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Dear Douglas,thank you very much for your help; I run the recon of MNI152_T1_1mm_brain.nii.gz (which I moved into a directory called MNI_1mm).Then I run the following command, as you suggested:$mri_vol2surf --mov ROI_set1/LeftAngG.img  --regheader MNI_1mm --interp nearest --hemilh --out LeftAngG_tmp.mgh --projdist-max 0 1 0.1 --noreshape But then, in freeview I get the following result:

I also get an error when I try to load it as a surface:"LeftAngG_tmp.mgh' has 0 vertices!Probably trying to use a scalar data file as a surface!" What could be the mistake? Best regards,Eleni

On Thursday, July 2, 2020, 04:25:54 PM GMT+3, Douglas N. Greve dgreve@mgh.harvard.edu wrote:

Try running recon-all on the MNI152. Load the ROI onto the reconned MNI152; load the surfaces as well and make sure that the ROI intersects with the surface, then use #3 below with --regheader MNI152 instead of --reg tmp.dat. You can also specify --trgsubject fsaverage and mri_vol2surf will map the ROI all the way onto the fsaverage surface

On 7/1/2020 10:03 AM, Eleni Nikalexi wrote:

External Email - Use Caution         Dear Freesurfer developers, We have a series of MRI scans and we are trying to extract cortical thickness in certain regions of interest. The ROIs already exist - some are in .img and some in NIFTI format - and we want to tranform them into labels and then register them on fsaverage. The problem is that the ROIs are in MNI152 space (from SPM), with voxel size=2mm.   We have tried various commands to register one of the .img ROIs on fsaverage, but they all failed:

- $ fslregister --s fsaverage --mov ROI_set1/LeftAnGG.img --reg tmp.dat - $ tkmedit fsaverage T1.mgz -overlay ROI_set1/LeftAngG.img -overlay-reg tmp.dat - $ mri_vol2surf --mov ROI_set1/LeftAngG.img --reg tmp.dat --interp nearest --hemi lh --out Left_AngG_tmp.mgh --projdist-max 0 1 0.1 --noreshape - $ mri_vol2surf --mov ROI_set1/LeftAngG.img --reg tmp.dat --interp nearest --hemi lh --out Left_AngG_tmp.mgh --targ $SUBJECTS_DIR/fsaverage/mri/orig.mgz The result is that the ROI is either not in the right place, or the right size or we just end up with a weird 3D cross shape in freeview. Could you please suggest something that we could do to fix this? Thank  you so much in advance! Best regards, Eleni

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Dear Bruce and Douglas,Thank you very much for the prompt, indeed it worked. Since the ROIs were originally obtained in 2mm voxel size, I used the vol2surf command as you suggested, in order map the ROI all the way onto the fsaverage surface:

$mri_vol2surf --mov ROI_set1/LeftAngG.img --regheaderMNI_1mm --interp nearest --hemi lh --out Left_AngG_tmpfs.mgh --projdist-max 0 10.1 --noreshape --trgsubject fsaverage

I checked the result using:  $ freeview -f../data/scans/subject/fsaverage/surf/lh.inflated:overlay=Left_AngG_tmpfs.mgh

and the overlay is correct.Then, I tried to transform the Left_AngG_tmpfs.mgh to a label using the fsaverage as a reference. The command I used was:   $ mri_vol2label --i Left_AngG_tmpfs.mgh --id  1 --l LeftAngG_tmp.label  --surf fsaverage lh white

but permission was denied. If I try to use one of my subjects as a reference I get: ERROR: dim mismatch between surface (117900) and input (163842).What would you suggest? Thank you in advance,Best wishes,Eleni On Friday, July 3, 2020, 06:35:05 PM GMT+3, Fischl, Bruce bfischl@mgh.harvard.edu wrote:

#yiv2641346477 #yiv2641346477 -- _filtered {} _filtered {} _filtered {} _filtered {} _filtered {}#yiv2641346477 #yiv2641346477 p.yiv2641346477MsoNormal, #yiv2641346477 li.yiv2641346477MsoNormal, #yiv2641346477 div.yiv2641346477MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv2641346477 a:link, #yiv2641346477 span.yiv2641346477MsoHyperlink {color:blue;text-decoration:underline;}#yiv2641346477 a:visited, #yiv2641346477 span.yiv2641346477MsoHyperlinkFollowed {color:purple;text-decoration:underline;}#yiv2641346477 pre {margin:0in;margin-bottom:.0001pt;font-size:10.0pt;}#yiv2641346477 p.yiv2641346477msonormal0, #yiv2641346477 li.yiv2641346477msonormal0, #yiv2641346477 div.yiv2641346477msonormal0 {margin-right:0in;margin-left:0in;font-size:11.0pt;font-family:sans-serif;}#yiv2641346477 span.yiv2641346477HTMLPreformattedChar {font-family:Consolas;}#yiv2641346477 span.yiv2641346477EmailStyle22 {font-family:sans-serif;color:windowtext;}#yiv2641346477 .yiv2641346477MsoChpDefault {font-size:10.0pt;} _filtered {}#yiv2641346477 div.yiv2641346477WordSection1 {}#yiv2641346477 _filtered {}#yiv2641346477 ol {margin-bottom:0in;}#yiv2641346477 ul {margin-bottom:0in;}#yiv2641346477 Hi Eleni

What is your freeview command line? Note that in this case the output of mri_vol2surf is *not* a surface, but rather  a scalar field over the surface (that is, a file with one or more values per vertex location). To visualize it you need to load a surface, then load your overlay on top of it. Look at the freeview help on overlays, but it should be something like:

Freeview -f lh.inflated:overlay=LeftAngG_tmp.mgh

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.eduOn Behalf Of Eleni Nikalexi Sent: Friday, July 3, 2020 10:11 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Label on fsaverage failure

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Dear Douglas,

thank you very much for your help; I run the recon of MNI152_T1_1mm_brain.nii.gz (which I moved into a directory called MNI_1mm).

Then I run the following command, as you suggested:

$ mri_vol2surf --mov ROI_set1/LeftAngG.img  --regheader MNI_1mm --interp nearest --hemi lh --out LeftAngG_tmp.mgh --projdist-max 0 1 0.1 --noreshape

But then, in freeview I get the following result:

I also get an error when I try to load it as a surface:

"LeftAngG_tmp.mgh' has 0 vertices!

Probably trying to use a scalar data file as a surface!"

What could be the mistake?

Best regards,

Eleni

On Thursday, July 2, 2020, 04:25:54 PM GMT+3, Douglas N. Greve dgreve@mgh.harvard.edu wrote:

Try running recon-all on the MNI152. Load the ROI onto the reconned MNI152; load the surfaces as well and make sure that the ROI intersects with the surface, then use #3 below with --regheader MNI152 instead of --reg tmp.dat. You can also specify --trgsubject fsaverage and mri_vol2surf will map the ROI all the way onto the fsaverage surface

On 7/1/2020 10:03 AM, Eleni Nikalexi wrote:

External Email - Use Caution

Dear Freesurfer developers,

We have a series of MRI scans and we are trying to extract cortical thickness in certain regions of interest. The ROIs already exist - some are in .img and some in NIFTI format - and we want to tranform them into labels and then register them on fsaverage. The problem is that the ROIs are in MNI152 space (from SPM), with voxel size=2mm.

We have tried various commands to register one of the .img ROIs on fsaverage, but they all failed:

- $ fslregister --s fsaverage --mov ROI_set1/LeftAnGG.img --reg tmp.dat - $ tkmedit fsaverage T1.mgz -overlay ROI_set1/LeftAngG.img -overlay-reg tmp.dat - $ mri_vol2surf --mov ROI_set1/LeftAngG.img --reg tmp.dat --interp nearest --hemi lh --out Left_AngG_tmp.mgh --projdist-max 0 1 0.1 --noreshape - $ mri_vol2surf --mov ROI_set1/LeftAngG.img --reg tmp.dat --interp nearest --hemi lh --out Left_AngG_tmp.mgh --targ $SUBJECTS_DIR/fsaverage/mri/orig.mgz

The result is that the ROI is either not in the right place, or the right size or we just end up with a weird 3D cross shape in freeview.

Could you please suggest something that we could do to fix this?

Thank  you so much in advance!

Best regards,

Eleni

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

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