Re: [caret-users] projecting functional MRI to gii surfaces
Hi Yan, Could you use a terminal window or file manager to check whether the file exists, and if so, what its size is. We have seen cases before where the file was just a header -- no data. Inexplicably, the presence of a non-english character set on the system used has caused this sort of trouble. If there is a system nearby that does not have a non-english character set installed, you might see if Caret works there. Or remove any non-english character sets on your system and see if it helps. Donna On Jul 31, 2014, at 3:52 PM, Tang, Yan yan.t...@ttu.edu wrote: Dear all, I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. Now I want to map functional volumes to surfaces. In volume selection page, I choose my file 'ff001_010.nii'; In spec file and surface selection page, I choose the file 'study1.L.orig.164k_fs_LR'. I get a file 'map_data_0_31_Jul_2014_15_10_13.metric'. But I find I couldn't open this file. Which step is wrong? How can you do it? ___ 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] projecting functional MRI to gii surfaces
I am sure that the file exist and the size of file is 446KB. Is It correct? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [donna.dier...@sbcglobal.net] Sent: Friday, August 01, 2014 10:10 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, Could you use a terminal window or file manager to check whether the file exists, and if so, what its size is. We have seen cases before where the file was just a header -- no data. Inexplicably, the presence of a non-english character set on the system used has caused this sort of trouble. If there is a system nearby that does not have a non-english character set installed, you might see if Caret works there. Or remove any non-english character sets on your system and see if it helps. Donna On Jul 31, 2014, at 3:52 PM, Tang, Yan yan.t...@ttu.edu wrote: Dear all, I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. Now I want to map functional volumes to surfaces. In volume selection page, I choose my file 'ff001_010.nii'; In spec file and surface selection page, I choose the file 'study1.L.orig.164k_fs_LR'. I get a file 'map_data_0_31_Jul_2014_15_10_13.metric'. But I find I couldn't open this file. Which step is wrong? How can you do it? ___ 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 mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] projecting functional MRI to gii surfaces
Hmmm. Sounds like more than a header to me. When you open the spec file you selected when you mapped the data, and select the output file that is 446kb, what happens? You must make sure you select Metric on the D/C: Overlay/Underlay Surface menu (primary or secondary, typically). Else it won't display. On Aug 1, 2014, at 2:47 PM, Tang, Yan yan.t...@ttu.edu wrote: I am sure that the file exist and the size of file is 446KB. Is It correct? From: caret-users-boun...@brainvis.wustl.edu [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [donna.dier...@sbcglobal.net] Sent: Friday, August 01, 2014 10:10 AM To: Caret, SureFit, and SuMS software users Cc: Tang, Yiyuan Subject: Re: [caret-users] projecting functional MRI to gii surfaces Hi Yan, Could you use a terminal window or file manager to check whether the file exists, and if so, what its size is. We have seen cases before where the file was just a header -- no data. Inexplicably, the presence of a non-english character set on the system used has caused this sort of trouble. If there is a system nearby that does not have a non-english character set installed, you might see if Caret works there. Or remove any non-english character sets on your system and see if it helps. Donna On Jul 31, 2014, at 3:52 PM, Tang, Yan yan.t...@ttu.edu wrote: Dear all, I used the Freesurfer_to_fs_LR Pipeline to get 164k fs_LR surface. Now I want to map functional volumes to surfaces. In volume selection page, I choose my file 'ff001_010.nii'; In spec file and surface selection page, I choose the file 'study1.L.orig.164k_fs_LR'. I get a file 'map_data_0_31_Jul_2014_15_10_13.metric'. But I find I couldn't open this file. Which step is wrong? How can you do it? ___ 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 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
That file has multiple problems, the first being that it isn't plumb, the sform/qform have some rotation in them. Caret5 won't read those kinds of volumes correctly, and it is nontrivial to try to reverse-generate the equivalent in the volume space you need it in. The easiest way to get something that works may be to first remove obliques from your original T1 volume, and then rerun freesurfer, so that this file is no longer oblique. However, I'm not clear on why the third volume dimension has a different number of voxels - you might need to pad your original input volume or something. I haven't had to deal with these things in freesurfer, so someone else should probably give you some guidance. Tim On Thu, Jul 31, 2014 at 3:11 PM, SHAHIN NASR sha...@nmr.mgh.harvard.edu wrote: Hi Timothy, That may be the problem. When the output is like this: ribbon.nii.gz sizeof_hdr 348 data_type INT16 dim0 3 dim1 256 dim2 256 dim3 176 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 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 0.009315 -0.034602 -0.999358 87.028618 qto_xyz:2 -0.998443 0.054645 -0.011198 162.972198 qto_xyz:3 -0.054997 -0.997906 0.034039 140.719284 qto_xyz:4 0.00 0.00 0.00 1.00 qform_xorient Anterior-to-Posterior qform_yorient Superior-to-Inferior qform_zorient Right-to-Left sform_name Scanner Anat sform_code 1 sto_xyz:1 0.009315 -0.034602 -0.999358 87.028618 sto_xyz:2 -0.998443 0.054645 -0.011199 162.972198 sto_xyz:3 -0.054997 -0.997906 0.034039 140.719284 sto_xyz:4 0.00 0.00 0.00 1.00 sform_xorient Anterior-to-Posterior sform_yorient Superior-to-Inferior sform_zorient Right-to-Left file_type NIFTI-1+ file_code 1 descripFreeSurfer May 14 2013 aux_file As you see, dim3 is different than the T1 and T2. But I used the command the command that was mentioned in the instruction to generate ribbon (i.e. mri_convert -rl mri/rawavg.mgz mri/ribbon.mgz ribbon.nii.gz). Any suggestion how to correct this problem? On Thu, Jul 31, 2014 at 3:08 PM, Timothy Coalson tsc...@mst.edu wrote: 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, 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
