[Freesurfer] qcache option for post recon-all longitudinal data

2021-08-06 Thread Zeng, Qi
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Hi Freesurfer experts,

I've done running a longitudinal analysis pipeline for individuals in 3
groups. Now, I need to get prepared for QDEC group analysis. I cp all
groups of individuals to the same directory and each subject contains one
base and multiple long files. I want to run "-qcache" option for the prep.
Got a couple of questions here?
1) I failed to run "recon-all -s 001 -qcache", said: "missing
001/surf/lh.thickness", so for a longitudinal run, should I run "recon-all
-s 001_base -qcache" or 'recon-all -s 001_ses-1.long.001_base" instead?
2) Where will the output be stored for each individual?
3) To run multiple qcache in parallel, will the following code generate the
same outputs as that I run each individually: " find . -type d -name
'*_base" -exec bash -c 'for i in "$@"; do recon-all -s "$i" -qcache; done".
Thank you so much!

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

2021-08-06 Thread Adam Martersteck
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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
>>> 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:
>>>
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 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

[Freesurfer] Diffusion MRI postdoc position

2021-08-06 Thread Corinna Bauer
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We are seeking a full-time postdoctoral fellow with experience in diffusion
analysis with an emphasis on network-based approaches, NODDI, DKI, and
tract-specific analysis. The NIH-funded project employs structural,
diffusion, and relaxometry based MRI methods to target thalamo-cortical
changes in morphometry, neural networks, and MRI-based markers of myelin in
youths with perinatal brain injury.

We are seeking a candidate with the following qualifications:
• Doctoral degree in computer science, neuroscience, or related field
• Advanced skills in the processing and analysis of diffusion (including
connectivity, DKI, and NODDI approaches) data, particularly focusing on
network-based approaches are required
• Strong coding skills in python, MATLAB, bash, etc.
• Experience with fMRI design and analysis is a plus

Interested candidates should send a cover letter including, a brief summary
of their research interests and career goals, their C.V., and the names and
phone numbers of three references to Corinna Bauer (
corinna_ba...@meei.harvard.edu).

Additional details can be found at:
https://secure-web.cisco.com/1PRcDuRd4mfRf2yIwKkDZ9B-oKmLA-2p68m-jCGxuMCJA8f7glCaKVcnpLSpPymTt5LL_ZZz1U6rPVyfpHRKJLCccf5seuMcS1PXZEr8k1BHYaGIcq6Uath-xRSXPCk_uk4uupQNIGbsnwLQEe311E2piHwMds55ypOBZTLDS7Yr0a_lz1E_8gIKzILQjupT047BLy37LwFR3HEC-doUZ0nu0gx4y4ghXHSKkxWNkp5qn7nGIuXcrWbbdGoPcc8ClblJDqQ7sYU3Mp6_W6eZ_Ew/https%3A%2F%2Fpartners.taleo.net%2Fcareersection%2Fmee%2Fjobdetail.ftl%3Fjob%3D3145087%26tz%3DGMT-05%253A00%26tzname%3DAmerica%252FNew_York
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