Hi Carolin
I think our lab manager Leah Morgan (ccd) is going to find an RA to take a
look. Leah: has anyone had a chance yet?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Caroline Chwiesko
Sent: Thursday, April 8, 2021 3:52 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to edit GM when WM is ok
External Email - Use Caution
Hello Bruce,
I haven't heard back from you so I just wanted to follow up and ask if you had
the chance to look at the data that I uploaded.
Cheers
Carolin
On Mon, Mar 29, 2021 at 4:01 PM Caroline Chwiesko
<cchwi...@uci.edu<mailto:cchwi...@uci.edu>> wrote:
Because the dataset is already uploaded would it be possible to also look at
the following in this dataset?:
For editing of the subcortical segmentation in the aparc+aseg file, there is a
spot where I can not figure out if this structure is supposed to be part of the
caudate or the choroid plexus. In most of my subjects it is segmented as
caudate but based on the shape I don t think that this is correct. I am
wondering if there is somewhere a dataset that we can download and that
displays an optimal/correct segmentation of the subcortical structures to serve
as a guide for editing?
The coordinates for the location I am not sure about are:
for right :RAS 8.24 10.85 33.75, in the aparc+aseg file its 118 124 144
for left: RAS -12.76 14.71 29.46, in the aparc+aseg file its 139 128 148
Thank you very much in advance for your help!
Carolin
On Mon, Mar 29, 2021 at 3:32 PM Caroline Chwiesko
<cchwi...@uci.edu<mailto:cchwi...@uci.edu>> wrote:
RAS: 6.11, 57.54, 60.36
brainmask [120, 98, 191]
Talairach 115.59, 127.61, 202.35
On Mon, Mar 29, 2021 at 3:08 PM Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
Thanks. What are the voxel coords of the location you wanted us to take a look
at?
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 Caroline Chwiesko
Sent: Monday, March 29, 2021 5:54 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to edit GM when WM is ok
External Email - Use Caution
Hello Bruce,
i don t have a good understanding of how the upload works so i just called
those files img1.png, img2.png and img3.png thinking that you will be able to
connect those files with my email address. I uploaded now the entire zipped
subject directory. This file is called carolinechwiesko.zip. It includes also a
directory called images which includes images of the problematic spot in all 3
orientations.
I got the following output in the terminal while uploading my file. I hope that
this means that the upload was successful:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> put carolinechwiesko.zip
local: carolinechwiesko.zip remote: carolinechwiesko.zip
200 PORT command successful. Consider using PASV.
150 Ok to send data.
Again thank you very much for your help with this!
Cheers
Carolin
On Sat, Mar 27, 2021 at 8:35 AM Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Carolin
What did you name them? Also, we won’t really be able to diagnose things unless
you upload the entire tarred/gzipped subject directory
Cheers
Bruce
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 Caroline Chwiesko
Sent: Friday, March 26, 2021 8:04 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to edit GM when WM is ok
External Email - Use Caution
Thank you for your response! I followed the instructions for FTP file exchange.
And did then:
ftp> cd transfer/incoming
ftp> put filename.txt
Are the images not there?
Cheers
Carolin
On Fri, Mar 26, 2021 at 3:20 PM Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Carolin
Where did you upload the images?
Bruce
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 Caroline Chwiesko
Sent: Friday, March 26, 2021 6:08 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to edit GM when WM is ok
External Email - Use Caution
Hello Bruce,
I wrote a week ago to this mailing list to ask for advice about how to edit an
issue where an entire Gyrus will not be captured by the pial surface. I
uploaded some images to show what that looks like. I just wanted to send a
friendly reminder to make sure it won't be forgotten ;)
Thank you very much for any help!
Cheers
Carolin
On Fri, Mar 19, 2021 at 4:54 PM Caroline Chwiesko
<cchwi...@uci.edu<mailto:cchwi...@uci.edu>> wrote:
Hi Bruce,
thank you very much for taking a look at that. I uploaded 3 images in different
orientations. I can not see any white matter.
Cheers
Carolin
On Fri, Mar 19, 2021 at 7:26 AM Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Carolin
Yes, I guess send along images using all 3 orientations. There has to be some
white matter there somewhere….
Cheers
Bruce
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 Caroline Chwiesko
Sent: Friday, March 19, 2021 12:28 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] How to edit GM when WM is ok
External Email - Use Caution
Hello Freesurfer experts,
i am doing some editing after recon-all. I have the issue that one gyrus is not
captured by the pial surface. There is no wm that is wrong and that i could
correct. It looks like this gyrus has a weird angle so there is actually no WM
visible. How can such an error be corrected? I am happy to send a couple images
if needed.
Thank you very much in advance for any help!
Cheers
Carolin
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