Hi Elisabetta

we would need the entire subject directory. Did you look at the surfaces I suggested?

cheers Bruce On Fri, 20 Nov 2015, Elisabetta del Re wrote:

Hi Bruce, thank you so much. I attach here T1 of 2 of the cases. Thank you again, regards, Elisabetta

On 11/4/15, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Elisabetta

I don't think that's an error, just a warning. That said, a defect with 38K vertices is awfully big, almost 1/4 of the surface, which usually means

something big is wrong (e.g. cerebellum or skull attached to the hemi). Can

you look at the orig.nofix or the inflated.nofix and see what is wrong? If you upload one of the subjects I'll take a look

cheers Bruce

On Wed, 4 Nov 2015, Elisabetta del Re wrote:

...

Dear FreeSurfer team,we are running FreeSurfer on 1.5T cases. For a few of them we get error messages that I am attaching. Mostly the message error relates to excessive topological defect. Any suggestions you can give to us? Thank you, regards, Elisabetta

-- Elisabetta C. del Re, Ph.D. Instructor, Department of Psychiatry Harvard Medical School phone 617 9675569 mail elisabetta_delre@hms.harvard.edu

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Hi Elisabetta

can you describe what you did in this case? I'm puzzled because the brain.finalsurfs.mgz and the wm.mgz both contain skull in them and don't like they have been skull stripped at all, but the brainmask.auto.mgz (which is the output of our skull stripping) looks like it worked well (that is, brainmask.auto.mgz doesn't have any skull in it). Despite this things seem to have gone ok. To visualize the defects load the rh or lh.inflated.nofix surface as:

freeview -f lh.inflated.nofix:overlay=lh.defect_labels:overlay_threshold=1,120

then click the "3D" button to show the surface. This will show you every defect as a different color. You can click on them then find where they are in the volume to fix them if you need to (that is, also load the brain.finasurfs.mgz and the wm.mgz and edit the wm.mgz or add control points).

In this case though it seems that the skull stripping worked, but you somehow reintroduced the unstripped volume back into the pipeline

cheers Bruce

On Fri, 20 Nov 2015, Elisabetta del Re wrote:

Hi Bruce, thank you so much. I attach here T1 of 2 of the cases. Thank you again, regards, Elisabetta

On 11/4/15, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Elisabetta

I don't think that's an error, just a warning. That said, a defect with 38K vertices is awfully big, almost 1/4 of the surface, which usually means

something big is wrong (e.g. cerebellum or skull attached to the hemi). Can

you look at the orig.nofix or the inflated.nofix and see what is wrong? If you upload one of the subjects I'll take a look

cheers Bruce

On Wed, 4 Nov 2015, Elisabetta del Re wrote:

...

Dear FreeSurfer team,we are running FreeSurfer on 1.5T cases. For a few of them we get error messages that I am attaching. Mostly the message error relates to excessive topological defect. Any suggestions you can give to us? Thank you, regards, Elisabetta

-- Elisabetta C. del Re, Ph.D. Instructor, Department of Psychiatry Harvard Medical School phone 617 9675569 mail elisabetta_delre@hms.harvard.edu

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.