Re: [Freesurfer] Fixing error with pial surface {Disarmed}

Try these instructions

From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log  into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.

On 11/3/2020 12:38 PM, Julie Ottoy wrote:

External Email - Use Caution

Hi Bruce,

Thanks for your answer and cc'ing Rob. I did use anonymous as the username.

Thanks, Julie

On Tue, 3 Nov 2020 at 11:44, Fischl, Bruce <BFISCHL@mgh.harvard.edu mailto:BFISCHL@mgh.harvard.edu> wrote:

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
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
<freesurfer-bounces@nmr.mgh.harvard.edu
<mailto: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
<mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* Re: [Freesurfer] Fixing error with pial surface {Disarmed}

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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 <mailto: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
    <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
    <freesurfer-bounces@nmr.mgh.harvard.edu
    <mailto: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
    <mailto: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 <mailto: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
        <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
        <freesurfer-bounces@nmr.mgh.harvard.edu
        <mailto: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
        <mailto: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
        <https://secure-web.cisco.com/1gpx46tpa8CTIUNay0UrrJ-gxsIj8Mag4YGO8J8nyhFBk_vUGzoIRj4Mcbd6QhCbXxxACP5NekTgpkwy1i_7hReP5AFQqNeKWbPlOKFgTdD71o6FOQEC25-2mLI9VIZ3DCCUILUIjSEHeA8PQm-jSQuf2Q35SRlvA0gE74LLqJnkql0Rs2lM9RWexhSh3jGixx7QPZFpX0y4nDvIsDFmhtQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FPialEditsV6.0>
        ), 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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