Am 29.11.2020 um 18:17 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>:

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 <dgreve@mgh.harvard.edu>:

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 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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