Thank you so much for your response, Nick! I uploaded "ROI5.nii" (i.e., abc.nii) just now. This ROI has been in Talarich space. Actually, it is from my group functional data. So I did not have corresponding T1-data.

BTW: when can I read the web page describing the steps taken to get cortical thickness from an ROI defined by a volume mask? I hope I can read it ASAP. If it is possible, could you please do me a favor and send the draft to me? Thanks, again!

Xiaochu Zhang PhD

Visiting Research Fellow

Neuroimaging Research Branch

National Institute on Drug Abuse - IRP

Biomedical Research Center

251 Bayview Blvd.

Suite 200 (NIDA)

Baltimore MD

21224

Tel: 443-740-2619

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Monday, November 17, 2008 12:59 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] RE: for cortical thickness

Xiaochu,

I'm putting together a web page describing the steps taken to get cortical thickness from an ROI defined by a volume mask. Can you send me these two files so that I can make sure the steps work correctly?

1) the ROI mask file (what you are calling 'abc.nii') 2) the T1-weighted anatomical volume of the subject from which abc.nii was created. i need this file to register to a template volume.

You can post those files (available only to me) by uploading to our file drop:

https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Nick

On Sat, 2008-11-15 at 00:48 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote:

Hi, FreeSurfer export,

Thank you very much for response! Now, under some export's help, I used to the mri_surf2vol to transfer

cortex thickness into nifti.

The below line is what I used. mri_surf2vol --surfval ../surf/lh.thickness --hemi lh --fillribbon --template orig.mgz --volregidentity ${subid} --outvol lh.ribbon.nii

I checked the result and found the voxel outside the gray matter is

always zero and in the gray matter is about 0-3. Could you please do me a favor and tell me whether these data is cortex thickness or not?

If they are cortex thickness, why are they always different. In my

mind, it should be same in one direction because we calculate the distance between the white matter line and the gray matter line.

Thanks a lot! All the best, Xiaochu

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Nick, Thank you very much for your help in the previous email. Recently, I read and thought your manual very carefully and tried some other ways.

The first one: I tried to transfer ROI5.nii directly to subject's surface (not via fsaverage). i.e.,

cd $SUBJECTS_DIR/subjid/surf Fslregister --s subjid --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_subjid.dat Mri_vol2surf --mov /path/to/ROI5.nii --reg TT_avg152T1_to_subjid.dat --projdist 0 1 0.1 --interp nearest --hemi lh --out lh.ROI5.mgh Mri_segstats --seg lh.ROI5.mgh --in lh.thickness --sum segstats-ROI5.txt

Is it OK? What is the benefit for using fsaverage data? I got the same error information to that after strictly following your manual (see details in the last email I sent to you).Do you the reason for this error informaton?

Another way is transfering all data into volume. i.e.,

Mri_surf2vol --surfval lh.thickness --hemi lh --fillribbon --template orig.mgz --volregidentity subjid --outvol lh.ribbon.nii Mri_convert lh.ribbon.nii --apply_transform transforms/talairach.auto.xfm -o lh-talairach.ribbon.nii

Is it OK? This followship works without any error information. However, I do not know what is the value in each voxel in "lh-talairach.ribbon.nii". Do you know it?

Thanks, again!

Xiaochu Zhang PhD

Visiting Research Fellow

Neuroimaging Research Branch

National Institute on Drug Abuse - IRP

Biomedical Research Center

251 Bayview Blvd.

Suite 200 (NIDA)

Baltimore MD

21224

Tel: 443-740-2619

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Friday, November 21, 2008 5:15 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: Freesurfer Mailing List; Allison Stevens Subject: RE: [Freesurfer] RE: for cortical thickness

Zhang,

The web page describing the steps to extract cortical thickness data for your volume-space defined ROI is found here:

https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness

Nick

On Mon, 2008-11-17 at 14:02 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote:

Thank you so much for your response, Nick! I uploaded "ROI5.nii" (i.e., abc.nii) just now. This ROI has been in Talarich space. Actually, it is from my group functional data. So I did not have corresponding T1-data.

BTW: when can I read the web page describing the steps taken to get cortical thickness from an ROI defined by a volume mask? I hope I can read it ASAP. If it is possible, could you please do me a favor and send the draft to me? Thanks, again!

Xiaochu Zhang PhD

Visiting Research Fellow

Neuroimaging Research Branch

National Institute on Drug Abuse - IRP

Biomedical Research Center

251 Bayview Blvd.

Suite 200 (NIDA)

Baltimore MD

21224

Tel: 443-740-2619

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Monday, November 17, 2008 12:59 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] RE: for cortical thickness

Xiaochu,

I'm putting together a web page describing the steps taken to get cortical thickness from an ROI defined by a volume mask. Can you send

me these two files so that I can make sure the steps work correctly?

1. the ROI mask file (what you are calling 'abc.nii')
2. the T1-weighted anatomical volume of the subject from which abc.nii

was created. i need this file to register to a template volume.

You can post those files (available only to me) by uploading to our file drop:

https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Nick

On Sat, 2008-11-15 at 00:48 -0500, Zhang, Xiaochu (NIH/NIDA) [F]

wrote:

...

Hi, FreeSurfer export,

Thank you very much for response! Now, under some export's help, I used to the mri_surf2vol to transfer

cortex thickness into nifti.

...

The below line is what I used. mri_surf2vol --surfval ../surf/lh.thickness --hemi lh --fillribbon --template orig.mgz --volregidentity ${subid} --outvol lh.ribbon.nii

I checked the result and found the voxel outside the gray matter is

always zero and in the gray matter is about 0-3. Could you please do me a favor and tell me whether these data is cortex thickness or not?

...

If they are cortex thickness, why are they always different. In my

mind, it should be same in one direction because we calculate the distance between the white matter line and the gray matter line.

...

Thanks a lot! All the best, Xiaochu

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Zhang,

You could perform the steps you show in 1., where you sample your ROI directly to the subjects surface, rather than going through the fsaverage subject. Ultimately, you would (or should) end-up with the same result as that from following the steps in the wiki page (going through fsaverage). The difference is that you only need to do the sampling of the ROI to fsaverage only once, whereas with what you want to do, you do it for every subject. Not a big deal if you dont have that many subjects. btw, fsaverage is in talairach space, so its not distorting things much by performing that registration (the .dat file from fslregister has very small values).

I'm not sure about the useful of performing 2., where you sample the thickness data to the volume. This is not usually done (I dont think). You will have a volume with voxel values equal to the thickness of the cortex around that voxel, but there is no hard meaning of that value for that voxel. Typically mri_surf2vol is used to sample parcellation labels into volume space.

I'm not sure why you are getting dimension mismatch errors. Use mri_info on the files in question to get the dimensions. Note this part of the wiki instructions in the last two steps:

cd $SUBJECTS_DIR/subjid/surf

noting that 'subjid' is the name of your subject. If you remain in the $SUBJECTS_DIR/fsaverage/surf directory from the previous steps, you will get the mismatch error (which i just discovered myself).

Nick

On Fri, 2008-12-05 at 15:06 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote:

Hi Nick, Thank you so much for your help! Recently, I tested it strictly following your instruction. However, I met a problem in the last step "mri_segstats ". They gave me the error information: "ERROR: dimension mismatch between input volume and seg". I checked the old mails in the list. Some one talked about dimension mismatch but not related to my issue. Could you please do me a favor and give some suggestion for the reason?

There are another two issues:

1. I noted you transfer ROI5.nii to fsaverage space. Because my ROI5.nii

have been in the Talairach space, can I transfer it to subjects's space directly? For example: cd $SUBJECTS_DIR/subjid/surf Fslregister --s subjid --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_subjid.dat Mri_vol2surf --mov /path/to/ROI5.nii --reg TT_avg152T1_to_subjid.dat --projdist 0 1 0.1 --interp nearest --hemi lh --out lh.ROI5.mgh Mri_segstats --seg lh.ROI5.mgh --in lh.thickness --sum segstats-ROI5.txt

Is it OK? What is the benefit for using fsaverage data? BTW, I got the same dimension mismatch error information in the last step.

2. Can we transfer all data into the volume space. i.e.,

Mri_surf2vol --surfval lh.thickness --hemi lh --fillribbon --template orig.mgz --volregidentity subjid --outvol lh.ribbon.nii Mri_convert lh.ribbon.nii --apply_transform transforms/talairach.auto.xfm -o lh-talairach.ribbon.nii

I tried it and no error information appear. However, I don't know it is correct or not.

Thanks, again!

Xiaochu Zhang PhD

Visiting Research Fellow

Neuroimaging Research Branch

National Institute on Drug Abuse - IRP

Biomedical Research Center

251 Bayview Blvd.

Suite 200 (NIDA)

Baltimore MD

21224

Tel: 443-740-2619

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Friday, November 21, 2008 5:15 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: Freesurfer Mailing List; Allison Stevens Subject: RE: [Freesurfer] RE: for cortical thickness

Zhang,

The web page describing the steps to extract cortical thickness data for your volume-space defined ROI is found here:

https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness

Nick

On Mon, 2008-11-17 at 14:02 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote:

...

Thank you so much for your response, Nick! I uploaded "ROI5.nii" (i.e., abc.nii) just now. This ROI has been in Talarich space. Actually, it is from my group functional data. So I did not have corresponding T1-data.

BTW: when can I read the web page describing the steps taken to get cortical thickness from an ROI defined by a volume mask? I hope I can read it ASAP. If it is possible, could you please do me a favor and send the draft to me? Thanks, again!

Xiaochu Zhang PhD

Visiting Research Fellow

Neuroimaging Research Branch

National Institute on Drug Abuse - IRP

Biomedical Research Center

251 Bayview Blvd.

Suite 200 (NIDA)

Baltimore MD

21224

Tel: 443-740-2619

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Monday, November 17, 2008 12:59 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] RE: for cortical thickness

Xiaochu,

I'm putting together a web page describing the steps taken to get cortical thickness from an ROI defined by a volume mask. Can you send

...

me these two files so that I can make sure the steps work correctly?

1. the ROI mask file (what you are calling 'abc.nii')
2. the T1-weighted anatomical volume of the subject from which abc.nii

...

was created. i need this file to register to a template volume.

You can post those files (available only to me) by uploading to our file drop:

https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Nick

On Sat, 2008-11-15 at 00:48 -0500, Zhang, Xiaochu (NIH/NIDA) [F]

wrote:

...

...

Hi, FreeSurfer export,

Thank you very much for response! Now, under some export's help, I used to the mri_surf2vol to transfer

cortex thickness into nifti.

...

The below line is what I used. mri_surf2vol --surfval ../surf/lh.thickness --hemi lh --fillribbon --template orig.mgz --volregidentity ${subid} --outvol lh.ribbon.nii

I checked the result and found the voxel outside the gray matter is

always zero and in the gray matter is about 0-3. Could you please do me a favor and tell me whether these data is cortex thickness or not?

...

If they are cortex thickness, why are they always different. In my

mind, it should be same in one direction because we calculate the distance between the white matter line and the gray matter line.

...

Thanks a lot! All the best, Xiaochu

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Xiaochu,

The dimensions for lh.thickness.fsaverage.mgh are correct, the ones for lh.fsaverage.ROI5.mgh are not. They should be the same (163842x1x1). Did you create lh.fsaverage.ROI5.mgh like this:

cd $SUBJECTS_DIR/fsaverage/surf mri_vol2surf \ --mov /path/to/ROI5.nii \ --reg TT_avg152T1_to_fsaverage.dat \ --projdist-max 0 1 0.1 \ --interp nearest \ --hemi lh \ --out lh.fsaverage.ROI5.mgh

Nick

On Fri, 2008-12-05 at 16:56 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote:

I just checked the demension information and found they are not same. Do you think which one is wrong? Thanks a lot!

Volume information for lh.thickness.fsaverage.mgh type: MGH dimensions: 163842 x 1 x 1 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5

Volume information for lh.fsaverage.ROI5.mgh type: MGH dimensions: 23406 x 1 x 7 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 23406.000 dof: 0 xstart: -11703.0, xend: 11703.0 ystart: -0.5, yend: 0.5 zstart: -3.5, zend: 3.5

Xiaochu Zhang PhD

Visiting Research Fellow

Neuroimaging Research Branch

National Institute on Drug Abuse - IRP

Biomedical Research Center

251 Bayview Blvd.

Suite 200 (NIDA)

Baltimore MD

21224

Tel: 443-740-2619

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Friday, December 05, 2008 3:51 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] RE: for cortical thickness

Zhang,

You could perform the steps you show in 1., where you sample your ROI directly to the subjects surface, rather than going through the fsaverage subject. Ultimately, you would (or should) end-up with the same result as that from following the steps in the wiki page (going through fsaverage). The difference is that you only need to do the sampling of the ROI to fsaverage only once, whereas with what you want to do, you do it for every subject. Not a big deal if you dont have that many subjects. btw, fsaverage is in talairach space, so its not distorting things much by performing that registration (the .dat file from fslregister has very small values).

I'm not sure about the useful of performing 2., where you sample the thickness data to the volume. This is not usually done (I dont think). You will have a volume with voxel values equal to the thickness of the cortex around that voxel, but there is no hard meaning of that value for that voxel. Typically mri_surf2vol is used to sample parcellation labels into volume space.

I'm not sure why you are getting dimension mismatch errors. Use mri_info on the files in question to get the dimensions. Note this part of the wiki instructions in the last two steps:

cd $SUBJECTS_DIR/subjid/surf

noting that 'subjid' is the name of your subject. If you remain in the $SUBJECTS_DIR/fsaverage/surf directory from the previous steps, you will get the mismatch error (which i just discovered myself).

Nick

On Fri, 2008-12-05 at 15:06 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote:

...

Hi Nick, Thank you so much for your help! Recently, I tested it strictly following your instruction. However, I met a problem in the last step "mri_segstats ". They gave me the error information: "ERROR: dimension mismatch between input volume and seg". I checked the old mails in the list. Some one talked about dimension mismatch but not related to my issue. Could you please do me a favor and give some suggestion for the reason?

There are another two issues:

1. I noted you transfer ROI5.nii to fsaverage space. Because my

ROI5.nii have been in the Talairach space, can I transfer it to subjects's space directly? For example: cd $SUBJECTS_DIR/subjid/surf Fslregister --s subjid --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_subjid.dat Mri_vol2surf --mov /path/to/ROI5.nii --reg TT_avg152T1_to_subjid.dat --projdist 0 1 0.1 --interp nearest --hemi lh --out lh.ROI5.mgh Mri_segstats --seg lh.ROI5.mgh --in lh.thickness --sum segstats-ROI5.txt

Is it OK? What is the benefit for using fsaverage data? BTW, I got the same dimension mismatch error information in the last step.

2. Can we transfer all data into the volume space. i.e., Mri_surf2vol

--surfval lh.thickness --hemi lh --fillribbon --template orig.mgz --volregidentity subjid --outvol lh.ribbon.nii Mri_convert lh.ribbon.nii --apply_transform transforms/talairach.auto.xfm -o lh-talairach.ribbon.nii

I tried it and no error information appear. However, I don't know it is correct or not.

Thanks, again!

Xiaochu Zhang PhD

Visiting Research Fellow

Neuroimaging Research Branch

National Institute on Drug Abuse - IRP

Biomedical Research Center

251 Bayview Blvd.

Suite 200 (NIDA)

Baltimore MD

21224

Tel: 443-740-2619

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Friday, November 21, 2008 5:15 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: Freesurfer Mailing List; Allison Stevens Subject: RE: [Freesurfer] RE: for cortical thickness

Zhang,

The web page describing the steps to extract cortical thickness data for your volume-space defined ROI is found here:

https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness

Nick

On Mon, 2008-11-17 at 14:02 -0500, Zhang, Xiaochu (NIH/NIDA) [F]

wrote:

...

...

Thank you so much for your response, Nick! I uploaded "ROI5.nii" (i.e., abc.nii) just now. This ROI has been in

...

...

Talarich space. Actually, it is from my group functional data. So I did not have corresponding T1-data.

BTW: when can I read the web page describing the steps taken to get cortical thickness from an ROI defined by a volume mask? I hope I can read it ASAP. If it is possible, could you please do me a favor and send the draft to me? Thanks, again!

Xiaochu Zhang PhD

Visiting Research Fellow

Neuroimaging Research Branch

National Institute on Drug Abuse - IRP

Biomedical Research Center

251 Bayview Blvd.

Suite 200 (NIDA)

Baltimore MD

21224

Tel: 443-740-2619

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Monday, November 17, 2008 12:59 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] RE: for cortical thickness

Xiaochu,

I'm putting together a web page describing the steps taken to get cortical thickness from an ROI defined by a volume mask. Can you send

...

me these two files so that I can make sure the steps work correctly?

1. the ROI mask file (what you are calling 'abc.nii')
2. the T1-weighted anatomical volume of the subject from which

abc.nii

...

was created. i need this file to register to a template volume.

You can post those files (available only to me) by uploading to our file drop:

https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Nick

On Sat, 2008-11-15 at 00:48 -0500, Zhang, Xiaochu (NIH/NIDA) [F]

wrote:

...

...

Hi, FreeSurfer export,

Thank you very much for response! Now, under some export's help, I used to the mri_surf2vol to transfer

cortex thickness into nifti.

...

The below line is what I used. mri_surf2vol --surfval ../surf/lh.thickness --hemi lh --fillribbon

...

...

...

--template orig.mgz --volregidentity ${subid} --outvol lh.ribbon.nii

I checked the result and found the voxel outside the gray matter is

always zero and in the gray matter is about 0-3. Could you please do

...

...

me a favor and tell me whether these data is cortex thickness or

not?

...

...

...

If they are cortex thickness, why are they always different. In my

mind, it should be same in one direction because we calculate the distance between the white matter line and the gray matter line.

...

Thanks a lot! All the best, Xiaochu

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Xiaochu,

My bad, I see the problem now. I was using our 'dev' enviro, which doesnt 'reshape' the data (never mind that detail) whereas 'stable' (public) does.

So, just add --reshape to the end of the mri_surf2surf command, as the updated instruction here show:

https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness

and the dimensions of those two files should match (correct is 23406 x 1 x 7).

Nick

On Fri, 2008-12-05 at 17:21 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote:

I RUN: xzhang@magneto:/data2/379/ASL/temp/fsaverage/surf> mri_vol2surf --mov ../../ROI5.nii --reg TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fsaverage.ROI5.mgh

THE OUTPUT: srcvol = ../../ROI5.nii srcreg = TT_avg152T1_to_fsaverage.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = 0.5 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data2/379/ASL/temp/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /data2/379/ASL/temp/fsaverage/surf/lh.white.avg.area.mgh Done reading source surface Reading thickness /data2/379/ASL/temp/fsaverage/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0 0 1 vol2surf_linear: nhits = 163842/163842 2 0.1 0 1 vol2surf_linear: nhits = 163842/163842 3 0.2 0 1 vol2surf_linear: nhits = 163842/163842 4 0.3 0 1 vol2surf_linear: nhits = 163842/163842 5 0.4 0 1 vol2surf_linear: nhits = 163842/163842 6 0.5 0 1 vol2surf_linear: nhits = 163842/163842 7 0.6 0 1 vol2surf_linear: nhits = 163842/163842 8 0.7 0 1 vol2surf_linear: nhits = 163842/163842 9 0.8 0 1 vol2surf_linear: nhits = 163842/163842 10 0.9 0 1 vol2surf_linear: nhits = 163842/163842 Done mapping volume to surface Number of source voxels hit = 75048 Reshaping 7 (nvertices = 163842) Writing to lh.fsaverage.ROI5.mgh Dim: 23406 1 7

Xiaochu Zhang PhD

Visiting Research Fellow

Neuroimaging Research Branch

National Institute on Drug Abuse - IRP

Biomedical Research Center

251 Bayview Blvd.

Suite 200 (NIDA)

Baltimore MD

21224

Tel: 443-740-2619

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Friday, December 05, 2008 5:10 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] RE: for cortical thickness

Xiaochu,

The dimensions for lh.thickness.fsaverage.mgh are correct, the ones for lh.fsaverage.ROI5.mgh are not. They should be the same (163842x1x1). Did you create lh.fsaverage.ROI5.mgh like this:

cd $SUBJECTS_DIR/fsaverage/surf mri_vol2surf \ --mov /path/to/ROI5.nii \ --reg TT_avg152T1_to_fsaverage.dat \ --projdist-max 0 1 0.1 \ --interp nearest \ --hemi lh \ --out lh.fsaverage.ROI5.mgh

Nick

On Fri, 2008-12-05 at 16:56 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote:

...

I just checked the demension information and found they are not same. Do you think which one is wrong? Thanks a lot!

Volume information for lh.thickness.fsaverage.mgh type: MGH dimensions: 163842 x 1 x 1 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5

Volume information for lh.fsaverage.ROI5.mgh type: MGH dimensions: 23406 x 1 x 7 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 23406.000 dof: 0 xstart: -11703.0, xend: 11703.0 ystart: -0.5, yend: 0.5 zstart: -3.5, zend: 3.5

Xiaochu Zhang PhD

Visiting Research Fellow

Neuroimaging Research Branch

National Institute on Drug Abuse - IRP

Biomedical Research Center

251 Bayview Blvd.

Suite 200 (NIDA)

Baltimore MD

21224

Tel: 443-740-2619

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Friday, December 05, 2008 3:51 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] RE: for cortical thickness

Zhang,

You could perform the steps you show in 1., where you sample your ROI directly to the subjects surface, rather than going through the fsaverage subject. Ultimately, you would (or should) end-up with the same result as that from following the steps in the wiki page (going through fsaverage). The difference is that you only need to do the sampling of the ROI to fsaverage only once, whereas with what you want

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to do, you do it for every subject. Not a big deal if you dont have that many subjects. btw, fsaverage is in talairach space, so its not distorting things much by performing that registration (the .dat file from fslregister has very small values).

I'm not sure about the useful of performing 2., where you sample the thickness data to the volume. This is not usually done (I dont

think).

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You will have a volume with voxel values equal to the thickness of the

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cortex around that voxel, but there is no hard meaning of that value for that voxel. Typically mri_surf2vol is used to sample parcellation

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labels into volume space.

I'm not sure why you are getting dimension mismatch errors. Use mri_info on the files in question to get the dimensions. Note this part of the wiki instructions in the last two steps:

cd $SUBJECTS_DIR/subjid/surf

noting that 'subjid' is the name of your subject. If you remain in the $SUBJECTS_DIR/fsaverage/surf directory from the previous steps, you will get the mismatch error (which i just discovered myself).

Nick

On Fri, 2008-12-05 at 15:06 -0500, Zhang, Xiaochu (NIH/NIDA) [F]

wrote:

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Hi Nick, Thank you so much for your help! Recently, I tested it strictly following your instruction. However, I met a problem in the last step "mri_segstats ". They gave me the error information: "ERROR: dimension mismatch between input volume and

seg".

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I checked the old mails in the list. Some one talked about dimension

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mismatch but not related to my issue. Could you please do me a favor

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and give some suggestion for the reason?

There are another two issues:

1. I noted you transfer ROI5.nii to fsaverage space. Because my

ROI5.nii have been in the Talairach space, can I transfer it to subjects's space directly? For example: cd $SUBJECTS_DIR/subjid/surf Fslregister --s subjid --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_subjid.dat Mri_vol2surf --mov /path/to/ROI5.nii --reg

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TT_avg152T1_to_subjid.dat --projdist 0 1 0.1 --interp nearest --hemi

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lh --out lh.ROI5.mgh Mri_segstats --seg lh.ROI5.mgh --in lh.thickness --sum segstats-ROI5.txt

Is it OK? What is the benefit for using fsaverage data? BTW, I got the same dimension mismatch error information in the last

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step.

2. Can we transfer all data into the volume space. i.e.,

Mri_surf2vol --surfval lh.thickness --hemi lh --fillribbon --template orig.mgz --volregidentity subjid --outvol lh.ribbon.nii Mri_convert lh.ribbon.nii --apply_transform transforms/talairach.auto.xfm -o lh-talairach.ribbon.nii

I tried it and no error information appear. However, I don't know it

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is correct or not.

Thanks, again!

Xiaochu Zhang PhD

Visiting Research Fellow

Neuroimaging Research Branch

National Institute on Drug Abuse - IRP

Biomedical Research Center

251 Bayview Blvd.

Suite 200 (NIDA)

Baltimore MD

21224

Tel: 443-740-2619

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Friday, November 21, 2008 5:15 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: Freesurfer Mailing List; Allison Stevens Subject: RE: [Freesurfer] RE: for cortical thickness

Zhang,

The web page describing the steps to extract cortical thickness data

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for your volume-space defined ROI is found here:

https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness

Nick

On Mon, 2008-11-17 at 14:02 -0500, Zhang, Xiaochu (NIH/NIDA) [F]

wrote:

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Thank you so much for your response, Nick! I uploaded "ROI5.nii" (i.e., abc.nii) just now. This ROI has been in

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Talarich space. Actually, it is from my group functional data. So I did not have corresponding T1-data.

BTW: when can I read the web page describing the steps taken to get cortical thickness from an ROI defined by a volume mask? I hope I can read it ASAP. If it is possible, could you please do me

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a favor and send the draft to me? Thanks, again!

Xiaochu Zhang PhD

Visiting Research Fellow

Neuroimaging Research Branch

National Institute on Drug Abuse - IRP

Biomedical Research Center

251 Bayview Blvd.

Suite 200 (NIDA)

Baltimore MD

21224

Tel: 443-740-2619

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Monday, November 17, 2008 12:59 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] RE: for cortical thickness

Xiaochu,

I'm putting together a web page describing the steps taken to get cortical thickness from an ROI defined by a volume mask. Can you send

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me these two files so that I can make sure the steps work

correctly?

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1. the ROI mask file (what you are calling 'abc.nii')
2. the T1-weighted anatomical volume of the subject from which

abc.nii

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was created. i need this file to register to a template volume.

You can post those files (available only to me) by uploading to our file drop:

https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Nick

On Sat, 2008-11-15 at 00:48 -0500, Zhang, Xiaochu (NIH/NIDA) [F]

wrote:

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Hi, FreeSurfer export,

Thank you very much for response! Now, under some export's help, I used to the mri_surf2vol to transfer

cortex thickness into nifti.

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The below line is what I used. mri_surf2vol --surfval ../surf/lh.thickness --hemi lh --fillribbon

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--template orig.mgz --volregidentity ${subid} --outvol lh.ribbon.nii

I checked the result and found the voxel outside the gray matter

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is

always zero and in the gray matter is about 0-3. Could you please do

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me a favor and tell me whether these data is cortex thickness or

not?

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If they are cortex thickness, why are they always different. In my

mind, it should be same in one direction because we calculate the distance between the white matter line and the gray matter line.

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Thanks a lot! All the best, Xiaochu

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