Hi Mohamed

it depends on how you computed it. I believe that the one in the exvivo.stats file computes it directly from the surfaces (i.e. sum of the volumes of the tetrahedra or something like that). If you sample it into the volume and add up voxels you will get discretization artifacts that will change the volume.


cheers
Bruce


On Thu, 8 Feb 2018, m.ba...@uliege.be wrote:

Dear Bruce,

Many thanks for you kind answer.
I sampled the perirhinal roi label into the volume using the suggested command 
line:
"mri_label2vol --subject s6904 --fill-ribbon --label lh.perirhinal.label --o 
lh.perirhinal.volume.nii --hemi lh --identity".
The obtained mask seems to cover well the perirhinal structure.

Now, I calculate the perirhinal volmue (mm3) based on the obtained mask but I found that the obtained value does not match the one obtained during the Freesurfer cortical reconstruction (values in the stat folder: files : rh/lh-BA_exvivo.stats). did I messed something?

Thank you very much in advance,

Best regards,

Mohamed

----- Mail original -----
De: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
À: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Envoyé: Lundi 22 Janvier 2018 16:12:10
Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

oh, then I think you are just showing the surface-based label, which will
only fill voxels that intersect with the white surface I believe. To
sample it into the volume try mri_label2vol with the --fill-ribbon flag
(the help is pretty extensive).

cheers
Bruce
On Mon, 22 Jan 2018, m.ba...@uliege.be
wrote:

Dear Bruce,

Thank you for your answer!

I just display the "T1.mgz" image (mri folder) using Freeview and then loaded the 
"lh/rh.perirhinal_exvivo.label" rois (label folder).

If this is not the good way to do it, please, could you explain more the 
procedure? What do you mean by MT and PC?

Thank you very much in advance,

Best regards,

Mohamed


----- Mail original -----
De: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
À: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Envoyé: Vendredi 19 Janvier 2018 16:53:18
Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Hi Mohamed

how are you visualizing the MT or PC ROIs. Did you sample them into the
volume? If so, can you tell me where the file ROIs are in the data you
sent me?

cheers
Bruce
On Fri, 19 Jan 2018, m.ba...@uliege.be wrote:

Dear Bruce,

Many thanks for your kind help!

I put the subject data on your ftp site (s8201.tar).

Best regards,

Mohamed



----- Mail original -----
De: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
À: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Envoyé: Jeudi 18 Janvier 2018 16:37:10
Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Hi Mohamed

if you tar, gzip and ftp this subject to our ftp site we will take a look
cheers
Bruce
On
Thu, 18 Jan 2018, m.ba...@uliege.be wrote:

Dear Bruce,

Attached is the screen shot of the results of the segmentation of the 
perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented Roi 
does not cover the entire cortical thickness of the region. Is there any other 
alternative to get a better segmentation of this region?

Many thanks in advance,

Best regards,

Mohamed

----- Mail original -----
De: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
À: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Envoyé: Mardi 9 Janvier 2018 14:50:16
Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Hi Mohamed

I'm pretty sure this was an issue with the ribbon-filling in V5 that is
better in V6. Try using it and see if it is fixed.

cheers
Bruce
On Tue, 9 Jan 2018,
m.ba...@uliege.be wrote:

Dear Freesurfer experts,

We would like to use volume and cortical thickness measures obtained for the 
perirhinal cortex in Freesurfer 5. When checking the region that has been 
segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem 
to cover the entire cortical thickness of the region. On the coronal slice 
shown in example (attached file), one can see that there are still a few voxels 
of gray matter between the external border of the ROI and the external boundary 
of the cortex. How reliable is this segmentation? Is there a reason why the ROI 
appears so thin?

Many thanks in advance,

Best regards,



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