Fixing error with pial surface

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Julie Ottoy

11 Oct 2020 11 Oct '20

3:51 p.m.

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 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

Attachments:

attachment.html (text/html — 1.1 KB)
screenshot_T1.png (image/png — 115.4 KB)
screenshot_skullstrip.png (image/png — 66.6 KB)

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Fischl, Bruce

12 Oct 12 Oct

1:55 p.m.

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 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

Julie Ottoy

3:41 p.m.

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 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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Fischl, Bruce

3:47 p.m.

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,

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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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 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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Julie Ottoy

3 Nov 3 Nov

11:12 a.m.

New subject: 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 https://secure-web.cisco.com/1gpx46tpa8CTIUNay0UrrJ-gxsIj8Mag4YGO8J8nyhFBk_v... ), 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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1aSysztaOg72LTSrHZ8IMlAHyx36lqzh_mhacRbfU85DOTL...

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1aSysztaOg72LTSrHZ8IMlAHyx36lqzh_mhacRbfU85DOTL...

Fischl, Bruce

11:40 a.m.

New subject: Fixing error with pial surface {Disarmed}

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:

Could you help me out with this? Thanks Julie

On Mon, 12 Oct 2020 at 15:48, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Fixing error with pial surface

External Email - Use Caution Hi Bruce,

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.edumailto: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

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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1aSysztaOg72LTSrHZ8IMlAHyx36lqzh_mhacRbfU85DOTLuITwz3kWnasOayZnNZpzHZSWb5yin6dOCPVg41bA3XaEhUSmu2qLzGmwvcmvNrteWu-9Bq02pR9SPHPFq5coAaCcaqLAJPYFbqOglbTzBLSd3Jj0DTqAj7WlndHsL0y2Oth1Io1uSTzIyh1lgScLGMaZlhF10kZeZegItM5w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1aSysztaOg72LTSrHZ8IMlAHyx36lqzh_mhacRbfU85DOTLuITwz3kWnasOayZnNZpzHZSWb5yin6dOCPVg41bA3XaEhUSmu2qLzGmwvcmvNrteWu-9Bq02pR9SPHPFq5coAaCcaqLAJPYFbqOglbTzBLSd3Jj0DTqAj7WlndHsL0y2Oth1Io1uSTzIyh1lgScLGMaZlhF10kZeZegItM5w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Julie Ottoy

12:38 p.m.

New subject: Fixing error with pial surface {Disarmed}

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 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 < 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://secure-web.cisco.com/1POCEML4QLGqdTfIf8StL0SUvgpIg3DncxT_ePZTsjRJHXG... 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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1EifvyV6KDi8xRojSTCOF_0h85ZTUKALs1YwF9ySx1YcICW... https://secure-web.cisco.com/1aSysztaOg72LTSrHZ8IMlAHyx36lqzh_mhacRbfU85DOTLuITwz3kWnasOayZnNZpzHZSWb5yin6dOCPVg41bA3XaEhUSmu2qLzGmwvcmvNrteWu-9Bq02pR9SPHPFq5coAaCcaqLAJPYFbqOglbTzBLSd3Jj0DTqAj7WlndHsL0y2Oth1Io1uSTzIyh1lgScLGMaZlhF10kZeZegItM5w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1EifvyV6KDi8xRojSTCOF_0h85ZTUKALs1YwF9ySx1YcICW... https://secure-web.cisco.com/1aSysztaOg72LTSrHZ8IMlAHyx36lqzh_mhacRbfU85DOTLuITwz3kWnasOayZnNZpzHZSWb5yin6dOCPVg41bA3XaEhUSmu2qLzGmwvcmvNrteWu-9Bq02pR9SPHPFq5coAaCcaqLAJPYFbqOglbTzBLSd3Jj0DTqAj7WlndHsL0y2Oth1Io1uSTzIyh1lgScLGMaZlhF10kZeZegItM5w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1EifvyV6KDi8xRojSTCOF_0h85ZTUKALs1YwF9ySx1YcICW...

Douglas N. Greve

5 Nov 5 Nov

9:41 a.m.

New subject: 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}

*        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 <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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Julie Ottoy

6 Nov 6 Nov

7:20 p.m.

New subject: Fixing error with pial surface {Disarmed}

External Email - Use Caution

Dear Bruce and Douglas,

Thanks for the help, I have now uploaded the data. This is called subject_FS_upload.zip

Please refer to the antsdn.brain.mgz (for T1) and the pial surface. As described below, the freesurfer output did not delineate some parts of the frontal lobe and medial temporal lobe correctly and this was not fixed by putting control points (as there is no white matter in this area). Also adapting the skull stripping did not help. For my dataset with a lot of atrophic brains, the issue particularly in the medial temporal lobe is very common (about 15% of my dataset)

Any tips / help would be appreciated! Julie

On Thu, 5 Nov 2020 at 09:42, Douglas N. Greve dgreve@mgh.harvard.edu wrote:

...

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 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 < 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://secure-web.cisco.com/1DuJrjwUJPwh5Gk7RCl73Io-xKugWO2CwXlTMkR0SOwoaOZ... 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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Douglas N. Greve
Fischl, Bruce
Julie Ottoy