[Freesurfer] help

2022-10-25 Thread Sarah Lavelle 
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Dear freesurfer,

Are there any additional resources on how to make cuts? I have found this
https://secure-web.cisco.com/18_liDyv7h8S0t-GuSrqbS0mexl0ornQBxqLR6v5JlLJUxICtX_m72JgFOKgqmcmDmNUv_rPvux5Bj3HvJdGS1wmDMB49Af-BJx9Q5hozmhhuUcgnG8xeUpfoO4g2LSz1OdFi_9on9h5ngyGR9FDKKAgMIOCzYJezDsIESZYkKSRdPHkAWMlYTYYAHYx4iD-JqVc30z2DimXPHyrLEyGpNChw8D4PkkLoasWz2jf7w4Pefp9yJvvDnZx-gyl0BhCk8ul3x-2cGVK0SVa-LKxKQHzToFKqsURPjIXBXX2NOr8s_VgCRqHl8WzMW3bCwJiearZFL1Avboe-CZ8CLgZe_w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all%23Flattening
 but it isn't
enough for the project I am doing. I want to flatten the whole surface but
I may need to change where I am cutting from patient to patient. How do you
know how big the hole should be? and how many relaxation cuts should you
make? How long should they be? If you have any more guidance on how to cut
to minimise distortion, please let me know!

Also when I perform the mris_flatten function using my patch, my terminal
gives me a % near the end saying "41% total metric distortion". Can you
confirm that this value is the total metric distortion from an inflated
surface to a flatmap surface using my chosen patch?

Many thanks,
Sarah Lavelle
Trinity College Dublin
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Re: [Freesurfer] help

2022-10-25 Thread Fischl, Bruce R.,PHD 
Hi Sarah

Sorry, I’m not sure we have much to add. We don’t flatten much any longer, and 
the cuts are kind of ad hoc – the one around the medial wall to get rid of 
non-cortical stuff, then the radial ones from there to remove particularly the 
curvature from the 3 poles. Mostly we just follow what Anders and Marty started 
doing way back when
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Sarah Lavelle
Sent: Tuesday, October 25, 2022 5:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] help


External Email - Use Caution
Dear freesurfer,

Are there any additional resources on how to make cuts? I have found this 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Flattening
 but it isn't enough for the project I am doing. I want to flatten the whole 
surface but I may need to change where I am cutting from patient to patient. 
How do you know how big the hole should be? and how many relaxation cuts should 
you make? How long should they be? If you have any more guidance on how to cut 
to minimise distortion, please let me know!

Also when I perform the mris_flatten function using my patch, my terminal gives 
me a % near the end saying "41% total metric distortion". Can you confirm that 
this value is the total metric distortion from an inflated surface to a flatmap 
surface using my chosen patch?

Many thanks,
Sarah Lavelle
Trinity College Dublin
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[Freesurfer] MRI recon-all failed at talairach

2022-10-25 Thread Jonany, Vincent Joe 
External Email - Use Caution


Dear FreeSurfer Developers,

I am encountering a weird error in performing recon-all in my dicom directory. 
I believe the problem is here (snippet copied from talairach_avi.log. I have 
also attached here the recon-all.log, as well as the talaraich_avi.log. Does 
anyone know or have seen this problem before? I will appreciate any kind of 
help, please let me know if I need to provide anything else.

FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: MacOS Monterey (apple silicon)

$Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $
/Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img
256 256 256 1
1.00 1.00 1.00
orientation T byte_order littleendian
Reading image: 
/Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img
dimensions: 256 256 256
mmppix: 1. -1. -1.
center: 128. -129. -129.
talsrcimg_g11.4dfp.img
256 256 256 1
1.00 1.00 1.00
orientation T byte_order littleendian
Reading image: talsrcimg_g11.4dfp.img
dimensions: 256 256 256
mmppix: 1. -1. -1.
center: 128. -129. -129.
t4_read: talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4pupuÀþN
èEÑ�àÔ�àÔ7SÎ0°þN
#Öô>ÖxþN
°þN
�þN
SÎðþN

þN
Ñ@
àþN
�
Ñ read error
t4_read: transform initialized to I4
rotation matrix determinant 1.00

Thank you in advance! I appreciate any help!

Best,

Vincent
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[Freesurfer] Preproc-sess crashed - 3dvolreg.afni error

2022-10-25 Thread Gillian Grennan 
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Hello FreeSurfer Developers,

I downloaded Freesurfer v7.3.2

 onto my local drive
and am attempting to run preprocessing through FSFAST. I wasn't able to get
access to the .tar.gz Darwin file but downloaded Xquartz, Freesurfer, FSL,
and Matlab individually and was able to source Freesurfer using the
following commands:

export FREESURFER_HOME=/Applications/freesurfer/7.3.2

export PROJECT_DIR=/Users/angelafang/Library/CloudStorage/OneDrive-UW/VicExt

export SUBJECTS_DIR=$PROJECT_DIR/subjects

source $FREESURFER_HOME/SetUpFreeSurfer.sh


However, when I run preproc-sess in my analysis folder I get the following
error:


command: preproc-sess -sf subjectlist -fsd bold -stc siemens -surface
fsaverage lhrh -mni305 -fwhm 5 -per-run


error message:

++ Initializing alignment base

Choleski factorization failure in startup_lsqfit

mri_startup_lsqfit: bad call to startup_lsqfit!

++ Starting final pass on 44 sub-bricks: 0

Fatal Signal 11 (SIGSEGV) received

   mri_3dalign_one

  3dvolreg main

 Bottom of Debug Stack

** AFNI version = AFNI_2011_12_21_1014  Compile date = May 22 2013

** [[Precompiled binary macosx_10.7_Intel_64: May 22 2013]]

** Program Abort **

** If you report this crash to the AFNI message board,

** please copy the error messages EXACTLY, and give

** the command line you used to run the program, and

** any other information needed to repeat the problem.

** You may later be asked to upload data to help debug.

ERROR: 3dvolreg.afni

Invalid null command.


I'm confused on what more I need to install? Is there a way I can get an
updated link to the tar file with the relevant software packages needed to
run FSFAST?


Best,

Gillian Grennan
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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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>>

[Freesurfer] Glasser parcellation labelling

2022-10-25 Thread Paulk, Angelique C.,PhD 
Hello,
I have yet another, likely obvious, question and I apologize if this is 
answered elsewhere. I ran the below series of functions to apply the HCP-MM1 
(Glasser) atlas to the FreeSurfer output. I was able to produce an annotation 
file that had the labels in the right locations and mapping.

Yet, when I look at the output HCP-MMP1.mgz and HCP-MMP1+aseg.mgz files in 
FreeView or 3DSlicer, the old DKT FreeSurfer labels are applied to the brain 
labels (which are inaccurate). Is there an additional step I need to convert 
the labels such as using a modified HCP-MMP1 LUT look up table (such as linked 
here)?

using the HCP-MMP1 annotation files:
https://figshare.com/articles/dataset/HCP-MMP1_0_projected_on_fsaverage/3498446?file=5528837

And the use of mri_surf2volseg in the following sequence:
https://github.com/ftadel/IntrAnat/issues/7#issuecomment-768996270

Thank you for any and all help,
Angelique
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[Freesurfer] response?? Fail to install FreeSurfer 7 from the *.deb package

2022-10-25 Thread ?????? 
External Email - Use Caution

Hi R,


Thank you for your kind help. I re-downloaded the package and the installation 
was finished with error.


Best,
Qunjun





 




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