Re: [Freesurfer] FreeView cannot open any images

2022-12-01 Thread Fischl, Bruce R.,PHD 
Hi Greta

Make sure you are in the "3D" view (the icon that looks like a little head next 
to the coronal/axial/sagittal ones)

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Greta Tuckute
Sent: Thursday, December 1, 2022 6:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FreeView cannot open any images

Hello,

I am attempting to use FreeView (have used it successfully for a few years, but 
suddenly it stopped working — cannot identify any cause. Have not updated 
operating system or similar). 
The problem is that nothing is loaded or shown. I cannot load e.g., an inflated 
LH surface from fsaverage. Running:

❯ freeview -f /Applications/freesurfer/subjects/fsaverage/surf/lh.inflated

Only opens FreeView and shows the background. lh.inflated is shown under 
“Surfaces” in the upper left corner, but nothing is shown. Nothing changes with 
“Reset view”. I tried:

- Updating FreeView (did not help)
- Reinstalled FreeSurfer (did not help either)

Any idea what is going on? No error message. Other FreeSurfer commands work 
fine.

FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg (FreeView: 
freesurfer-darwin-macOS-dev-freeview.tar.gz from 

Operating system: macOS Catalina, version 10.15.7 (19H1824)


Thanks so much,
Greta



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[Freesurfer] FreeView cannot open any images

2022-12-01 Thread Greta Tuckute 
Hello,

I am attempting to use FreeView (have used it successfully for a few years, but 
suddenly it stopped working — cannot identify any cause. Have not updated 
operating system or similar). 
The problem is that nothing is loaded or shown. I cannot load e.g., an inflated 
LH surface from fsaverage. Running:

❯ freeview -f /Applications/freesurfer/subjects/fsaverage/surf/lh.inflated

Only opens FreeView and shows the background. lh.inflated is shown under 
“Surfaces” in the upper left corner, but nothing is shown. Nothing changes with 
“Reset view”. I tried:

- Updating FreeView (did not help)
- Reinstalled FreeSurfer (did not help either)

Any idea what is going on? No error message. Other FreeSurfer commands work 
fine.

FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg (FreeView: 
freesurfer-darwin-macOS-dev-freeview.tar.gz from 

Operating system: macOS Catalina, version 10.15.7 (19H1824)


Thanks so much,
Greta




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[Freesurfer] ERROR: fast_mat2vol

2022-12-01 Thread stdp82 
External Email - Use Caution

 I would extract the rs-fMRI timeseries from Yeo’s Network components. 


 I’m running: 
preproc-sess -s ${1} -fsd rest -sliceorder up -surface self lhrh -fwhm 0 
-per-runfcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config 
fcseed-sess -s ${1} -cfg wm.configfcseed-config -vcsf -fcname vcsf.dat -fsd 
rest -pca -cfg vcsf.configfcseed-sess -s ${1} -cfg vcsf.config


 mkanalysis-sess -analysis fc.noseed.surf.lh -surface self lh -fwhm 0 -notask 
-nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest 
-TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten 
 mkanalysis-sess -analysis fc.noseed.surf.rh -surface self rh -fwhm 0 -notask 
-nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest 
-TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten 


 The line below produced this error: 


 selxavg3-sess -s ${1} -a fc.noseed.surf.lh -no-con-ok -svres 
Saving rho1

ERROR: fast_mat2vol: szvol inconsistent with mat2d  nv = 151008, size(mat,2) = 
142954  run 2t= 1.6reading data ... 0.518631Temporally filteringSaving rho1

ERROR: fast_mat2vol: szvol inconsistent with mat2d  nv = 151008, size(mat,2) = 
142954Found 0 voxels with corrected AR1 > 0.90Not WhiteningFound 8054 
zero-valued voxelsComputing contrasts

The res folder in fc.noseed.surf.lh or fc.noseed.surf.rh contains

 res-001.nii.gz 158KB 
 res-002.nii.gz 158KB 


 that cannot be opended. 


 Stefano ___
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[Freesurfer] [Tracula] ERRORS when using trac-all -prep

2022-12-01 Thread h21ms-utsumi 
External Email - Use Caution

Dear Freesurfer experts

I'm attempting to running TRACULA in a two subjects(one visit per 
subject and multiple deffusion scans per visit), as described on the 
TRACULA tutorial 
(https://secure-web.cisco.com/1YZplCc8ElxyKpvsfXb9OH_SNhToXmmPHixjCRlcZ51VHS12nUQQG4rMQybDPmP5RRwTYpZXLYBDCgi-aVwgAkIbD7f1nuv3qCRerbwqiEFE3PYEbp8GmUG0QZj8fv0kGh0sKwEI4r8ULPKz8OVdmWBr0me7wibJF1a8l5S74YstX_dkTB88f-aX5wFUKO798aWohHBR8zND-FMrt7oygYVYxsL29Q_PPvrSO9pY3WzpuLzpxcRYLe5zFQCaLJXJBW7T8VmIUQnJULc6AZpBWEUkPcavsBb5sLnWOQo8mARajKxbGYJ0zVdvJ3F9BgYZk/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula,
 
https://secure-web.cisco.com/1nYtHW48eZdU7uUKv6TSjlFm9HP9CHGRmfSeoCOA7uunK3kIdhbSPNPcLfk5dxLcxWFiX2iHtjYsKFFHkoFhohA_CBpmhn00TFI7dj_A6_Ysx-lUshF_hf_8PUjxAdpehn-lqUTRnrPxgpYcsx8A0aJH2TTRWCAIqy17bdWBFVgQAQXbJRvtSUG4WJIHGUl8JnW7AvLKo8ViJ0qpfJKeQBkqJjtDD6vV1cJ-eyupl192QAfm_n0WbMnvunlfpzAz7Gt1ah6Mj6aSc5x3uQJeB0H0geYTLMZzvPA2AGFf8b1ADynWtOKW4a5-jHY9CyqkY/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fdmrirc,
 and 
https://secure-web.cisco.com/1i1x3WraESWH3k6zfmnPSieIq0qc66z7vq-nTTa6dKs81QaXyWb6SELvy3WVyD4G2zXOxWyMoa9XtbxMRvjRsZ8tCmHNGXEDfM3VvK19JRnw0BNx6bRO_1uIqy-6a2bcwHFYJ8Wpsym4MKm4wLCe8sqjV1P1uLv0rPNiOI771Wzr84BYMrpjzpwRR71UoYzZtPxhIN-6WqahEpeiW4OVNDbAMgz1WtV3OkZCxRKIR2CiF8R5TgCo6YpME4qVk5AgiEQFOpb86ElM97aPZcBORWVC4QR_7uCE_2Wrn1yTXf-9xfT2DGJhaCR9NpAzjOaVZ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FRunningTracula),
 
but for my subjects I get the following error when I run the trac-all -
prep:

cp dwi.nii.gz /media/sf_share\freesurfer\7.3.2/subjects/diffusion_
tutorial/trc/subject1/dmri/data.nii.gz 
cp: cannot stat 'dwi.nii.gz': No such file or directory.

I checked the "dmri" directory and found that "data.nii.gz" was missing 
and "dwi.nii.gz " was there.

I've searched the archive list and I found the following two things;
 the dwi.nii.gz file is the DWI after all corrections have been made 
and the data.nii.gz file is a symbolic link to the other, so they should 
be the exact same file.
(https://secure-web.cisco.com/1qq_o3GFIoLx7Luv5Fgj2ZN5KBHCJCZzPPrZqzLzT3BdzI8z8iY0s3aw9ZiV1ZqrrmxTI8XTA7nXUIB1qpFj5LqqBdPnBFaZ7iS_mKC527GAIGxaf0Xr1d2hXyykfiJOg9la8SZsvG8hbRNzs9LKMucBEe_Qsq-Te92e_afgT0lgv8YjlwRCN8x4bLchbzgTax5xSIp36ImbKD-ULL5sKdOAT5Pt0iuy9S3llRWzxBj7k662wVU597F1GBdua-M2DqRsS_Ma2-VjUuqnpz_xJdR-CTlUc7ijJhoRDUMxdkCoZUzK06Oqx9Idmes9tVreb/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg39432.html)

 the data.nii.gz file is necessary for the process of "trac-all -bedp", 
not "trac-all -prep." 
(https://secure-web.cisco.com/1pjKE3HFIeU-FqIoHgU1xkoI3rom-BBboaeTQQ7MDiNVT78circo6cATHKBmSd6J0ggcrbRvJqQf9IqYLORohmBgZdmcnpjU0riT_Om05ORgE8YJiCXCAmGSQgA6bQw4ha8P5_aKiMWMMgVUnzTTyI4H1y9WPnVdAAGVvbf1a7xYUQHr4BKvE2zHSekVxYMsuHjf7wzvKK8F5QBedOY7m2_gAJA1y5HMgkJegAV_UG7qtaryWKAw2h2YWsWvJaig4iDNnu3bIRvxRxdg57lv8ZdiG6JgvjMwo1IsofvAdHvq9F47TrXAwtRnT8bgoBDMu/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg24254.html).


However, no similar errors have been reported. Does anyone have any 
thoughts on how to trouble-shoot this one? Also, Ive attached the dmrirc.
tutorial, trac-all.log, pre-diffusion_tutorial_tree.text, and post-
diffusion_tutorial_tree.text in case it's of any use. 

Best regards, 

Tomohiro Utsumi.


 
Tomohiro Utsumi, PhD Student.
Department of Psychiatry, The Jikei University School of Medicine, Tokyo,
 Japan.




dmrirc.tutorial
Description: Binary data
brain@l4n:/media/sf_share/freesurfer/7.3.2/subjects/diffusion_tutorial$ tree
.
|-- diffusion_tutorial_tree.txt
|-- fs
|   |-- subject1
|   |   |-- label
|   |   |   |-- BA_exvivo.ctab
|   |   |   |-- BA_exvivo.thresh.ctab
|   |   |   |-- aparc.annot.DKTatlas.ctab
|   |   |   |-- aparc.annot.a2009s.ctab
|   |   |   |-- aparc.annot.ctab
|   |   |   |-- lh.BA1_exvivo.label
|   |   |   |-- lh.BA1_exvivo.thresh.label
|   |   |   |-- lh.BA2_exvivo.label
|   |   |   |-- lh.BA2_exvivo.thresh.label
|   |   |   |-- lh.BA3a_exvivo.label
|   |   |   |-- lh.BA3a_exvivo.thresh.label
|   |   |   |-- lh.BA3b_exvivo.label
|   |   |   |-- lh.BA3b_exvivo.thresh.label
|   |   |   |-- lh.BA44_exvivo.label
|   |   |   |-- lh.BA44_exvivo.thresh.label
|   |   |   |-- lh.BA45_exvivo.label
|   |   |   |-- lh.BA45_exvivo.thresh.label
|   |   |   |-- lh.BA4a_exvivo.label
|   |   |   |-- lh.BA4a_exvivo.thresh.label
|   |   |   |-- lh.BA4p_exvivo.label
|   |   |   |-- lh.BA4p_exvivo.thresh.label
|   |   |   |-- lh.BA6_exvivo.label
|   |   |   |-- lh.BA6_exvivo.thresh.label
|   |   |   |-- lh.BA_exvivo.annot
|   |   |   |-- lh.BA_exvivo.thresh.annot
|   |   |   |-- lh.FG1.mpm.vpnl.label
|   |   |   |-- lh.FG2.mpm.vpnl.label
|   |   |   |-- lh.FG3.mpm.vpnl.label
|   |   |   |-- lh.FG4.mpm.vpnl.label
|   |   |   |--