[Freesurfer] Several faculty jobs at University of Chicago in Aging + Alzheimer's and related dementias

[Adam Martersteck]

External Email - Use Caution

*Apologies for cross-posting*

The University of Chicago's Department of Neurology is recruiting several
faculty members at any rank to join the Healthy Aging & Alzheimer’s
Research Care (HAARC) Center. We welcome candidates with research interests
that align with our mission including topics and methods such as digital
biomarkers, blood-based biomarkers, imaging biomarkers (MRI, PET),
large-dataset curation, social determinants of health, assessment of
cognition, memory, psychosocial wellbeing, functional outcomes,
neuropathologic, nonpharmacologic interventions, and implementation
science.

We are looking for (1) a tenure track faculty (any rank, with or without
tenure), (2) a non-tenure track faculty (any rank), (3) a behavioral
neurologist, and (4) a full professor of neuroimmunology to direct a
program in neuroinflammation.

Clinical neuropsychologists, behavioral neurologists, and cognitive
neuroscientists with an interest in contributing to a collaborative
multidisciplinary research center are encouraged to apply. We especially
welcome applicants from URM groups, which are African American, Latino,
Native American, Pacific Islanders, women, and individuals with
disabilities.

For more information see our website:
https://secure-web.cisco.com/10L7_lboSnfTgH5hrqe1sUZtGSywMbqb47r96NhJAp4tK2nOorN27NkJvDmmqD6on6dFVSd_UQlK9xq0TY-LKv7O0YwxSlCOYNEGg2vmxpRcpVwsp8eqiD7SGPeLZ7FJSrRZkuqTTXt2n13a-wyj53S_XcroxdWBdlPKgL8OqTJ27-EehXUjPQ2nmJ-plWeGk_imYOba3Ne7Kx1ue1PU00q7fmc7Mvl_UukLjfL0prukuobfkh3y5PW7BBhhMz-B0BAn2E1S5Z80D5mkeEu2qw7AUFqreSRcRHAxo4rcFPYm7sbRMMaTy6tPkqYLhJSs0rmM4PIxp4pggOIkLkwRsRg/https%3A%2F%2Fhaarc.center.uchicago.edu%2Femployment-opportunities
Tenure track faculty position: 
https://secure-web.cisco.com/1OeZ6fDc9_LaXQp8riD9fIo6-CzZ7ojZNXgL4wc93ARP8I8-gKxHdKzfAxE4r6NRmD3sKUgzyX48yXMfJ4WoPvcR70lbgbHT2jdMlhXQ0kNdHN56w88mPPRg9PjxVe8oyYwPJu2z8YlI_Y2G3OyWVmdOTVLO0rRh9sts_kgxCAOIJfPrT8tDkNyNzoFfylstNPa-BqNNCGKwbVgsC_DwXz2Z0UtWlvK9gH-H0rNEG8yDfYeYBOn5BJBPLK9VXtTW6a65F88a_M3YpEqSlD1AAMeM2v9xByHsayoTVZ7xQPZ2oZCQHfmNc5XEVhOF0vJCzNuZ2TGWrkaMfHAx19bsu4Q/https%3A%2F%2Fapply.interfolio.com%2F141590
Non-tenure track faculty position: 
http://secure-web.cisco.com/17J6yWYJ2zsoku90RYF2YU_thqO3lxxSRJXfK4HSbPzjCannkCOhzR7s5uZ6jgb2oHJVS2PYIzigvOx0tgGFEA4cDDIp_CPjc5YQxoPlCzuK6n8cCuPg5zjt24Uh6AeBfXe2PDTh-tE228rLVKFd2RkajbY6OBMk7VmTxztfHXMWTWvdq5pOjyHM91Ry9T_YrZil0A4rKMRv-hcxkZObvyYr-BXS9E-Oqo56Y3cvO4vdx6jj19zFodH7yfGPx8K4FxVNhHfGRG-R-Mk1DZRZNUyaj7vPpHxJvegwtoHe6EVKN5FWo_uLbzMcGcgGd1KJ2NpF3zk7lxEz8xHSNm5bPRQ/http%3A%2F%2Fapply.interfolio.com%2F141591
Behavioral neurologist: 
https://secure-web.cisco.com/1ZT7et8OCIVgBMktDPuQAx1nX2C27i0IwlduDjDBH2QFZffVyzLTqfD8x4GShtjcxO9SOXwjgxwDqQ99wjUxwVi1g3iE1kusOGa7RatrX_CSWOyYz4erkYK3s_eyp3SyzAciLD1N1qMIHbTXiiarFkjURr6UCGhBmL17ARIPCGEEhBWyhHrgTfc6f0n2CGb-PvYsSvx-uxgtZcvgWTJC6fVbQtPi6rRnZLWBRE0FAITqacs90PXCplpYpdrMkLR7jeM2N_6oXEBKgpzsdLlvMrWF73MjtAJ18k6i3okMqq1ERRhWEjZ3t_FiMIlqznWQiqYV1RWYn-l3MrK5l1cNZJw/https%3A%2F%2Fapply.interfolio.com%2F119788
Tenured full professor in neuroimmunology, with endowed chair:
https://secure-web.cisco.com/1aGaEvfSfHQUMYR0p_DyIC-4_q2Xse9-YUKKvf1BxySfjoOzdFh0reO4k1DoGB0wcpnrgNlXdYWH7FdbMyxTVK2-BEuUAWnPq8HbY39qxTChBfaUeN2WTE94tfjXYCspSexf3zkFEsQ-ZrFouNqM_e9GXgIq2FWjfUhH_ZS-tqxA58GDpjFCsUn6zjj1OFbVrWipbYErwpGWX8kQYHZhOJsf6pZdsEwahYNqD5f35h43w2SHKTv8A-880LQ3_7dJNTeCQ5d91xie-sXJXvrR1FdfeB-mHCVRIFUtYODq3xnGM6pHEPmDWl__wu7uaR4VS8JgPUxVEFXY1hv3Fb7HKLw/https%3A%2F%2Fapply.interfolio.com%2F140371

-- 

*Adam Martersteck, PhD *
*(he/him)**Assistant Professor of Neurology* | The University of Chicago,
Healthy Aging & Alzheimer's Research Care (HAARC) Center
*Address *| 850 East 58th Street | Chicago, IL 60637
*Phone *| 773-795-1683

*Email *| marterst...@uchicago.edu
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[Freesurfer] Job at University of Chicago, neuroimaging for aging/Alzheimer

[Adam Martersteck]

External Email - Use Caution

*Apologies for cross-posting listservs*

The University of Chicago’s Neurology Department is seeking a data
scientist focused on neuroimaging in aging and Alzheimer’s disease. See the
full job posting here.
<https://secure-web.cisco.com/1yaxNMxhk779aUROY3cicfsnJIUzCUvaeqRL_tkMqoQ7VBuJ0HAYRGzEwlSVIx5Isug3uGgRbcfx2kZcJpH-1uU8PvCXc3DqrmHvyoOP-wAqal6nHxtjPqnOSqpGjEJDshVuImdTvjxpzas7IeRL-ywQ49a1TSGyOCCVSw_YsqClXawXXS3g1te7EBKl7Fy_BA_MZMqHw6HyP4rmJBWLV3HNX8Rqb8I97rkdnu5Tdz4MKHg-oIiYZYTmmEbB0-aVCis71X_ZlD1p_QBS7IT5rC6MdweZRc74-iBW6vA85X2LaxbnfIMv5mHB6Wi_kVsEqZKkleoep93O6UZKB_ZNfYQ/https%3A%2F%2Fuchicago.wd5.myworkdayjobs.com%2Fen-US%2FExternal%2Fjob%2FChicago-IL%2FData-Science--Specialist-in-Neuroimaging_JR22662>

University of Chicago’s new Healthy Aging & Alzheimer’s Research Care
Center is focused on SuperAging, a phenotype of successful aging, and
atypical Alzheimer’s disease and related dementia syndromes. Prior
experience with Alzheimer’s disease or aging is *not* a requirement.

The primary responsibilities of the positions are to use analytical,
statistical, and programming skills to help collect, curate, analyze, and
interpret biomedical data, including neuroimaging and biomarker
derivatives. The candidate will work alongside investigators and clinicians
to develop data-driven solutions and answer scientific questions. See the
full list of responsibilities in the job posting for more information.

Candidates should have some prior experience with neuroimaging software
libraries, and Python and/or R. Experience with high-performance cluster
shell scripting and schedulers, and machine learning libraries are
desirable.

Apply through the portal, but feel free to reach out with questions (
marterst...@uchicago.edu).

*Adam Martersteck, PhD *
*(he/him)**Assistant Professor of Neurology* | The University of Chicago,
Healthy Aging & Alzheimer's Research Care (HAARC) Center
*Address *| 850 East 58th Street | Chicago, IL 60637
*Phone *| 773-795-1683

*Email *| marterst...@uchicago.edu
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Re: [Freesurfer] [EXTERNAL] Re: Longitudinal PET analysis

[Adam Martersteck]

External Email - Use Caution

On other thought: You may want to do Doug's suggestion of calculating the
paired-diff in the longitudinal stream's subject-specific unbiased template
space of each participant instead of doing it all in fsaverage. Then take
the resultant file, the symmetrized percent change, or pc1, etc. from the
subject-specific template space to fsaverage for your group statistics.

On Wed, Sep 21, 2022 at 12:39 PM Gomar, Jesus  wrote:

> External Email - Use Caution
>
> Thank you Doug, I will follow your suggestion.
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas N. Greve
> *Sent:* Wednesday, September 21, 2022 9:58 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [EXTERNAL] Re: [Freesurfer] Longitudinal PET analysis
>
>
>
> *External Email. Do not click links or open attachments unless you trust
> the sender and content. Report suspicious emails using Report Phishing
> button or forward email to ph...@northwell.edu *
>
> You may be able to use one of the paired diff options in mris_preproc. Run
> it with --help. I also put some info on it below. QDEC has been deprecated
>
>
>
> --paired-diff
>
> After concatenating all the inputs together, create a new output file by
> computing paired differences, ie, Input1-Input2, Input3-Input4, etc.
> There must be an even number of inputs. The inputs are "pruned" before
> taking the difference, meaning that values for all inputs are set to 0
> if any individual is 0.
>
> --paired-diff-norm
>
> Same as --paired-diff, but normalizes by average of time points, ie,
> (Input1-Input2)/((Input1+Input2)/2).
>
> --paired-diff-norm1
>
> Same as --paired-diff, but normalizes by time point 1, ie,
> (Input1-Input2)/Input1.
>
> --paired-diff-norm2
>
> Same as --paired-diff, but normalizes by time point 2, ie,
> (Input1-Input2)/Input2.
>
>
> On 9/20/2022 3:31 PM, Gomar, Jesus wrote:
>
> *External Email - Use Caution*
>
> Hello Freesurfer developers,
>
>
>
> I am interested in analyzing PET data following a longitudinal design.
>
> I have co-registered each PET image to the closest MRI in time processed
> through the longitudinal stream.
>
> I have sampled each co-registered PET image time-point onto fsaverage
> surface via the individual's subject surface (mri_vol2surf).
>
> From this point:
>
> 1.   Is it possible to obtain spc (symmetrized percent change) using
> long_mris_slopes for each subject?
>
> 2.   Is there a way to input the sampled surfaces into a qdec file
> for long_mris_slopes command?
>
>
>
> 1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.2.0.
>
> 2) Platform: Ubuntu 18,04.6 LTS
>
> 3) uname -a: Linux ubuntu 5.4.0-122-generic-Ubuntu UTC 2022 x86_64 x86_64
> x86_64 GNU/Linux
>
>
>
>
>
> Thank you!
>
>
>
> Jesus
>
> The information contained in this electronic e-mail transmission and any
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>  
> 

[Freesurfer] Jobs at Northwestern’s Alzheimer’s Disease Center

[Adam Martersteck]

External Email - Use Caution

*Apologies for cross-posting listservs*

Northwestern University’s Mesulam Center for Cognitive Neurology and
Alzheimer’s Disease 
<http://secure-web.cisco.com/1os8bjA2GGuqsqLRdnOyst5hgeqVHhHK23L0gkUDEg90RCl1JBoWzCjup90HBePvvAj5Ii_uFkgYs4BsO-AIpTU-G2usTEBCrtIdpL-LrOywQrJJKaRvR6TLM1R3syjQzEIoQNhiBCg0-JqiVbjVR3du-_-OTglI0-Aibkp-EuxJ4_v69-RMxjk7nfyJt8SEZjmQTpdfVsTqBzbVPNNqcb-8DAH9Z85dKpXqqY0AQ_sOO0frdUjXrKqfr3GUsRLIbPPZJGaRbufXb5DNSa0xwjJ6vJb9mm0U4N_zpicOPzm9am9rwxM9hFVOPes-yvJA8vQq0pzQU6wz2EM2SlAqlmQ/http%3A%2F%2Fbrain.northwestern.edu>
 is seeking a research
data analyst and research study assistant.

Northwestern’s Mesulam Center is 1 of 33 NIA-funded Alzheimer’s Disease
Research Centers, and home to the SuperAging Project and studies of
atypical dementia syndromes. We are located on Chicago’s downtown campus,
nestled between the Magnificent Mile and the city's beautiful lakefront.

Prior experience with Alzheimer's disease is *not a requirement*.

The primary responsibilities of the two positions are to use analytical,
statistical, and programming skills to help collect, curate, analyze, and
interpret biomedical data, including neuroimaging and biomarker
derivatives. Both roles will work alongside PhD investigators to develop
data-driven solutions and answer scientific questions about aging,
Alzheimer’s disease, and related dementia syndromes.

Successful candidates for the two positions will have proportional prior
experience and education:
(1) The research data analyst will have a MS or PhD, and/or several years’
experience in data science, computer science, biomedical engineering, or
neuroscience.
(2) The research study assistant should have a BA or BS and be interested
in learning the fundamentals of neuroimaging, from data collection to
analysis.

Apply online:
For the Research Data Analyst Associate position
<https://secure-web.cisco.com/1PFgc4rrfnmIjp1zwwdmU41IfrJXRNft07y-F8-PLVAyp4IMTDD6jvbH372fKx2cH-_3KNWsA7Br5Y3Oa86dKma-mfqaPlLO5A5DnXgvAD7LRXXXWd9YUQ3Bf8ZfYO0gDk7EDwxfGkPIV3V_iNHCMG2vW3LSaD5YrqRwmJ1ZDP1wBzFKXHyhwmxK2kzLvRMG-g-H73s0z3ABkNaSzeplEL3SYjXfZPw-7zinkt46CF-LjKq4JDdyuYXpPdT7z4QZv5E28yWh9Bcbv_MZowgUCpLN8-bKxyVVzQNHjYleY_V1FTl-Sr1PdPxaxL77_v8_fG1xbKThoKub-Vx_xYifyYQ/https%3A%2F%2Fcareers.northwestern.edu%2Fpsp%2Fhr857prd_er%2FEMPLOYEE%2FHRMS%2Fc%2FHRS_HRAM_FL.HRS_CG_SEARCH_FL.GBL%3FPage%3DHRS_APP_JBPST_FL%26Action%3DU%26FOCUS%3DApplicant%26SiteId%3D1%26JobOpeningId%3D45172%26PostingSeq%3D1>
(MS, PhD, or years of experience)
For the Research Study Assistant position
<https://secure-web.cisco.com/1xJCiZZXB5CJMqC_9HOhbuER7ZRIeV4HGEI0CeGE4ENBmgNegoV0ZFn4VfbxPlqUqmsUxI8ogOIUEmvXs9DH_VtR4RvKQjX049Pq5M4nnAxDRUVe9kIEgxQp8eQX8u7mZyIikFtyNyD8Sgyi4ZglxhWA3ZK-ZsZU_QG6l3pvNgDHuFJ-CMszxCj-zax-6ipebNZ92VyT43ImErbWTJIxPRhIot-1fJrryYHSktz2h9prpzCe3DDQf5-A0QQC2ooKS99djaI3jCCwCuB0Ok_joP2cYtq4-fSTGYaHAEKl6w9s9bq1d31LZhzmfTs9jbKj-8W-QhGeoZSrxI2NA8aE15g/https%3A%2F%2Fcareers.northwestern.edu%2Fpsp%2Fhr857prd_er%2FEMPLOYEE%2FHRMS%2Fc%2FHRS_HRAM_FL.HRS_CG_SEARCH_FL.GBL%3FPage%3DHRS_APP_JBPST_FL%26Action%3DU%26FOCUS%3DApplicant%26SiteId%3D1%26JobOpeningId%3D45255%26PostingSeq%3D1>
(BA, BS, less prior experience)

*Adam Martersteck, PhD*
Assistant Professor
Northwestern University
Feinberg School of Medicine, Department of Radiology
Mesulam Center for Cognitive Neurology and Alzheimer's Disease
300 E. Superior Street, Tarry 8-729, Chicago IL 60611
312-503-5632 (office)  |  amarterst...@northwestern.edu
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Re: [Freesurfer] Advice? Re: Freeview 7.1.1 won't start on Mac: segmentation fault

[Adam Martersteck]

External Email - Use Caution

Hi Sam,

I can tell from your crash report you have a LG HDR 4K, 3840 x 2160
(2160p/4K UHD 1 - Ultra High Definition) plugged in.
You might try unplugging any external monitors and just having your native
laptop display on then starting FreeView and seeing if it works.

I had the same issue; see here:
https://secure-web.cisco.com/1QAQ9qaYk0cRXE_tuE6_6VTlZGnx-wmKlQEPhui0Cjq32oTS_dSjTGlD3YbSR2s8pjQlBQBaN8hPpw_z7qWk_EmhDjAWKngTk92DSUaYOQPyRrJxwc5NL7wvjLUpLp3AfwsyOV7Sc-zKHrd8POYuILI_JX-B6WhP1RKwzv6ygwBPKkIEqZ9teGBuqXwAAw5Q8p5ZEXisP4b-5xu2ap9PK2pukM2s4h55D3xyAa99wiF9P6kZGroIrog7Ue0hLecEc9mkqQrVFnIJgwU42zqwwtOMzyjKGhjoDGroLAFjrzpA_KmoJFkpu255YVZFofHCCXgpMy_wzdg8ODImbcHY-1A/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg70721.html
Still unresolved. Can open FreeView fine without a monitor plugged in but
get a segmentation fault whenever I'm using an external display.

-Adam

On Tue, Mar 1, 2022 at 4:04 PM Sam Buck Johnson 
wrote:

> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I am writing to request technical assistance with freeview. I use
> freesurfer and freeview in my current research, where they are very
> valuable tools. However, upon upgrading my macbook's OS to macOS Monterey,
> Version 12.2.1, I now am unable to open freeview; it quits immediately upon
> starting. The error message indicates a segmentation fault, and in fact my
> error (and the error message) appears to be exactly the same as the one
> encountered by Alex White in this thread:
> https://secure-web.cisco.com/1IXdnFyTKmN2mh6oaF1iVQ3_Ho1Z9szlPmaAOZrSIy7EZwFSGBaRz93qDmsCiQy2Z6Qu1MlfziSSlmz6_q4xH7dp6jWhtuz18sAR4YqlHt-uhVfECWgtUIajup6ToOMrtI21BszCMS3Hm_T5vsdfqldD--V9-BvmSEW30VQWsJgLj43SWhxbHhg9KdLrvQTamGOv2uE-NWdprChzhAyZzDujkMV9BIck4KXxAkJdty3M8iwplk047j56UI0xeeKds_0MEbvRViDuarya-0fuQVEEEBjpkBoJxgsZdlqpgFYb_af8AiWOAL4uJbIFlakyC2-hddR2bv3IQY792SuvOXA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67739.html
>
> I have been in correspondence with Alex, and he mentioned that you were
> able to help him resolve the issue, but that it required you to send him a
> patched version of freeview (or freesurfer?). I have the identical problem
> on freeview 7.1.1 and 7.2.0, but if possible I would prefer to continue
> working with your latest version, 7.2.0.
>
> Please do let me know if further information could help you understand
> this issue better. For the time being, I have copied the error message that
> prints to terminal and the full error report, both below.
>
> Any help/advice is much appreciated.
>
> Sincerely,
>
> Sam Johnson
> Postdoctoral Scholar
> Yeatman Brain and Education Lab, Stanford University GSE
>
> -
>
>
> # terminal error message:
>
> (base) samjohns@DNab40bbcb 7.2.0 % freeview
> /Applications/freesurfer/7.2.0/bin/freeview: line 2:  1968 Segmentation
> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
>
>
> # full crash report
>
> -
> Translated Report (Full Report Below)
> -
>
> Process:   freeview [1673]
> Path:
> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview
> Identifier:com.freesurfer.freeview
> Version:   ???
> Code Type: X86-64 (Translated)
> Parent Process:Exited process [1672]
> Responsible:   Terminal [1587]
> User ID:   502
>
> Date/Time: 2022-03-01 15:12:51.8713 -0800
> OS Version:macOS 12.2.1 (21D62)
> Report Version:12
> Anonymous UUID:DCA45306-7159-2569-6BDE-CF94BEE1E522
>
>
> Time Awake Since Boot: 1200 seconds
>
> System Integrity Protection: enabled
>
> Crashed Thread:0  Dispatch queue: com.apple.main-thread
>
> Exception Type:EXC_BAD_ACCESS (SIGSEGV)
> Exception Codes:   KERN_INVALID_ADDRESS at 0x545845545f67
> Exception Codes:   0x0001, 0x545845545f67
> Exception Note:EXC_CORPSE_NOTIFY
>
> Termination Reason:Namespace SIGNAL, Code 11 Segmentation fault: 11
> Terminating Process:   exc handler [1673]
>
> VM Region Info: 0x545845545f67 is not in any region.  Bytes after previous
> region: 92257060675432  Bytes before following region: 12815019253913
>   REGION TYPESTART - END [ VSIZE] PRT/MAX
> SHRMOD  REGION DETAIL
>   commpage (reserved)10-70   [384.0G] ---/---
> SM=NUL  ...(unallocated)
> --->  GAP OF 0x5f90 BYTES
>   MALLOC_NANO  6000-6800 [128.0M] rw-/rwx
> SM=PRV
>
> Thread 0 Crashed::  Dispatch queue: com.apple.main-thread
> 0   freeview   0x104ec0ff8 0x104ce2000 +
> 1961976
> 1   QtWidgets  0x12046c6ed
> QWidget::event(QEvent*) + 1117
> 2   QtWidgets  0x12057dc45
> QMainWindow::event(QEvent*) + 277
> 3   Qt

Re: [Freesurfer] Dividing surface overlays

[Adam Martersteck]

External Email - Use Caution

Hi Dylan,

Give this a try:
fscalc gm_lh.nii.gz div wm_lh.nii.gz --o gmwmratio_lh.nii.gz

On Wed, Feb 23, 2022 at 12:24 PM Tisdall, Dylan <
mtisd...@pennmedicine.upenn.edu> wrote:

> External Email - Use Caution
>
> Hi all,
>
> I've generated two surface overlays, using mri_vol2surf with positive and
> negative projfrac to get a GM and WM samples (gm_lh.nii.gz and
> wm_lh.nii.gz). I'd now like to take the vertex-wise ratio of these two
> overlays, and make a new one (gmwmratio_lh.nii.gz). I've tried doing this
> as:
>
> fslmaths gm_lh.nii.gz -div wm_lh.nii.gz gmwmratio_lh.nii.gz
>
> but the result is:
>
> Image Exception: #22 :: Failed to read volume gm_lh.nii.gz
> Error : Error: Nonsensical ROI for gm_lh.nii.gz
>
> Is there another tool I can use to compute this ratio? Is there a better
> workflow than making two surfaces and dividing?
>
>
> Thanks,
> Dylan
>
>
>
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>
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Re: [Freesurfer] PETsurfer

[Adam Martersteck]

External Email - Use Caution

PETsurfer wasn't released until the v6.0.0 stable build. You can see it in
the release notes here:
https://secure-web.cisco.com/1n9uot8CDL1X4zb4xQXVdkvdqbv2ngmmjy0xI-YpaJo1tCft8AUJ0fOq2tnIi9H-neObzRYbNnzQ_f-6Te5NpdO_gdoIcUF7wBpGrIgl62EZEaig2VymVFjCNARkni1wUTJ13czIyMTklgwK4iZYXxPXCi62hXdypysMt1AovGhIBjCBbxwxARFiBo7UK4yxCu_DkX3qIclp985He7UPMP41zXb2euSPBiCtR_UvI2e1n30GWDH8BltpJ7syxjN2U7Gvsjo_ROof_krSJUUDh2A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes

I'd suggest downloading the newest release which will have the most updated
code.

You should be able to run PETsurfer from FS builds v6.0, v7.1, v7.2+
(gtmseg, mri_gtmpvc, etc.) on v5.3.0 reconstructions. (Note: it's often
recommended for reproducibility sake to use the same version of FS if you
can spare the compute time).

On Wed, Nov 3, 2021 at 8:07 AM Brusaferri, Ludovica <
lbrusafe...@mgh.harvard.edu> wrote:

> Hi!
>
> Thanks a lot. I have freesurfer 5.3.0 installed. If I type on the terminal
> commands such as tkregister it works , but if I try PETsurfer commands I
> have errors such as "mri_gtmpvc: Command not found”.
> Any idea?
>
> Thank you,
> Ludovica
>
> On Nov 3, 2021, at 10:05, Douglas N. Greve  wrote:
>
> There is nothing special you have to do. What version of FS do you have?
> You still have to source the FS environment. If you can run recon-all, you
> should be able to run PETsurfer
>
> On 11/1/2021 12:26 PM, Brusaferri, Ludovica wrote:
>
> Hi!
>
> I have been using freesurfer regularly and I am now trying to implement a
> few commands from PETsurfer
> https://secure-web.cisco.com/1BqgJn5GtD8lBmMhFIdkypD8JUZh4G9z6XnAbXLEtWVfk5ajdnK2tMbsx-SPWVIKjr-pvrXHZkfmuy822Z5VxuFrJPxx1uk4mN5QrGBjkWDzSIIb2mqQM8GVyIgapEgf8nTKrJooRayERS_AT_qr18crszq0A-mVtb3-oyYRRpGnUWMHEYJ0c9HDY4jv0xzEi3hUz7v4hsPpfk4MreO51RBUg69F_vA1eLD3NJOnCWDMFQBWsa9ugagsp6DyfQmNDEP2oIcThnq9fsmkqvQt6zw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer.
> It seems like I cannot use any of the commands listed in the wiki (such as
> gtmseg or mri_coreg), although they should be part of the freesurfer
> package (as PETsurfer is part of freesurfer). Do I need to follow a
> specific pipeline to install the PETsurfer extension? If so, could you
> please guide me through?
> Thanks so much in advance!
>
> Kindly,
> Ludovica
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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>
>
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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> The information in this e-mail is intended only for the person to whom it
> is addressed. If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
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Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly

[Adam Martersteck]

External Email - Use Caution

Sure thing. I'm not sure if my last email was sent as it contained images >
listserv allowable size, so I've reposted it here, hosting the images on
imgur.

I've tested it on 4 monitors, all at 2560x1440p native resolutions. An ASUS
PB278, an ASUS ROG PG278Q, a GIGABYTE M27Q, an an ACER XV272U. Here are the
mac display preferences testing each individually:
https://secure-web.cisco.com/16lOiIxQERu3wh-MTKeMFlvUWq-wGbKK7Og-Z9-0MVKa9UwQCDVwTeKHc--TAn3cWFYyiV0PM33EbLnEjkBbhEdDxMb-JK6jmF62tTKgJLS4hJ3jdW2ps1Z1ZELCuT6fZr1DRFkwT-mI0q8R4SXUsRLvuzHU0fKhjdzvDgn227HnFa91fa9_yMIZmz_J7anB5tmP90ta9lKOrJBZz2xIGjPgxfPy574gtgwt2Gid4KxuMg0j458uUjEsJbzYpOfUfoUBzgMg16HqEla_8yEh0PA/https%3A%2F%2Fimgur.com%2Fa%2FAcryUsH

I tested with and without "Default for display" and "Scaled". Each time the
monitor was set to "Default for display" or scaled to 2560x1440p or scaled
to any resolution > 1600x900, FreeView seg faults at:
"
loaded library
"/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqwebp.dylib"
/Applications/freesurfer/7.2.0/bin/freeview: line 2: $NUMBER Segmentation
fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
"

Not that I think it would make a difference, but for completeness, I also
tested jittering the refresh rate between 30 and 144Hz, and tested with a
USB-C-to-USB-C, displayport-to-USB-C, and HDMI-to-USB-C. Neither the
adapter nor the refresh rate made a difference in behavior.

On Mon, Aug 2, 2021 at 3:08 PM fsbuild  wrote:

> Thanks Adam for pointing out different behavior at different screen
> resolutions.   I would be interested to know if those resolutions are not
> the native resolution of the external monitor.  The manual/info for any
> monitor should state what it’s native resolution is, e.g., for a 4K monitor
> native resolution is  3840 X 2160.   If you don’t have the displays
> mirrored, I think when you select System Preferences -> Displays a window
> will appear on each monitor.  Under the Display tab try checking the box
> "default for display" for any external monitor and not the "scale" option
> for the hardware to scale the image up/down in size.
>
> - R.
>
> On Aug 2, 2021, at 16:08, Adam Martersteck  wrote:
>
> External Email - Use Caution
>
> I started getting segfaults again but I was able to diagnose what was
> different.
>
> It turns out it was *not the license file for me*. I registered a new
> license file this morning --> it worked on my Mac and I assumed it was the
> new license; I went into the office --> plugged my MacBook into my external
> monitor --> segfaults.
>
> Having a display with resolution > 1600x900 caused segfaults. At both
> 2048x1152 or 2560x1440, I am able to 100% replicate segfault error.
> FreeView does not launch.
> When I downsample the monitor to 1600x900 or 720p or unplug the monitor, I
> can open FreeView without error.
>
> Hope this helps other people out there.
>
> My graphics card on the 13" MacBook Pro is the Intel Iris Plus Graphics
> (1536 MB) from the Quad-Core Intel i5.
>
> On Mon, Aug 2, 2021 at 10:28 AM Adam Martersteck 
> wrote:
>
>> I should add: I've used this license file for several years wtih FS
>> v.5.1, v5.3, v6, v7+ and developer versions. It runs FreeSurfer perfectly
>> on two MacOS computers and on a RedHat Linux cluster where it has run
>> thousands of recons + additional processing.
>>
>> The license file continued to work -- I could run FreeSurfer commands
>> with it and it never reported a missing or unreadable license file.
>>
>> So if you are getting segfaults and you think you have a good license --
>> try requesting a new one just in case.
>>
>> On Mon, Aug 2, 2021 at 10:10 AM Adam Martersteck 
>> wrote:
>>
>>> Confirm, just requesting a new license file fixed my FreeView MacOS 11.4
>>> segfault errors.
>>>
>>> Requesting a new license file with my same credentials produced an
>>> identical text file (same email, same license #, same two strings of random
>>> letter/digit/symbols).
>>>
>>> *I didn't even need to download the new license file* (as the identical
>>> one was already present) or move it into the /Applications/freesurfer/7.2.0
>>> directory -- FreeView just began to work perfectly fine with my previously
>>> present license.
>>>
>>> This fixed my unusable FreeView in /Applications/freesurfer/7..1.1/
>>> also. Same license file was present there, never needed to download the
>>> newly requested one. Just the *act of requesting a new license file
>>>

Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly

[Adam Martersteck]

External Email - Use Caution

I started getting segfaults again but I was able to diagnose what was
different.

It turns out it was *not the license file for me*. I registered a new
license file this morning --> it worked on my Mac and I assumed it was the
new license; I went into the office --> plugged my MacBook into my external
monitor --> segfaults.

Having a display with resolution > 1600x900 caused segfaults. At both
2048x1152 or 2560x1440, I am able to 100% replicate segfault error.
FreeView does not launch.
When I downsample the monitor to 1600x900 or 720p or unplug the monitor, I
can open FreeView without error.

Hope this helps other people out there.

My graphics card on the 13" MacBook Pro is the Intel Iris Plus Graphics
(1536 MB) from the Quad-Core Intel i5.

On Mon, Aug 2, 2021 at 10:28 AM Adam Martersteck  wrote:

> I should add: I've used this license file for several years wtih FS v.5.1,
> v5.3, v6, v7+ and developer versions. It runs FreeSurfer perfectly on two
> MacOS computers and on a RedHat Linux cluster where it has run thousands of
> recons + additional processing.
>
> The license file continued to work -- I could run FreeSurfer commands
> with it and it never reported a missing or unreadable license file.
>
> So if you are getting segfaults and you think you have a good license --
> try requesting a new one just in case.
>
> On Mon, Aug 2, 2021 at 10:10 AM Adam Martersteck 
> wrote:
>
>> Confirm, just requesting a new license file fixed my FreeView MacOS 11.4
>> segfault errors.
>>
>> Requesting a new license file with my same credentials produced an
>> identical text file (same email, same license #, same two strings of random
>> letter/digit/symbols).
>>
>> *I didn't even need to download the new license file* (as the identical
>> one was already present) or move it into the /Applications/freesurfer/7.2.0
>> directory -- FreeView just began to work perfectly fine with my previously
>> present license.
>>
>> This fixed my unusable FreeView in /Applications/freesurfer/7.1.1/ also.
>> Same license file was present there, never needed to download the newly
>> requested one. Just the *act of requesting a new license file fixed it*.
>>
>> Strange, right? Doesn't sound like a Mac OS permission problem, sounds
>> like an issue with my license registration?
>>
>>
>> On Mon, Aug 2, 2021 at 4:41 AM fsbuild  wrote:
>>
>>> External Email - Use Caution
>>>
>>> After some feedback and some more testing, I can reproduce that
>>> freeview.app in the 7.2.0 release will segfault on MacOS 11.4 if the
>>> license file cannot be found or it cannot be read.  One user reported that
>>> he had to get a new license file in order for it to work.  The link for
>>> that is here,  
>>> https://secure-web.cisco.com/1JT3c7LfejGgdeFtwp5oXVewAdlgS-PXun8Ll2vrvO3YVB4MLUBp6y5E6-moEJz-n3__ZoHW9nv47Vz-rEnv3yCVZWjr06kLa-8j0W6M3By99rzKoyk0Z3mKWDuyucyiBcvV-UP4u4Iq9OoGR7kWUwvOKoY69EADHqSBQ2FIFoYRD--obaSUHHWuG9W-CmGbbInwqbrdVlIq1puTTtffxc-jSWIALoj2Lars9kYDqMEsHjFZcbYyYih8n6FF9WveXFQi_Zs9tYevF5KSNiYFm2g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
>>>
>>> - R..
>>>
>>> On Jul 29, 2021, at 14:34, Adam Martersteck  wrote:
>>>
>>> External Email - Use Caution
>>>
>>> Here's a log from a completely clean install of FreeSurfer 7.2.0.
>>>
>>> On an Intel processor MacBook Pro, running macOS Big Sur (11.4).
>>>
>>> __Starting with a completely clean install of FreeSurfer 7.2.0__
>>> Copied license file over from 7.1.1.
>>> (Confirmed license file works by running mri_convert)
>>>
>>> MacBook-Pro:freesurfer adam$ freeview
>>> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38945 Segmentation
>>> fault: 11  $FREESURFER_HOME/Freeview..app/Contents/MacOS/freeview "$@"
>>> MacBook-Pro:freesurfer adam$ freeview
>>> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38951 Segmentation
>>> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
>>> MacBook-Pro:freesurfer adam$ freeview
>>> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38954 Segmentation
>>> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
>>> MacBook-Pro:freesurfer adam$ freeview
>>> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38974 Segmentation
>>> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
>>> MacBook-Pro:freesurfer adam$ freeview
>>> /Applications/freesurfer/7.2.0

Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly

[Adam Martersteck]

External Email - Use Caution

I should add: I've used this license file for several years wtih FS v.5.1,
v5.3, v6, v7+ and developer versions. It runs FreeSurfer perfectly on two
MacOS computers and on a RedHat Linux cluster where it has run thousands of
recons + additional processing.

The license file continued to work -- I could run FreeSurfer commands
with it and it never reported a missing or unreadable license file.

So if you are getting segfaults and you think you have a good license --
try requesting a new one just in case.

On Mon, Aug 2, 2021 at 10:10 AM Adam Martersteck  wrote:

> Confirm, just requesting a new license file fixed my FreeView MacOS 11.4
> segfault errors.
>
> Requesting a new license file with my same credentials produced an
> identical text file (same email, same license #, same two strings of random
> letter/digit/symbols).
>
> *I didn't even need to download the new license file* (as the identical
> one was already present) or move it into the /Applications/freesurfer/7.2.0
> directory -- FreeView just began to work perfectly fine with my previously
> present license.
>
> This fixed my unusable FreeView in /Applications/freesurfer/7.1.1/ also.
> Same license file was present there, never needed to download the newly
> requested one. Just the *act of requesting a new license file fixed it*.
>
> Strange, right? Doesn't sound like a Mac OS permission problem, sounds
> like an issue with my license registration?
>
>
> On Mon, Aug 2, 2021 at 4:41 AM fsbuild  wrote:
>
>> External Email - Use Caution
>>
>> After some feedback and some more testing, I can reproduce that
>> freeview.app in the 7.2.0 release will segfault on MacOS 11.4 if the
>> license file cannot be found or it cannot be read.  One user reported that
>> he had to get a new license file in order for it to work.  The link for
>> that is here,  
>> https://secure-web.cisco.com/1ET788Mna2WVAEWKpm4YiU1xXU3qn8bJGFhxXkO9s6jJXdtKLbhrUhl8OTrwNFjiqhXcjsJb86Yz-6R-DTgfHSEAzWDL0QgznDOjerB7-xv-KJYP9ECT_vGza0i7LICmv8c0YsLHQn7E8y2Bl3u8WH2t_ntW9Bbu7Zowx9ubjV4nrif-rv2oBgs3t4dO1En3qw4YxfrHuldvBQUvKX32TAyKrafsDcqI42e4hmx1fb3P-FTEwsLgeSqUyPcDTSVwcYI51XgdwgrICJqOfSNQtzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
>>
>> - R..
>>
>> On Jul 29, 2021, at 14:34, Adam Martersteck  wrote:
>>
>> External Email - Use Caution
>>
>> Here's a log from a completely clean install of FreeSurfer 7.2.0.
>>
>> On an Intel processor MacBook Pro, running macOS Big Sur (11.4).
>>
>> __Starting with a completely clean install of FreeSurfer 7.2.0__
>> Copied license file over from 7.1.1.
>> (Confirmed license file works by running mri_convert)
>>
>> MacBook-Pro:freesurfer adam$ freeview
>> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38945 Segmentation
>> fault: 11  $FREESURFER_HOME/Freeview..app/Contents/MacOS/freeview "$@"
>> MacBook-Pro:freesurfer adam$ freeview
>> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38951 Segmentation
>> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
>> MacBook-Pro:freesurfer adam$ freeview
>> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38954 Segmentation
>> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
>> MacBook-Pro:freesurfer adam$ freeview
>> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38974 Segmentation
>> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
>> MacBook-Pro:freesurfer adam$ freeview
>> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38977 Segmentation
>> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
>>
>> (Line numbers that it faults at are linearly increasing?)
>>
>> With export QT_DEBUG_PLUGINS=1
>>
>> I have attached the output log from "freeview
>> > freeview_QT_DEBUG_log.txt".
>> The tail of it is:
>> "
>> loaded library
>> "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqtiff.dylib"
>> loaded library
>> "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqwbmp.dylib"
>> loaded library
>> "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqwebp.dylib"
>> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 39147 Segmentation
>> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
>> "
>>
>> It perfectly replicates in FreeSurfer 7.1.1. Same error, same debug log.
>>
>> -Adam
>>
&

Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly

[Adam Martersteck]

External Email - Use Caution

Confirm, just requesting a new license file fixed my FreeView MacOS 11.4
segfault errors.

Requesting a new license file with my same credentials produced an
identical text file (same email, same license #, same two strings of random
letter/digit/symbols).

*I didn't even need to download the new license file* (as the identical one
was already present) or move it into the /Applications/freesurfer/7.2.0
directory -- FreeView just began to work perfectly fine with my previously
present license.

This fixed my unusable FreeView in /Applications/freesurfer/7.1.1/ also.
Same license file was present there, never needed to download the newly
requested one. Just the *act of requesting a new license file fixed it*.

Strange, right? Doesn't sound like a Mac OS permission problem, sounds like
an issue with my license registration?


On Mon, Aug 2, 2021 at 4:41 AM fsbuild  wrote:

> External Email - Use Caution
>
> After some feedback and some more testing, I can reproduce that
> freeview.app in the 7.2.0 release will segfault on MacOS 11.4 if the
> license file cannot be found or it cannot be read.  One user reported that
> he had to get a new license file in order for it to work.  The link for
> that is here,  
> https://secure-web.cisco.com/102goTLYZghbG1one7hITbEMVONyU-O0jWQPIskDdkuDmhaxukoGaD5jlQDVIL4CtgvPnUVDXBXw9XKnoFnMInD9ikZqA2brbFYnISp85z7Hc9trSiRbOP4QaFGptReMLpFauRZaqFaFbqFoDVkvD1kx1BZxSteV2e5Q6jrFPf-YEcIImmcloqwIqP8Lh2lnSy5aLFUp8K9mERr6dYmb0OhnvW_rEkD7__biFcC5PAxgQXOLA-8GdeO0SES2PBZDvT6wg4_mvqRFFPHORULo23A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
>
> - R..
>
> On Jul 29, 2021, at 14:34, Adam Martersteck  wrote:
>
> External Email - Use Caution
>
> Here's a log from a completely clean install of FreeSurfer 7.2.0.
>
> On an Intel processor MacBook Pro, running macOS Big Sur (11.4).
>
> __Starting with a completely clean install of FreeSurfer 7.2.0__
> Copied license file over from 7.1.1.
> (Confirmed license file works by running mri_convert)
>
> MacBook-Pro:freesurfer adam$ freeview
> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38945 Segmentation
> fault: 11  $FREESURFER_HOME/Freeview..app/Contents/MacOS/freeview "$@"
> MacBook-Pro:freesurfer adam$ freeview
> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38951 Segmentation
> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
> MacBook-Pro:freesurfer adam$ freeview
> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38954 Segmentation
> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
> MacBook-Pro:freesurfer adam$ freeview
> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38974 Segmentation
> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
> MacBook-Pro:freesurfer adam$ freeview
> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38977 Segmentation
> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
>
> (Line numbers that it faults at are linearly increasing?)
>
> With export QT_DEBUG_PLUGINS=1
>
> I have attached the output log from "freeview > freeview_QT_DEBUG_log.txt".
> The tail of it is:
> "
> loaded library
> "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqtiff.dylib"
> loaded library
> "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqwbmp.dylib"
> loaded library
> "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqwebp.dylib"
> /Applications/freesurfer/7.2.0/bin/freeview: line 2: 39147 Segmentation
> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
> "
>
> It perfectly replicates in FreeSurfer 7.1.1. Same error, same debug log.
>
> -Adam
>
> On Wed, Jul 28, 2021 at 8:53 PM fsbuild  wrote:
>
>> External Email - Use Caution
>>
>>
>> If you have not already done so, see if you get a different result by
>> double clicking on the Freeview.app icon under
>> /Applications/freesurfer/7.2.0 with the mouse.
>>
>> You can try this variation on what's been previously suggested.
>>
>> 1) run a bash shell
>> $ bash
>>
>> 2) setup freesurfer environment
>> $ export FREESURFER_HOME=/Applications/freesurfer/7.2.0
>> $ source $FREESURFER_HOME/SetUpFreeSurfer.sh
>>
>>  freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME   /Applications/freesurfer/7.2..0
>> FSFAST_HOME   /Applications/freesurfer/7.2.0/fsfast
>> FSF_OUTPUT_FORMAT nii

Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly

[Adam Martersteck]

External Email - Use Caution

Here's a log from a completely clean install of FreeSurfer 7.2.0.

On an Intel processor MacBook Pro, running macOS Big Sur (11.4).

__Starting with a completely clean install of FreeSurfer 7.2.0__
Copied license file over from 7.1.1.
(Confirmed license file works by running mri_convert)

MacBook-Pro:freesurfer adam$ freeview
/Applications/freesurfer/7.2.0/bin/freeview: line 2: 38945 Segmentation
fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
MacBook-Pro:freesurfer adam$ freeview
/Applications/freesurfer/7.2.0/bin/freeview: line 2: 38951 Segmentation
fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
MacBook-Pro:freesurfer adam$ freeview
/Applications/freesurfer/7.2.0/bin/freeview: line 2: 38954 Segmentation
fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
MacBook-Pro:freesurfer adam$ freeview
/Applications/freesurfer/7.2.0/bin/freeview: line 2: 38974 Segmentation
fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
MacBook-Pro:freesurfer adam$ freeview
/Applications/freesurfer/7.2.0/bin/freeview: line 2: 38977 Segmentation
fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"

(Line numbers that it faults at are linearly increasing?)

With export QT_DEBUG_PLUGINS=1

I have attached the output log from "freeview > freeview_QT_DEBUG_log.txt".
The tail of it is:
"
loaded library
"/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqtiff.dylib"
loaded library
"/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqwbmp.dylib"
loaded library
"/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqwebp.dylib"
/Applications/freesurfer/7.2.0/bin/freeview: line 2: 39147 Segmentation
fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
"

It perfectly replicates in FreeSurfer 7.1.1. Same error, same debug log.

-Adam

On Wed, Jul 28, 2021 at 8:53 PM fsbuild  wrote:

> External Email - Use Caution
>
>
> If you have not already done so, see if you get a different result by
> double clicking on the Freeview.app icon under
> /Applications/freesurfer/7.2.0 with the mouse.
>
> You can try this variation on what's been previously suggested.
>
> 1) run a bash shell
> $ bash
>
> 2) setup freesurfer environment
> $ export FREESURFER_HOME=/Applications/freesurfer/7.2.0
> $ source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
>  freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer/7.2.0
> FSFAST_HOME   /Applications/freesurfer/7.2.0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/7.2.0/subjects
> MNI_DIR   /Applications/freesurfer/7.2.0/mni
>
> 3) Locate your license file (I name mine license.txt) in your home
> directory and check you can read its contents,
> $ export FS_LICENSE=$HOME/license.txt
> $ cat $FS_LICENSE
> ... check the output ...
> ... first line should contain email address ...
> ... followed by 3 more lines ...
>
> 4) set environment variable for debug
> $ export QT_DEBUG_PLUGINS=1
>
> 5) run freeview with no arguments
> $ which freeview
> /Applications/freesurfer/7.2.0/bin/freeview
> $ freeview
>
> ... an empty freeview window should appear and persist on the screen ...
>
> At this point the last few lines of output in the terminal window should
> now be:
>
> Got keys from plugin meta data ("svg", "svgz", "svg.gz")
> QFactoryLoader::QFactoryLoader() checking directory path
> "/Applications/freesurfer/7.2.0/Freeview.app/Contents/MacOS/iconengines" ...
> QFactoryLoader::QFactoryLoader() checking directory path
> "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/accessible"
> ...
> QFactoryLoader::QFactoryLoader() checking directory path
> "/Applications/freesurfer/7.2.0/Freeview.app/Contents/MacOS/accessible" ...
>
> 6) Use the freeview application "File" pull down menu to select "load
> volume".  In the window that comes up, click on the yellow folder icon to
> the r.h.s of the folder/file entry box under "Select Volume File".  In the
> Finder window that comes up, navigate to
> /Applications/freesurfer/7.2.0/subjects/bert/mri and select the brain.mgz
> file..  Click on OPEN. That path/filename will appear in the load volume
> text entry box.  Don't check/change any of the options for loading the
> volume and click OK.
>
> The steps above worked for me to load that volume using an Intel MacPro
> laptop with the 7.2.0 release running under either MacOS 10.15.7 (Catlaina)
> or MacOS 11.4 (Big Sur) w/o freeview exiting or producing any further
> output in the terminal window.  If it fails on your machine, you could send
> along the Qt debug output after the lines listed above.  Please do not send
> the output from cat'ing your license file though.
>
> - R.
>
> On Jul 28, 2021, at 14:53, fsbuild  wrote:
>
> External

[Freesurfer] 2 surface mri_glmfit as independent variables

[Adam Martersteck]

External Email - Use Caution

Hi FreeSurfer team,

I have a question about running mri_glmfit with 2 different surface
modalities as the independent variable and a single value per participant
as the dependent variable. I'm trying to examine the unique and shared
contribution of the 2 surfaces to predict a cognitive measure.
E.g. Cognition ~ ?h.thickness + ?h.PET

I tried mri_glmfit with the "--table" option, giving it a column of scores
per participant (in the aseg2stats table format), and then using "--pvr
lh.thickness-stack.fsaverage.mgh" and a second "--pvr
lh.PET-stack.fsaverage.mgh", using contrasts matrices as [0 0 1], [0 1 0],
and [0 1 1].

*When I run mri_glmfit it returns:*
ERROR: mri_reshape: number of elements cannot change
  nv1 = 163842, nv1 = 1

It continues to run, but all surface maps are full of zeroes. Any
suggestions? Is there a better way to do this?

Thanks,
Adam
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Re: [Freesurfer] fsaverage label into functional space

[Adam Martersteck]

External Email - Use Caution

To confirm, your label is starting on the fsaverage surface. You can open
tksurfer fsaverage ?h pial and open the label and it shows up?

From my experience using fcseed-sess & fcseed-config using FS v6.0.0 what
you want to do is move the label from fsaverage -> subject native surface
-> subject native T1 volume and it will take care of the rest

So you would run:
label=your_label (without the .label at the end)
subject=your_new_subject
hemi=lh (or rh)

mri_label2label --srclabel $SUBJECTS_DIR/fsaverage/label/$label.label
--trglabel $SUBJECTS_DIR/$subject/label/$label.label --trgsubject $subject
--srcsubject fsaverage --hemi $hemi --srchemi $hemi --trghemi $hemi
--regmethod surface
mri_label2vol --label $SUBJECTS_DIR/$subject/label/$label.label --temp
$SUBEJCTS_DIR/$subject/mri/brainmask.mgz --fill-ribbon --subject $subject
--hemi $hemi --regheader $SUBJECTS_DIR/$subject/mri/brainmask.mgz --o
$SUBJECTS_DIR/$subject/mri/$label.mgz

The new file is what you would input as the "-seg $label.mgz" in the
fcseed-config command

On a related note -- in my tests of -proj-frac vs. -fill-ribbon == if you
want the full ROI from edge of the white surface to the pial surface you
should use -fill-ribbon -- see attached screenshot

[image: projfrac_vs_fill-ribbon.png]

On Thu, Oct 10, 2019 at 12:03 PM Lauri Tuominen  wrote:

> External Email - Use Caution
>
> Dear FreeSurfers!
>
> I would like to confirm something before I proceed with my analyses. I
> think I am just confused again.
>
> I am doing resting state analysis using fsfast. I am trying to use a label
> defined in the fsaverage space as a seed using the fcseed-config &
> fcseed-sess commands. Now these commands say that the label should be in
> fuctional space, which I gather is the space of the f.nii.
>
> So in order to move the label into functional space I say:
>
> mri_label2vol --subject fsaverage --label lh.mylabel.in-fsaverage.label
> --o lh.mylabel.individualized.in-functional.mgz --proj frac 0 1 0.01
> --hemi lh --temp ${projectdir}/${sessionj}/rest/001/f.nii --fill-ribbon
> --reg ${projectdir}/${session}/rest/register.dof6.lta
>
> To my surprise, the voxel size here corresponds to the anatomical
> (orig.mgz) but not the functional space (f.nii). To test this further I
> did:
>
> mri_label2vol --subject fsaverage --label lh.mylabel.in-fsaverage.label
> --o lh.mylabel.individualized.in-functional.mgz --proj frac 0 1 0.01
> --hemi lh --temp $SUBJECTS_DIR/$/${sessionj}/mri/orig.mgz --fill-ribbon
> --reg ${projectdir}/${session}/rest/register.dof6.lta
>
> And I get exactly the same ROI in the volume.
>
> So just to confirm, is this what I want for the fcseed -commands?
>
> Thank you so much again!
>
> Lauri Tuominen
>
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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[Freesurfer] Accessing the FS mail archive online

[Adam Martersteck]

External Email - Use Caution

Hi Freesurfer team,

Just in case this hasn't been brought to your attention -- it looks like
the online mail archive requires a martinos center login. Accessing links
to past questions and answers via google or just
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/ prompts for a
login.

I can replicate this on multiple computers, phones, on and off different
VPNs.

It's been happening for the last week or two.

-Adam
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[Freesurfer] Advantage of having skull for longitudinal processing?

[Adam Martersteck]

External Email - Use Caution

Hi Freesurfer team,

I'm thinking of pre-skullstrip'ing my brains prior to being input into
FreeSurfer.

My fear was this information in the skull might be useful during
mri_robust_register or mri_robust_template for longitudinal analyses:

Martin discusses this in his Freesurfer workshop talk at 9 minutes in
(youtube: http://www.youtube.com/watch?v=vxJODPBLd3M&t=9m21s) where the
heatmap covers parts of the skull and the Freesurfer wiki which mentions
that the Tukey biweight will deweight regions of noise like tongue/eye/neck
differences.

But it appears the longitudinal stream registers everything on each
cross-sectional's norm.mgz to create the fused norm -- which is
skullstripped and missing neck/tongue/eyes/skull already.

Am I missing something? Is it alright if my T1.mgz, rawavg.mgz, orig.mgz,
etc. do not have a skull for longitudinal processing?

Thanks,
Adam
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[Freesurfer] Postdoc or Research Associate/Scientist at Northwestern in Chicago

[Adam Martersteck]

External Email - Use Caution

*Apologies for cross-posting*

Northwestern University’s Mesulam Center for Cognitive Neurology and
Alzheimer’s Disease Imaging Core is seeking a research associate or
postdoctoral fellow.

Prior experience with Alzheimer's disease is *not a requirement*.

The primary responsibility of this position is to develop and automate the
preprocessing and analysis of large-scale neuroimaging datasets involving
PET and MR imaging. This will involve implementing state of the art
methodologies, including signal processing and statistical learning, on a
high performance computing cluster. The individual may participate in
publications and presentations resulting from the work.

This individual will work with Emily Rogalski (Imaging Core Leader) and her
collaborators Todd Parrish (director of the Center for Translation Imaging)
and Lei Wang (director of the Applied Computational Anatomy Lab) at
Northwestern University’s Feinberg School of Medicine. The Mesulam Center
is located on the downtown campus, nestled between the Magnificent Mile and
the city's beautiful lakefront.

Successful candidates will have a Ph.D. or M.S. in computer
science/engineering, biomedical engineering, neuroscience, or a related
field. A successful applicant will be proficient in programming (Python or
related language); be familiar with scientific-computing such as NumPy,
SciPy, and Pandas and neuroimaging libraries such as FreeSurfer, FSL, AFNI,
SPM; have the ability to work effectively in a multidisciplinary
collaborative environment.

Experience with a single imaging modality (sMRI, DTI, rsfMRI and/or PET) is
required with a particular emphasis on multimodal approaches.

Interested applicants should send a CV and cover letter stating experience
and interests, two or three peer-reviewed publications, and at least two
letters of recommendation to a...@northwestern.edu.
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Re: [Freesurfer] mri_convert

[Adam Martersteck]

External Email - Use Caution

mri_convert can do lots of things but I would actually try mri_probedicom
to get the DICOM timings. If you have AFNI installed you could also try
dicom_hinfo which has more examples in the AFNI wiki than mrI_probedicomi.
You could just loop over dicoms writing stdout to a text file.

On Wed, Feb 20, 2019 at 10:45 AM john Anderson 
wrote:

> External Email - Use Caution
>
> hi FS experts.
> I would like to inquire about the command mri_ convert
> I use this command to convert fMRI and PET 4D volumes from dicom format to
> nifti.
>
> Are there any flags that can be used in mri_convert command line to enable
> it to extract a text file contain each series time in seconds?
>
> thanks
> John
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] PET PVC transforms and MG voxels

[Adam Martersteck]

External Email - Use Caution

Hi Freesurfer team,

Just wanted to bump this to see if anyone had any thoughts.

Thanks,
Adam

On Tue, Jan 29, 2019 at 10:21 AM Adam Martersteck 
wrote:

> Hi FreeSurfer team,
> I have two comments/questions about PET PVC & Doug’s 2016 Neuroimage paper:
>
> 1) It looks like the 2 rigid transforms created during mri_gtmpvc found at
> [$pvc_directory/aux/anat2bbpet.lta] and [$pvc_directory/aux/bbpet2anat.lta]
> are misnamed and the file names should be swapped. I noticed this isn’t a
> problem during mri_vol2surf (e.g. the PetSurfer wiki) because mri_vol2surf
> is “smart” and will automatically detect and invert the transform -- but it
> was causing problems for me when I used them during mri_vol2vol thinking
> the bbpet2anat.lta was from pet space to anat space. I apologize if you
> already knew about this – I couldn’t find anything in the FSv6 “Known
> Issues” or on the PetSurfer page.
>
> 2) I am using the MG PVC stream and a fairly conservative GM PVF threshold
> of 30% (similar to Doug’s paper). I noticed when the PVF is < 0.3 it sets
> the corrected [mg.nii.gz] image to zero in those voxels. Intuitively, I
> would have thought this would just “cap” all values < 0.3 to 0.3 and divide
> voxels by 0.3 to get a MG corrected voxel. I went back to Doug’s paper and
> found, indeed, the paper says, *“In this study, we varied the threshold
> from 1% to 50%. The TACs in voxels that did not meet this criterion were
> set to zero.”*
>
> So when I take the mg.nii.gz and use vol2surf as Doug did, I get a
> significant number of “patches” of zero values across the cortex (see
> attached image; every voxel along the normal is zero). I would then have
> smoothed this surface -- artificially lowering the entire neighborhood of
> vertices. Did you guys do something else for the Neuroimage paper when you
> were going from vol2surf? Or did you smooth the zeroes into the surrounding
> vertices? Maybe this isn't a problem in healthy brains and the projfrac 0.5
> voxel is always a non-zero?
>
> Since I am working with significantly atrophied Alzheimer brains -- would
> “capping” the PVF make sense here to balance over correcting noise while
> avoiding non-zero vertices? Is there a command in fscalc to set all values
> between 0.0001 and 0.3 to 0.3 so I could do this?
>
> Thanks!
> Adam
>
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[Freesurfer] Postdoctoral Fellow at Northwestern's Alzheimer's Disease Center

[Adam Martersteck]

External Email - Use Caution

*Apologies for cross-posting*
Northwestern University’s Mesulam Center for Cognitive Neurology and
Alzheimer’s Disease is seeking candidates for a postdoctoral fellowship in
Neuroimaging of Aging and Dementia. The fellow will focus on analyzing
multimodal MR, amyloid PET, and tau PET data for our NIA-funded Alzheimer’s
Disease Center.

The fellow may develop, adapt, implement and/or optimize analysis pipelines
for our newly funded AD Center Imaging Core, which will substantially
contribute to imaging biomarker discoveries and enhance data sharing
procedures. The fellow may participate in publications and presentations
resulting from the work. The fellow will work with Dr. Rogalski (Imaging
Core Leader) and her collaborators Dr. Todd Parrish (Director of the Center
for Translation Imaging) and Dr. Lei Wang (Director of the Applied
Computational Anatomy Lab). The Mesulam Center is located on the downtown
campus, nestled between the Magnificent Mile and the city's beautiful
lakefront.

Successful candidates will have a PhD in neuroscience, physics, psychology,
bioengineering or a related field. Experience with analysis of sMRI, DTI,
rsfMRI and/or PET is required with a particular emphasis on multimodal
approaches. Interested applicants should send a CV and cover letter stating
experience and interests, 2-3 peer-reviewed publications, and at least two
letters of recommendation. The start date is negotiable and the position
will remain open until filled. Please send application materials to
a...@northwestern.edu.
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Re: [Freesurfer] Computation time

[Adam Martersteck]

External Email - Use Caution

Hi Dawn,

See
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Step-wiseDirectives-1
for an approximate beakdown of computational time per step. The parallel
flag in FS v6 will decrease this to about 3 hours total on a 4 core
machine.

(time varies depending on your workstation, surface defects, etc; if using
a cluster, check with network admins about using -parallel)

Volume, thickness, area, curv are all going to be seconds to minutes
calculations and would not meaningfully impact your recon-all time.

-Adam

On Fri, Nov 16, 2018 at 3:47 PM Dawn Matthews  wrote:

> External Email - Use Caution
>
> Dear Freesurfer team,
>
>
>
> Thank you for your continued efforts and advances on the Freesurfer tool,
> which have benefitted the community and quest for therapy advances.  I
> wondered whether there is an assessment of the computation time breakout
> between volume calculation vs. cortical thickness, area, and mean
> curvature.  Is it possible to reduce time by calculating only volumes (no
> CT, area, MC), and if so, what reduction would be anticipated (recognizing
> that the answer is proportional as the absolute time would depend upon
> hardware etc.)?  As a second question, there was a previous mention in
> listserv comments regarding running left and right hemispheres in
> parallel.  Is this done, and is it an approach that can be combined with
> the parallel processing flag?  Thank you for any insights on these
> questions.
>
>
>
> Dawn
>
>
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Re: [Freesurfer] T2pial correction options

[Adam Martersteck]

External Email - Use Caution

Re-posting to see if anyone has had this problem before and solutions
they've implemented.


> Hi Freesurfer team,
>
> We’re having some trouble with the T2pial option. We are currently getting
> the Martinos Center ABCD project Tisdall/van der Kouwe vNav MPRAGE and
> T2SPACE at 0.8mm^3, bandwidth matched for distortion.
>
> Linked below are 2 gifs were we have found areas we thought the T2 and
> –T2pial option would help differentiate brain from non-brain:
> https://goo.gl/dc9pjj
> https://goo.gl/AsCCbA
>
> I’ve read the discussion by Bruce, Matt, and Antonin about altering the
> final lh/rh mris_make_surface command with the T2. Has anyone found more
> optimal numbers for the nsigma_above and nsigma_below arguments?
>
> Is there anything else I could try to get this working better?
>
> Thanks!
> -Adam
>
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[Freesurfer] T2pial correction options

[Adam Martersteck]

External Email - Use Caution

Hi Freesurfer team,

We’re having some trouble with the T2pial option. We are currently getting
the Martinos Center ABCD project Tisdall/van der Kouwe vNav MPRAGE and
T2SPACE at 0.8mm^3, bandwidth matched for distortion.

Linked below are 2 gifs were we have found areas we thought the T2 and
–T2pial option would help differentiate brain from non-brain:
https://goo.gl/dc9pjj
https://goo.gl/AsCCbA

I’ve read the discussion by Bruce, Matt, and Antonin about altering the
final lh/rh mris_make_surface command with the T2. Has anyone found more
optimal numbers for the nsigma_above and nsigma_below arguments?

Is there anything else I could try to get this working better?

Thanks!
-Adam
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Re: [Freesurfer] bbregister error

[Adam Martersteck]

External Email - Use Caution

Are you sure you're terminal is setup in tcsh or csh? If you're using bash
instead, you want "export SUBJECTS_DIR=/project/bil/Nada"
Take a look at:
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac or
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux to see
if you may have missed something.

On Wed, Aug 22, 2018 at 4:37 AM Nada Naguib  wrote:

> External Email - Use Caution
>
> Hello,
>
> I have been using bbregister in this format
>
> bbregister —mov dkti4d.nii —s NewT2out —init-fsl —bold —lea register.lta
>
> NewT2out is the output of the free surfer processing on the T1 image and
> dkti4d.nii is the template file I want to use for the registration.
>
> it has worked before but now there is a new error
>
> ERROR: cannot find NewT2out in
> /project/iconic/apps/freesurfer/5.3.0/install/subjects
>
> even though I have already ran the command:
>
> setenv SUBJECTS_DIRECTORY /project/bil/Nada
>
>
> This path is where both NewT2out and dkti4d.nii are located.
>
> I don’t understand what is going wrong
>
> Best
> Nada
>
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>
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> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
> HelpLine at
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Re: [Freesurfer] resting state motion censoring

[Adam Martersteck]

External Email - Use Caution

Hi Freesurfer team & Doug,

Thought I would check in again about censoring volumes and using fcseedcor.

I was thinking about if it hasn't been incorporated yet -- could I create
my own first level covariate .dat file and run fcseedcor on a per subject
basis and pass the new .dat to xreg? I assume the .dat file would be
difference than the one we use for selxavg3 (currently just passing a .dat
file with just a single column of a list of volumes that violate criteria).

The new xreg file would have to be *m* rows long (where *m* is the number
of TRs).
And if frame 119, 120, and 121 where to be excluded: then it would be a *m* by
3 matrix with column 1, row 119 set to 1; row 120 column 2 set to 1; row
121 column 3 set to 1.

Is that all correct?

Thanks,
Adam

On Thu, Mar 15, 2018 at 9:47 AM, Adam Martersteck 
wrote:

> Hi Freesurfer team & Doug,
>
> Just thought I'd check back in as you had asked! Any thoughts on censoring
> resting state volumes for fcseedcorr?
>
> Thanks,
> Adam
>
> On Thu, Feb 15, 2018 at 12:57 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Currently there is no way to do this. But it might not be hard to add.
>> If I don't get back in a couple of weeks, send me a reminder.
>>
>>
>> On 02/14/2018 12:13 PM, Adam Martersteck wrote:
>> > Just a quick follow-up question,
>> > For FD/DVARS or other "censoring" criteria -- using -tpexclusion
>> > worked great for surface based analysis with mkanalsysis and selxavg3.
>> > Is there a way to do this for seed-to-seed analysis (fcseedcor)?
>> >
>> > Thanks!
>> >
>> > On Thu, Jan 25, 2018 at 4:00 PM, Douglas N Greve
>> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>> >
>> > Yes,you need a time point exclusion file (-tpexclude filename
>> > option to
>> > mkanalysis-sess). Run mkanalysis with -help to get more info on how
>> to
>> > create it.
>> >
>> > On 01/25/2018 04:43 PM, Adam Martersteck wrote:
>> > > Hi Freesurer experts,
>> > >
>> > > I’m looking to censor (drop volumes) from my resting state fMRI
>> time
>> > > series that violate a predetermined motion and signal threshold
>> (FD
>> > > and DVARS). I've already determined which volumes violate X and Y
>> > > criteria.
>> > >
>> > > Is there a way to to tell FS to "ignore" these time points in the
>> > > analysis such as in preproc-sess or mkanalysis-sess?
>> > >
>> > > If there is not and if I were to drop the volumes directly from
>> > the 4D
>> > > file before starting any pre-processing and analysis  – would
>> > that be
>> > > a problem for finding and regressing the auto-correlation in the
>> > time
>> > > series?
>> > >
>> > > Thanks!
>> > > Adam
>> > >
>> > >
>> > > ___
>> > > Freesurfer mailing list
>> > > Freesurfer@nmr.mgh.harvard.edu
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>> >
>> > --
>> > Douglas N. Greve, Ph.D.
>> > MGH-NMR Center
>> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>> > Phone Number: 617-724-2358 
>> > Fax: 617-726-7422 
>> >
>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> > <https://gate.nmr.mgh.harvard.edu/filedrop2>
>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> > Outgoing:
>> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.har
>> vard.edu>
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesur

Re: [Freesurfer] resting state motion censoring

[Adam Martersteck]

Hi Freesurfer team & Doug,

Just thought I'd check back in as you had asked! Any thoughts on censoring
resting state volumes for fcseedcorr?

Thanks,
Adam

On Thu, Feb 15, 2018 at 12:57 PM, Douglas N Greve  wrote:

> Currently there is no way to do this. But it might not be hard to add.
> If I don't get back in a couple of weeks, send me a reminder.
>
>
> On 02/14/2018 12:13 PM, Adam Martersteck wrote:
> > Just a quick follow-up question,
> > For FD/DVARS or other "censoring" criteria -- using -tpexclusion
> > worked great for surface based analysis with mkanalsysis and selxavg3.
> > Is there a way to do this for seed-to-seed analysis (fcseedcor)?
> >
> > Thanks!
> >
> > On Thu, Jan 25, 2018 at 4:00 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > Yes,you need a time point exclusion file (-tpexclude filename
> > option to
> > mkanalysis-sess). Run mkanalysis with -help to get more info on how
> to
> > create it.
> >
> > On 01/25/2018 04:43 PM, Adam Martersteck wrote:
> > > Hi Freesurer experts,
> > >
> > > I’m looking to censor (drop volumes) from my resting state fMRI
> time
> > > series that violate a predetermined motion and signal threshold (FD
> > > and DVARS). I've already determined which volumes violate X and Y
> > > criteria.
> > >
> > > Is there a way to to tell FS to "ignore" these time points in the
> > > analysis such as in preproc-sess or mkanalysis-sess?
> > >
> > > If there is not and if I were to drop the volumes directly from
> > the 4D
> > > file before starting any pre-processing and analysis  – would
> > that be
> > > a problem for finding and regressing the auto-correlation in the
> > time
> > > series?
> > >
> > > Thanks!
> > > Adam
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.
> harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> >
> > The information in this e-mail is intended only for the person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > http://www.partners.org/complianceline
> > <http://www.partners.org/complianceline> . If the e-mail was sent
> > to you in error
> > but does not contain patient information, please contact the
> > sender and properly
> > dispose of the e-mail.
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/

Re: [Freesurfer] resting state motion censoring

[Adam Martersteck]

Just a quick follow-up question,
For FD/DVARS or other "censoring" criteria -- using -tpexclusion worked
great for surface based analysis with mkanalsysis and selxavg3. Is there a
way to do this for seed-to-seed analysis (fcseedcor)?

Thanks!

On Thu, Jan 25, 2018 at 4:00 PM, Douglas N Greve 
wrote:

> Yes,you need a time point exclusion file (-tpexclude filename option to
> mkanalysis-sess). Run mkanalysis with -help to get more info on how to
> create it.
>
> On 01/25/2018 04:43 PM, Adam Martersteck wrote:
> > Hi Freesurer experts,
> >
> > I’m looking to censor (drop volumes) from my resting state fMRI time
> > series that violate a predetermined motion and signal threshold (FD
> > and DVARS). I've already determined which volumes violate X and Y
> > criteria.
> >
> > Is there a way to to tell FS to "ignore" these time points in the
> > analysis such as in preproc-sess or mkanalysis-sess?
> >
> > If there is not and if I were to drop the volumes directly from the 4D
> > file before starting any pre-processing and analysis  – would that be
> > a problem for finding and regressing the auto-correlation in the time
> > series?
> >
> > Thanks!
> > Adam
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> but does not contain patient information, please contact the sender and
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> dispose of the e-mail.
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[Freesurfer] resting state motion censoring

[Adam Martersteck]

 Hi Freesurer experts,

I’m looking to censor (drop volumes) from my resting state fMRI time series
that violate a predetermined motion and signal threshold (FD and DVARS).
I've already determined which volumes violate X and Y criteria.

Is there a way to to tell FS to "ignore" these time points in the analysis
such as in preproc-sess or mkanalysis-sess?

If there is not and if I were to drop the volumes directly from the 4D file
before starting any pre-processing and analysis  – would that be a problem
for finding and regressing the auto-correlation in the time series?

Thanks!
Adam
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Re: [Freesurfer] Descriptions of regions in Yeo 2011 Network atlases

[Adam Martersteck]

Hi Dr. Yeo,

Just a related question -- do you have an opinion on if one of the network
solutions corresponds to the language network? I realize they are all
bilateral, with no significantly left lateralized one. But do you think one
of the DMN solutions (such as Default B in the paper you linked, much more
representative on the LH surface view) might represent the language network?

-Adam

On Thu, Oct 5, 2017 at 2:07 AM, Thomas Yeo  wrote:

> Hi Chintan,
>
> Sorry. At that time, we wanted to not bias the interpretation of the
> networks by naming them. But that may be a bit idealistic. We have
> subsequently named the networks.
>
> To map networks 1 to 17 to the names, the easiest way is to load the annot
> in freeview and hover your mouse over it and then visually match it to
> Figure 1 of this paper (http://people.csail.mit.edu/y
> thomas/publications/2015SleepDeprivation-NeuroImage.pdf). When I do so, I
> get the following, but you probably want to double check!
>
> 1) Network 1: Visual A
>
> 2) Network 2: Visual B
>
> 3) Network 3: SomMot A
>
> 4) Network 4: SomMot B
>
> 5) Network 5: DorsAttn A
>
> 6) Network 6: DorsAttn B
>
> 7) Network 7: Sal/VentAttn A
>
> 8) Network 8: Sal/VentAttn B
>
> 9) Network 9: Limbic B
>
> 10) Network 10: Limbic A
>
> 11) Network 11: Control C
>
> 12) Network 12: Control A
>
> 13) Network 13: Control B
>
> 14) Network 14: TempPar
>
> 15) Network 15: Default C
>
> 16) Network 16: Default A
>
> 17) Network 17: Default B
>
> Regards,
> Thomas
>
>
> On Thu, Oct 5, 2017 at 2:54 AM, Mehta, Chintan 
> wrote:
>
>> Dear Freesurfer users,
>>
>> I am examining the Yeo 2011 17 Network atlases in Freesurfer 6.0. The
>> regions are labeled 1 through 17. Is there a reference table mapping these
>> numbers with the names of cognitive networks described by Yeo, et al.
>> (2011) ( 
>> https://www.ncbi.nlm.nih.gov/pubmed/21653723)? For example, would
>> network 1 correspond to visual networks? I cannot find descriptions in the
>> readme files except the color look-up table.
>>
>>
>> Thank you.
>>
>> Best,
>>
>> Chintan
>>
>> ___
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>>
>>
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>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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Re: [Freesurfer] Long-stream comparing differing resolutions

[Adam Martersteck]

Just bumping to the top to see if anyone has ideas about comparing 0.8mm
vs. 1mm data using the long stream.


Dear FS Experts,

I’m trying to compare multiple T1-weighted sequences taken across multiple
scanners in the same day in 15 individuals using the longitudinal stream.

One question we had was how different cortical thickness estimates would be
using a 0.8mm^3 resolution vs. our standard 1mm^3 MPRAGE.

Unfortunately, during the initial long-stream norm fusion, the –hires
enabled 0.8mm data has a mismatch in dimensions compared to the standard
1mm data.

Given this limitation -- what would be the best way to compare these two
sequences?

Thanks,
Adam
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[Freesurfer] Long-stream comparing differing resolutions

[Adam Martersteck]

 Dear FS Experts,

I’m trying to compare multiple T1-weighted sequences taken across multiple
scanners in the same day in 15 individuals using the longitudinal stream.

One question we had was how different cortical thickness estimates would be
using a 0.8mm^3 resolution vs. our standard 1mm^3 MPRAGE.

Unfortunately, during the initial long-stream norm fusion, the –hires
enabled 0.8mm data has a mismatch in dimensions compared to the standard
1mm data.

Given this limitation -- what would be the best way to compare these two
sequences?

Thanks,
Adam
___
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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] freesurfer 6.0 with some of the analyses

[Adam Martersteck]

You are correct that the former is true.

Run recon-all -all on your existing subject directories after moving them
to a new v6 directory (with the new fsaverage, etc.) -- it will rerun all
the commands and use your brainmask.mgz deleted voxels, and your wm.mgz 255
voxels to correct the surfaces.

You will still need to open your subjects up in tkmedit or freeview and
inspect the surfaces for errors.

On Fri, Jan 27, 2017 at 11:13 AM Rizvi, Batool 
wrote:

>
>
>
>
>
>
>
>
>
>
>
>
> Thanks for your responses!
>
>
>
>
>
>
> Sorry for the naive question, but I'm wondering which commands I'd use to
> re-process all the data from 5.3. Can I run recon-all -all, and it will go
> through all the steps that it would if I ran it from the start? Or would it
> skip certain steps if it finds
>
> certain files existing already. I'm pretty sure the former is true, but
> just wanted to confirm.
>
>
>
>
>
>
>
> Thanks again!
>
>
>
>
>
>
>
> Batool
>
>
>
>
>
>
> --
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez,
> Eugenio [e.igles...@ucl.ac.uk]
>
>
> *Sent:* Thursday, January 26, 2017 11:01 AM
>
>
> *To:* Freesurfer support list
>
>
> *Subject:* Re: [Freesurfer] freesurfer 6.0 with some of the analyses
>
>
>
>
>
>
>
>
>
> Dear Batool,
>
> Sorry for missing your message.
>
>
> And dear Adam:
>
>
> Thanks for covering me! That’s exactly my standard answer to that question
> ;-)
>
>
>
>
>
>
>
>
>
>
>
>
>
> Juan Eugenio Iglesias
>
>
>
>
> ERC Senior Research Fellow
>
>
> Translational Imaging Group
>
>
> University College London
>
>
> http://www.jeiglesias.com
>
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On 26 Jan 2017, at 15:55, Adam Martersteck  wrote:
>
>
>
>
>
>
>
> I believe Dr. Iglesias previous responses on this exact question have
> been, "yes it's possible, but your results may be harder to
>
> reproduce"
>
>
> e.g. If someone wanted to replicate your study they may have a harder time
> having to download 2 different versions of freesurfer
>
> to achieve comparable results with your study.
>
>
>
>
>
>
>
> I think the general consensus is "how many subjects do you have?" -- if
> it's less than 50, you may want to just rerun
>
> v6 on your subjects as it should preserve the edits -- but it's
> recommended you still open them up and double check.
>
>
>
>
>
>
>
> -Adam
>
>
>
>
>
>
>
> On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool 
> wrote:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Hi,
>
>
>
>
>
> Can anyone comment on my question below?
>
>
>
>
>
>
>
>
> I think the FAQ page mentions that the same version should be used to
> process all cases within a dataset, but my question is whether I can have
> the same dataset used for two different versions for separate analyses?
> This is considering
>
> that I've already
>
>
>
>
>
> processed all my data with 5.3, but am interested in getting hippocampal
> subfields through 6.0.
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Thanks so much!
>
>
>
>
>
>
>
>
> Batool
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
>
>
>
>
>
>
>
>
>
>
> *From:* Rizvi, Batool
>
>
>
>
>
>
>
>
> *Sent:* Wednesday, January 25, 2017 12:54 PM
>
>
>
>
>
>
>
>
> *To:*
>
> freesurfer@nmr.mgh.harvard.edu
>
>
>
>
>
>
>
>
> *Subject:* freesurfer 6.0 with some of the analyses
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Hi,
>
>
>
>
>
>
>
>
> I'm wondering if it's oka

Re: [Freesurfer] freesurfer 6.0 with some of the analyses

[Adam Martersteck]

I believe Dr. Iglesias previous responses on this exact question have been,
"yes it's possible, but your results may be harder to reproduce"
e.g. If someone wanted to replicate your study they may have a harder time
having to download 2 different versions of freesurfer to achieve comparable
results with your study.

I think the general consensus is "how many subjects do you have?" -- if
it's less than 50, you may want to just rerun v6 on your subjects as it
should preserve the edits -- but it's recommended you still open them up
and double check.

-Adam

On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool 
wrote:

>
>
>
>
>
>
>
>
>
>
>
>
> Hi,
>
> Can anyone comment on my question below?
>
>
> I think the FAQ page mentions that the same version should be used to
> process all cases within a dataset, but my question is whether I can have
> the same dataset used for two different versions for separate analyses?
> This is considering that I've already
>
> processed all my data with 5.3, but am interested in getting hippocampal
> subfields through 6.0.
>
>
>
>
>
>
>
>
>
>
>
>
> Thanks so much!
>
>
> Batool
>
>
>
>
> --
>
>
> *From:* Rizvi, Batool
>
>
> *Sent:* Wednesday, January 25, 2017 12:54 PM
>
>
> *To:* freesurfer@nmr.mgh.harvard.edu
>
>
> *Subject:* freesurfer 6.0 with some of the analyses
>
>
>
>
>
>
>
>
>
>
>
>
>
> Hi,
>
>
> I'm wondering if it's okay to run some of the analyses within one study
> on v.5.3 and the other hippocampal analyses on 6.0?
>
> Or do you recommend us starting over for the analyses we've already done
> in 5.3 for that study?
>
>
>
>
>
>
> Thank you!
>
>
> Batool
>
>
>
>
>
>
>
>
>
>
> ___
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
> The information in this e-mail is intended only for the person to whom it
> is
>
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
>
> contains patient information, please contact the Partners Compliance
> HelpLine at
>
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
>
> but does not contain patient information, please contact the sender and
> properly
>
> dispose of the e-mail.
>
>
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] PET PVC - CSF estimation

[Adam Martersteck]

Hi,

Just want to bump this to the top now that the weekend is over!

Thanks for any insights about the CSF estimation,
Adam

On Fri, Oct 21, 2016 at 1:03 PM, Adam Martersteck 
wrote:

> Thanks for replying Doug,
>
> Yes, I would like to use my own mask if the choroid plexus is included but
> *only* for Tau PET. There is high off-target binding of the new tau PET
> ligand AV1451 (formerly called T807) in choroid plexus. I wanted to avoid
> that high signal when estimating CSF.
>
> I think choroid plexus being included for all the other types of PET I
> plan on using (FDG or amyloid PET) is great -- because it bridges the
> ventricles at the septum pellucidum (intended or not) -- and makes the
> erosion of 3mm much less 'harsh' because it's eroding from a connected mass
> of 1 segmentation instead of two independent segmentations (left and right
> ventricles).
>
> if choroid plexus is not included -- then no worries, I'll continue using
> it for AV1451 Tau PET just like for amyloid and FDG PET as planned. If it
> is -- is there a way to expose the CSF estimation in the script so that I
> could input my own estimation (just the ventricles)?
>
> Thanks!
> Adam
>
> On Thu, Oct 20, 2016 at 3:24 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> What do you mean? You have your own CSF segmentation and you want to use
>> that instead of the one created by gtmseg?
>>
>>
>>
>> On 10/20/2016 11:32 AM, Adam Martersteck wrote:
>> > Hi FreeSurfer team,
>> >
>> > Hopefully Doug or someone familiar with the new PET PVC implementation
>> > can answer a few things I can't seem to find on
>> > http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer or either of Doug's
>> > PVC publications (2013 or 2016).
>> >
>> > 1) Is the choroid plexus included in the binarized then 3mm eroded
>> > segmentation to find the mean ventricular CSF signal?
>> >
>> > 2) Is there a way to input my own estimation of ventricular CSF signal
>> > to mri_gtmpvc?
>> >
>> > Thanks!
>> > Adam
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] PET PVC - CSF estimation

[Adam Martersteck]

Thanks for replying Doug,

Yes, I would like to use my own mask if the choroid plexus is included but
*only* for Tau PET. There is high off-target binding of the new tau PET
ligand AV1451 (formerly called T807) in choroid plexus. I wanted to avoid
that high signal when estimating CSF.

I think choroid plexus being included for all the other types of PET I plan
on using (FDG or amyloid PET) is great -- because it bridges the ventricles
at the septum pellucidum (intended or not) -- and makes the erosion of 3mm
much less 'harsh' because it's eroding from a connected mass of 1
segmentation instead of two independent segmentations (left and right
ventricles).

if choroid plexus is not included -- then no worries, I'll continue using
it for AV1451 Tau PET just like for amyloid and FDG PET as planned. If it
is -- is there a way to expose the CSF estimation in the script so that I
could input my own estimation (just the ventricles)?

Thanks!
Adam

On Thu, Oct 20, 2016 at 3:24 PM, Douglas N Greve 
wrote:

> What do you mean? You have your own CSF segmentation and you want to use
> that instead of the one created by gtmseg?
>
>
>
> On 10/20/2016 11:32 AM, Adam Martersteck wrote:
> > Hi FreeSurfer team,
> >
> > Hopefully Doug or someone familiar with the new PET PVC implementation
> > can answer a few things I can't seem to find on
> > http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer or either of Doug's
> > PVC publications (2013 or 2016).
> >
> > 1) Is the choroid plexus included in the binarized then 3mm eroded
> > segmentation to find the mean ventricular CSF signal?
> >
> > 2) Is there a way to input my own estimation of ventricular CSF signal
> > to mri_gtmpvc?
> >
> > Thanks!
> > Adam
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] PET PVC - CSF estimation

[Adam Martersteck]

Hi FreeSurfer team,

Hopefully Doug or someone familiar with the new PET PVC implementation can
answer a few things I can't seem to find on
http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer or either of Doug's PVC
publications (2013 or 2016).

1) Is the choroid plexus included in the binarized then 3mm eroded
segmentation to find the mean ventricular CSF signal?

2) Is there a way to input my own estimation of ventricular CSF signal to
mri_gtmpvc?

Thanks!
Adam
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] bbregister problems with PET data

[Adam Martersteck]

Thanks Martin and Doug,

I'll give both robust_register with robent and mri_coreg a try.

RE: Doug
The PET tracer is Avid's amyloid compound -- F18-florbetapir (aka amyvid,
aka AV45).
The asymmetric signal is a result of the population -- individuals with a
non-amnestic language dementia with underlying Alzheimer's pathology. I
realize the focal left lateralized atrophy could play a role in partial
voluming, next step is PVC.

Thanks again,
Adam

On Thu, Mar 31, 2016 at 12:13 PM, Douglas N Greve  wrote:

> btw, what tracer is this? And the asymmetry you are talking about is
> between the hemispheres? Is that typical for this tracer or is this a
> phenomena with this subject (or population)?
>
> On 03/30/2016 03:41 PM, Adam Martersteck wrote:
> > Hi Freesurfer team,
> >
> > I’m encountering a problem using bbregister on PET data:
> >
> > -- When I attempt to register a PET volume to T1-space the asymmetric
> > tracer uptake of the PET throws off proper registration. (Treating the
> > PET as a T1 because of the non-specific white matter uptake > grey
> > matter signal).
> >
> > -- You can really see the bbregister mis-registration in this gif
> > here: https://goo.gl/iM6yrT
> >
> > -- It (expectedly) attempts to find the best match between signal
> > intensities on both the left and right surfaces, but is inherently
> > biased by the asymmetric uptake shifts the entire volume to the right.
> >
> > -- Are there any suggestions for dealing with asymmetric scans like
> > this? Stick with just a simple FLIRT? It doesn't seem to do that great
> > a job for everyone.
> >
> > Cutting left and right hemispheres apart and register separately?
> >
> > Using Martin’s new robust register for multi-modal data? Any
> > suggestions on the parameters of ROBENT?
> >
> > Thanks,
> > Adam
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] bbregister problems with PET data

[Adam Martersteck]

 Hi Freesurfer team,

I’m encountering a problem using bbregister on PET data:

-- When I attempt to register a PET volume to T1-space the asymmetric
tracer uptake of the PET throws off proper registration. (Treating the PET
as a T1 because of the non-specific white matter uptake > grey matter
signal).

-- You can really see the bbregister mis-registration in this gif here:
https://goo.gl/iM6yrT

-- It (expectedly) attempts to find the best match between signal
intensities on both the left and right surfaces, but is inherently biased
by the asymmetric uptake shifts the entire volume to the right.

-- Are there any suggestions for dealing with asymmetric scans like this?
Stick with just a simple FLIRT? It doesn't seem to do that great a job for
everyone.

Cutting left and right hemispheres apart and register separately?

Using Martin’s new robust register for multi-modal data? Any suggestions on
the parameters of ROBENT?

Thanks,
Adam
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] v5.3 fsaverage (accidentally) in v5.1 directory

[Adam Martersteck]

 Hi Freesurfer team,

*Short question: *Will (accidentally) using the fsaverage v5.3 subject in
our v5.1 directory influence our reconstructions?

*Long question:* Our server has 2 different freesurfer environments. A
recon was accidentally run on a single v5.1 subject in the v5.1 directory
with freesurfer version 5.3. During the “balabels” stage of autorecon3,
because FS 5.3 couldn’t find the perirhinal label – it deleted our 5.1
symlink and replaced it with the correct 5.3 symlink. We realized it had
happened and correct the subject, but didn’t catch that the symlink had
been changed.

We have run multiple (hundreds) of brains through v5.1 since then – with
the v5.3 fsaverage in the v5.1 directory.

A cursory glance over the release notes from 5.1 to 5.3 makes me think
nothing has fundamentally changed – only new files have been added to
fsaverage 5.3 (e.g. cortical parcellation networks). No new GCA atlas or
anything that would change how FS 5.1 reconstructs the brain?

Thanks for any thoughts!
Adam
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[Freesurfer] Using N3 MNI and N3 FS corrections

[Adam Martersteck]

Hi Freesurfer users,

I have a question about using the N3 algorithm twice for processing ADNI
data:

Is it okay for data to have undergone the ADNI N3 correction (Boyes et al.
2008 http://www.ncbi.nlm.nih.gov/pubmed/18063391) AND then pushed through
the Freesurfer pipeline and undergo FS N3 correction (Zheng, Chee, and
Zagorodnov 2009 http://www.ncbi.nlm.nih.gov/pubmed/19559796)?

The problem stems from the fact that recent ADNI data has either undergone
gradient warping correction (http://www.ncbi.nlm.nih.gov/pubmed/16300968)
AND N3 correction or no corrections at all. The optimal solution would to
have just been able to download the grad warp’d data and push that through.


Thanks for any thoughts!
Adam
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Re: [Freesurfer] problems with Surface-based Interhemispheric Registration

[Adam Martersteck]

Just to provide some additional insight,

I noticed that the xhemireg file was missing from
<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg>
the ftp on January 28th, 2014 and emailed the listserv:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33639.html

Doug quickly emailed back after hosting it with "sorry, try now".

I downloaded the new xhemireg and installed it in my FS v5.1.0 directory,
and got an identical error as Angela.
Xhemireg fails at -cortparc, trying to generate the rh.aparc.annot (The
label directory is empty).

For curiosity, I used v5.3.0 and compared log files.

Differences:
*xhemireg that was hosted for versions below FSv5.2.0 is xhemireg v1.12*
--> mri_convert {volumes}.mgz --> tkregister2 -> mri_surf2surf for each
hemi --> copies only surfaces --> generate annots/cortex label from
-cortparc

cp surf/lh.curv {subject}/xhemi/surf/rh.curv
cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc
cp surf/lh.area {subject}/xhemi/surf/rh.area
cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial
cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial
cp surf/lh.avg_curv {subject}/xhemi/surf/rh.avg_curv
cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H
cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K
cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness
Goes on to try -cortparc for right hemi to generate the rh.aparc.annot, but
fails because rh.cortex.label does not exist in {subject}/label/ directory

*xhemireg that v5.3.0 uses is v1.12.4.3* and is much more efficient -->
mri_vol2vol --> mri_surf2surf each hemi --> copies surfaces and
annots/labels for each hemi

cp surf/lh.curv {subject}/xhemi/surf/rh.curv
cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc
cp surf/lh.area {subject}/xhemi/surf/rh.area
cp surf/lh.volume {subject}/xhemi/surf/rh.volume
cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness
cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H
cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial
cp surf/lh.area.mid {subject}/xhemi/surf/rh.area.mid
cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial
cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K


*cp label/lh.aparc.annot {subject}/xhemi/label/rh.aparc.annotcp
label/lh.BA.annot {subject}/xhemi/label/rh.BA.annotcp
label/lh.aparc.a2009s.annot {subject}/xhemi/label/rh.aparc.a2009s.annot*
(Not explicit, but the ?h.cortex.label appears at the same time; presumably
just from the corresponding ?h.aparc.annot)

Hope that was helpful!
Adam Martersteck


On 01/28/2014 11:26 AM, Adam Martersteck wrote:
>
> Hi Freesurfer team,
>
> I noticed that the xhemireg file is missing from:
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg
>


On Thu, Jul 3, 2014 at 3:44 PM,  wrote:

> Hi all,
> I am trying again to perform Surface-based Interhemispheric Registration
> in another computer (same version of FS 5.0) and by building my own atlas.
> However, there is an error while running xhemireg command (please find the
> log attached).
>
> I also noted that the command xhemireg took a lot of time to run (more
> than 30 min) while you wrote on the wiki that it would take a few minutes
> to finish.
>
> If anyone can give some hints it would be great
>
> thank you
>
> Angela
>
> >
> >
> > I'm not sure why this is failing. Are there other things in the xhemi
> > folder? What version of FS are you using?
> > doug
> >
> > On 07/01/2014 11:06 AM, angela.fav...@unipd.it wrote:
> >> sure! thank you
> >>
> >>
> >>> Can you send the log file (or the full terminal output)?
> >>> On 06/30/2014 03:11 PM, angela.fav...@unipd.it wrote:
> >>>> Hi all,
> >>>> I have a problem with 'Surface-based Interhemispheric Registration'
> >>>>
> >>>> I followed the instructions and all seem to work, but the command:
> >>>> 'surfreg --s $subject --t fsaverage_sym --lh --xhemi'
> >>>>
> >>>> finish with the error below
> >>>> (indeed in the xhemi/label directory, there is no file)
> >>>>
> >>>> What can I do?
> >>>> Thank you for any help!
> >>>> Angela
> >>>>
> >>>> #@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014
> >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts
> >>>> \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz
> >>>> -seed
> >>>> 1234 subj024/xhemi rh ../surf/rh.sphere.reg
> >>>>
> /Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killia

[Freesurfer] xhemi - xhemireg file

[Adam Martersteck]

Hi Freesurfer team,

I noticed that the xhemireg file is missing from:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg



I'm assuming the xhemireg for v5.3.0 (found in v5.3.0's
$FS_HOME/bin/xhemireg) is identical and I can use that with v5.1.0?


Thanks,

Adam
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[Freesurfer] reg.dat for ICBM152 to MNI305 (fsaverage)

[Adam Martersteck]

Hi Freesurfer experts,

Question related to transforming volumes/masks in ICBM-152 space to MNI-305
space for use with fsaverage.

1. What is the proper registration file while utilizing mri_vol2vol?
A. The registration file
{$FREESURFER_HOME}/subjects/fsaverage/mri/transforms/reg.mni152.2mm.dat
>>Same file as {$FREESURFER_HOME}/average/mni152.register.dat

OR

B. The different registration file
{$FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat

2. Are VOI-masks that are ALREADY in SPM2/FSL’s MNI-305 space (i.e. 2mm^3,
90x108x90) resliced to 256^3 -- usable with fsaverage without any further
alteration?
>> If not: Different linear transform from MNI-305 to ‘fsaverage MNI-305’?

Thanks!
Adam Martersteck

Cognitive Neurology and Alzheimer's Disease Center
Northwestern University Feinberg School of Medicine
320 E. Superior Street, Searle 11
Chicago, IL 60611
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[Freesurfer] freeview v5.3 reposition surface

[Adam Martersteck]

Hi Freesurfer experts,

I noticed that Freeview has gotten an upgrade from v5.1 to v5.3 and the
reposition tool now has a GUI and it works!

Dr. Fischl said in response to Dr. Pietro De Rossi on October 24th, 2012
that the pipeline for the reposition surface tool was not yet implemented
and you still needed to rerun “mris_make_surface (including mris_thickness
to regenerate the thickness map)”. [
https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2012-October/026209.html
I noticed that the freeview virtual representation of the surfaces are
immediately regenerated.

Should I be running the mris_make_surface command after saving the new
surface(s)?

Thanks,

Adam Martersteck

Cognitive Neurology and Alzheimer's Disease Center
Northwestern University Feinberg School of Medicine
320 E. Superior Street, Searle 11
Chicago, IL 60611
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[Freesurfer] FS 5.1: white matter holes in wm.mgz

[Adam Martersteck]

Hey all,

Problem: I am getting white matter ‘holes’ of varying sizes on the wm.mgz


I’ve uploaded 6 images to show an example of such a hole that was created.
It is the same wm hole from all 3 views shown in brainmask.mgz and wm.mgz.

The album with all 6 images can be found at photobucket.com/FS51



Background:

The hole appears within the first or second recon-all (after edits made)

They are appearing in multiple subjects

If they do appear in a subject - it is usually between 2-3 per volume

I am using FS 5.1 on a mac (recon on a linux)

I am performing pial/wm/cp edits



I was curious if anyone had ever run into this error and a solution for
avoiding it in the future.



Thanks in advance for the help!



Adam Martersteck

Cognitive Neurology and Alzheimer’s Disease Center

brain.northwestern.edu
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