Re: [Freesurfer] Infant Freesurfer exiting without error

[COLLEEN PLETCHER]

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Thanks so much for the help!

-Colleen

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Wednesday, May 12, 2021 2:16 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error

I included the list of FS labels with their IDs. When you know the 
correspondences, you should be able to use scripts / FS commands to change the 
labels automatically.
Lila

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of COLLEEN PLETCHER 

Sent: Tuesday, May 11, 2021 4:28 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error


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Hello,

Getting a list of the labels would be fantastic! Also, when relabeling the 
segmentations, do you normally just do that by hand?

Thanks so much,

Colleen

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Thursday, May 6, 2021 4:14 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error

Hi Colleen,
The segmentations just need to be relabled in order to match the labels that 
are produced by the infantFS pipeline. I am happy to send you a list of lables 
that get generated by our tool and then you can match those up with the ones 
that you get with FSL.
Best, Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of COLLEEN PLETCHER 

Sent: Tuesday, April 27, 2021 4:11 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error


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Hi,

I was using FSL anat in order to do the initial segmentation for the --segfile 
input. I am not sure how to put FS aseg labels in something that is not a 
freesurfer aseg file. Can you offer any advice on how to do this?

Thanks so much for the help!

-Colleen

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Saturday, April 24, 2021 2:14 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error

Hi Colleen,
Do you have all the FS aseg lables in your input segmentation file?
Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of COLLEEN PLETCHER 

Sent: Friday, April 23, 2021 3:01 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error


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Hi,

Just checking in about this question. Please let me know if you need anything 
else from me!

Thanks,

Colleen

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of COLLEEN PLETCHER 

Sent: Tuesday, April 13, 2021 12:48 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error


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Hello,

I have attached the log file and the command used is the first line, please let 
me know if you need anything else.

-Colleen

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Tuesday, April 13, 2021 12:33 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error

Hi Colleen,

 Can you send the exact command that you used and also the log file for more 
information?

Best, Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of COLLEEN PLETCHER 

Sent: Tuesday, April 13, 2021 1:29 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Infant Freesurfer exiting without error


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Hi,

I am trying to run infant freesurfer using the --segfile and --masked options. 
When I attempt to run it, it runs for a bit and then I get this:


USAGE: mri_or   fname1 fname2 ..



After this, the program exits. I am not getting any error, so I am confused 
about why it is exiting suddenly?


Thank you very much!


-Colleen
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Re: [Freesurfer] how to visualize statistical maps in FS7.1?

[Douglas N. Greve]

your tksurferfv command line is wrong

On 5/12/2021 6:06 AM, Bernardoni, Fabio wrote:
>  External Email - Use Caution
>
> Dear Freesurfers
>
> I recently moved to FS7.1 and I was trying to reproduce my workflow I had 
> with FS5.3.
>
> To visualize statistical maps, I had always used tksurfer. It seems, however, 
> it is no longer maintained.
>
> When I launch it it fails to find out the tix, tcl, etc libraries. Following 
> this thread:
> https://secure-web.cisco.com/1v7sQGKZgCQ9d6BT0fUpIf9QvmP5selhkoGYWs1-X9TSsF6ebf9WkfXQKwNGkJnbQTNihRlUwkt3d_MtgGepc7G9MM_ZkCKisZX1hKBJ9twis_mX1rWvKXW84_u67FO-1Nf-Nw0XV4e4TaksCUTJbLoVykRInrujR5kv4RuP668hB4uZuRSUTzw5Wv0cdJpuX2G2CxoXrNGsfZPGI9wEQy2xuY0fWpzXbjw3A6IN30dlVGcFiz2RxbN4DmxS9mgJACyaWUAW4XrSh_mrEyukmaw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg66219.html
>
> I tried to use tksurferfv.  However, when trying to overlay the sig.mgh 
> output of mriglmfit, on an inflated fsaverage surface, the program shuts 
> down, with this error:
>
> freeview -f 
> /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:curvature=/usr/local/freesurfer/subjects/fsaverage/surf/lh.curv
>  -viewport 3d
> terminate called after throwing an instance of 'int'
> Abort (core dumped)
>
>
>
>
>
> What would you suggest to visualize statistical maps in FS7? Is my problem 
> expected?
>
> Thank you in advance for your attention
>
> Fabio
>
>
> Dr. Fabio Bernardoni
> wiss. Mitarbeiter
>
> Division of Psychological & Social Medicine and Developmental Neurosciences
> http://secure-web.cisco.com/1fJ-kcGEyM5xIf9EYKEBdxq9jOYgp4LWrcrsRqW2VW0t2XhEyJg3GuHzjb7IPAU-FCiyn7epXi34kENaICaL_blhCQ8oexcOBMTiefsG3_aAP0L5sU_H9y1xYVTw6Wh6hIqLbAa4i4vAgC5EkA-lRurbVwk8nsJ2OkIW9GfadFxibvScxITahbmnRCznxGJlPF-53t2LTXrv5ovrctRRUr3HCbs6q1-FfiwpZbapsJCpLgnVMXDIXmR9FalmQ1tAveKdaDRqfq1X5OnoG5ccMFg/http%3A%2F%2Fwww.transdenlab.de%2F;
>  
> http://secure-web.cisco.com/1xug_1JvXuCXLAVwiFYmOgWpcXQT14Ee7lkNin2N9gXlkJe_rVe8WFPk8CrMRmNwa_OuMhrKZXOFFO-FGw4FoQLrEFxfrO0Bmrs52S58GLUHqIsCPDL1IlMhZljPMxwDvqHheBhbH3FY9WwkZleNf0vOcLN7T--LeyLSKHC_sDn8owSIUefCSKVrRFaCMbFr5M04ZXYBHqA2QiHHZt1TpSnAlfoaQMAYejGip5Lnf_rIw4wUFl8P8g9z1Vi1EDDQW72FYV0DvC7gVAebazbP_AQ/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
> +49 (0351) 458-5245
> Universitätsklinikum Carl Gustav Carus
> an der Technischen Universität Dresden
> Anstalt des öffentlichen Rechts des Freistaates Sachsen
> Fetscherstraße 74, 01307 Dresden
> http://secure-web.cisco.com/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EBtyOQOncARekE9xGU6ufm0K3AsWqpT_QNy_QstYzolatBvaWI4t7eMeALTKskxEvWoxokVkLLB4HMJ0YkwdqKEe8ljROpTHIFtyq1qCflRlJTMWaL3-X3wy0Xoc3l8aqALWtblfOLH8ZWHGuYKuFG4ZDS2lawCB8R4FPsst51f44nwNGvWALB0xsX_5W2NQbQ4wnfuAoIXlyw0pV5MKnAhp5Uh9k6uZlMYG5XgZw/http%3A%2F%2Fwww.uniklinikum-dresden.de
>
> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
> Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
> USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
>
> http://secure-web.cisco.com/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EBtyOQOncARekE9xGU6ufm0K3AsWqpT_QNy_QstYzolatBvaWI4t7eMeALTKskxEvWoxokVkLLB4HMJ0YkwdqKEe8ljROpTHIFtyq1qCflRlJTMWaL3-X3wy0Xoc3l8aqALWtblfOLH8ZWHGuYKuFG4ZDS2lawCB8R4FPsst51f44nwNGvWALB0xsX_5W2NQbQ4wnfuAoIXlyw0pV5MKnAhp5Uh9k6uZlMYG5XgZw/http%3A%2F%2Fwww.uniklinikum-dresden.de
> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
> Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
> USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
>
>
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[Freesurfer] Re NEUROIMAGINGPOSITION IN EPILEPSY Available

[Xiaozhen You]

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*NEUROIMAGING POSITION IN EPILEPSY*

*AT CHILDREN’S NATIONAL HOSPITAL AND THE GEORGE WASHINGTON UNIVERSITY*



A position is available starting *Spring/Summer 2021* in the Comprehensive
Pediatric Epilepsy Program at Children’s National Hospital affiliated with
George Washington University in Washington DC (Polerlab.org
).
 This position involves the application of
state-of-the-art functional and structural MRI imaging methods applied in
clinical research. The candidate will apply methods previously developed
but not used in epilepsy as well as develop novel computational imaging
methods. Our aim is to apply sophisticated approaches to answer clinical
questions (e.g, identify seizure focus; develop sensitive MRI metrics of
cognitive reorganization; examine pre- and post-surgical changes
structurally and functionally to build sensitive predictive models).



The candidate will have the opportunity to initiate his/her own research
projects, mine existing data, and collaborate with a multidisciplinary team
including neurologists, neurosurgeon, neuropsychologists, fellows, graduate
students, and undergraduate research assistants.



Candidate qualifications and educational background are flexible and the
position will be tailored accordingly. We prefer a postdoctoral level;
however, will consider an advanced graduate student. An early career
faculty position is an option as well. Appointments are for two years
minimum, renewable upon mutual agreement. Candidates should have graduate
school training in engineering, neuroscience, computational, or other
biological sciences. Experience with computer programming and image
processing is essential. Familiarity with fMRI analysis software including
SPM, FSL, AFNI, and Freesurfer, as well as programming environments such as
MATLAB or Python is highly desirable. Children’s National Hospital is an
equal opportunity employer. Full-time employees receive full benefits,
competitive salaries, and excellent resources for career development.



To apply, please send a letter describing research interests and
experience, curriculum vita, and names and contact information of three
references to William Gaillard, MD at wgail...@childrensnational.org and
Madison Berl, PhD at mb...@childrensnational.org.
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[Freesurfer] Sulcus represented in wm.mgz filled in lh.white

[Dierker, Donna]

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Hi freesurfer experts,

I have some cases where sulci near the occipital pole are reflected in the 
wm.mgz, but are filled in the white surface.
Attached is a capture showing the sulcus near the image center, where the 
crosshairs are located.

Might the topology fixer have filled in this sulcus, to reduce topological 
errors?
This was generated using recon-all -all, freesurfer 6.0, ubuntu 18.04.3.

Thanks,

Donna



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