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 CautionHi 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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