Re: [Freesurfer] How to edit GM when WM is ok

[Fischl, Bruce]

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 
 On Behalf Of Caroline Chwiesko
Sent: Thursday, April 8, 2021 3:52 PM
To: Freesurfer support list 
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 
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 
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 
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>>
 On Behalf Of Caroline Chwiesko
Sent: Monday, March 29, 2021 5:54 PM
To: Freesurfer support list 
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 
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>>
 On Behalf Of Caroline Chwiesko
Sent: Friday, March 26, 2021 8:04 PM
To: Freesurfer support list 
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 
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>>
 On Behalf Of Caroline Chwiesko
Sent: Friday, March 26, 2021 6:08 PM
To: Freesurfer support list 
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 
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 

Re: [Freesurfer] How to edit GM when WM is ok

[Caroline Chwiesko]

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  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 
> 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 
>> 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 <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Caroline Chwiesko
>>> *Sent:* Monday, March 29, 2021 5:54 PM
>>> *To:* Freesurfer support list 
>>> *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 
>>> 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 <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Caroline Chwiesko
>>> *Sent:* Friday, March 26, 2021 8:04 PM
>>> *To:* Freesurfer support list 
>>> *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 
>>> wrote:
>>>
>>> Hi Carolin
>>>
>>>
>>>
>>> Where did you upload the images?
>>> Bruce
>>>
>>>
>>>
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Caroline Chwiesko
>>> *Sent:* Friday, March 26, 2021 6:08 PM
>>> *To:* Freesurfer support list 
>>> *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 
>>> 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 

Re: [Freesurfer] mri_convert problem

[Hoopes, Andrew]

Have you made sure that you have read permission to open those files? What is 
the output of `ls -l asta.mgh`? And asta.nii doesn’t seem to be a file in your 
working directory.

Best,
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Pierpaolo Croce 

Date: Thursday, April 8, 2021 at 11:32 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] mri_convert problem

External Email - Use Caution
Dear List,
I have installed the ubuntu version of freesurfer (creating the VM as in the 
tutorial)
I would like to run the following command:

mri_convert -c -oc 0 0 0 asta.mgh orig.mgz

I always get the error in the screen shot. Can someone help me?
also using asta.nii format
--

Ing. Pierpaolo Croce, PhD.
Institute for Advanced Biomedical Technologies - ITAB
and
Department of Neuroscience and Imaging
University of Chieti "G. D'Annunzio"
Via dei Vestini, 33
66013 Chieti, Italy
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Re: [Freesurfer] thalamic nuclei segmentation

[Iglesias Gonzalez, Juan E.]

Dear Sara,
You can download Freesurfer 7, install it side by side with FreeSurfer 6, and 
run the thalamic module on the already reconned subjects.
Cheers,
/E


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of Sara PONTICORVO 

Reply-To: Freesurfer support list 
Date: Thursday, April 8, 2021 at 03:22
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] thalamic nuclei segmentation


External Email - Use Caution
Hi Freesurfer experts,
I processed ~150 subjects with freesurfer v6 (recon-all) and I was wondering if 
it is possible to use the script for the segmentation of the thalamic nuclei on 
these subjects.
I know this part of the processing is now integrated in the v7 of freesurfer, 
but I'm thinking if there is a way to avoid re-run all the reconstruction with 
the new version.
I looked in the wiki page, and it seems that there was a way to integrate the 
scripts in the  fs-v6, but I don't  find any downloadable package or scripts.

Thanks for your help,
Sara


--
Sara Ponticorvo, PhD
Department of Medicine Surgery and Dentistry
University of Salerno
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[Freesurfer] Decompressed problem during reconall

[Banu Femir]

External Email - Use Caution

Dear FreeSurfer Developers,

I've a problem that cannot solve for the last week. I am using virtual box,
FS7 on my windows. I run reconall for Bert and checked that it is working.I
have an MRI scan of sepstic patients that I got via CD, these are DICOM
files but does not end with .dcm.

When I try to run reconall, for dcm images I got the following error (the
longer version is in the attachment)


Loading pixel data
JPEG compressed, decompressing
cd /home/developer/Documents/7.1.0-1/subjects/sepsis2
fsdcmdecompress --i
/home/developer/Documents/7.1.0-1/subjects/D_01/F_01 --o
/tmp/developer.tmp.decompressed.dcm.0oOV4x --jpeg >&
/tmp/developer.tmp.decompressed.dcm.0oOV4x.dcmdjpeg.out
ERROR: 512, see /tmp/developer.tmp.decompressed.dcm.0oOV4x.dcmdjpeg.out for
more details
Command exited with non-zero status 1
@#@FSTIME  2021:04:08:08:29:16 mri_convert N 2 e 1.97 S 1.19 U 0.60 P 91% M
9200 F 2 R 999 W 0 c 174 w 356 I 32240 O 0 L 0.55 0.33 0.41
@#@FSLOADPOST 2021:04:08:08:29:18 mri_convert N 2 0.55 0.33 0.41
Linux developer-VirtualBox 5.3.0-53-generic #47~18.04.1-Ubuntu SMP Thu May
7 13:10:50 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sepsis2 exited with ERRORS at Thu Apr  8 08:29:18 EDT 202


I converted files to nii, this time I decided to run reconall on nii
images, it took more time but again failed on talairach transform.

I tried to run on different shells but ended up with the same problem. Is
it related with my MRI data or computer, how can I understand that?

Many thanks!
Banu


recon-all.log
Description: Binary data
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[Freesurfer] thalamic nuclei segmentation

[Sara PONTICORVO]

External Email - Use Caution

Hi Freesurfer experts,
I processed ~150 subjects with freesurfer v6 (recon-all) and I was
wondering if it is possible to use the script for the segmentation of the
thalamic nuclei on these subjects.
I know this part of the processing is now integrated in the v7 of
freesurfer, but I'm thinking if there is a way to avoid re-run all the
reconstruction with the new version.
I looked in the wiki page, and it seems that there was a way to integrate
the scripts in the  fs-v6, but I don't  find any downloadable package or
scripts.

Thanks for your help,
Sara


-- 
Sara Ponticorvo, PhD
Department of Medicine Surgery and Dentistry
University of Salerno
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