers, Colin ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
[caret-users] myelin mapping
Hi - I had a data accident a while ago. I lost a freesurfer dir. But, since I was importing to caret I have lh and rh white and pial from freesurfer, and I have the thickness files for each. And I have the appropriate MRIs. These files took a LONG time to get right, and then it took quite a while to register them to F99 in a way I found acceptable. So I'm not sure about doing it again, for this animal anyway. I can get a ribbon volume using mri_ribbon. It's one file for each hemisphere. I presume I can just merge them, and call it ribbon,mgz what I'm missinng, for myelin mapping, are the rh.curv and lh.curv. there are two programs: mris_curvature mris_curvature_stats the former outputs a mean and gaussian curvature file (I think these files are an intermediate in making "rh.curv"; mris_make_surfaces does generate them I think anyway) then the other program makes this stuff rh.smoothwm.K.crv rh.smoothwm.H.crv rh.smoothwm.k1.crv rh.smoothwm.k2.crv rh.smoothwm.S.crv rh.smoothwm.C.crv rh.smoothwm.BE.crv can I make the curv file that you want for myelin mapping from any of the above files? maybe just renaming the mean curvature file or gaussian curvature file to "rh.curv" would be fine? Also, my voxels are 1mm in freesurfer, but 0.25 in reality. is that going to be a problem for this (curvature, thickness)? Probably not. but making sure. cheers, Colin ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] myelin mapping
It would work to provide the image you want to use for the myelin map (i.e. the MTR) and then a volume of ones for the T2. Then format the ribbon volume like a FreeSurfer ribbon file (in terms of the numbers that correspond to particular labels). Peace, Matt. _ From: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Timothy Coalson Sent: Sunday, April 22, 2012 10:49 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] myelin mapping Since what the myelin mapping maps is basically T1/T2, you may be able to adjust your data to be in a plausible range for these values, and then fake the T2 by taking an image that looks like a T1 and dividing it by this adjusted data. As long as your data is not discontinuous at the edge of the ribbon, it should work because myelin mapping ignores voxels outside the ribbon. If you don't have a volume that looks like a T1, you can probably use nearly anything as long as its grey matter is fairly consistent and far from zero. Alternatively, if you have the workbench alpha, its volume to surface mapping now has a ribbon mapping option which uses data from all voxels inside the ribbon, rather than just ones close enough to matter for interpolation, though you will need surfaces that approximate the white and pial surfaces: tim@timsdev:~$ wb_command -volume-to-surface-mapping MAP VOLUME TO SURFACE wb_command -volume-to-surface-mapping [-trilinear] [-enclosing] [-ribbon-constrained] [-volume-roi] [-voxel-subdiv] [-subvol-select] ... This doesn't have the artifact correction code from myelin mapping in it, though that code in myelin mapping is partly based on the kinds of artifacts that show up in T1/T2, and may not apply to your data. Tim On Sun, Apr 22, 2012 at 12:06 PM, Colin Reveley wrote: hello - I'm interested in using your myelin mapping algorithm, however: I don't have a t1w imgage I don't have a t2w image I don't have any freesurfer data. what do I have? I have, instead, a magnetization transfer ratio image from an ex-vivo sample. and, it's very high resolution (250um). I have a pretty good ribbon made in FAST. I have a caret surface made from a downasmpled 500um of the MTR. while the MTR is maybe not a perfect correlate of GM myelin content, it's pretty good and and it's what I have. I don't have time to go through the freesurfer process for this data. since the resolution is good, in principle it's possible to take the caret surefit surface and expand and shrink it so that I can map the MTR and get some vague gesture at laminar differences in myelin. so far the results of this seems to make some sense, although it's hardly exact. I'd like to apply your algorithm, and it does seem to me that the essential data is there (especially as you've previously given me insturction on how to get a ribbon that's suitable using only FAST). so, in effect, I have a midthickness, the equiv of a T1/T2 (I understand it's not the same, but we don't have time to get T1w and t2w from the sample, which won't behave the same in fixed tissue anyway - the MTR is ok. Someone else other than me has made that determination, so let's accept his view) and pretty much a cortical ribbon. however, the inputs to appropriate caret-command aren't right. even though the data is surely ok as input to the algorithm. and I still want to make use of your smart algorithm to process the data using ribbon, instead of just volume->surface metric making. It may validate, or not, claims of more fine tuned (laminar *related*) info. the laminar possibility is nice, but it's of course all over the place in practical terms of surface mapping, even as the data is there. attach screen (crude, top ctx layers shaved off). clearly it can work. if I knew how to fool caret_command by giving it the right data or "fake" data just so I can take advantage of your work with the ribbon, and the things the you wrote about recently. and that would be a help, and progress. best, Colin ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] myelin mapping
Since what the myelin mapping maps is basically T1/T2, you may be able to adjust your data to be in a plausible range for these values, and then fake the T2 by taking an image that looks like a T1 and dividing it by this adjusted data. As long as your data is not discontinuous at the edge of the ribbon, it should work because myelin mapping ignores voxels outside the ribbon. If you don't have a volume that looks like a T1, you can probably use nearly anything as long as its grey matter is fairly consistent and far from zero. Alternatively, if you have the workbench alpha, its volume to surface mapping now has a ribbon mapping option which uses data from all voxels inside the ribbon, rather than just ones close enough to matter for interpolation, though you will need surfaces that approximate the white and pial surfaces: tim@timsdev:~$ wb_command -volume-to-surface-mapping MAP VOLUME TO SURFACE wb_command -volume-to-surface-mapping [-trilinear] [-enclosing] [-ribbon-constrained] [-volume-roi] [-voxel-subdiv] [-subvol-select] ... This doesn't have the artifact correction code from myelin mapping in it, though that code in myelin mapping is partly based on the kinds of artifacts that show up in T1/T2, and may not apply to your data. Tim On Sun, Apr 22, 2012 at 12:06 PM, Colin Reveley wrote: > hello - > > I'm interested in using your myelin mapping algorithm, however: > > I don't have a t1w imgage > I don't have a t2w image > I don't have any freesurfer data. > > what do I have? > > I have, instead, a magnetization transfer ratio image from an ex-vivo > sample. and, it's very high resolution (250um). > > I have a pretty good ribbon made in FAST. > > I have a caret surface made from a downasmpled 500um of the MTR. > > while the MTR is maybe not a perfect correlate of GM myelin content, it's > pretty good and and it's what I have. > > I don't have time to go through the freesurfer process for this data. > > since the resolution is good, in principle it's possible to take the caret > surefit surface and expand and shrink it so that I can map the MTR and get > some vague gesture at laminar differences in myelin. so far the results of > this seems to make some sense, although it's hardly exact. > > I'd like to apply your algorithm, and it does seem to me that the > essential data is there (especially as you've previously given me > insturction on how to get a ribbon that's suitable using only FAST). > > so, in effect, I have a midthickness, the equiv of a T1/T2 (I understand > it's not the same, but we don't have time to get T1w and t2w from the > sample, which won't behave the same in fixed tissue anyway - the MTR is ok. > Someone else other than me has made that determination, so let's accept his > view) and pretty much a cortical ribbon. > > however, the inputs to appropriate caret-command aren't right. even though > the data is surely ok as input to the algorithm. > > and I still want to make use of your smart algorithm to process the data > using ribbon, instead of just volume->surface metric making. It may > validate, or not, claims of more fine tuned (laminar *related*) info. > > the laminar possibility is nice, but it's of course all over the place in > practical terms of surface mapping, even as the data is there. > > attach screen (crude, top ctx layers shaved off). > > clearly it can work. if I knew how to fool caret_command by giving it the > right data or "fake" data just so I can take advantage of your work with > the ribbon, and the things the you wrote about recently. > > and that would be a help, and progress. > > best, > > Colin > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
