[Freesurfer] Fw: TRACULA error- segmentation fault

[Shanika Jayakody]

External Email - Use Caution

Dear TRACULA team

I got an error in pre processing that
"Writing output files to 
/gs/gsfs0/users/helena_blumen_lab/TRACULA/30285/dlabel/syn/lh.cst_avg16_syn_bbr_*
Writing spline volume to 
/gs/gsfs0/users/helena_blumen_lab/TRACULA/30285/dlabel/syn/lh.cst_avg16_syn_bbr_cpts_7.nii.gz
Segmentation fault (core dumped)
Linux cpu-769.cluster.local 4.18.0-305.19.1.el8_4.x86_64 #1 SMP Tue Sep 7 
07:07:31 EDT 2021 x86_64 x86_64 x86_64 GNU/Linux"
I checked Freesurfer mail and found it could happen when older version are used 
but I use 7.2
I have attached the configuration file.
Thank you for any suggestions. This happened for another ID as well but for a 
different tract. I have been using similar configuration files and trac-prep 
finished without error for my other subjects
Regards
Oshadi
setenv SUBJECTS_DIR  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set dtroot =  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set subjlist = 30285
set runlist = 1
set dcmroot =  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set dcmlist = 
30285/20190619_600891701_701_WIP_110_DTI66d_2mm_SF3_SENSE_110_DTI66d_2mm_SF3_SENSE.nii
set bvecfile = 30285/bvecs.txt
set bvalfile = 30285/bvals.txt
set dob0 = 0
set doeddy = 0
set intrareg = 3
set intradof = 9
set intrarot = 90
set interreg = 5
set intertrg =  
/public/apps/freesurfer/7.2.0/trctrain/hcp/MGH35_HCP_FA_template.nii.gz
set segname = aparc+aseg
set usethalnuc = 0
set usemaskanat = 1
set thrbet = 0.3
set trainfile =  /public/apps/freesurfer/7.2.0/trctrain/hcp/trainlist.txt
set nstick = 2
set nburnin = 200
set nsample = 7500
set nkeep = 5
set reinit = 0
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Re: [Freesurfer] Longitudinal stream bug ?

[Lauri Tuominen]

External Email - Use Caution

Apologies to all. This command seems to be running just fine if I remove the 
--fwhm flag all together. I was just confused by the error message. I suspect 
that since I did not include qcache option in the initial recon-all command, 
this might have messed things up, maybe.

Have a nice day!

Lauri



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lauri Tuominen 

Sent: November-03-22 2:39 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal stream bug ?

CAUTION: External Mail. Do not click on links or open attachments you do not 
trust.
ATTENTION: Courriel externe. Ne cliquez pas sur des liens et n'ouvrez pas de 
pièces jointes auxquelles vous ne faites pas confiance.


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Hi FreeSurfer Developers,
I am trying to run a longitudinal analysis on Ubuntu 20.04.1 LTS, 
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551, and Python 3.8.5.

I use the following command:

long_mris_slopes --qdec ../tables/long.all.table.dat \
  --meas thickness \
  --hemi lh \
  --sd $SUBJECTS_DIR \
  --do-spc --do-label \
  --generic-time \
  --fwhm 15 \
  --qcache fsaverage \
  --stack-spc ../group/lh.generictime.thickness-spc.stack.mgh \
  --isec-labels lh.generictime.fsaverage.cortex.label

Error message I get is this:

mris_calc -o ./tmp-template_P08_lh_thickness_mfuld5s6/betam.mgh 
./tmp-template_P08_lh_thickness_mfuld5s6/betam.mgh add 
./tmp-template_P08_lh_thickness_mfuld5s6/beta0.mgh

Saving result to './tmp-template_P08_lh_thickness_mfuld5s6/betam.mgh' (type = 
MGH )   [ ok ]

Traceback (most recent call last):
  File "/mnt/scratch/software/freesurfer//python/scripts/long_mris_slopes", 
line 1005, in 
if fwhm > 0:
TypeError: '>' not supported between instances of 'str' and 'int'

I tried to search for this error but did not see anything. Would anyone have 
any thoughts on how to fix this?
Thanks in advance
Lauri Tuominen?
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[Freesurfer] Longitudinal stream bug ?

[Lauri Tuominen]

External Email - Use Caution

Hi FreeSurfer Developers,
I am trying to run a longitudinal analysis on Ubuntu 20.04.1 LTS, 
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551, and Python 3.8.5.

I use the following command:

long_mris_slopes --qdec ../tables/long.all.table.dat \
  --meas thickness \
  --hemi lh \
  --sd $SUBJECTS_DIR \
  --do-spc --do-label \
  --generic-time \
  --fwhm 15 \
  --qcache fsaverage \
  --stack-spc ../group/lh.generictime.thickness-spc.stack.mgh \
  --isec-labels lh.generictime.fsaverage.cortex.label

Error message I get is this:

mris_calc -o ./tmp-template_P08_lh_thickness_mfuld5s6/betam.mgh 
./tmp-template_P08_lh_thickness_mfuld5s6/betam.mgh add 
./tmp-template_P08_lh_thickness_mfuld5s6/beta0.mgh

Saving result to './tmp-template_P08_lh_thickness_mfuld5s6/betam.mgh' (type = 
MGH )   [ ok ]

Traceback (most recent call last):
  File "/mnt/scratch/software/freesurfer//python/scripts/long_mris_slopes", 
line 1005, in 
if fwhm > 0:
TypeError: '>' not supported between instances of 'str' and 'int'

I tried to search for this error but did not see anything. Would anyone have 
any thoughts on how to fix this?
Thanks in advance
Lauri Tuominen?
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[Freesurfer] Extracting GWC values from mask

[Fulton, Travis]

External Email - Use Caution

Hello FreeSurfer Developers,
I am trying to extract gray/white contrast stats for a specific area within a 
cortical region. I was able generate a mask of the significant area with:

mri_binarize --i lh.RegionOfInterest.sig.mgh --o 
lh.SignificantAreaOfROI.sig.mgh --min 1.3

However, I'm not sure how to extract the values from this mask now. 
aparcstats2table doesn't have the --stats=lh.w-g.pct.stats option that 
asegstats2table uses and I'm not sure how to proceed.

Is there a way to extract the gray/white contrast stats for this specific area 
for each of my subjects?
Any help would be greatly appreciated!
Thank you,


Travis Fulton, MS
Graduate Student
Molecular and Systems Pharmacology
Laney Graduate School | Emory University
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Re: [Freesurfer] Global diffusion metrics

[Max Korbmacher]

External Email - Use Caution

And perhaps to add, I'm particularly interested in whole-brain grey matter 
diffusion metrics.
Best,
Max

Max Korbmacher
PhD student
Western Norway University of Applied Sciences
Bergen, Norway

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Max Korbmacher 

Sent: Thursday, November 3, 2022 5:39:47 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Global diffusion metrics


External Email - Use Caution

Dear all,

I have been trying a few things to compute global (not regional) average
diffusion metrics.

Is there a function available?

Best,

Max
Max Korbmacher

PhD student
Western Norway University of Applied Sciences
Bergen, Norway
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Global diffusion metrics

[Max Korbmacher]

External Email - Use Caution

Dear all,

I have been trying a few things to compute global (not regional) average
diffusion metrics.

Is there a function available?

Best,

Max
Max Korbmacher

PhD student
Western Norway University of Applied Sciences
Bergen, Norway
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Requesting Pass Code for FS_7_2_0_ubuntu_18_04_06.ova VirtualBox Image

[Preston Bowman]

External Email - Use Caution

Good morning,

I would like to kindly request the pass code for the 
FS_7_2_0_ubuntu_18_04_06.ova VirtualBox Image.

Thanks,
Preston
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contains patient information, please contact the Mass General Brigham 
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this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] T1w/T2w ratio maps: acquisition parameters T1w and T2w

[Glasser, Matt]

External Email - Use Caution

Giving cubic volumes of voxels is a bit confusing, but I assume what you meant 
to say is that you have 1mm T1w images and 0.7mm T2w images.  Although you can 
certainly can register these and take the ratio (and FreeSurfer bbregister is 
the recommended way to do this as it has the highest accuracy of methods we 
have tested), keep in mind that your resolution of the T1w/T2w will only be as 
good as your lower resolution image.  A better study design is to match the 
spatial resolution of your T1w and T2w images so that you don’t sacrifice 
resolution or SNR and to have the spatial resolution of both T1w and T2w 0.8mm 
isotropic or better.  1mm is too coarse to accurately measure the thinnest 
cortical areas that are 1.6mm and T1w/T2w myelin mapping is especially 
demanding of surface quality, as if either the white or pial surface is not in 
the right place you will get wildly inaccurate values.  I am also assuming your 
study is at 3T and in vivo.  If those aren’t the case, many other issues can 
come into play.

Matt.

From:  on behalf of Steve Petersen 

Reply-To: Freesurfer support list 
Date: Thursday, November 3, 2022 at 3:57 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] T1w/T2w ratio maps: acquisition parameters T1w and T2w



External Email - Use Caution

Dear FreeSurfer experts,

I would like to calculate myelin maps using the ratio between T1w and T2w 
scans. However, the acquisition parameters of the T2w images are slightly 
different (e.g. voxel size T1w = 1mm3 vs voxel size T2w = 0.35 mm3 ; T1w 
matrix: 240 x 240 vs T2w matrix: 640 x 640). The first step of the protocol 
would involve a robust registration between the two MRI images (e.g. bbregister 
method) which would lead to a downsampling of the T2w images. My question is, 
could I conduct a reliable analysis of T1w/T2w ratio maps despite these 
differences in the acquisition parameters between both MRI sequences?.

Thank you very much in advance.

Best regards,

Steve.





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Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Freeview on WSL in Windows 10

[Dicamillo, Robert]

Hello Monica,

The login page you display is not accessible to the public.   We have 
information about how to get started with WSL on the public wiki pages, e.g., 
https://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wslWe talk about installing 
WSL version 1 and WSL version 2, though it reads like you already have a 
version of WSL up and running and a version of Linux installed.

With WSL running Linux, you should download the appropriate freesurfer binary 
linux .rpm or .deb installer and use that to install freesurfer.  Those are 
available per OS (CentOS 7, 8 and Ubuntu 18, 20, 22) via a link on the WSL 
pages above to here, https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads.

For Freeview to display graphics, you need to install a 3rd party X windows 
server on your windows host.  We demonstrate using Xming but some users have 
not been able to get Xming to work but have had success with MobaXterm.

WSL is a work in progress and can change without notice when Microsoft 
automatically updates your Windows machine.  We cannot guarantee the current 
version of WSL, the 3rd party X-servers, and the specifics graphics 
card/hardware in your computer are all going to cooperate to allow X-windows 
graphics to work.

If WSL does not work for you, an alternative its to use a different 
virtualization technology like VirtualBox instead of WSL.   We have a 
pre-installed version of Freesurfer 7.2.0 inside an Ubuntu 18 VM that runs 
under Virtualbox.  That eliminates having to use/install an X-server on your 
Windows machine.  Information about installing VierualBox and running the 
Freesurfer Ubuntu 18 VM can be found under, https://freesurfer.net/fswiki/VM_67

- R.

On Nov 3, 2022, at 04:11, Monica Crotti 
mailto:monica.cro...@kuleuven.be>> wrote:

External Email - Use Caution

Dear Freesurfer developers,

I am writing to you with regard to two issue I would like to address:

1. I subscribe to the email list but when I am trying to access the page 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://mail.nmr.mgh.harvard.edu/NMRAuth/GLOBAL/LOGIN
 I got the following error


2. I installed Freesurfer on a WSL2 environment on my computer Windows 10. 
Neverthless, I am unable to run the freeview command. I looked into web for 
solutions related to the error I got which is the following

freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: 
cannot open shared object file: No such file or directory

Following what I found on the web, I run the following commands

$sudo add-apt-repository ppa:ubuntuhandbook1/ppasudo

apt-get install qt4-dev-tools libqt4-dev libqtcore4 libqtgui4

and I get the following errors

base) root@GBW-L-W3359:/usr/local/KUL_apps/freesurfer# cd bin/
(base) root@GBW-L-W3359:/usr/local/KUL_apps/freesurfer/bin# ldd 'freeview.bin' 
| grep not
libvtkverdict.so.5.6 => not found
libvtkGraphics.so.5.6 => not found
libvtkmetaio.so.5.6 => not found
libvtkpng.so.5.6 => not found
libvtkzlib.so.5.6 => not found
libvtksqlite.so.5.6 => not found
libvtkImaging.so.5.6 => not found
libvtkFiltering.so.5.6 => not found
libvtkCommon.so.5.6 => not found
libvtksys.so.5.6 => not found
libvtkGenericFiltering.so.5.6 => not found
libvtkexoIIc.so.5.6 => not found
libvtkNetCDF.so.5.6 => not found
libvtkVolumeRendering.so.5.6 => not found
libvtkRendering.so.5.6 => not found
libvtkftgl.so.5.6 => not found
libvtkWidgets.so.5.6 => not found
libvtkHybrid.so.5.6 => not found
libvtkIO.so.5.6 => not found
libvtkDICOMParser.so.5.6 => not found

I was wondering if you could help me in solving this issue.

Thank you in advance,
Best regards

Monica
Monica Crotti, M.Sc. | PhD Student
Locomotor and Neurological Disorders Group
Department of Development and Regeneration
KU Leuven, Belgium

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[Freesurfer] Password request for the FS_7_2_0_Ubuntu_18_04_06.ova VirtualBox image

[Siemerkus Jakob]

External Email - Use Caution

Dear FreeSurfer community,

I just downloaded the Virtualbox S_7_2_0_Ubuntu_18_04_06.ova - image
and would kindly like to ask if you could send me the password for
unzipping the archive.

Thank you very much in advance,
J

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[Freesurfer] T1w/T2w ratio maps: acquisition parameters T1w and T2w

[Steve Petersen]

External Email - Use Caution

Dear FreeSurfer experts,

I would like to calculate myelin maps using the ratio between T1w and T2w
scans. However, the acquisition parameters of the T2w images are slightly
different (e.g.* voxel size T1w* = 1mm3* vs* *voxel size T2w* = 0.35 mm3 ;*
T1w matrix:* 240 x 240 *vs* *T2w matrix:* 640 x 640). The first step of the
protocol would involve a robust registration between the two MRI images
(e.g. bbregister method) which would lead to a downsampling of the T2w
images. My question is, could I conduct a reliable analysis of T1w/T2w
ratio maps despite these differences in the acquisition parameters between
both MRI sequences?.

Thank you very much in advance.

Best regards,

Steve.
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