Hmmm, did you log in as anonymous? I’ll cc Rob who should be able to help

 

Cheers

Bruce

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Julie Ottoy
Sent: Tuesday, November 3, 2020 11:12 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Fixing error with pial surface {Disarmed}

 

        External Email - Use Caution        

Hi Bruce

 

Thank you!

Meanwhile, I tried to upload the subject on the server but I always get the following error:

 

230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> put subject_FS_upload.zip
local: subject_FS_upload.zip remote: subject_FS_upload.zip
421 Service not available, remote server has closed connection

 

Could you help me out with this?

Thanks

Julie

 

On Mon, 12 Oct 2020 at 15:48, Fischl, Bruce <BFISCHL@mgh.harvard.edu> wrote:

Hi Julie

 

It’s really hard to diagnose this way. Are you able to upload the subject? If so, please send us the coordinates of the region where you think things are going wrong

 

Cheers

Bruce

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Julie Ottoy
Sent: Monday, October 12, 2020 3:42 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Fixing error with pial surface

 

        External Email - Use Caution        

Hi Bruce,

 

Thanks for your answer. I have checked the wm.mgz but it does not seem to be a topological error I think.

I have added coronal, axial, and sag views in attachment (see the red cursor). Also I have added the first (coronal) slice that starts to show white matter (couple slices later).

 

Let me know if you still would like me to upload the data.

 

Best

Julie

 

On Mon, 12 Oct 2020 at 14:23, Fischl, Bruce <BFISCHL@mgh.harvard.edu> wrote:

Hi Julie

 

It’s hard to tell from the single slice. Is there white matter in the wm.mgz that doesn’t have surface (?h.white) covering it? That would indicate a topological defect.

If you upload the entire gzipped and tarred subject’s directory we will take a look

 

Cheers

Bruce

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Julie Ottoy
Sent: Sunday, October 11, 2020 3:51 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Fixing error with pial surface

 

        External Email - Use Caution        

Dear Freesurfer team,

 

I have a question related to fixing the pial surface when a part was missed (see attachment). On the freesurfer website, I only found how to erase the pial when there was too much (see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEditsV6.0 ), but I could not find what to do when there was too little.

As there is no white matter in this particular area, it is also not an option to place control points. Also the skull stripping did not change anything: I tried both the freesurfer skull stripping and an in-house skull stripping algorithm.

 

Thank you for your help.

Best regards

Julie

 

 

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