[Freesurfer] Problem with tkregister2/tkregisterfv

[Nadvar, Negin]

External Email - Use Caution

Good afternoon,


I’m trying to run “tkregister2” in the following code for a manual registration 
correction:
 tkregister2 --mov ./fMRI_run1.nii.gz --reg ./Reg.lta --surfs  --sd 
${SubjectsFolder}


The above command works fine in older versions of FreeSurfer, but with the new 
version that I have, I’m getting the following error:

 Tcl_Init failed: Can't find a usable init.tcl in the following directories:
/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4
This probably means that Tcl wasn't installed properly.


I get the same error with "tkregisterfv". Here’s more info about my system, in 
case it helps. OS: Linux Ubuntu 18, FreeSurfer version: 
freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460, Python version: Python 
3.11.4, FSL version: 6.0.7.1

Please let me know if there's a known solution for this issue.

Thank you,

Negin

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[Freesurfer] Longitudinal multimodal processing

[gabriel robert]

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Dear experts in longitudinal neuroimaging

We carefully read the papers about possible biases introduced by treating
timepoints images differently (Reuter and Fischl NI 2011, for example) to
estimate unbiased anatomical and functional changes of brain development in
healthy individuals. We took good note that treating each time point
independently would remove asymmetry biases at the cost of reduced power.

In our project, we would like to analyze about 800 scans both 3DT1,
diffusion (FA preprocessed with fsl TBSS) and functional task BOLD at 3
time points (14 years-old, 19 years-old and 23 years-old).

Each time point scans are preprocessed individually and normalized to a
specific group-based template at the corresponding time point (not a
within-subject midpoint symmetric space) and to the standard MNI space.

Our question: We'd like to use a home-made study-specific multimodal atlas
to resample ROI BOLD mean contrasts and fractional anisotropy at each time
point but this atlas is *based on the last time point only (23 years-old).*
Does this situation fall into the 'asymmetry-induced bias in longitudinal
processing' ?

Our feeling is most probably yes but given the sample size this is likely
to be marginal compared to the effect size and results would still be
interpretable... ?

Many thanks for time, interest and insight,

Best wishes

Gabriel
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Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan

[KennethSPrice]

External Email - Use Caution

I looked through the thread and downloaded VirtualBox. Freesurfer 5.1 
installation was working fine but mounting my drive and sharing folders 
required so many libraries which are now defunct, it just wasn't worth it. I 
wrangled with the machine for a while but it seems easier to just process 
everything with freesurfer 7.4.

Thanks,
K
--- Original Message ---
On Monday, September 18th, 2023 at 8:02 AM, Huang, Yujing 
 wrote:

> External Email - Use Caution
>
> You are using Freesurfer 5.1 
> (freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0). I’m wondering if it is 
> software compatibility issue.
>
> There are suggestions on how to run Freesurfer 5.1 from container in this 
> posting - [MailScanner has detected a possible fraud attempt from 
> "secure-web.cisco.com" claiming to be 
> https://secure-web.cisco.com/18JSemI8UZisRAbamkAD4iEpeHnPbUto45vp33zIyv6IxlxH6YY_ccXNVq1bmims4D73UhRQQc55skHaxr7mL7bmo19VXhughEQHs2oC_SgCBJM6Pspz18oq8ETY0yiZ1gy_iRlnnHVgzkRWKKBU7p8dUY_RNJ_fp0F9C4ruTUINzQs8aE-tbwUm-j7sbo67BsA1NUuAarLEtmv7TBc0UASWbPhDkfweJtDJ3L6B75NnbOyr3i0vR2CYwEgegY0UcJ8KS_XX7uqmR6GcFKyqky_Tz-Zpj_rxSLW8dM8V85Hz-FiK6aR0GUgu-JXHRsTQE/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74552.html](https://secure-web.cisco.com/1zoee5Wuv_DvRaT0fpKqBwycBeglhqic772BD4C6VpO6izm3ko3HbKPFAhhiSvHUnH2VQsVbbE6SCsil2t_uZiXawtT72CtBfi8VIAFZuWUn25D4ubxeaap7woc9mG9Yy1Wu1Es0agG-DTknpF_Wehz_xUywjWQyLGqahiHTWbSDXkJDIkMD-VXedp_TMcIAgjTWyYdyMA1Vy2cRruqatwVaE03hCpnXnjrovVfhMKBXrWCBilDshe2qF6UT2gEt4/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74552.html)
>
> Hope this helps.
>
> Best,
>
> Yujing
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of KennethSPrice
> Sent: Sunday, September 17, 2023 11:35 AM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) 
> synthsr scan
>
> External Email - Use Caution
>
> I've set the coredumpsize to unlimited, and still get the same error. Could 
> it be something with the installation?
>
> build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
>
> Linux DESKTOP-MRI 4.4.0-19041-Microsoft #3393-Microsoft Mon Aug 14 14:52:00 
> PST 2023 x86_64 x86_64 x86_64 GNU/Linux
>
> cputime unlimited
>
> filesize unlimited
>
> datasize unlimited
>
> stacksize 8192 kbytes
>
> coredumpsize unlimited
>
> memoryuse unlimited
>
> vmemoryuse unlimited
>
> descriptors 1024
>
> memorylocked 64 kbytes
>
> maxproc 7823
>
> maxlocks unlimited
>
> maxsignal 7823
>
> maxmessage 819200
>
> maxnice 0
>
> maxrtprio 0
>
> maxrttime unlimited
>
> total used free shared buff/cache available
>
> Mem: 16643620 4264632 12149636 17720 229352 12245256
>
> Swap: 29192228 0 29192228
>
> --- Original Message ---
> On Saturday, September 16th, 2023 at 9:49 PM, fsbuild  
> wrote:
>
>> External Email - Use Caution
>>
>> Hello Ken,
>>
>> The output from your linux shell limits in the log show the following,
>>
>> cputime unlimited
>>
>> filesize unlimited
>>
>> datasize unlimited
>>
>> stacksize 8192 kbytes
>>
>> coredumpsize 0 kbytes
>>
>> memoryuse unlimited
>>
>> vmemoryuse unlimited
>>
>> descriptors 1024
>>
>> memorylocked 64 kbytes
>>
>> maxproc 7823
>>
>> maxlocks unlimited
>>
>> maxsignal 7823
>>
>> maxmessage 819200
>>
>> maxnice 0
>>
>> maxrtprio 0
>>
>> maxrttime unlimited
>>
>> I would set at least coredumpsize to something non-zero so you can at least 
>> get a core file saved that could be looked at. By default the limits on my 
>> Ubuntu 22 system are:
>>
>> $ ulimit -a
>>
>> real-time non-blocking time(microseconds, -R) unlimited
>>
>> core file size(blocks, -c) unlimited
>>
>> data seg size (kbytes, -d) unlimited
>>
>> scheduling priority (-e) 0
>>
>> file size (blocks, -f) unlimited
>>
>> pending signals (-i) 378881
>>
>> max locked memory (kbytes, -l) 64
>>
>> max memory size (kbytes, -m) unlimited
>>
>> open files(-n) 1048576
>>
>> pipe size(512 bytes, -p) 8
>>
>> POSIX message queues (bytes, -q) 819200
>>
>> real-time priority(-r) 0
>>
>> stack size(kbytes, -s) 8192
>>
>> cpu time (seconds, -t) unlimited
>>
>> max user processes(-u) unlimited
>>
>> virtual memory(kbytes, -v) unlimited
>>
>> file locks(-x) unlimited
>>
>> You can try setting the core file size to unlimited with,
>>
>> $ ulimit -c unlimited
>>
>> ... then check the value was changed to something > 0 ...
>>
>> $ ulimit -a
>>
>> You could increase memory size (and as many shell limits as possible) to 
>> unlimited to get the max size allowed by the system in the script you use to 
>> run recon-all, and then try running recon-all again to see if you can 
>> retrieve a core dump file.
>>
>> - R.
>>
>>> On Sep 16, 2023, at 09:55, KennethSPrice  
>>> wrote:
>>>
>>> External Email - Use Caution
>>>
>>> OK, I've attached the log file.
>>>
>>> --- Original Message ---
>>> On Friday, September 15th, 2023 at 2:59 PM, fsbuild  
>>> wrote:
>>>
 External Email - 

Re: [Freesurfer] freeview upgrade isn’t working/library issue

[fsbuild]

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I don't think we can guarantee upgrading freeview will work with the 
existing libraries in a sufficiently old freeview distribution. I’m not 
sure what version of Ubuntu is running from the kernel listed below, but you 
could create a backup of your existing freesurfer tree (if you need to keep 
it), and then run the .deb freesurfer 7.4.1 installer matching your system 
(Ubuntu 18, 20, 22) which you can download from,
https://secure-web.cisco.com/1W5Z7do8RHfQJIQIHZ9EbWhe5GYVhLQ8shO8lqEwhsAE6gDaexj3KfFN5zXfZdCA7mfyFvRUV606uEVX8q8IDVG0LNCC0MZeeiPwAtx_-ZxvtEW4-pSlPhehcCbUhEw62kOvNMbYel7i60_-I4om9lr8wCgQc4VQO3UDbDmVYy7BHSKG7VWmKi_tDBsO0qgu5TkBA4znCgxcoZom8erNkPY1dTUq2y5hUZ73nRKztQ4HU7CbYVPgsEOkDiB0P7MIm4uK7VAY2YIXUAPB2HVffR_qC0byOa-k5I7Iw2kPda10T0X0yWknO4wH7-RH0OuZWCBOv1vPCtSOENEHGX5Zf0w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
- R.

On Sep 19, 2023, at 15:33, Hoptman, Matthew (NKI) 
matthew.hopt...@nki.rfmh.org 
wrote:External Email - Use 
CautionTO:freesur...@nmr.mgh.harvard.eduFROM:matthew.hopt...@nki.rfmh.orgSUBJECT:
 freeview upgrade isn’t working/library issueHello FreeSurfer 
Developers,I followed the instructions here to upgrade 
freeview:MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeviewI am now getting the 
error:freeview: error while loading shared libraries: 
libvtkDomainsChemistry-7.1.so.1: cannot open shared object file: No such file 
or directoryI saw that it was recommended to install the package 
libvtk7.1, but that isn’t working:E: Unable to locate package libvtk7.1E: 
Couldn't find any package by glob 'libvtk7.1'Any help is appreciated. I 
am using:5.4.0-122-generic #138-Ubuntu SMP Wed Jun 22 15:00:31 UTC 2022 x86_64 
x86_64 x86_64 GNU/LinuxThanks,MattIMPORTANT NOTICE: This 
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cooperation.___Freesurfer 
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listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Recall: freeview upgrade isn’t working/library issue

[Hoptman, Matthew (NKI)]

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Hoptman, Matthew (NKI) would like to recall the message, "freeview upgrade 
isn’t working/library issue".



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[Freesurfer] freeview upgrade isn’t working/library issue

[Hoptman, Matthew (NKI)]

External Email - Use Caution

TO: freesurfer@nmr.mgh.harvard.edu
FROM: matthew.hopt...@nki.rfmh.org
SUBJECT: freeview upgrade isn’t working/library issue

Hello FreeSurfer Developers,

I followed the instructions here to upgrade freeview:
https://secure-web.cisco.com/1Fr1m43dMDo6PfZjwvbGiKtV6gtUUqAq08NIpRJf8nkhbpl6t_xCxggb1kwbhGAFGwTRhGkv4sWJDCjuHWTgohXGwrq-nAIvtq0Nfdd0_tSvmjvKWkv0IlMgpiIVnUf21uW4udZFN11ePTzTN75eirFuiyPk5w32ox5i_idq8DjZL2rE1Lhw9aSRLi3dL4VfG-EQQoTkGSI8C9oJRQKc6GjfomWHQ9wZBHqlQ-up71hJye297HHynBTUWYmHHjdXxRE8hiF6oPiasyVgS3wzts8TCnn2zZEmlDUcp4aN9Vjx2Xj6vUXf5no1SeK6B6hk0/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FUpdateFreeview

I am now getting the error:
freeview: error while loading shared libraries: 
libvtkDomainsChemistry-7.1.so.1: cannot open shared object file: No such file 
or directory

I saw that it was recommended to install the package libvtk7.1, but that isn’t 
working:
E: Unable to locate package libvtk7.1
E: Couldn't find any package by glob 'libvtk7.1'

Any help is appreciated. I am using:
5.4.0-122-generic #138-Ubuntu SMP Wed Jun 22 15:00:31 UTC 2022 x86_64 x86_64 
x86_64 GNU/Linux

Thanks,
Matt


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