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Thank you for your reply. It worked to convert to surface label :) When i overlay the surface labels on the pial surface, I can view a histogram showing the number of vertices versus the numbers of labels i have. As a follow-up question, do you know how I could extract a txt file that gives me the vertices with their corresponding label number. For example, for 10,000 vertices and 100 labels, I'd like to get a txt file with 10,000 rows and each row has a label value between 1 and 100.

Thank you for your help!

On Fri, 10 Jul 2020 at 16:28, Douglas N. Greve dgreve@mgh.harvard.edu wrote:

That will create a volume label, not a surface label (but it should not have been empty -- look in the label (it is just a text file)). To get a surface label, first map the volume to the surface with something like mri_vol2surf --mov parcellationvolumes.nii.gz --projfrac-max -.5 1 .1 --hemi lh --o lh.parcellationvolumes.mgz --regheader subject mri_cor2label --i lh.parcellationvolumes.mgz --id 20 --surf subject lh --l lh.20.label

On 7/10/2020 3:46 PM, Julie Ottoy wrote:

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Hi Freesurfer team

I am trying to convert parcellation (cortical) volumes that I acquired through another platform into surface labels using freesurfer. I tried following code to convert the volume with ID 20 from the parcellationvolumes.nii.gz file into a label

mri_cor2label --i dir/parcellationvolumes.nii.gz --id 20 --l dir/20.label

Although the code runs fine and finishes successfully, whenever I try to open the created label in freeview, it says that the label is empty.

Any idea what I am doing wrong? Do you have an easier way to project all ROI volumes onto the surface?

A second related question: I have run the recon-all for T1 of the subject and it creates rh.pial and lh.pial. I was wondering whether the transformation to go from T1 volume to the surface is saved somewhere and whether I can apply this transformation to convert my cortical volume parcellations into surface parcellations?

Thank you for your help! Best regards Julie

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There is no tool (I know of) which does exactly what you want, but it should be easy in Matlab or R.

So if I understand correctly you have several label files for one subject, and you want to apply all of them and get a single text file that should have one label per vertex of the subjects's surface. (Basically a text version of an anottation file, without the color lookup table.)

Two questions: 1) What value for vertices which were not matched by any label? 2) What should happen to vertices matched by more than one label?

Best,

Tim

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

On July 17, 2020 at 4:59 PM Julie Ottoy julie.jj.ottoy@gmail.com wrote:

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Hi FS team,

I was wondering if you could take a look at the question below. Thanks!

---------- Forwarded message --------- From: Julie Ottoy julie.jj.ottoy@gmail.com Date: Fri, 10 Jul 2020 at 20:49 Subject: Re: [Freesurfer] Fwd: question regarding mri_vol2label To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu

Thank you for your reply. It worked to convert to surface label :) When i overlay the surface labels on the pial surface, I can view a histogram showing the number of vertices versus the numbers of labels i have. As a follow-up question, do you know how I could extract a txt file that gives me the vertices with their corresponding label number. For example, for 10,000 vertices and 100 labels, I'd like to get a txt file with 10,000 rows and each row has a label value between 1 and 100.

Thank you for your help!

On Fri, 10 Jul 2020 at 16:28, Douglas N. Greve dgreve@mgh.harvard.edu wrote:

...

That will create a volume label, not a surface label (but it should not have been empty -- look in the label (it is just a text file)). To get a surface label, first map the volume to the surface with something like mri_vol2surf --mov parcellationvolumes.nii.gz --projfrac-max -.5 1 .1 --hemi lh --o lh.parcellationvolumes.mgz --regheader subject mri_cor2label --i lh.parcellationvolumes.mgz --id 20 --surf subject lh --l lh.20.label

On 7/10/2020 3:46 PM, Julie Ottoy wrote:

    External Email - Use Caution

Hi Freesurfer team

I am trying to convert parcellation (cortical) volumes that I acquired through another platform into surface labels using freesurfer. I tried following code to convert the volume with ID 20 from the parcellationvolumes.nii.gz file into a label

mri_cor2label --i dir/parcellationvolumes.nii.gz --id 20 --l dir/20.label

Although the code runs fine and finishes successfully, whenever I try to open the created label in freeview, it says that the label is empty.

Any idea what I am doing wrong? Do you have an easier way to project all ROI volumes onto the surface?

A second related question: I have run the recon-all for T1 of the subject and it creates rh.pial and lh.pial. I was wondering whether the transformation to go from T1 volume to the surface is saved somewhere and whether I can apply this transformation to convert my cortical volume parcellations into surface parcellations?

Thank you for your help! Best regards Julie

---

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Try mri_convert parcellationvolumes.mgz --ascii parcellationvolumes.txt

On 7/10/2020 8:49 PM, Julie Ottoy wrote:

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Thank you for your reply. It worked to convert to surface label :) When i overlay the surface labels on the pial surface, I can view a histogram showing the number of vertices versus the numbers of labels i have. As a follow-up question, do you know how I could extract a txt file that gives me the vertices with their corresponding label number. For example, for 10,000 vertices and 100 labels, I'd like to get a txt file with 10,000 rows and each row has a label value between 1 and 100.

Thank you for your help!

On Fri, 10 Jul 2020 at 16:28, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:

That will create a volume label, not a surface label (but it
should not have been empty -- look in the label (it is just a text
file)). To get a surface label, first map the volume to the
surface with something like
mri_vol2surf --mov parcellationvolumes.nii.gz --projfrac-max -.5 1
.1 --hemi lh --o lh.parcellationvolumes.mgz --regheader subject
 mri_cor2label --i lh.parcellationvolumes.mgz --id 20 --surf
subject lh --l lh.20.label


On 7/10/2020 3:46 PM, Julie Ottoy wrote:

...

        External Email - Use Caution

Hi Freesurfer team

I am trying to convert parcellation (cortical) volumes that I
acquired through another platform into surface labels using
freesurfer. I tried following code to convert the volume with ID
20 from the parcellationvolumes.nii.gz file into a label

mri_cor2label  --i dir/parcellationvolumes.nii.gz --id 20 --l
dir/20.label

Although the code runs fine and finishes successfully, whenever I
try to open the created label in freeview, it says that the label
is empty.

Any idea what I am doing wrong? Do you have an easier way to
project all ROI volumes onto the surface?

A second related question: I have run the recon-all for T1 of the
subject and it creates rh.pial and lh.pial. I was wondering
whether the transformation to go from T1 volume to the surface is
saved somewhere and whether I can apply this transformation to
convert my cortical volume parcellations into surface parcellations?

Thank you for your help!
Best regards
Julie

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