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.eduwrote:
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
- 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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