On 09/10/2012 03:49 PM, Garikoitz Lerma Usabiaga wrote:
Hi Doug, Many thanks! now it's working!
I have two new follow up questions: 1.- I understand that I should convert the .mgh to .label with mri_cor2label then? mri_cor2label --i /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh --surf Surfrend_Colin27 lh --id 1 --l /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.label
Correct
2.- As the ROI-s I want to export to FS are in Colin27, I am using a FS version of Colin27 (I updated with recon-all the FS_spm_CanonicalBrain distributed with SurfRend). I think I have near perfect translation of the ROI-s to FS now, I couldn't obtain them when translating to fsaverage. In order to obtain CT averages for that .label, is it ok if the source is my Colin27 instead of the standard fsaverage? mri_label2label --srclabel /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.label--srcsubject Surfrend_Colin27--trgsubject bert --trglabel lh.BA44-45-47Colin27_to_bert --regmethod surface --hemi lh
and then: mris_anatomical_stats -l lh.BA44-45-47Colin27_to_bert.label -t lh.thickness -b -f bert/stats/lh.BA44-45-47Colin27_to_bert.stats bert lh
Yes, that is fine.
Many many thanks for your help again! Gari
On 2012-09-10, at 16:44, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Gary, don't load it as a label, load it as an overlay. Another thing to note is that you should not specify both --projfrac and --projfrac-max (or --projdist-max). In your first case, it won't make a difference because --projfrac-max is last, but it will make a difference in your second call below. doug
On 09/09/2012 06:13 PM, Garikoitz Lerma Usabiaga wrote:
Dear freesurfers, I am trying to create .mgh labels in order to obtain CT averages from several subjects.
I register the ROI-s with bbregister and I get the .nii which renders nicely in tksurfer: /tksurfer Surfrend_Colin127 lh inflated /-overlay /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii -overlay-reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat
-fthresh 1
The problem arises when I try to use mri_vol2surf. I've been trying with many different options, for example:
mri_vol2surf--mov /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii--reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat
--projfrac 0.5 --projfrac-max 0 1 .01--hemi lh--out /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh
or
mri_vol2surf --mov /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii--reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat
--projdist-max 0 1 0.1 --projfrac 1 --interp nearest --hemi lh --out /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh
When I try to visualize it with tksurfer, it gives me nothing: /tksurfer Surfrend_Colin27 lh inflated -label/ /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh -fthresh 1
How should I use mri_vol2surf in order to obtain results? What are the alternatives in order to have surface labels? Creating a label tracing the border of the .nii label in tksurfer is a posible solution?
Thank you very much for your attention, Gari
[iMacGari:~] garikoitz% mri_vol2surf --mov /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii --reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat
--projfrac 0.5 --projfrac-max 0 1 .01 --hemi lh --out /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh srcvol = /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii srcreg = /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 Done loading volume Reading surface /Applications/freesurfer/subjects/Surfrend_Colin127/surf/lh.white Done reading source surface Reading thickness /Applications/freesurfer/subjects/Surfrend_Colin127/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0 0 1 using old 2 0.01 0 1 using old 3 0.02 0 1 [...] 99 0.979999 0 1 using old 100 0.989999 0 1 using old 101 0.999999 0 1 using old Done mapping volume to surface Number of source voxels hit = 32875 Writing to /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh Dim: 165607 1 1
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