[Freesurfer] Password request for virtual machine installation

2023-07-28 Thread Aaron S. 
External Email - Use Caution

Hello, just looking to get the password so I can unzip the virtual machine
file 'FS_7_2_0_ubuntu_18_04_06.ova.zip' as per the instructions found here:
https://secure-web.cisco.com/1ob4AXDbhbzqTxV6efnVHiFC74uJpjprhjdwl-BnfsqSh5rHA4eLKGZPKYOsRA6pehGDrYTtqDYBkVA-nQlCcHv93h7F8CDpjn2tOijm3xiHfRzYRj4mORvbuwy-m7-jd3RjjgaibYZ5vY_wLg1XNFlmwydxhDePxgE1pKSSybtkmxN6GZz_kDe5wKDY8NlPUizLkux3Avxgsi2Hlu7rlboIi6QYnjKsYc0kHHtAMwHmEpyko-NGWIuaUPrYlkinLkIR2PesmK7596RLkbtTaeNNIbbzW26O_sDNV3UWLfkUlyCHNZAFDCp3cO7aywchp800Zm3INlPyJ2aJLrMe0Uw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67

I recently got an MRI of my brain done and would like to 3D print a model
for personal use.

Thanks for your time!
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[Freesurfer] Passcode for virtual machine

2023-07-28 Thread Noelle Abbott 
External Email - Use Caution

Hello,

Can someone please provide me with the passcode
for FS_7_2_0_Ubuntu_18_04_06.ova.7z ?

Thanks,
Noelle
*~ ~ **~ ~ **~ ~ **~ ~ **~ ~ **~ ~ **~ ~ **~ ~ **~ ~ *
*Noelle Abbott, Ph.D. Candidate*
*SDSU/UCSD Joint Doctoral Program in Language and Communicative Disorders*
*SLP Essentials Instructor*
*Lab Manager, Language and Neuroscience Group, SDSU*


*6505 Alvarado Rd, Ste 204San Diego, California 92120**Phone: 619.594.7878 *
*https://secure-web.cisco.com/1bly9ydSxqTaYKuSFaH35yNknmiJLZ23JS3L_K2hsle1wsRjfr5cl0ucXbfnY0PQcMZ3_-u8MgkAmnYXTSzcwrU0CXJiVY9prBkGWpkRRttX9GExycg8lgeKeF-jKHbiVJQHiy2pPGFUVRBzhcsBVZLoRPiMWm1_vc0UXDEoPERDA12_HptApaJfGKhHhdyG5cXu3fmybMcsVA2jXwLXSaI7qkfyrIQtXPv0_Wwf0zRflSL38RRqQHHMpwf5-pAa87qUb-7fypGcxIaJAmUCHWORP4-5TsldZhR4zLoDk8ZjmWzCL2p3sSpiHQT3YqLwy3prn3MGC0XvxTmin7sMrvA/https%3A%2F%2Fslhs.sdsu.edu%2Flang%2F*
 


*Pronouns: she/her/hers*
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Re: [Freesurfer] PetSurfer, PET data format, mri_convert

2023-07-28 Thread Wighton, Paul 
External Email - Use Caution

Hi Zeyu,

It looks like your files are in 'interfile' format.

If you have access to pmod, you might be able to use that to convert your files 
to nifti.
https://secure-web.cisco.com/1zqVVdVIc7totHjAN-r1V2oHpo0YeUbAKoFLyEzf5hGF_2QpNKUkYjapa61k7l3PSjeARv8qdfQNsmsWgyLM_x7yRo7uvps9iIp9uwO7a2TINpqT1lUcfZcSARBl8Fns-rGgqjVdinmxYTRRJW7qEhjB7TFy_Akeg1X6PozmQwtUClLKAap1CgLy0N6P-i1td6Epv8GJIS-_NewalfMvYf-uyOe7TemfME6k238__pKMda6B1y1hwLdR5PEBewmHUOTI5Z0xkuVuplriFkvuAaw/https%3A%2F%2Fwww.pmod.com%2Ffiles%2Fdownload%2Fv31%2Fdoc%2Fpbas%2F684.htm%23%3A%7E%3Atext%3DInterfile%2520is%2520a%2520file%2520format,version%203.3%2C%20Nucl%20Med%20Commun.

Or you could try using this: 
https://secure-web.cisco.com/1V87W-pEHHar2tKNTfSutV2rBhxv4QVhkEBhm-a5RZ9q6Gz-7E2XdigrjJkwDqcX7klh7tFuRWLL-91eC6kvPzjRRqZhQnS5wwjEH2gT566KrsPTsUSgBpXi1HnBlucbgC5JunCkl-6FVnKsvzu3cCbBMp82g0-NeCBdJM_xFIERvYEYDp6ArkE6kKJ18zQhGHc3KX4095fGBoZgt7_PI5_RP7B5AEA-HCHemz72hJe_7FTpJkw6Giy3l28FBafW09nazM9MZx3-XJ1nWYzDVRA/https%3A%2F%2Fgithub.com%2Frordenlab%2Fi2nii

Good luck!

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zhou, Zeyu 

Sent: Friday, July 28, 2023 10:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] PetSurfer, PET data format, mri_convert

External Email - Use Caution

Hi Freesurfer developers,

I am new to PET and FreeSurfer. I am trying to go through the PetSurfer 
tutorial (MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1WIdRjlXspzVNAAubGnxONoOi-JQqlKFaZgFpmpGW_4cj_NGoWMbZCmxAW1Lx2XUGPrto07cKnoNmWSMabwUBhdizuJ3mimj9Xd_MWpUSafdFT4ojOiEHnwrT0iBPizzRaKXMlYsvKENtDO5ccRa8UEo9gWeMyQ0bNS2k2tUOQgdDchNUPKBRvJq54IaFi4y0eKS3ZSLgf78xNoL7Ng6qOqEMXMWX71tcHgARz3rerCE6795uAmZuqzjgij7h-thEDV9w3pPcJD-2qnuXbJpekQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer).
 In Part 4 "Reg
 ister your PET image with the anatomical", the PET data format in example is 
.nii.gz. However, here are the PET data I have (collected from SIEMENS HRRT 
PET):

309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame1_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame1_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame2_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame2_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame3_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame3_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame4_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame4_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame5_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame5_3D.i.hdr

I tried converting the .i file to (for example) an .nii file by mri_convert but 
got the following error message:

mri_convert 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i 309Fally0.nii
ERROR: cannot determine file type for 
309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i

Then I changed the .i file's extension to .img and the .i.hdr file's extension 
to .hdr and run mri_convert, but still got an error message:

mri_convert 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.img 309Fally0.nii
reading from 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.img...
error: ReadAnalyzeHeader: unsupported data type 17741

I couldn't find anywhere about how to process PET data in .i and .i.hdr files. 
Any suggestions? I attached one .i.hdr file for your reference.


1) FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
2) Platform: macOS Ventura 13.4.1 (c)
3) uname -a: Darwin rad-rsch-pc85 22.5.0 Darwin Kernel Version 22.5.0: Thu Jun  
8 22:22:23 PDT 2023; root:xnu-8796.121.3~7/RELEASE_ARM64_T6020 arm64


Thanks.

Best,
Zeyu Zhou


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[Freesurfer] Postdoc position at MGH / Harvard Medical School: locus coeruleus connectomics of resilience

2023-07-28 Thread Jacobs, Heidi (NP) 
External Email - Use Caution

Postdoc position in locus coeruleus connectomics of resilience

at 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 and Dr. Sepulcre. 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, cognitive 
assessments and non-invasive vagus nerve stimulation. The Sepulcre lab is 
focused on connectomics, brain organization methods and the integration with 
genomics in neurodegenerative diseases. This project is focused on identifying 
locus coeruleus functional network properties conferring resilience against 
Alzheimer’s disease-cognitive decline in the face of pathology and identifying 
network properties indicating risk of Alzheimer’s disease. This project will 
require pulling and harmonizing large imaging datasets together to investigate 
locus coeruleus function across the disease continuum (e.g. ADNI, HABS, A4, 7T 
lifespan dataset,..). The Jacobs Lab consists of a multidisciplinary team of 
one instructor, five postdocs, three PhD-students, three clinical research 
coordinators and one project manager. The Sepulcre lab consists of one 
Assistant Professor, three postdocs and several students.

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 and Dr. Sepulcre are 
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), collaboration with partners within and outside MGH, and 
manuscript preparation for publication in high impact journals. In addition, 
both Dr. Jacobs and Dr. Sepulcre have 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, Neuroimaging, Psychology (Biological) or related 
disciplines. Strong analytical, quantitative and programming skills and 
experience in fMRI are essential. Experience in connectomics or graph theory 
and physiological modeling would be beneficial. 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.

[cid:image001.png@01D9C144.C546D1F0]MGH & HMS are equal-opportunity, 
affirmative action employers. Women and minority candidates are encouraged to 
apply.



[cid:image002.png@01D9C144.C546D1F0]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, Associate Professor of Radiology, at 
hjac...@mgh.harvard.edu








Dr. Heidi Jacobs
Associate Professor of Radiology

Massachusetts General Hospital
Harvard Medical School
Department of Radiology
Gordon Center for Medical Imaging
149 13th Street
Charlestown, MA 02129
hjac...@mgh.harvard.edu
http://secure-web.cisco.com/14oqD7dprcCf49eSlNAiGL3

[Freesurfer] PetSurfer, PET data format, mri_convert

2023-07-28 Thread Zhou, Zeyu 
External Email - Use Caution

Hi Freesurfer developers,

I am new to PET and FreeSurfer. I am trying to go through the PetSurfer 
tutorial 
(https://secure-web.cisco.com/1SgXjbJz8ibehnENjVYIj14hM83pSJC3l0yNLV0Ubo9CVpoRewK5OxES53m1g56UEZ-L0ETzo4Rc8IsDydiXIeeWmtig-JVTf38MrXJgEig7jBCmIH1m-rCOdppmfFR5wfgg1_moJvMlaGmh_k1ETKxXWg2Wacf0cZvhVYuR5DFR1BJXYCAXEtP7FsfLzyU1CzhIPaI_b5kMDFt1eR8x60qTqr2FUBBzv_u8-A5VIvRrR-59G_W4Aac7OxqLCUzVxEYoa18Z0bBEgjXS-hCBj12Hv8QQmoyM5U0sU9HZrh0U40Wqke505AyMtqaJUm9EXuWiDjKfFEkEzXAenqlKtQA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer).
 In Part 4 "Register your PET image with the anatomical", the PET data format 
in example is .nii.gz. However, here are the PET data I have (collected from 
SIEMENS HRRT PET):

309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame1_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame1_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame2_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame2_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame3_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame3_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame4_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame4_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame5_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame5_3D.i.hdr

I tried converting the .i file to (for example) an .nii file by mri_convert but 
got the following error message:

mri_convert 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i 309Fally0.nii
ERROR: cannot determine file type for 
309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i

Then I changed the .i file's extension to .img and the .i.hdr file's extension 
to .hdr and run mri_convert, but still got an error message:

mri_convert 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.img 309Fally0.nii
reading from 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.img...
error: ReadAnalyzeHeader: unsupported data type 17741

I couldn't find anywhere about how to process PET data in .i and .i.hdr files. 
Any suggestions? I attached one .i.hdr file for your reference.


1) FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
2) Platform: macOS Ventura 13.4.1 (c)
3) uname -a: Darwin rad-rsch-pc85 22.5.0 Darwin Kernel Version 22.5.0: Thu Jun  
8 22:22:23 PDT 2023; root:xnu-8796.121.3~7/RELEASE_ARM64_T6020 arm64


Thanks.

Best,
Zeyu Zhou


309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i.hdr
Description: 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i.hdr
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Re: [Freesurfer] Longitudinal Pipeline

2023-07-28 Thread Huang, Yujing 
External Email - Use Caution

Here is the tutorial page for longitudinal pipeline - 
https://secure-web.cisco.com/1DcUJ0a_skONZSHVRpSGkgbTHuJUYN0f05kxjKkGh8ULxXW5lqtpzszfBoN-Xtfji8oIhv9vRccou8zbWsrBEOjLdmo0rTMcvCMZxYlfgwwj9WhTkMxZjPQXRIllql_rFkKSHG62EwrEuQ-E69bA0inHgOQJ7ZBwMv0T0u6l4NK6aCGAw_C5Dz8H3TS_qFlJDhaFv6Z1RzMJDTcBIPCGKbIPF8cz0m_l0mkH528Meg0J0mttU67tqAWOdr3KFVBAtTpqx8axSHsTpQG_Bs18idA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalProcessing

In step 1 (cross),  recon-all -all -s  -i path_to_tpN_dcm
you should have processed each of your time points separately, for example, 
 = tp1, tp2, tp3 (these are the subjectIDs you choose for your 
subject/timepoint).
In step 2 (base), recon-all -base  -tp  -tp  ... -all
1. Choose an unique subjectID as your  (for example, 
base_tp1_tp2_tp3).
2. -tp  ... are the subjectIDs (tp1, tp2, tp3) from your cross process.
In step 3 (long), 'recon-all -long   -all'.
It should output in directory .long..

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Atwater, Emanuel R
Sent: Thursday, July 27, 2023 6:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] (no subject)


External Email - Use Caution
Hello FreeSurfer Team,

I recently messaged about running a longitudinal scan on a couple of images.

The response told me to utilize "timepoints":
For base processing, specify each timepoint with -tp <> (not the nii file).
recon-all -base  -tp  -tp  ... -all

I've attempted to review the youtube videos and instructions made available 
online but am unsure what "timepoints" are. Can I have some clarification on 
what exactly a timepoint is, please.

FS version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b
Recon-all.log: see attached

V/r,
Emanuel Atwater

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The information in this e-mail is intended only for the person to whom it is 
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contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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[Freesurfer] Fw: cortical boundary and center of gravity

2023-07-28 Thread alexandra.ko...@uksh.de 
External Email - Use Caution

Dear Freesurfer expert,

Please receive my email as a kind reminder of my previous one: Can I extract 
the cortical boundary as a spatial series and the center of the mass in the 
grey matter segmented images using the FreeSurfer? Can you please let me know 
how to?

Many thanks in advance,
Dr. -Ing. Alexandra Korda

Forschung & Lehre
Zentrum für Integrative Psychiatrie ZIP gGmbH
Campus Lübeck
Ratzeburger Allee 160 I Haus B7 I 23538 Lübeck
Tel.: +49 451 500-98715
alexandra.ko...@uksh.de I 
http://secure-web.cisco.com/1pjc_SGUWZLRg8chpXIrtY4lF77fMNhpz7khzIO23axlH1vIGy0EYPjLTmc9YQmqqYtzAi5DANHmu56-ULCwVGSQeEGpQJcs5UtZbN0PsYMZSuo9866B14gkhOW2stBLiQg4aqeH73rVFP9m21QQHYafIrF4q-jPfzOxHv48bcRr86Gsth7o6fDvCl7WhcHZcyiFqIXoJrmHfF0t1rlh3NM9D25rlUtEMlbyMj3JfoxDS3mI88qvdZNtEryj3wrHBXtE2tEnCpfA0FbGXGUpL1HCuslrQnn8yYgXQ93HSIlQ6NoNnb5Zp6eS_k8ax2C3fD55ZZiPoPzLmX1jyHg7wtw/http%3A%2F%2Fwww.zip.uksh.de
https://secure-web.cisco.com/15uhZPgBC1AIlkY28uAICPQga2oSml8UpQWNMpilTQ-llrsqEHhfbkwHxPfHFlJUjTV_RUzR6M1HwJOaz88fv-fV2sMxRW3Wt_tIV7PKNOVG3ysLBAjnNepy8od_fPJtK8AxgHx-8kmzSrViMgSlOfFQMv_wQcshGtHbVQb9WQPwlDe47soDUFgWGQ2SKXOBru-dHs3VVBM95TheE7IZgdksibNF3VVdNBnd75v4zRU4Wier85yZe5ucAtOJwWoXpFW8tEz0RgJr36uQJqAGzzuwCMgEVszYME1u78YwHQVyqxKs3LXVSrZZth3cHJ7tNqycV-NWxDwXSMAT75oTv4Q/https%3A%2F%2Ftranslationalpsychiatry.de%2Falexandra-korda%2F

From: Korda, Alexandra
Sent: 25 July 2023 08:36:07
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cortical boundary and center of gravity


Dear Freesurfer expert,


Please receive my email as a kind reminder of my previous one: Can I extract 
the cortical boundary as a spatial series and the center of the mass in the 
grey matter segmented images using the FreeSurfer? Can you please let me know 
how to?


Many thanks in advance,

Dr. -Ing. Alexandra Korda

Forschung & Lehre
Zentrum für Integrative Psychiatrie ZIP gGmbH
Campus Lübeck
Ratzeburger Allee 160 I Haus B7 I 23538 Lübeck
Tel.: +49 451 500-98715
alexandra.ko...@uksh.de I 
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From: Korda, Alexandra
Sent: 21 July 2023 15:53:02
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cortical boundary and center of gravity


I am sorry, I mean the grey matter segmented images. What I wanted to do is to 
measure the complexity of the cortical boundary.

I have run an analysis using VBM in which I used the segmented brain MR images, 
calculate the center of the mass in these images and the cortical boundary (per 
slice, but this is not a problem to use the 3D cortical boundary 
spatial-series). Then, I calculated the distances between the center of the 
mass and the cortical boundary.


Is it possible to replicate this analysis using the FreeSurfer?


Many thanks for the help.


Dr. -Ing. Alexandra Korda

Forschung & Lehre
Zentrum für Integrative Psychiatrie ZIP gGmbH
Campus Lübeck
Ratzeburger Allee 160 I Haus B7 I 23538 Lübeck
Tel.: +49 451 500-98715
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