[Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

2023-08-22 Thread Eric BARDINET 
External Email - Use Caution

Hello Freesurfer Developpers,

I attempted to run mri_easyreg (Freesurfer 7.4) between two MP2RAGE UNI 
images (acquired on a SIEMENS PRISMA 3T).

First, I did not include segmentations, as I understood that EasyReg 
would run it for me.

But it didn't. I don't know why.

Then I first ran mri_synthseg with the --parc option on the two images.

I checked the results, and saw cortical labels on both hemispheres.

But when I ran again mri-easyreg adding these images (--ref_seg 
--flo_reg), I get again the > no cortical parcels.

What did I do wong?

Any hints?

Thanks in advance for your help.

Best,

Eric




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[Freesurfer] Password for unzipping Virtual Box Image file

2023-08-22 Thread mkassinopoulos 
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Hi,

 

I would like to request the passcode for unzipping the Virtual Box Image
file (i.e. FS_7_2_0_ubuntu_18_04_06.ova.7z).

 

Best regards,

Michalis

 

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Re: [Freesurfer] T2 FLAIR Images

2023-08-22 Thread Douglas N. Greve 
   External Email - Use Caution


Sorry, you need to pass it to recon-all with --flair or --T2

On 8/21/2023 1:19 PM, Alan Francis wrote:


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Hi Doug:

Thanks for your reply. I am trying to set the T1.nii.gz as 001.mgz and 
the T2.nii.gz as 002.mgz. So will the following command work?


mri_convert t2.nii.gz --flair 002.mgz

or is it:

mri_convert --flair t2.nii,gz 002.mgz

Thanks,

Alan

On Sun, Aug 20, 2023 at 4:17 PM Douglas N. Greve 
 wrote:


External Email - Use Caution

How did you set up the T2? Did you set 001.mgz to be the T1 and
the 002.mgz to be the T2FLAIR? If so, that will not work. You
should pass the FLAIR with the --flair flag. recon-all will
register them together. Or do you just want to register them
outside of recon-all?

On 8/14/2023 2:46 PM, Alan Francis wrote:


External Email - Use Caution

Good evening Doug et all:

I am trying to coregister T1 and T2 images and run the recons.
However, the T2's are giving me an error message. Please see
below: I opened the T2 image on Freeview. It looks normal. I
tried running a second brain.  Same problem. Appears normal on
Freeview but recons wont run.

So I tried running the recons on the T1 alone and it ran without
problems.

Thanks,

Alan

[DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid
NCANDA_S00042/
fs-check-version --s NCANDA_S00042 --o
/var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1
Mon Aug  7 16:06:21 CDT 2023

setenv SUBJECTS_DIR /Users/alanfrancis/SUBJECTS
cd /Users/alanfrancis/SUBJECTS
/Applications/freesurfer/7.4.1/bin/fs-check-version --s
NCANDA_S00042 --o
/var/folders/z4/3sg7yzm101vbwnsmzcdx70n4gq/T//tmp.W6p7a1
-rwxrwxr-x@ 1 alanfrancis faculty 18565 Jun 13 23:24
/Applications/freesurfer/7.4.1/bin/fs-check-version

freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
$Id$
Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul
 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64
pid 9192
Current FS Version
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
Subject does not have a bstampfile, copying
/Applications/freesurfer/7.4.1/build-stamp.txt
Subject FS Version:
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
No constraints on version because REQ=UnSet and FsVerFile=NotThere
#@#% fs-check-version match = 1
fs-check-version Done
INFO: SUBJECTS_DIR is /Users/alanfrancis/SUBJECTS
Actual FREESURFER_HOME /Applications/freesurfer/7.4.1
Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul
 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64
#
#@# MotionCor Mon Aug  7 16:06:22 CDT 2023
Found 2 runs
/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz
/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz
Checking for (invalid) multi-frame inputs...
Checking for (invalid) multi-frame inputs...
#---
/Users/alanfrancis/SUBJECTS/NCANDA_S00042
\n mri_robust_template --mov
/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz
/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz
--average 1 --template
/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz --satit
--inittp 1 --fixtp --noit --iscale --iscaleout
/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001-iscale.txt
/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002-iscale.txt
--subsample 200 --lta
/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.lta
/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.lta \n
7.4.1

--mov: Using
/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz as
movable/source volume.
--mov: Using
/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz as
movable/source volume.
    Total: 2 input volumes
--average: Using method 1 for template computation.
--template: Using
/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz as
template output volume.
--satit: Will estimate SAT iteratively!
--inittp: Using TP 1 as target for initialization
--fixtp: Will map everything to init TP!
--noit: Will output only first template (no iterations)!
--iscale: Enabling intensity scaling!
--iscaleout: Will perform intensity scaling and output results
--subsample: Will subsample if size is larger than 200 on all axes!
--lta: Will output LTA transforms
Setting iscale ...
reading source
'/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz'...
converting source
'/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz' to
bspline ...
MRItoBSpline degree 3
reading source
'/Users/alanfrancis/SUBJECTS/NCAND

[Freesurfer] How to register single voxel spectroscopy VOI to FreeSurfer processed brain

2023-08-22 Thread Lauren Stephens 
External Email - Use Caution

Dear FreeSurfer,

I am trying to extract tissue composition of %GM, %WM, and %CSF from a 
Freesurfer processed brain. I have the coordinates for the voxel but do not 
know how to place a voxel on the brain in FreeSurfer before running 
mri_compute_volume_fractions.  Can anyone provide direction on how to do this 
in FreeSurfer using a Mac running Ventura 13.4.1?

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu

P: (650)-725-1716

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[Freesurfer] Job Position: Postdoc Research Associate at the Center for Healthy Minds

2023-08-22 Thread Center for Healthy Minds Human Resources 
External Email - Use Caution

The Center for Healthy Minds at the University of 
Wisconsin–Madison
 is seeking multiple highly motivated postdoctoral researchers to work on 
intervention studies in U.S. adults to promote wellbeing and prevent suicide.



Areas of research include the evaluation and mechanistic examination of 
behavioral and physiological interventions in healthy and distressed adults 
using multiple types of MRI, passive measures of behavior and physiology, and 
survey measurements.

The postdoctoral research associates will have opportunities to participate in 
activities related to neuroimaging methods development and evaluation, study 
data collection and analyses, research publications, grant writing and are 
expected to make

positive scholarly contributions to this interdisciplinary and highly 
collaborative research program.



Qualifications:

Required

Ph.D. in medical physics, psychology, neuroscience, and/or a related field

Prior experience with brain imaging techniques (e.g. MRI, DTI, and/or fMRI) 
and/or behavioral data

Strong communication and organization skills are a must.

Preferred

Experience with brain image analysis software tools, MATLAB, Python, C++ and/or 
other computer programming (e.g., R, Mplus)

Experience with large and complex research studies and/or clinical trials

Emerging track record of publishing in academic journals, strong analytic 
skills, and excel at working in a collaborative environment.



We are an equal opportunity/affirmative action employer. We promote excellence 
through diversity and encourage all qualified individuals to apply.



To view the full posting with application instructions please go to 
https://secure-web.cisco.com/1VdOrlXBZlLhFv9xXJTvkxUg9UcYvjBez8PJM194TBa2Rz4hV78F7Wla7fsgKOf33hoTV3UJlcyKEuZpNjiqWV4ToPsBzMFjfb7CQb1EeeMh2YXc6ZtAT5DUOFyQlLz23oNpgGYohiG9pifz3-QSjRorEtduAlC2hjpHctdiBLMPuO9xl-JHrTX4cE_osEPwYeS2llKGtpk8-kJSx00jXZ55xgNut95AZVJM-BTALBs_awNapky6DUvrF9Z060r5nMYMnH9pRRlUncrs7h7xsoNLMAWRXW_Hkfs8PYrVJjtFZ2seUnuLjMLyKQwNc-O6XObq2zAqA1OI7jdGluo8qnA/https%3A%2F%2Fcenterhealthyminds.org%2Fassets%2Ffiles-publications%2FPostDoc_DARPA-FINAL-COPY.pdf
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Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

2023-08-22 Thread Iglesias Gonzalez, Juan E. 
External Email - Use Caution

Dear Eric,
Thanks for the interest in our tool!
Can you please send us the exact command line that you used, and the full 
output of  mri_easyreg?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
http://secure-web.cisco.com/1U33kJUEZ__sfspXazQKQX0hyZheFOuaPY4ZYQX7M1oqicMzMIhcwB7IXyPqhLqRQSzRrVfcmO5sRw0JCKEmGnCWGmXfSPa1_mmxNgT_JkO-bBaMQp7fRvDZlsEuuU-oEf0Ca4pBrQQ7XDE0oMkn09jboq6mrKi1y1ohW2Na3ERNUJvbV_x4kHPgIl2Ez_MQX5B7hk47NG4V9rHOKxytJ8Q41um8ARqtElBIGdjj2sIHdF7JHTyv7FRRIVZ1rJIfI/http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Eric BARDINET 

Date: Tuesday, August 22, 2023 at 04:57
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with 
--parc option ?
External Email - Use Caution

Hello Freesurfer Developpers,

I attempted to run mri_easyreg (Freesurfer 7.4) between two MP2RAGE UNI
images (acquired on a SIEMENS PRISMA 3T).

First, I did not include segmentations, as I understood that EasyReg
would run it for me.

But it didn't. I don't know why.

Then I first ran mri_synthseg with the --parc option on the two images.

I checked the results, and saw cortical labels on both hemispheres.

But when I ran again mri-easyreg adding these images (--ref_seg
--flo_reg), I get again the > no cortical parcels.

What did I do wong?

Any hints?

Thanks in advance for your help.

Best,

Eric




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Re: [Freesurfer] Freeview output viewing error

2023-08-22 Thread fsbuild 
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 If you search the freesurfer mail archives for WSL you should find 
postings about how to setup an  X-server on the windows host in order for 
Linux applications to run in WSL and use X-Windows to display images.   We 
provide some documentation, however we cannot guarantee these settings work 
with the current version of the 2nd iteration of WSL, i.e., WSL2, which you are 
running. 
 See,https://secure-web.cisco.com/11H-L4FbGidKmZY-de-JntjYeQLAeVrQ1XgpdUHaMqg8CCouWlZ-csPc_4IeioBAVAqHhk45el9cRUZPv7wIb0Fa33nZc9N4PkjKI0dF1RPJVN-he9XBt1Ua6a4QSVeD_w5bZnfOLabOM5n15lkCAJOV069NjUvo7wvfKDC7ihp4tfFZRlqy04d4Ulv8M3XzFbXzHa3_X6PzLyLptMRW0DpSEH15MxILMfCaw2aXqyXv8WbtHT_dWkB1oPK8nKUInT_c31S6utPE9VzRLR2IkzwjB7r2AqOCZO1vkEd_sd-w--NZS1-g316PnttbIo3N5Ia8In0FQw1pQlYDew151jQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl
Some people have found Moba X-term to be easier to setup and use compared to 
Xming for the 
X-server.https://secure-web.cisco.com/1wbbTwhirUX48Lj_j7Zcog0e6ACmMB4oLvaYMUSE6loHwKKH6rYEiMDQ_-1MsBcWWJ3dpd-OBkNiaLAOkgjmtSZ7JWjzkEua8MwktH6pGmclIPg9mYSOIZGoNJqa8TyOhIyULOcXHVCIwSrp1q7QmTmYGBmMt1RXf29SR5i7iBMuAElxCOfXtvqo5wRPR9HlFUq9YF3tI-JWR9ZV0DuGS-nlAMxp2FK8AZkA1JIcN9VK9U6c3gbDeHRkrBKUAB3cFvtv5i1SwGP3i-UzJh2-KSIxX1ezMDxvbg_rkI2XjKSvA8qTaTX0hmxVxg3O3Fd1B50G-W2xhwfmR-OPMEtPh0A/https%3A%2F%2Fmobaxterm.mobatek.net
Before trying to run freeview, check that simple X-windows programs like 
“xclock” or “glxgears” run directly from the terminal window inside linux, 
i.e., you should see a clock displayed,$ xclock… and spinning gears ...$ 
glxgears
An alternative to WSL is to run the VirtualBox VM we provide with freesurfer 
7.2.0 pre-installed running on Ubuntu 
18,https://secure-web.cisco.com/1vK-WU9hm5IesyZObbEUx1tWoPmNR_OvT3eg0YDwj-sSQIXzdhv-YwluzAWgB4gG9phXhLQcVB_o2cNHMOGnK9Gp9XWPjB8FgTqezBrM26yU2u5N756v_OP8sEXvbixcSFk6pTTTGbu3wEJMe_5kxVgYIInMdlJVcY40F7nAa8KOLYdDPEcKUtp7gnSXtBSNLE4rpSwwlEQr2t1r_26eI3pnjxD9fv1Z2pFrryslOZVdLTsNVxs6jZcYOZZYcGKMTjoPot6uYkAjYPe0eKi-U441Xz0011uiNKcTTbbhPOQ4bs6_q6eY9BWkFuxm6JBvP1WaMMtWPal2bAZD488thEA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67
You can upgrade the VM from Ubuntu 18, to 20, etc….  Similarly you can 
uninstall freesurfer 7.2.0 and install the latest 7.4.1 rpm matching the Ubuntu 
OS you are running from the Freesurfer downloads 
page,https://secure-web.cisco.com/1m70yw-FWa8H1WUCpyYEQ2AgIFTjm9W5pcTX0PejadT4Xt5J_YSvLLKb8_hi0_CHsZkjcfaQJCEMoo1FR4a9GG9tUh6CWii4M9OYVfYi_14SBVGd6at8Lq4qJl4P52yuupYfLSlf4et8HVuNu-BSrFq_g6gQPHt7TDv0XpvqiAcUFOZflBvLAt77eCm7hGGXLN1fDoqdOUQwkVMKxE_fQKUtGggn2wVVcPGGKMn0c6cY2qTSjq4IujXwEdI3Q1R9TCQhHO3yRJUrQQ5_fmbPjy10RA6O0dq6U8snOAcvQBrLVHTurrJ96BgrBP2v5L89SDuPgaqSHlT1K2QIOorRFLA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
Advantages to the VM are it will run (thru Virtualbox) on most Linux, Mac, or 
Windows hosts and since the X-server is built into the VM, there is no need to 
install and configure a 3rd party X-server on a Windows host.  Some users 
have switched to VirtualBox because they found it easier to use. 
 See,https://secure-web.cisco.com/1vK-WU9hm5IesyZObbEUx1tWoPmNR_OvT3eg0YDwj-sSQIXzdhv-YwluzAWgB4gG9phXhLQcVB_o2cNHMOGnK9Gp9XWPjB8FgTqezBrM26yU2u5N756v_OP8sEXvbixcSFk6pTTTGbu3wEJMe_5kxVgYIInMdlJVcY40F7nAa8KOLYdDPEcKUtp7gnSXtBSNLE4rpSwwlEQr2t1r_26eI3pnjxD9fv1Z2pFrryslOZVdLTsNVxs6jZcYOZZYcGKMTjoPot6uYkAjYPe0eKi-U441Xz0011uiNKcTTbbhPOQ4bs6_q6eY9BWkFuxm6JBvP1WaMMtWPal2bAZD488thEA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67
- R.


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