Dear Bruce and freesurfers, Someone has suggested to me that my problem is a result of the poor resolution of the original MPRAGE data. If I know that my volume index of a problematic point is (152,91,124), how can I map it onto my original MPRAGE data and check?
Thank you very much! Sincerely, Ye On Thu, Jul 4, 2013 at 4:40 PM, ye tian <tianye...@gmail.com> wrote: > 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 yt...@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 <tianye...@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 <fis...@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 <tianye...@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 >>>> >>>> >>>> >>>> >>>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >>> If the e-mail was sent to you in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> >> >
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