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

[Caroline Chwiesko]

External Email - Use Caution

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 7:26 AM Fischl, Bruce 
>> 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 <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Caroline Chwiesko
>> *Sent:* Friday, March 19, 2021 12:28 AM
>> *To:* Freesurfer support list 
>> *Subject:* 

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

[Caroline Chwiesko]

External Email - Use Caution

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 7:26 AM Fischl, Bruce 
> 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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Caroline Chwiesko
> *Sent:* Friday, March 19, 2021 12:28 AM
> *To:* Freesurfer support list 
> *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
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> 

[Freesurfer] functional to anatomical registration question

[Nasiriavanaki, Zahra]

Dear Freesurferers,

I have a question and I appreciate it much if you could please reply.
I need to know how to check subcortical functional to anatomical registration. 
I know for checking the cortical registration I can use the below command:

tkregister2 --s $subj --mov  template.nii.gz  --surf --reg 
init.register.dof6.dat

Could you please tell me what command should I use to check the registration in 
subcortex?

Thanks
MOna



Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Boston, MA, USA, 02129

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

[Fischl, Bruce]

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

From: 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 
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 any white matter.

Cheers
Carolin


On Fri, Mar 19, 2021 at 7:26 AM Fischl, Bruce 
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>>
 On Behalf Of Caroline Chwiesko
Sent: Friday, March 19, 2021 12:28 AM
To: Freesurfer support list 
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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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] How to edit GM when WM is ok

[Caroline Chwiesko]

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 7:26 AM Fischl, Bruce 
> 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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Caroline Chwiesko
> *Sent:* Friday, March 19, 2021 12:28 AM
> *To:* Freesurfer support list 
> *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
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1J_oIoYOhJvnRwnRW-4mvRYHkbS5YnJ-4a7ToFYTxtnkArwteHXKuS4d4Wbv1jNBOAxWg-iEK4odlolDNbypwWrlvCH1BW_KMwQ9tHAPOKCgj4XUClFwsEmf0AR5-6yBvIMJ19n4JeUOabYx10eAx82aCv3dCpQDue-uBJz6hYzhzm3UpZWjYZUB1O0AyetRlARVuEpcPRWza5ygSj1w6L2i9jbFvdlCCfuJVUs_y-p5TjAcxJyMHLB4Es4tx8h3kS5XOIkL9CKBoeUCArT5Hkw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 
>
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> 

[Freesurfer] Running recon-all with FLAIR

[Edina Szabó]

External Email - Use Caution

Dear All,

We are running recon-all on the latest version of FreeSurfer (v7.1.1). We
are using both T1 and FLAIR images to better define the pial surfaces, but
when we run the recommended command line (recon-all -subject subjectname -i
/path/to/input_volume -FLAIR /path/to/FLAIR_volume -FLAIRpial -all) the
pial surface is very underestimated (?.pial.FLAIR – and the aseg volume is
based on these surfaces), and we get better results without the FLAIR.
It seems that FreeSurfer mis-registers the FLAIR to the T1 during the
process. Is there a separate step we should do to register FLAIR to T1?

Thank you,
Edina
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[Freesurfer] Fwd: Three researcher positions (doctoral candidates) in visual perception and educational neuroscience

[Mareike Grotheer]

   External Email - Use Caution

The Educational Neuroscience Lab at the Philipps Universität Marburg 
(Germany) is currently recruiting up to three Doctoral Candidates. Two 
positions are aimed at candidates who are interested in simultaneously 
pursuing their doctorate as well as training as a child and adolescent 
psychotherapists. These two positions are described here: 
https://secure-web.cisco.com/1u41B3o1_wCuZdmyXcMyyhvPMvChH9Gk-uVYt5UJ5WOx7sVoOZdGP7xhPr8uscUr9VKZyJzTe7XOuydsk6PaVsESkajzNZMoiJsNWygnlcM6W-mEALXwUVnatcba-94RKILSnnBDcT_aJJLxDG1cp5QidYPHQ0jjfZCANlQRcJbBTDQ0a7-wTiOCqveaFRw_lhvIQI-VT0gbUywJdpKbpgyrgAnkS_5Z5Ymei12X-LQ5upTobZxbhWctqJCDSSkD9dPGOsOugJxvp8stSKOix1w/https%3A%2F%2Fwww.psychjob.eu%2Fde%2Fjob%2F1-2-stipendien-im-rahmen-des-marburger-modells-neuronale-grundlagen-13241 
. 
The third position is focused on research only and is described below.


In the Department of Psychology and the Center for Mind Brain and 
Behavior (CMBB), the Education Neuroscience Lab headed by Junior Group 
Leader Dr. Mareike Grotheer is currently accepting applications for a 
*Researcher (Doctoral Candidate)*.


The position is offered for a period of 3 years, if no former times of 
qualification must be considered. The starting date is as soon as 
possible. The position is part-time (65 % of regular working hours) with 
salary and benefits commensurate with a public service position in the 
state Hessen, Germany (TV-H E 13, 65 %).


The successful candidate will be highly motivated to conduct research on 
the neural substrates of visual perception as well as reading and 
mathematical cognition. The lab strives to employ a multimodal approach 
and the successful candidate will therefore have the opportunity to 
acquire multiple cutting-edge MRI techniques, such as functional, 
diffusion and quantitative MRI. By combining these tools with behavioral 
measures as well as computational models, the successful candidate will 
explore the interplay of brain function and structure, learning-induced 
changes in the brain and/or brain development. The successful candidate 
will plan, carry out and analyze experiments as well as prepare 
publications and conference presentations of their work. The lab is part 
of a larger research network, with excellent links to scientists in 
Europe and the US. Marburg is a beautiful university town, located just 
90 km north of Frankfurt, right in the heart of Germany.


The position is limited to a time period deemed adequate for the 
completion of a doctoral degree. As part of the assigned duties, there 
will be ample opportunity to conduct the independent scientific research 
necessary for the completion of a doctorate. The limitation complies to 
§ 2, 1 WissZeitVG.


The successful applicant will hold an MSc-degree (or equivalent) in 
Psychology, Neuroscience, Biology, Computer Science, or related fields. 
The applicant will further be keen to learn new techniques and to expand 
their quantitative and programming skills. He/she should also enjoy 
working in a team, as well as, independently. Experience with MRI, 
programming in Matlab or Python and good written and verbal English 
skills are desirable. Disposition to own scientific qualification (e.g. 
a doctorate project in the area of Education Neuroscience) is expected.


Feel free to contact Dr. Mareike Grotheer at 
groth...@staff.uni-marburg.de for more information.


We actively support the professional development of junior researchers, 
e.g. by the offers of Marburg Research Academy (MARA), the International 
Office, the Higher Education Didactics Office and the Human Resources 
Development Office.


We support women and strongly encourage them to apply. In areas where 
women are underrepresented, female applicants will be preferred in case 
of equal qualifications. Applicants with children are welcome – 
Philipps-University is certified as a family-friendly university. 
Sharing a full-time position (§ 8 Abs. 2 S. 1 HGlG) as well as a 
reduction of working time is possible. Applicants with a disability as 
described in SGB IX (§ 2 Abs. 2, 3) will be preferred in case of equal 
qualifications. Application and interview costs can not be refunded.


Please send your application mentioning registration number 
fb04-0025-wmz-2021 as a single PDF file to 
groth...@staff.uni-marburg.de, before the 9th of April, 2021.


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Re: [Freesurfer] make_average_subject error

[Jordan Mullins]

External Email - Use Caution

Hi Douglas,

Just following up on this. Thanks!

On Wed, Mar 17, 2021 at 6:12 PM Jordan Mullins 
wrote:

> Yes! Results attached.
>
> On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve 
> wrote:
>
>>
>> Can you run
>> ls -l $FREESURFER_HOME/bin/mri_aparc2aseg
>> $FREESURFER_HOME/bin/make_average_subject
>> and send the result?
>>
>> Also, the result of
>> which mri_aparc2aseg
>> which make_average_subject
>>
>>
>>
>> On 3/17/2021 8:36 PM, Jordan Mullins wrote:
>>
>> External Email - Use Caution
>> Yes, I had seen that report and had downloaded the patch, but still got
>> the same error. Are there any other steps I can take?
>>
>> On Wed, Mar 17, 2021 at 2:59 PM Douglas N. Greve 
>> wrote:
>>
>>> This problem is documented (along with a fix) on our release notes
>>> *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/1u1Z-uFR5fxuGqNlR5v1xrK8erCTHmH3u-GMZLm7k-SucWfLQ_ZGnDhkfR3eHFG2BYz4n4fFD_IphMenUgkeHN6_KDGkBXZKw2dD2lXqcIkrJNrRKqNsjFTAiDMC7-z4k6WGP8lSmOzdCyk7vG0ZpBli-I2mTyzQSi7j1Gj3tyHImeatyu_KS1BG54P2UK8RpEowofIba-HUt-sH0P0hjgD0r-L6Z3OxeZBCpegAPyCz8bmz_iKyyhZb4JD8npYtXZzE7pQmEt-icPsvs9i6fvQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes
>>> 
>>>
>>>
>>> On 3/16/2021 3:39 PM, Jordan Mullins wrote:
>>>
>>> External Email - Use Caution
>>> Yes, I used the make_average_subject command. I've attached a text file
>>> below of the command line and terminal output from my attempt to average
>>> two subjects. I get the same error when I try this with the full sample.
>>>
>>> On Tue, Mar 16, 2021 at 9:12 AM Douglas N. Greve 
>>> wrote:
>>>
 What command are you using? make_average_subject? Send the command line
 and terminal output

 On 3/10/2021 3:53 PM, Jordan Mullins wrote:

 External Email - Use Caution
 Hello,

 I am trying to create an average subject from a set of subjects, but
 keep getting an error that says "mghRead(mri/norm.mgz, -1): could not open
 file". I've read that several others have solved this issue by installing
 the patch available at *MailScanner has detected a possible fraud
 attempt from "secure-web.cisco.com" claiming to be*
 http://secure-web.cisco.com/1PFeDAVc139N82htFQiJN3EfkbyA7F5UAzXWNALk8zD7J-ELJBX3mhFTTg1bjNL3feCaiBf4Qu3pMFMD4F8yiNEV4pVgA-MhL1o8NrZMbXzXcNCoBvyDEtQdE1FRVuC2FCurEQF9-QkjKoG52S5y2_sjizkwZRGzs78OOoWeWWXHHdqBPJb7yYYPnvtuylms-MFEz64YdzkufSjRrvgDt-DHvi_6E4nhZiR_8ckN1Eq0YjzIrTrmUmD9v_r_w47fQGF-2q1SEfF9cozdxI0nZAg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F6.0.0-patch%2F
 .
 I did this, but continue to get the same error. I'm working with Freesurver
 Version 6.0.0 and MacOS Big Sur Version 11.2.3. I've attached the
 recon-all.log below, but please let me know if you need additional
 information.

 Any insight on this would be appreciated! Thank you!

 Jordan

 --
 *Jordan L. Mullins, B.A.*
 Doctoral Student, Department of Psychology
 University of California, Riverside
 *MailScanner has detected a possible fraud attempt from
 "secure-web.cisco.com" claiming to be* 
 http://secure-web.cisco.com/1fpwAcAdfpPcgXwG26yDXqSP95kASeRHLMrJFeIUyDibUdqUVH2p0VRezzhwnATWC6T9xIybL_yMoJMsNYkzaaVhiVJdvQu1-4tRXyaLHYAOvnAYvGKVrX8cOnPzcAg5idnKgh43DE29cfOdy3c4LUI1r_TID4tgkTklyuy2ABBPRZ2zSpiirU0OI5NjaFLgnMDI_7ogEQ9p2DJ4NhEZz8pjoQRTmM3jYxd9v5Zi-6dvsU6pgZDmP-fTnealh-Gpw3Ga8ejexqF6eJ9hhYpEf2w/http%3A%2F%2Fucrkindlab.com
 


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 Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
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[Freesurfer] Postdoctoral position at Massachusetts General Hospital / Harvard Medical School

[Jacobs, H (NP)]

External Email - Use Caution

Postdoc Position in the Department of Radiology,

Massachusetts General Hospital / Harvard Medical School



The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at 
Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in 
Boston, Massachusetts, has an opening for highly qualified individuals at the 
post-doctoral level to work with Dr. Heidi Jacobs. The Jacobs lab is part of 
the Gordon Center for Medical Imaging at MGH and focused on improving the early 
detection and early treatment of Alzheimer’s disease. The lab focuses on the 
neuromodulatory subcortical nuclei, in particular the locus coeruleus, using a 
variety of approaches, including 7T MRI, PET imaging, pupil measurements, 
physiological recording, blood-based markers and cognitive assessments. This 
postdoc will be involved in a new NIA-funded R01 project using 7T imaging and 
non-invasive stimulation of the vagus nerve to modulate cognitive performance 
and locus coeruleus activity in older individuals at risk for Alzheimer’s 
disease. Our team and this project are closely affiliated with the Harvard 
Aging Brain Study (HABS). The position is available from June 2021. Most of the 
work in this project will be performed at the Athinoula A. Martinos Center for 
Biomedical Imaging, Charlestown Navy Yard. The candidate will be part of 
ongoing collaborations and be able to work in a stimulating and inspiring 
environment.

The Department of Radiology at MGH is equipped with the first mobile PET/CT, 
the first brain PET/MRI, the first whole-body PET/MRI in the USA and several 
MRI scanners, including two 7T ultra-high-field scanner. It is equipped with a 
large-scale shared memory computing facility for parametric image analysis, 
tomographic reconstruction, Monte Carlo simulation, and other computationally 
intensive research applications.

Our research group values open communication, motivation, optimism, mutual 
respect, teamwork, and innovative thinking. Dr. Jacobs is highly committed to 
individualized mentoring to help trainees achieve the most out of their 
postdoctoral candidature and to move forward in their career. At a minimum, the 
training environment will include professional development, one-on-one 
meetings, group lab meetings, frequent seminars and journal clubs, 
opportunities to present their work at national and international scientific 
conferences (i.e. Human Amyloid Imaging, Alzheimer’s Association International 
Conference, OHBM), and manuscript preparation for publication in high impact 
journals. In addition, Dr. Jacobs has a strong funding record and will strongly 
encourage and provide mentorship in grant applications.



Requirements: Candidates should have a Ph.D. in Cognitive Neuroscience, 
Computational Neuroscience, Medical Physics, Computer Science, Biomedical 
Engineering or related disciplines. Strong analytical, quantitative and 
programming skills are essential (e.g., fMRI-physiological data analyses, data 
modeling, simulations). Prior experience in fMRI, non-invasive neurostimulation 
methods and physiological investigation is advantageous.  The candidate should 
be highly motivated, a strong communicator, possess internal drive to learn 
independently, but also be comfortable with working as part of a larger 
collaborative team. A real necessity is a passion for science, strong 
scientific writing and organizational skills, and a positive attitude. 
Experience in Alzheimer’s disease dementia or aging would be beneficial.

MGH & HMS are equal-opportunity, affirmative action employers. Women and 
minority candidates are encouraged to apply.

[cid:image001.png@01D724BE.5F90F2C0]

Apply: The successful candidate will have joint appointments at MGH and HMS. If 
interested, please send your CV, letter describing interests, background, major 
achievements, skills, goals and contact information for three professional 
references. Please send application materials to Dr. Heidi Jacobs, Assistant 
Professor of Radiology, at 
hjac...@mgh.harvard.edu



Postdoc Position.pdf
Description: Postdoc Position.pdf
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