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ok. Thank you very much :)

On Thu, Apr 8, 2021 at 1:19 PM Fischl, Bruce <BFISCHL@mgh.harvard.edu> wrote:

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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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

 

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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 <cchwiesk@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 <cchwiesk@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 <BFISCHL@mgh.harvard.edu> wrote:

Thanks. What are the voxel coords of the location you wanted us to take a look at?

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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>
Subject: Re: [Freesurfer] How to edit GM when WM is ok

 

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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 <BFISCHL@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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>
Subject: Re: [Freesurfer] How to edit GM when WM is ok

 

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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 <BFISCHL@mgh.harvard.edu> wrote:

Hi Carolin

 

Where did you upload the images?
Bruce

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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>
Subject: Re: [Freesurfer] How to edit GM when WM is ok

 

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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 <cchwiesk@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 <BFISCHL@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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>
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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