#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 <dgreve@mgh.harvard.edu>:
please send the command line

On 11/16/2020 7:20 AM, Alina Rojas wrote:
External Email - Use Caution
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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness 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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