Great!!
On 08/11/2015 12:06 PM, Emma Thompson wrote:
Thanks Ani.
Yes, I am simply trying to copy the cases to a new location
(directory), so I can access and run my FS analyses from there. I had
tried what you mentioned initially, following the wiki instructions
for setup config, but I couldn't get it to source properly (I kept
getting an error stating that -bash didn't recognize the setenv
command). I started to think it just wasn't possible, really naive I
know. I realize now after reading your post and perusing the
listserve/internet for answers that this was because I was sourcing
incorrectly in bash shell, so when I tried using the following
'export' command instead of 'setenv' everything works fine:
export SUBJECTS_DIR=''/pathtomynewdirectory/subjects''
Thanks again!!!
On Mon, Aug 10, 2015 at 3:09 PM, Ani Varjabedian
<a...@nmr.mgh.harvard.edu <mailto:a...@nmr.mgh.harvard.edu>> wrote:
Hi Emma,
You should be able to just copy the subject folders in question to
a new location. When you want to work with them just set your
SUBJECTS_DIR variable to whatever that new path is. Could you
explain why you think you will have to recreate surface
reconstructions? That should not be the case. You are simply going
to copy the cases to a new location, correct?
-Ani
On 08/10/2015 02:49 PM, Emma Thompson wrote:
Thanks Christopher for your response. I have read the
tutorials/wiki page. My subject directory is set up somewhat
similarly (See below). The problem is I would like to create and
move the "PP*" patients to an entirely new and different FS
'subjects' directory while keeping the "MM*" patients in the
current FS 'subjects' directory...Anybody have any ideas on how I
can implement this? Thanks in advance!
|-- STUDY A
|-- DTI
|-- FS
|-- subjects
|-- MM01
|-- bem
|-- label
|-- mri
|-- scripts
|-- src
|-- stats
|-- surf
|-- tmp
|-- touch
|-- trash
|-- MM02
|-- bem
|-- label
|-- mri
|-- scripts
|-- src
|-- stats
|-- surf
|-- tmp
|-- touch
|-- trash
|-- PP01
|-- bem
|-- label
|-- mri
|-- scripts
|-- src
|-- stats
|-- surf
|-- tmp
|-- touch
|-- trash
|-- PP02
|-- bem
|-- label
|-- mri
|-- scripts
|-- src
|-- stats
|-- surf
|-- tmp
|-- touch
|-- trash
On Mon, Aug 10, 2015 at 2:26 PM, Watson, Christopher
<christopher.wat...@childrens.harvard.edu
<mailto:christopher.wat...@childrens.harvard.edu>> wrote:
I think it's a bit unclear what you're asking for. Have you
followed the tutorials on the wiki? Can you post your
directory structure?
What I do on my system is keep studies separate from one
another. Each study directory has its own FS directory, and I
keep the raw images separate. So something like the following:
.
|-- Study A
|-- DTI
|-- MPRAGE
|-- raw
|-- subj01
|-- subj01_mprage.nii.gz
|-- subj01_DICOMS
|-- subj02
|-- Freesurfer
|-- subj01
|-- subj02
|-- FMRI
...and so on
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of
Emma Thompson [vonecono...@gmail.com
<mailto:vonecono...@gmail.com>]
*Sent:* Monday, August 10, 2015 2:16 PM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] creating a new subject directory
using imported data from existing subject directory
Hi,
I'm re-posting my query in case it got buried on the listserve:
Dear Freesurfers,
I created a single subject directory and then imported sdata
from two separate studies, in the end I realized I should
have created two subject directories and would like to now
rectify the situation. My question is, 1) how do I create a
second subject directory in a different location? and 2) how
do I transfer my existing subjects' data from my current
subject directory to this new subject directory without
having to redo any of my work (surface reconstruction). Is
this even possible at this point? Or is it that I should only
have one FS directory after all and perhaps I should just
move the location of this directory so it is more accessible
for both of my studies? If this is the case, could you advise
me on how to go about doing this?
BTW I'm using bash shell.
I hope my questions are clear. Thanks!!!
On Sat, Aug 8, 2015 at 1:24 PM, Emma Thompson
<vonecono...@gmail.com <mailto:vonecono...@gmail.com>> wrote:
Dear Freesurfers,
I created a single subject directory and then imported
sdata from two separate studies, in the end I realized I
should have created two subject directories and would
like to now rectify the situation. My question is, 1) how
do I create a second subject directory in a different
location? and 2) how do I transfer my existing subjects'
data from my current subject directory to this new
subject directory without having to redo any of my work
(surface reconstruction). Is this even possible at this
point? Or is it that I should only have one FS directory
after all and perhaps I should just move the location of
this directory so it is more accessible for both of my
studies? If this is the case, could you advise me on how
to go about doing this?
BTW I'm using bash shell.
I hope my questions are clear. Thanks!!!
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dispose of the e-mail.
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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
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