[Freesurfer] Thalamic segmentation with FGATIR not running

2024-03-12 Thread Amrita Pal 
External Email - Use Caution

Hi

While doing thalamic segmentation with FGATIR additional volume, I am
getting an error that
"BIAS field corrected version of additional volume found; no need to recompute
error: No such file or directory
error: WARNING: 419053 NaNs found in volume tempT1.mgz..
and I get a blank ThalamicNucleiv.12.FGATIR.mgz

Can you please help spot the error?

Thanks and regards

-- 
Amrita


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Re: [Freesurfer] Thalamic segmentation tool: question about input files from recon

2023-01-05 Thread Douglas N. Greve 
I think it has to go through the whole recon as it uses wmparc.mgz and 
that is one of the last things created


On 1/5/2023 4:16 AM, Verónica E wrote:


External Email - Use Caution

Dear all,

I am planning to run the thalamic segmentation (as implemented on 
FreeSurfer 7.1). The data has been already preprocessed with 
FreeSurfer 5.3, but I want to rerun the recon step on the newer 
FreeSurfer version. My question is, which recon output images does the 
thalamic segmentation use as input? It would make a considerable 
difference for us if we could only rerun up to e.g. the normalization 
instead of the whole recon (e.g. to get the aseg.mgz file) in 
FreeSurfer 7.


Sincerely,
Verónica

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[Freesurfer] Thalamic segmentation tool: question about input files from recon

2023-01-05 Thread Verónica E 
External Email - Use Caution

Dear all,

I am planning to run the thalamic segmentation (as implemented on FreeSurfer 
7.1). The data has been already preprocessed with FreeSurfer 5.3, but I want to 
rerun the recon step on the newer FreeSurfer version. My question is, which 
recon output images does the thalamic segmentation use as input? It would make 
a considerable difference for us if we could only rerun up to e.g. the 
normalization instead of the whole recon (e.g. to get the aseg.mgz file) in 
FreeSurfer 7.

Sincerely,
Verónica
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Re: [Freesurfer] Thalamic segmentation error

2022-10-25 Thread Alan Francis 
External Email - Use Caution

Thank you Eugenio and R. It works great.

On Wed, Oct 19, 2022 at 4:04 PM fsbuild  wrote:

>
> You shouldn’t be getting errors about libcuda (which we do not support).
>
> If you have not already done so, please try the script we provide to
> install the Matlab runtime environment,
>
> $ cd $FREESURFER_HOME/bin
> $ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr  R2014b
>
> - R.
>
> On Oct 19, 2022, at 16:41, Alan Francis  wrote:
>
> External Email - Use Caution
>
> Hi Eugenio -
>
> Thanks for your reply. We have a Linux Tech. He installed it for me.
> Should I reinstall the runtime ?
>
> Thanks,
>
> Alan
>
> On Tue, Oct 18, 2022 at 2:59 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
>> Dear Alan,
>> How did you install the runtime? Did you follow the instructions in the
>> wiki?
>> Cheers,
>> /Eugenio
>>
>> Juan Eugenio Iglesias
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be* 
>> http://secure-web.cisco.com/1NxrZiMBZIdOtAR8_r0nmuYuSKlfrnrMQ1VsI-DCGLHVaFe67Jmp6vDjJys7VNCUAtlxQu8zVVkZucqVuJTst6se9e57PrcV1H4IsHrGXpL0J-xOa2Bsj_ZrPxy3v6kb3-_sfC6kxTN7XC01Gj2wkhaKy5Hm5q2jKK96UcRRs-19EN9T3FRRhNQqs802nFdzbH_fe5FPiuaf5uu_r8G7zFfuNNMExlUDnl9--VSlvUZ8II2vCfDYHH-2UKuhOAnFVFkX77l84F9bXexJUkrTCsb96rzLUSSnTNG275pUsWjh_WvXvOHdgodhF8dNVBj-L/http%3A%2F%2Fwww.jeiglesias.com
>> 
>>
>>
>> On Oct 18, 2022, at 2:37 PM, Alan Francis 
>> wrote:
>>
>> External Email - Use Caution
>>
>> Hi Eugenio -
>>
>> Hope all is well. I am running FS 7.2. I have installed the MATLAB
>> Runtime 2014b. However when I run the thalamic segmentation routine I get
>> this error. Please help.
>>
>> Thanks,
>>
>> Alan
>>
>> copernicus:~/IMAGING> segmentThalamicNuclei.sh 973770
>> Setting ITK threads to 1
>> #
>> #@# Thalamic Nuclei processing Tue Oct 18 12:25:06 PM CDT 2022
>> --
>> Setting up environment variables
>> ---
>> LD_LIBRARY_PATH is
>> .:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:
>> /usr/local/freesurfer/bin/SegmentThalamicNuclei: error while loading
>> shared libraries: libicudata.so.52: cannot open shared object file: No such
>> file or directory
>> Command exited with non-zero status 127
>> @#@FSTIME  2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 e 0.01 S
>> 0.00 U 0.00 P 33% M 2256 F 11 R 621 W 0 c 1 w 25 I 1776 O 0 L 0.69 0.22 0.07
>> @#@FSLOADPOST 2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 0.69
>> 0.22 0.07
>> 127
>> Linux copernicus 5.15.0-50-generic #56-Ubuntu SMP Tue Sep 20 13:23:26 UTC
>> 2022 x86_64 x86_64 x86_64 GNU/Linux
>>
>> Thalamic nuclei exited with ERRORS at Tue Oct 18 12:25:06 PM CDT 2022
>>
>> For more details, see the log file
>> /home/alanfrancis/IMAGING/FREESURFER_SUBJECTS//973770/scripts/thalamic-nuclei-mainFreeSurferT1.log
>>
>> --
>> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>>
>>
>>
>> *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
>> Neuroscience*
>> *University of Texas, School of Medicine*
>>
>> *Rio Grande Valley*
>>
>> *Texas.*
>>
>>
>> ___
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>>

Re: [Freesurfer] Thalamic segmentation error

2022-10-19 Thread fsbuild 
External Email - Use Caution

You shouldn’t be getting errors about libcuda (which we do not support).
If you have not already done so, please try the script we provide to install 
the Matlab runtime environment,

$cd $FREESURFER_HOME/bin$sudo FREESURFER_HOME=$FREESURFER_HOME 
./fs_install_mcr R2014b
- R.
On Oct 19, 2022, at 16:41, Alan Francis alandarkene...@gmail.com 
wrote:External Email - Use 
CautionHi Eugenio -Thanks for 
your reply. We have a Linux Tech. He installed it for me. Should I reinstall 
the runtime ?Thanks,AlanOn Tue, Oct 18, 2022 at 2:59 PM Iglesias Gonzalez, Juan 
E. jiglesiasgonza...@mgh.harvard.edu wrote:Dear Alan,How did you 
install the runtime? Did you follow the instructions in the 
wiki?Cheers,/EugenioJuan Eugenio IglesiasMailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to 
behttp://secure-web.cisco.com/1CU2rXmtEeXSOj0JKFwB3VuWcd145hFeSGV-cS6p3wsULZfgCrr0Eg1vbiZOdpl-djAZHbbmgSlnaxHA5s-bjBQkjtnq4MhkzbMkarBhcbP6CiSxCzDlsKYZuCp0DxHq9aJO27vKoy4FtiQJCyOYXPSGomTWVUUwSGclXPk4rhzVDJcQSnQKiYnvtrSFvURyYy6xcscqanTCtJAvcKOOotIqBkoa3VsDMmJlZCoiR1Mb8R7zWXe5Wa-v68GOSE45zlgnP2yImIYOsq1G-F2hrwMdQsM99zSKu_w3OCFiPPFh8lKQWDvFc1guSKr5siSaWVUklTU3unjAVgqoyqUxHgA/http%3A%2F%2Fwww.jeiglesias.comOn
 Oct 18, 2022, at 2:37 PM, Alan Francis alandarkene...@gmail.com 
wrote:External Email - Use 
CautionHi Eugenio -Hope 
allis well. I am running FS 7.2. I have installed the MATLAB Runtime 
2014b. However when I run the thalamic segmentation routine I get this error. 
Please help.Thanks,Alancopernicus:~/IMAGING segmentThalamicNuclei.sh 
973770Setting ITK threads to 1##@# 
Thalamic Nuclei processing Tue Oct 18 12:25:06 PM CDT 
2022--Setting up environment 
variables---LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/freesurfer/bin/SegmentThalamicNuclei:
 error while loading shared libraries: libicudata.so.52: cannot open shared 
object file: No such file or directoryCommand exited with non-zero status 
127@#@FSTIME 2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 e 0.01 
S 0.00 U 0.00 P 33% M 2256 F 11 R 621 W 0 c 1 w 25 I 1776 O 0 L 0.69 0.22 
0.07@#@FSLOADPOST 2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 0.69 
0.22 0.07127Linux copernicus 5.15.0-50-generic #56-Ubuntu SMP Tue Sep 20 
13:23:26 UTC 2022 x86_64 x86_64 x86_64 GNU/LinuxThalamic nuclei exited with 
ERRORS at Tue Oct 18 12:25:06 PM CDT 2022For more details, see the log file 
/home/alanfrancis/IMAGING/FREESURFER_SUBJECTS//973770/scripts/thalamic-nuclei-mainFreeSurferT1.log--|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|Alan
 N. Francis PhDAssistant Professor of NeuroscienceInstitute of 
NeuroscienceUniversity of Texas, School of MedicineRio Grande 
ValleyTexas.
   
   
   
   
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Re: [Freesurfer] Thalamic segmentation error

2022-10-19 Thread Alan Francis 
External Email - Use Caution

Hi Eugenio -

Thanks for your reply. We have a Linux Tech. He installed it for me. Should
I reinstall the runtime ?

Thanks,

Alan

On Tue, Oct 18, 2022 at 2:59 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:

> Dear Alan,
> How did you install the runtime? Did you follow the instructions in the
> wiki?
> Cheers,
> /Eugenio
>
> Juan Eugenio Iglesias
> http://secure-web.cisco.com/1-F2deM4oNalZVW-blsG0oWLgbKUPi9lklFoUJexQqa87w6TBW80F65uV3keXC_JNnhNLjdgs5T3DVG3xGEMIgcb7cMHk2Q_ALBFO9Oi6RrXZyCulsv9K8E_IWAPqNCnI1vFAlkCEf71E98zI0kcYlNH6bHeV9q3ASpBGrbdZM55ULbrYFlerLR3edJIPeSOZkReV7GSq0OlTnO8h6R0G38zKEZdDh-2r98CGtXw-xmmNTNyKlT9K-tpnOb9wFWu5viucqTNIlnzPhcp5yWDmDwUuQyb8g50ui9YFgpCNoMSrr0WMSkbg9zqr7LxhdyS4/http%3A%2F%2Fwww.jeiglesias.com
>
>
> On Oct 18, 2022, at 2:37 PM, Alan Francis 
> wrote:
>
> External Email - Use Caution
>
> Hi Eugenio -
>
> Hope all is well. I am running FS 7.2. I have installed the MATLAB Runtime
> 2014b. However when I run the thalamic segmentation routine I get this
> error. Please help.
>
> Thanks,
>
> Alan
>
> copernicus:~/IMAGING> segmentThalamicNuclei.sh 973770
> Setting ITK threads to 1
> #
> #@# Thalamic Nuclei processing Tue Oct 18 12:25:06 PM CDT 2022
> --
> Setting up environment variables
> ---
> LD_LIBRARY_PATH is
> .:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:
> /usr/local/freesurfer/bin/SegmentThalamicNuclei: error while loading
> shared libraries: libicudata.so.52: cannot open shared object file: No such
> file or directory
> Command exited with non-zero status 127
> @#@FSTIME  2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 e 0.01 S
> 0.00 U 0.00 P 33% M 2256 F 11 R 621 W 0 c 1 w 25 I 1776 O 0 L 0.69 0.22 0.07
> @#@FSLOADPOST 2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 0.69
> 0.22 0.07
> 127
> Linux copernicus 5.15.0-50-generic #56-Ubuntu SMP Tue Sep 20 13:23:26 UTC
> 2022 x86_64 x86_64 x86_64 GNU/Linux
>
> Thalamic nuclei exited with ERRORS at Tue Oct 18 12:25:06 PM CDT 2022
>
> For more details, see the log file
> /home/alanfrancis/IMAGING/FREESURFER_SUBJECTS//973770/scripts/thalamic-nuclei-mainFreeSurferT1.log
>
> --
> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>
>
>
> * Alan N. Francis PhD Assistant Professor of Neuroscience Institute of
> Neuroscience*
> *University of Texas, School of Medicine*
>
> *Rio Grande Valley *
>
> *Texas. *
>
>
> ___
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>

Re: [Freesurfer] Thalamic segmentation error

2022-10-18 Thread Iglesias Gonzalez, Juan E. 
Dear Alan,
How did you install the runtime? Did you follow the instructions in the wiki?
Cheers,
/Eugenio

Juan Eugenio Iglesias
www.jeiglesias.com


On Oct 18, 2022, at 2:37 PM, Alan Francis 
mailto:alandarkene...@gmail.com>> wrote:


External Email - Use Caution

Hi Eugenio -

Hope all is well. I am running FS 7.2. I have installed the MATLAB Runtime 
2014b. However when I run the thalamic segmentation routine I get this error. 
Please help.

Thanks,

Alan

copernicus:~/IMAGING> segmentThalamicNuclei.sh 973770
Setting ITK threads to 1
#
#@# Thalamic Nuclei processing Tue Oct 18 12:25:06 PM CDT 2022
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:
/usr/local/freesurfer/bin/SegmentThalamicNuclei: error while loading shared 
libraries: libicudata.so.52: cannot open shared object file: No such file or 
directory
Command exited with non-zero status 127
@#@FSTIME  2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 e 0.01 S 0.00 
U 0.00 P 33% M 2256 F 11 R 621 W 0 c 1 w 25 I 1776 O 0 L 0.69 0.22 0.07
@#@FSLOADPOST 2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 0.69 0.22 
0.07
127
Linux copernicus 5.15.0-50-generic #56-Ubuntu SMP Tue Sep 20 13:23:26 UTC 2022 
x86_64 x86_64 x86_64 GNU/Linux

Thalamic nuclei exited with ERRORS at Tue Oct 18 12:25:06 PM CDT 2022

For more details, see the log file 
/home/alanfrancis/IMAGING/FREESURFER_SUBJECTS//973770/scripts/thalamic-nuclei-mainFreeSurferT1.log

--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience
University of Texas, School of Medicine
Rio Grande Valley
Texas.

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[Freesurfer] Thalamic segmentation error

2022-10-18 Thread Alan Francis 
External Email - Use Caution

Hi Eugenio -

Hope all is well. I am running FS 7.2. I have installed the MATLAB Runtime
2014b. However when I run the thalamic segmentation routine I get this
error. Please help.

Thanks,

Alan

copernicus:~/IMAGING> segmentThalamicNuclei.sh 973770
Setting ITK threads to 1
#
#@# Thalamic Nuclei processing Tue Oct 18 12:25:06 PM CDT 2022
--
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:
/usr/local/freesurfer/bin/SegmentThalamicNuclei: error while loading shared
libraries: libicudata.so.52: cannot open shared object file: No such file
or directory
Command exited with non-zero status 127
@#@FSTIME  2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 e 0.01 S
0.00 U 0.00 P 33% M 2256 F 11 R 621 W 0 c 1 w 25 I 1776 O 0 L 0.69 0.22 0.07
@#@FSLOADPOST 2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 0.69
0.22 0.07
127
Linux copernicus 5.15.0-50-generic #56-Ubuntu SMP Tue Sep 20 13:23:26 UTC
2022 x86_64 x86_64 x86_64 GNU/Linux

Thalamic nuclei exited with ERRORS at Tue Oct 18 12:25:06 PM CDT 2022

For more details, see the log file
/home/alanfrancis/IMAGING/FREESURFER_SUBJECTS//973770/scripts/thalamic-nuclei-mainFreeSurferT1.log

-- 
*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*



*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
Neuroscience*
*University of Texas, School of Medicine*

*Rio Grande Valley*

*Texas.*
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Re: [Freesurfer] Thalamic segmentation error Big Sur

2021-07-16 Thread Iglesias Gonzalez, Juan E. 
Hi Daniel
This error is intriguing  because the code did run for a while… Is it possible 
that you ran out of RAM memory? How much RAM does your machine have? (you can 
find it by clicking on the apple on the top left corner and then “about this 
Mac”)
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

On Jul 16, 2021, at 07:08, Daniela Vecchio 
mailto:vecchio.d...@gmail.com>> wrote:

External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to segment thalamic nuclei, as described by the tutorial page 
(https://secure-web.cisco.com/1F9Cs4OMcQ2PV75K6Q0sKfyHoo5UBJNkIWoWVANuievmgb7YVmB72kOrHuNn1V8uoNhZN-KHe4ok9nSjzkSzoyH5n058ic0lLqwrMVHZ1ozpd7WV13-3izOOM4vTGZYclV0LEUE8KhAUx622iHqFKU9VFaY7mQtisbVEWK7YBKaAQw7RXbGIA71WJAz-5JKkJ0pl7BBS7MJrP4hFzbKx4mjI-PAgshzNpARL7zVl83KzC8c5y1v2hPafTqoIG4MC_6IeE6txqYTA7C8LF0xfIWg/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FThalamicNuclei),
 but I got an Matlab routine error. I’t happened after the upgrade to MacOS Big 
Sur and I guess it is a compatibility issue. I tried also to re-install the 
routine (by fs_install_mcr R2014b
) and to run the process by docker container but the process ended with the 
same error.
(Obviously, I got the same error also trying the hippocampus module).



  ERROR:

MATLAB is exiting because of fatal error
/Applications/freesurfer/bin/run_SegmentThalamicNuclei.sh: line 33:  3322 
Killed: 9   
/Applications/freesurfer/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei
 subjHC001/ /Applications/freesurfer/subjects 0.5 
/Applications/freesurfer/average/ThalamicNuclei/atlas/AtlasMesh.gz 
/Applications/freesurfer/average/ThalamicNuclei/atlas/AtlasDump.mgz 
/Applications/freesurfer/average/ThalamicNuclei/atlas/compressionLookupTable.txt
 0.05 L-BFGS v12 '/Applications/freesurfer/bin/fs_run_from_mcr 
/Applications/freesurfer/bin/' 1 0
Darwin iMac-di-Daniela.local 20.5.0 Darwin Kernel Version 20.5.0: Sat May  8 
05:10:33 PDT 2021; root:xnu-7195.121.3~9/RELEASE_X86_64 x86_64



I've searched the list and I didn’t found a way to fix it.
Does anyone have any thoughts on how to trouble-shoot this one?
Also, Ive attached the thalamic-nuclei-mainFreeSurferT1.log in case it's of any 
use.

Thanks in advance

Best regards,
Daniela





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[Freesurfer] Thalamic segmentation error Big Sur

2021-07-16 Thread Daniela Vecchio 
External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to segment thalamic nuclei, as described by the tutorial page 
(https://secure-web.cisco.com/1F9Cs4OMcQ2PV75K6Q0sKfyHoo5UBJNkIWoWVANuievmgb7YVmB72kOrHuNn1V8uoNhZN-KHe4ok9nSjzkSzoyH5n058ic0lLqwrMVHZ1ozpd7WV13-3izOOM4vTGZYclV0LEUE8KhAUx622iHqFKU9VFaY7mQtisbVEWK7YBKaAQw7RXbGIA71WJAz-5JKkJ0pl7BBS7MJrP4hFzbKx4mjI-PAgshzNpARL7zVl83KzC8c5y1v2hPafTqoIG4MC_6IeE6txqYTA7C8LF0xfIWg/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FThalamicNuclei),
 but I got an Matlab routine error. I’t happened after the upgrade to MacOS Big 
Sur and I guess it is a compatibility issue. I tried also to re-install the 
routine (by fs_install_mcr R2014b
) and to run the process by docker container but the process ended with the 
same error. 
(Obviously, I got the same error also trying the hippocampus module).


 
  ERROR: 

MATLAB is exiting because of fatal error
/Applications/freesurfer/bin/run_SegmentThalamicNuclei.sh: line 33:  3322 
Killed: 9   
/Applications/freesurfer/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei
 subjHC001/ /Applications/freesurfer/subjects 0.5 
/Applications/freesurfer/average/ThalamicNuclei/atlas/AtlasMesh.gz 
/Applications/freesurfer/average/ThalamicNuclei/atlas/AtlasDump.mgz 
/Applications/freesurfer/average/ThalamicNuclei/atlas/compressionLookupTable.txt
 0.05 L-BFGS v12 '/Applications/freesurfer/bin/fs_run_from_mcr 
/Applications/freesurfer/bin/' 1 0
Darwin iMac-di-Daniela.local 20.5.0 Darwin Kernel Version 20.5.0: Sat May  8 
05:10:33 PDT 2021; root:xnu-7195.121.3~9/RELEASE_X86_64 x86_64



I've searched the list and I didn’t found a way to fix it. 
Does anyone have any thoughts on how to trouble-shoot this one? 
Also, Ive attached the thalamic-nuclei-mainFreeSurferT1.log in case it's of any 
use. 

Thanks in advance

Best regards,
Daniela







thalamic-nuclei-mainFreeSurferT1.log
Description: Binary data
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Re: [Freesurfer] Thalamic segmentation in FS voxel space

2021-04-15 Thread Iglesias Gonzalez, Juan E. 
Dear George,
The volumes in the text files come from soft segmentations at high resolution. 
There are two factors contributing to the discrepancies:

  1.  The downsampling to 1mm isotropic
  2.  The use of soft vs hard segmentations when computing volumes. For 
example: if you’ve got 100 voxels with 1% probability of being in the VM, the 
volume will be one voxel. But if you count the number of voxels being labeled 
as VM, you’ll get zero.
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of "Thomas, George" 

Reply-To: Freesurfer support list 
Date: Thursday, April 15, 2021 at 07:07
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Thalamic segmentation in FS voxel space


External Email - Use Caution

External Email - Use Caution
Dear All,

I have run segmentThalamicNuclei.sh on a set of subjects with 1mm isotropic T1 
images.

I need to convert these labels into volumetric space for further analysis so 
have been using the output with the FSvoxelSpace suffix and converting .mgz to 
.nii using mri_convert

However, for some of the subnuclei there seems to be a large discrepancy 
between the surface-based volumetric measurement completed by 
quantifyThalamicNuclei.sh, and the number of voxels in the FSvoxelSpace output.

Across the whole dataset of ~130 subjects, the left and right VM nuclei have a 
mean volume of about 25mm^3 according to quantifyThalamicNuclei.sh but are only 
represented by about 2-3 voxels per subject in the FSvoxelSpace output and are 
sometimes absent entirely.

I have found this to be similar for the VAmc (~30mm^3) and CL nuclei (~40mm^3), 
both of which are represented many fewer voxels than one might expect (~6 and 
~20 voxels, respectively).

Of course, it will not always be possible to represent a given surface in 
voxel-space and you would expect some differences but am wondering why the 
discrepancy might be so large in these cases, and if there is anything that 
might be done to remedy this?

Many thanks,
George Thomas
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[Freesurfer] Thalamic segmentation in FS voxel space

2021-04-15 Thread Thomas, George 
External Email - Use Caution

Dear All,

I have run segmentThalamicNuclei.sh on a set of subjects with 1mm isotropic T1 
images.

I need to convert these labels into volumetric space for further analysis so 
have been using the output with the FSvoxelSpace suffix and converting .mgz to 
.nii using mri_convert

However, for some of the subnuclei there seems to be a large discrepancy 
between the surface-based volumetric measurement completed by 
quantifyThalamicNuclei.sh, and the number of voxels in the FSvoxelSpace output.

Across the whole dataset of ~130 subjects, the left and right VM nuclei have a 
mean volume of about 25mm^3 according to quantifyThalamicNuclei.sh but are only 
represented by about 2-3 voxels per subject in the FSvoxelSpace output and are 
sometimes absent entirely.

I have found this to be similar for the VAmc (~30mm^3) and CL nuclei (~40mm^3), 
both of which are represented many fewer voxels than one might expect (~6 and 
~20 voxels, respectively).

Of course, it will not always be possible to represent a given surface in 
voxel-space and you would expect some differences but am wondering why the 
discrepancy might be so large in these cases, and if there is anything that 
might be done to remedy this?

Many thanks,
George Thomas
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Re: [Freesurfer] Thalamic Segmentation of Post Contrast MRI

2020-05-26 Thread Iglesias Gonzalez, Juan E. 
Dear Baris,
It’s hard to tell without seeing images… Would you mind sharing a scan?
Cheers,
/E


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of barış genç 

Reply-To: Freesurfer support list 
Date: Sunday, May 24, 2020 at 06:21
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Thalamic Segmentation of Post Contrast MRI


External Email - Use Caution

Dear FreeSurfer Experts,





  I have a data set (control and patients) that has 3DT1 , acquired on 3 T

 Philips Achieva scanner after post contract (Gadolinium).



  Can I use his data set to measure the thalamic nuclei segmentation or 
amygdala segmentation?



  Is gadolinium can interferes results?





Any suggestions will be great.




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[Freesurfer] Thalamic Segmentation of Post Contrast MRI

2020-05-24 Thread barış genç 
External Email - Use Caution

Dear FreeSurfer Experts,


  I have a data set (control and patients) that has 3DT1 , acquired on 3 T
 Philips Achieva scanner after post contract (Gadolinium). 

  Can I use his data set to measure the thalamic nuclei segmentation or 
amygdala segmentation? 

  Is gadolinium can interferes results?


Any suggestions will be great.

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Re: [Freesurfer] thalamic segmentation analysis

2020-03-28 Thread Bruce Fischl 

Hi VP

you need to give us more information! What is going wrong? What kind of 
system are you installing/running on? Send us the commands you are running 
and their output including any error messages.


cheers
Bruce



On Sat, 28 Mar 2020, Parisi Veronica 
wrote:




External Email - Use Caution

Hi there,

I have been trying to learn and set-up Freesurfer for a research project I a
m working on, but I am having trouble with the set-up/installation process.

Once Freesurfer is set-up, I will be using it to measure thalami and define 
their sub nuclei.


I have followed the instructions online to the best of my ability but can't 
seem to figure this out. Any assistance would be very much appreciated. 


Thank you.

Best,

VP


Rispetta l’ambiente: non stampare questa mail se non è necessario.
Respect the environment: print this email only if necessary.


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[Freesurfer] thalamic segmentation analysis

2020-03-28 Thread Parisi Veronica 
External Email - Use Caution

Hi there,

I have been trying to learn and set-up Freesurfer for a research project I am 
working on, but I am having trouble with the set-up/installation process.

Once Freesurfer is set-up, I will be using it to measure thalami and define 
their sub nuclei.

I have followed the instructions online to the best of my ability but can't 
seem to figure this out. Any assistance would be very much appreciated.

Thank you.

Best,


VP


Rispetta l'ambiente: non stampare questa mail se non è necessario.
Respect the environment: print this email only if necessary.
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Re: [Freesurfer] Thalamic segmentation

2019-04-18 Thread Iglesias Gonzalez, Eugenio 
External Email - Use Caution

Dear Zheng
One of the other developers can help you with Freeview.
But, as a workaround, you can always use an earlier version of Freeview, and 
load the lookup table of the Dev version.
Cheers
Eugenio

Sent from mobile, please excuse brevity and typos

--

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 郑凤莲 

Sent: Thursday, April 18, 2019 5:59:15 AM
To: Freesurfer support list
Subject: [Freesurfer] Thalamic segmentation


External Email - Use Caution

Hi Expert,

In the latest version of FS, I have segmented the thalamic successfully. But I 
can't use Freeview to show the segmentation map. There is an error :"freeview: 
/usr/lib/libpng15.so.15:version 'PNG15_0' not found (required by 
/opt/freesurfer/bin/../lib/qt/lib/libQt5Gui.so.5)". May be I didn't install the 
latest version of Freeview. However, I can't find this version on 
Freesurferwiki.  Could you share me the install steps and the latest version? 
Thanks very much for your help.

Sincerely,
Zheng





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[Freesurfer] Thalamic segmentation

2019-04-18 Thread 郑凤莲 
External Email - Use Caution

Hi Expert,


In the latest version of FS, I have segmented the thalamic successfully. But I 
can't use Freeview to show the segmentation map. There is an error :"freeview: 
/usr/lib/libpng15.so.15:version 'PNG15_0' not found (required by 
/opt/freesurfer/bin/../lib/qt/lib/libQt5Gui.so.5)". May be I didn't install the 
latest version of Freeview. However, I can't find this version on 
Freesurferwiki.  Could you share me the install steps and the latest version? 
Thanks very much for your help.


Sincerely,
Zheng

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Re: [Freesurfer] Thalamic segmentation questions

2019-01-29 Thread Iglesias Gonzalez, Eugenio 
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Dear Manoj,

First question:
The one without the suffix is defined at higher resolution, on a voxel grid 
that does not correspond to the standard FS space (where norm.mgz, aseg.mgz, 
etc. live).
The one with the suffix lives on the voxel grid of norm.mgz, aseg.mgz, etc
Both of them live in the physical RAS coordinates or the other volumes, that’s 
why they look similar when you open them of FreeView. But if you zoom in 
enough, you’ll notice that the one without the suffix has higher resolution.

Second question:
Yes, you first need to register, manually or (preferably) automatically, e.g., 
with BBregister, mri_robust_register, etc.
Then, you can run:mri_convert   moving.nii.gz  deformed.nii.gz  -rl  nu.mgz 
-at  [YOURTRANSFORMFILE.LTA]  -rt nearest

I hope this helps.

/Eugenio


--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

Lecturer on Radiology
Harvard Medical School

http://www.jeiglesias.com


From:  on behalf of Manoj Saranathan 

Reply-To: Freesurfer support list 
Date: Tuesday, 29 January 2019 at 19:15
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Thalamic segmentation questions


External Email - Use Caution
The thalamic nuclei segmentation produces 2 mgz files. One has the FS suffix 
and other does not. Is the latter without the FS in the native space? If I 
import and view in freeview, they look same. I want it in native space so I can 
do some Dice calculations.

My manual segmentations are on a different data set very close to but not 
necessarily perfectly aligned to the T1 data set used in recon-all. I can use 
the mri_conver -rl 'reslice like' option but it does not do any registrations 
does it? It just reslices it in the orientation of the file argument to -rl 
right. I assume have to manually affine register and propagate the warps if 
they are not aligned?

Thanks,
manoj



From: Manoj Saranathan
Sent: Tuesday, January 29, 2019 5:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Thalamic segmentation questions

The thalamic nuclei segmentation produces 2 mgz files. One has the FS suffix 
and other does not. Is the latter without the FS in the native space? If I 
import and view in freeview, they look same. I want it in native space so I can 
do some Dice calculations.

My manual segmentations are on a different data set very close to but not 
necessarily perfectly aligned to the T1 data set used in recon-all. I can use 
the mri_conver -rl 'reslice like' option but it does not do any registrations 
does it? It just reslices it in the orientation of the file argument to -rl 
right. I assume have to manually affine register and propagate the warps if 
they are not aligned?

Thanks,
manoj


From: Manoj Saranathan
Sent: Tuesday, January 29, 2019 5:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Thalamic segmentation questions

The thalamic registration produces 2 mgz files. One has the FS suffix and other 
does not. Is the latter without the FS in the native space? If I import and 
view in freeview, they look same. I want it in native space so I can do some 
Dice with manual segmentation.

The 'reslice like' option of mri_convert does not do any registrations does it? 
It just reslices it in the orientation of the file argument to -rl right. I 
assume have to manually register and propagate the warps if they are not 
aligned.

Thanks,
manoj



Manoj Saranathan
Associate Professor, Dept. of Medical Imaging
University of Arizona
Ph: 520-626-6531
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[Freesurfer] Thalamic segmentation questions

2019-01-29 Thread Manoj Saranathan 
External Email - Use Caution

The thalamic nuclei segmentation produces 2 mgz files. One has the FS suffix 
and other does not. Is the latter without the FS in the native space? If I 
import and view in freeview, they look same. I want it in native space so I can 
do some Dice calculations.

My manual segmentations are on a different data set very close to but not 
necessarily perfectly aligned to the T1 data set used in recon-all. I can use 
the mri_conver -rl 'reslice like' option but it does not do any registrations 
does it? It just reslices it in the orientation of the file argument to -rl 
right. I assume have to manually affine register and propagate the warps if 
they are not aligned?

Thanks,
manoj




From: Manoj Saranathan
Sent: Tuesday, January 29, 2019 5:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Thalamic segmentation questions


The thalamic nuclei segmentation produces 2 mgz files. One has the FS suffix 
and other does not. Is the latter without the FS in the native space? If I 
import and view in freeview, they look same. I want it in native space so I can 
do some Dice calculations.

My manual segmentations are on a different data set very close to but not 
necessarily perfectly aligned to the T1 data set used in recon-all. I can use 
the mri_conver -rl 'reslice like' option but it does not do any registrations 
does it? It just reslices it in the orientation of the file argument to -rl 
right. I assume have to manually affine register and propagate the warps if 
they are not aligned?

Thanks,
manoj



From: Manoj Saranathan
Sent: Tuesday, January 29, 2019 5:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Thalamic segmentation questions


The thalamic registration produces 2 mgz files. One has the FS suffix and other 
does not. Is the latter without the FS in the native space? If I import and 
view in freeview, they look same. I want it in native space so I can do some 
Dice with manual segmentation.

The 'reslice like' option of mri_convert does not do any registrations does it? 
It just reslices it in the orientation of the file argument to -rl right. I 
assume have to manually register and propagate the warps if they are not 
aligned.

Thanks,
manoj


Manoj Saranathan
Associate Professor, Dept. of Medical Imaging
University of Arizona
Ph: 520-626-6531

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Re: [Freesurfer] thalamic segmentation

2018-09-10 Thread Vinny K 
External Email - Use Caution

Actually, I was able to match the boundaries with the referenced
publication.  So it's all good, thanks again for your help!

Vinny

On Mon, Sep 10, 2018 at 6:55 PM Vinny K 
wrote:

> Hi Eugenio,
>
> Thank you for your reply.  Somehow the display from my thalamic
> segmentation does not capture the colors in your publication and
> furthermore, the nuclei are not clearly delineated from each other visually
> since one color may encompass two or three different nuclei.  However, I
> see the label numbers ranging from 8100 to 8300 when hovering my mouse over
> the segmented thalamus and also these numbers change within the same color
> meaning that delineation does in fact exist; these new label numbers are
> different from the 14 FreeSurferColorLut.txt thalamic labels.  Is there a
> table that links these new label numbers with the names of the 26 thalamic
> nuclei?
>
> Thanks again for your help,
>
> Vinny
>
> On Mon, Sep 10, 2018 at 1:36 PM Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
>> External Email - Use Caution
>>
>> Hi Vinny,
>> The anatomical definitions can be found in the paper, which is open
>> access (see Table 2):
>> https://www.sciencedirect.com/science/article/pii/S1053811918307109
>> Kind regards
>> Eugenio
>>
>>
>>
>> Sent from my phone, please excuse brevity and typos
>>
>>
>>
>>
>>
>>
>> From: Vinny K
>> Sent: Monday, September 10, 10:35
>> Subject: Re: [Freesurfer] thalamic segmentation
>> To: freesurfer@nmr.mgh.harvard.edu
>>
>>
>> External Email - Use Caution
>> Hi,
>>
>> I ran recon-all to generate the required files for the thalamic
>> segmentation tool (http://freesurfer.net/
>> <http://freesurfer.net/fswiki/ThalamicNuclei>fswiki
>> <http://freesurfer.net/fswiki/ThalamicNuclei>/
>> <http://freesurfer.net/fswiki/ThalamicNuclei>ThalamicNuclei
>> <http://freesurfer.net/fswiki/ThalamicNuclei>) using the latest
>> development version of Freesurfer (06/09/2018) linux-cent06.  The segmented
>> thalamic nuclei were visualized but I could not find a table listing the
>> thalamic nuclei and its associated label to help identify the specific
>> nuclei.
>>
>> Any help would be greatly appreciated.
>>
>> Thanks,
>>
>> Vinny
>>
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>
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Re: [Freesurfer] thalamic segmentation

2018-09-10 Thread Vinny K 
External Email - Use Caution

Hi Eugenio,

Thank you for your reply.  Somehow the display from my thalamic
segmentation does not capture the colors in your publication and
furthermore, the nuclei are not clearly delineated from each other visually
since one color may encompass two or three different nuclei.  However, I
see the label numbers ranging from 8100 to 8300 when hovering my mouse over
the segmented thalamus and also these numbers change within the same color
meaning that delineation does in fact exist; these new label numbers are
different from the 14 FreeSurferColorLut.txt thalamic labels.  Is there a
table that links these new label numbers with the names of the 26 thalamic
nuclei?

Thanks again for your help,

Vinny

On Mon, Sep 10, 2018 at 1:36 PM Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> External Email - Use Caution
>
> Hi Vinny,
> The anatomical definitions can be found in the paper, which is open access
> (see Table 2):
> https://www.sciencedirect.com/science/article/pii/S1053811918307109
> Kind regards
> Eugenio
>
>
>
> Sent from my phone, please excuse brevity and typos
>
>
>
>
>
>
> From: Vinny K
> Sent: Monday, September 10, 10:35
> Subject: Re: [Freesurfer] thalamic segmentation
> To: freesurfer@nmr.mgh.harvard.edu
>
>
> External Email - Use Caution
> Hi,
>
> I ran recon-all to generate the required files for the thalamic
> segmentation tool (http://freesurfer.net/
> <http://freesurfer.net/fswiki/ThalamicNuclei>fswiki
> <http://freesurfer.net/fswiki/ThalamicNuclei>/
> <http://freesurfer.net/fswiki/ThalamicNuclei>ThalamicNuclei
> <http://freesurfer.net/fswiki/ThalamicNuclei>) using the latest
> development version of Freesurfer (06/09/2018) linux-cent06.  The segmented
> thalamic nuclei were visualized but I could not find a table listing the
> thalamic nuclei and its associated label to help identify the specific
> nuclei.
>
> Any help would be greatly appreciated.
>
> Thanks,
>
> Vinny
>
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] thalamic segmentation

2018-09-10 Thread Iglesias Gonzalez, Eugenio 
External Email - Use Caution

Hi Vinny,
The anatomical definitions can be found in the paper, which is open access (see 
Table 2):
https://www.sciencedirect.com/science/article/pii/S1053811918307109
Kind regards
Eugenio



Sent from my phone, please excuse brevity and typos






From: Vinny K
Sent: Monday, September 10, 10:35
Subject: Re: [Freesurfer] thalamic segmentation
To: freesurfer@nmr.mgh.harvard.edu


External Email - Use Caution
Hi,

I ran recon-all to generate the required files for the thalamic segmentation 
tool 
(http://freesurfer.net/<http://freesurfer.net/fswiki/ThalamicNuclei>fswiki<http://freesurfer.net/fswiki/ThalamicNuclei>/<http://freesurfer.net/fswiki/ThalamicNuclei>ThalamicNuclei<http://freesurfer.net/fswiki/ThalamicNuclei>)
 using the latest development version of Freesurfer (06/09/2018) linux-cent06.  
The segmented thalamic nuclei were visualized but I could not find a table 
listing the thalamic nuclei and its associated label to help identify the 
specific nuclei.

Any help would be greatly appreciated.

Thanks,

Vinny


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Re: [Freesurfer] thalamic segmentation

2018-09-10 Thread Vinny K 
External Email - Use Caution

Hi,

I ran recon-all to generate the required files for the thalamic
segmentation tool (http://freesurfer.net/fswiki/ThalamicNuclei) using the
latest development version of Freesurfer (06/09/2018) linux-cent06.  The
segmented thalamic nuclei were visualized but I could not find a table
listing the thalamic nuclei and its associated label to help identify the
specific nuclei.

Any help would be greatly appreciated.

Thanks,

Vinny
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