Dear Bruce and Freesurfers,

I am sorry that I am asking you this question, but I have trouble uploading my directory to freesurfer's ftp. I have tried the following

1. put /Path_to_subject/subjectDirectory                                            ---->     local: not a plain file

2. put -r /Path_to_subject/subjectDirectory                                         ---->     remote: Can't open '-r': No such file or directory

3. mput /Path_to_subject/subjectDirectory                                         ---->     [anpqy?] y  ---->  not a plain file

4. scp -r ytian@university.edu:~/Path_to_subject/subjectDirectory       ---->    ?Invalid command

5. I compressed the subject directory into subject.zip. put subject.zip ---->    local: Entering extended passive mode; could not create file

Is there any other way to upload a file to ftp without manually "put" all the files in the directories and subdirectories one by one?

I know that this question is unrelated to freesurfer, but I really appreciate it if someone can get me unstuck.

Thank you all for being so patient with me.

Sincerely,

Ye

On Thu, Jul 4, 2013 at 2:35 PM, ye tian <tianye730@gmail.com> wrote:

Dear Bruce and Christopher,

Thank you very much!

Yes, more white matter starts filling in afterwards. I am attaching the first slice from which the problem starts to the first slice where the problem is gone (4 total in Surfs.png).

I have trouble retrieving voxel coordinates. The command 

tkmedit subject orig.mgz -reg register.dat -ov mov.nii -surfs

returns Error: can not find overlay reg register.dat

Is it okay if I just click on the yellow surface and write down the "volume index" under "cursor" in tkmedit tool box?

Sincerely,

Ye

On Thu, Jul 4, 2013 at 11:32 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Ye

one is surface-based and the other is voxel-based. It's impossible to tell which is correct from just a single slice. If you upload the entire subject directory to our ftp server and give us the voxel coords of that point we will take a look

cheers
Bruce

On Thu, 4 Jul 2013, ye tian wrote:

Dear Freesurfers,
 
My first attempt of this message somehow didn't make it to the mailing
archive. In case it didn't go through, I am sending it again. Sorry to
bother you if you received the first message.  
 
Two things I was wondering
1) Why do the surfaces shown in the left and right panels disagree? (The
right one has a lot more white matter).
2) Do I need to edit the white matter? It seems unreasonable to have
+8mm thick of grey matter. If so, I will probably paint more voxels to
wm.mgz.
 
Thank you very much!
 
Sincerely,
Ye


On Wed, Jul 3, 2013 at 4:33 PM, ye tian <tianye730@gmail.com> wrote:
      Dear freesurfers,
I would like a second eye on my decision to edit wm.mgz. I think that
the boundary between the gray and the white is unrealistic (e.g.
Coronal.png). Furthermore, there is a discrepancy between -surfs and
-surfs -aseg (e.g. attached coronal_aseg.png). 

If I indeed need to edit these slices, which way is more preferable,
adding voxels or control points?

Thank you very much!

Sincerely,
Ye

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