Have you checked that the output of each of the stages is correct? Eg, does
mydata_T1.nii.mgz overlay with MNI152 and with ROI_MNI? At the end of
fslregister, there will be a tkregister command to visualize the regsitration.
Do those look ok?
On 11/17/2020 4:48 AM, Alina Rojas wrote:
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Thank you for your response! Here the commands:
#register image to MNIspace
flirt -in mydata_T1.nii.gz -ref fsl/data/standard/MNI152_T1_1mm -out
mydata_T1_MNI.nii.gz -omat mydata_T1_MNI.mat
#Create a registration from the ROI-anatomical volume to a freesurfer template
subject
fslregister --s fsaverage --mov mydata_T1_MNI.nii.gz --reg tmp.dat
#Map the ROI-mask to the fsaverage surface, to create an fsaverage-ROI surface
overlay.
mri_vol2surf --mov ROI_MNI.nii.gz --reg tmp.dat --projdist-max 0 1 0.1 --interp
nearest --hemi lh --out lh.fsaverage.ROI_MNI.mgh —noreshape
tkmeditfv fsaverage lh inflated -overlay lh.fsaverage.M1_L.mgh -fthresh 0.5
I tried with another threshold, and to change it while in Freeview and it’s
either the whole surface with the overlay or none.
Thank you for your help!
Alina Rojas
Am 16.11.2020 um 17:04 schrieb Douglas N. Greve
<[email protected]<mailto:[email protected]>>:
please send the command line
On 11/16/2020 7:20 AM, Alina Rojas wrote:
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Hello Freesurfer experts,
I am attempting to register a ROI (.nii) to the surface of fsaverage to get the
statistical output on the cortical thickness. I followed your instructions on
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behttps://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness<https://secure-web.cisco.com/1vMR3HBqveQVdV1izVoGaJ5VcRtbR7HBn6ADoe1ai7ok5utz9wmCB_PLEjDtsOmyziziVBQRSmBgczrdyk56eX0vaBWBNP1iIevBdxOho3o-JJ64DuVK1J6XpzIFNVqqzBDHDrU6O2cYjWTNnglb4Ow4OIdXr5Qq28eboicyUSvLl2KmB0P0lQY9abQIfjX6hs_1Q1FvwX1Tx7YnGwsbJIgqcpDRG0dkvqZc0pgeiBQbnNjLadwozbHME2Ale8Kt0-V-I2Urmgq5zbEhzlAPvCA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness>
but after mri_vol2surf I get this message, I can’t visualize the ROI on the
surface. I I’m using Freesurfer 7.0.1. How can I solve this? Thank you, Alina
Rojas.
srcvol = M1_L.nii.gz
srcreg = tmp.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjDist = 0.5
reshape = 0
interp = nearest
float2int = round
GetProjMax = 1
INFO: float2int code = 0
INFO: using NIfTI-1 qform
Done loading volume
INFO: This REGISTER_DAT transform is valid only for volumes between COR types
with c_(r,a,s) = 0.
Input reg is register.dat
-------- original matrix -----------
1.00000 0.00000 0.00000 2.49380;
0.00000 0.00000 1.00000 -22.50500;
0.00000 -1.00000 0.00000 -9.53872;
0.00000 0.00000 0.00000 1.00000;
-------- original matrix -----------
Reading surface /fsaverage/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
1 0 0 1
using old
2 0.1 0 1
using old
3 0.2 0 1
using old
4 0.3 0 1
using old
5 0.4 0 1
using old
6 0.5 0 1
using old
7 0.6 0 1
using old
8 0.7 0 1
using old
9 0.8 0 1
using old
10 0.9 0 1
using old
Done mapping volume to surface
Number of source voxels hit = 75073
Writing to lh.fsaverage.M1_L.mgh
Dim: 163842 1 1
surfcolor: Subscript out of range.
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