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 https://secure-web.cisco.com/1vMR3HBqveQVdV1izVoGaJ5VcRtbR7HBn6ADoe1ai7ok5ut... 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.
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 be* https://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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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:
External Email - Use CautionHello 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 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/182BqfOmZHFfN-HXG0WKcZl1t7mCNEi6craJT61YlVMJ8c1... https://secure-web.cisco.com/182BqfOmZHFfN-HXG0WKcZl1t7mCNEi6craJT61YlVMJ8c1BoYM9RlZhjXTzA4TeZ05e3OGT-xSV3Uin7CmBt_0BPg_0i1AWtJU1vZn2DKlHVGhyXp5WKXs1Q8ReIzK9xXEDa8NUDM3gsQVJpynhZD0gBj8FZlLEe9wNRv_4oDjFKtbqnX17Bqp5oWazA3LmrSeY0WMS-oVyt6_TjHFXCvvRLqx34lzCC8Be07NxJdDYc7K9_JaqoorFJc4KzIlIupp0UXZJiXV-VI33g3W95uw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/182BqfOmZHFfN-HXG0WKcZl1t7mCNEi6craJT61YlVMJ8c1... https://secure-web.cisco.com/182BqfOmZHFfN-HXG0WKcZl1t7mCNEi6craJT61YlVMJ8c1BoYM9RlZhjXTzA4TeZ05e3OGT-xSV3Uin7CmBt_0BPg_0i1AWtJU1vZn2DKlHVGhyXp5WKXs1Q8ReIzK9xXEDa8NUDM3gsQVJpynhZD0gBj8FZlLEe9wNRv_4oDjFKtbqnX17Bqp5oWazA3LmrSeY0WMS-oVyt6_TjHFXCvvRLqx34lzCC8Be07NxJdDYc7K9_JaqoorFJc4KzIlIupp0UXZJiXV-VI33g3W95uw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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:
External Email - Use Caution
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.edumailto: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/VolumeRoiCorticalThicknesshttps://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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/182BqfOmZHFfN-HXG0WKcZl1t7mCNEi6craJT61YlVMJ8c1BoYM9RlZhjXTzA4TeZ05e3OGT-xSV3Uin7CmBt_0BPg_0i1AWtJU1vZn2DKlHVGhyXp5WKXs1Q8ReIzK9xXEDa8NUDM3gsQVJpynhZD0gBj8FZlLEe9wNRv_4oDjFKtbqnX17Bqp5oWazA3LmrSeY0WMS-oVyt6_TjHFXCvvRLqx34lzCC8Be07NxJdDYc7K9_JaqoorFJc4KzIlIupp0UXZJiXV-VI33g3W95uw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Hello Douglas,
Thank you for your response. I seem to be having problems with registration. I tried:
#flirt -in T1w.nii.gz -ref fsl/data/standard/MNI152_T1_2mm -out T1w_MNI.nii.gz -omat T1w_MNI.mat #fnirt --in=T1w.nii.gz --aff=T1w_MNI.mat --cout=nonlinear_transf --config=T1_2_MNI152_2mm #applywarp --ref=/fsl/data/standard/MNI152_T1_2mm --in=T1w.nii.gz --warp=nonlinear_transf --out=warped_strucctural
->>this looks good, the ROI is where I expect it to be.
#fslregister --s fsaverage --mov T1w_MNI.nii.gz --reg /work/bav5809/subjects/severe/freesurfer_output/hand/${SUBJECTID}-${SESSIONID}/tmp.dat
#tkmeditfv fsaverage T1.mgz \ -overlay M1_L_bin.nii.gz \ -overlay-reg tmp.dat \ -fthresh 0.5 \
->>the problems seems to be in the registration because that does not look good.
Can you help me find the problem?
Many thanks,
Alina Rojas
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:
External Email - Use CautionThank 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 mailto:dgreve@mgh.harvard.edu>:
please send the command line
On 11/16/2020 7:20 AM, Alina Rojas wrote:
External Email - Use CautionHello 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 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1pFaTO-pjnktcJb-qCw2ZmMSSvyV9wLeBWqmkJXSfMxcQ6P... https://secure-web.cisco.com/182BqfOmZHFfN-HXG0WKcZl1t7mCNEi6craJT61YlVMJ8c1BoYM9RlZhjXTzA4TeZ05e3OGT-xSV3Uin7CmBt_0BPg_0i1AWtJU1vZn2DKlHVGhyXp5WKXs1Q8ReIzK9xXEDa8NUDM3gsQVJpynhZD0gBj8FZlLEe9wNRv_4oDjFKtbqnX17Bqp5oWazA3LmrSeY0WMS-oVyt6_TjHFXCvvRLqx34lzCC8Be07NxJdDYc7K9_JaqoorFJc4KzIlIupp0UXZJiXV-VI33g3W95uw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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fslregister should have printed out a tkregisterfv command to use to check the registration. Does that registartion look ok or not? If not, try mri_coreg instead of fslregister
On 12/11/2020 6:11 AM, Alina Rojas wrote:
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Hello Douglas,
Thank you for your response. I seem to be having problems with registration. I tried:
#flirt -in T1w.nii.gz -ref fsl/data/standard/MNI152_T1_2mm -out T1w_MNI.nii.gz -omat T1w_MNI.mat#fnirt --in=T1w.nii.gz --aff=T1w_MNI.mat --cout=nonlinear_transf --config=T1_2_MNI152_2mm#applywarp --ref=/fsl/data/standard/MNI152_T1_2mm --in=T1w.nii.gz --warp=nonlinear_transf --out=warped_strucctural
->>this looks good, the ROI is where I expect it to be.
[cid:part1.A0715EA3.F1997B19@mgh.harvard.edu][cid:part2.832C2D59.D5A0FCB1@mgh.harvard.edu]
#fslregister --s fsaverage --mov T1w_MNI.nii.gz --reg /work/bav5809/subjects/severe/freesurfer_output/hand/${SUBJECTID}-${SESSIONID}/tmp.dat
#tkmeditfv fsaverage T1.mgz \ -overlay M1_L_bin.nii.gz \ -overlay-reg tmp.dat \ -fthresh 0.5 \
->>the problems seems to be in the registration because that does not look good. [cid:part3.9F6D9A90.70B6235B@mgh.harvard.edu]
Can you help me find the problem?
Many thanks,
Alina Rojas
Am 29.11.2020 um 18:17 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto: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.edumailto: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/VolumeRoiCorticalThicknesshttps://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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freesurfer@nmr.mgh.harvard.edu
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Alina Rojas -
Douglas N. Greve -
Greve, Douglas N.,Ph.D.