[Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error

2022-06-29 Thread Andrew Beaudin 

  External Email - Use Caution
Hello Freesurfer Community,
  I am trying to use mri_robust_template (with its default 6 DOF
registration) outside of the Freesurfer longitudinal pipeline to
generate within-participant T1 templates from 2 time points. 
Unfortunately, I am coming up against a 'MyMatrix::RotationMean
input(s) not rotation' error on images acquired on our GE 3T
Discovery 750 system, but not our colleagues' Seimens 3T Prisma
images.  I have pasted the output from the --debug flag below (and
attached as text file - line 188 is the MyMatrix message).   If
helpful, images can be download from the following link:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://uofc-my.sharepoint.com/:f:/g/personal/abeaudin_ucalgary_ca/EmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ?e=lcovfR

Briefly: 
   - the images are skull-stripped niftis and I am running
Freesurfer 6.0
(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) on a
WSL2 Ubuntu 18.04 installation. 
   - the call is: mri_robust_template --mov 2001A_T1o_brain.nii.gz
2001B_T1o_brain.nii.mgz --lta 2001A2template.lta 2001B2template.lta
--average 1 --template 2001_template.nii.gz --satit

   -  I have tried the following with no success:
1) using the --iscale flag - same result as shown below.
2) using --inittp 0 - results in a 'Segmentation fault'
3) using --average 0 - same result as shown below
4) using Freesurfer v7.2 - same result as below
5) running mri_robust_template call on Catalina and Big Sur systems
with FS v6.0 - same result as below.

  Currently, the only way to get mri_robust_template to work with
our GE images is to run it with the --affine flag.  I would prefer
to use the rigid body registration but am at a loss for why these
images are failing using the rigid body registration is failing. Any
help/insights/recommendations are greatly appreciated.

Thank you very much.

Andrew


  Andrew Beaudin, PhD | Postdoctoral
Scholar
University of Calgary | Cumming School of Medicine
Department of Clinical Neurosciences
HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1
Phone: (403) 210-6273  
  

DEBUG REPORT:

$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter
Exp $

--mov: Using 2001A_T1o_brain.nii.gz as movable/source volume.
--mov: Using 2001B_T1o_brain.nii.gz as movable/source volume.
    Total: 2 input volumes
--lta: Will output LTA transforms
--average: Using method 1 for template computation.
--template: Using 2001_template.nii.gz as template output
volume.
--satit: Will estimate SAT iteratively!
--debug: Will output debug info and files!
reading source '2001A_T1o_brain.nii.gz'...
converting source '2001A_T1o_brain.nii.gz' to bspline ...
MRItoBSpline degree 3
reading source '2001B_T1o_brain.nii.gz'...
converting source '2001B_T1o_brain.nii.gz' to bspline ...
MRItoBSpline degree 3
Will use TP 2 as random initial target (seed 108242 ).

MultiRegistration::initializing Xforms (init 2 , maxres 0 ,
iterate 5 , epsit 0.01 ) : 

 MultiRegistration Parameters 

 Outdir:    ./
 TransOnly: false
 Rigid: true
 Robust:    true
 Satit: true
 Iscale:    false
 IscaleOnly:    false
 NoMulti:   false
 SubsampleSize: -1
 HighIt:    -1
 FixVoxel:  false
 KeepType:  true
 Average:   1
 DoublePrec:    false
 BackupWeights: false
 SampleType:    5
 CRASCenter:    false
 Debug: 1


[init] = TP 1 to TP 2
==
 Register TP 1 ( 2001A_T1o_brain.nii.gz )
  to  TP 2 ( 2001B_T1o_brain.nii.gz )

Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE )
   Type Source : 3  Type Target : 3  keeping type 
   Mov: (1, 1, 1)mm  and dim (176, 256, 256)
   Dst: (1, 1, 1)mm  and dim (176, 256, 256)
   Asserting both images: 1mm isotropic 
    - no Mov reslice necessary
    - no Dst reslice necessary


 Registration::findSaturation 
   - computing centroids 
   - computing initial transform
 -- using translation info
   - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 ) 
   - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 3 )

   - Build Gaussian Pyramid ( Limits min

[Freesurfer] How to project SPM image

2022-06-29 Thread Rachel Wagner 
External Email - Use Caution

Hello,

I am trying to project my SPM nii image onto an anatomical image to project 
them onto a cortical surface in Freesurfer, to generate images which look like 
this: Fig. 4: Refining neuroanatomical treatment targets for addiction. | 
Nature 
Medicine

Has anyone done this before and would be able to point me towards any resources 
to do so?

Thank you,
Rachel Wagner
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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.

[Freesurfer] recon-all error: mri_cc

2022-06-29 Thread cooperr1 
External Email - Use Caution

Dear FreeSurfer developers,

 

I'm attempting to run recon-all with the longitudinal stream, but one
subject (out of >500) fails recon-all (I've re-started many times). The
cross-sectional and base (i.e. steps 1 and 2 of the longitudinal processing)
have completed successfully; it's this final step that has the error. It
appears that the error lies in mri_cc.

The final lines of the recon-all.log are below:

 

#--

#@# CC Seg Wed Jun 29 14:56:47 AEST 2022

 

mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas
elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta
sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2V
Y

 

will read input aseg from aseg.auto_noCCseg.mgz

writing aseg with cc labels to aseg.auto.mgz

will write lta as
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas
elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta

reading aseg from
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas
elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz

error: No such file or directory

error: mri_cc: volume
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas
elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz
already has CC in it.

Run with -force to reprocess (not recommended)

 

@#@FSTIME  2022:06:29:14:56:47 mri_cc N 7 e 0.39 S 0.00 U 0.38 P 99% M 21240
F 0 R 1813 W 0 c 6 w 5 I 0 O 0 L 64.77 63.93 63.78

@#@FSLOADPOST 2022:06:29:14:56:47 mri_cc N 7 64.77 63.93 63.78

Linux spartan-bm112.hpc.unimelb.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP
Thu Jul 8 02:53:40 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

 

recon-all -s
sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2V
Y exited with ERRORS at Wed Jun 29 14:56:47 AEST 2022

 

 

Freesurfer version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b
(I have also attempted with version 7.1.0 with identical results)

Platform: centos7_x86_64

Recon-all.log: attached.

 

With thanks,

 

Rebecca

 



recon-all.log
Description: Binary data
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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] Tksurfer Error

2022-06-29 Thread fsbuild 
External Email - Use Caution

The tksurfer command is deprecated/no longer supported.
You could try using freeview directly or runtksurferfv, which may take 
the same options as tksurfer but run freeview to display things.
- R..

On Jun 29, 2022, at 16:33, Rachel Wagner rwag...@uwo.ca 
wrote:External Email - Use 
CautionHello,I am 
attempting to paint my spm functional data onto freesurfer’s anatomical 
image.I ran this code: tksurfer bert lh inflated -overlay updated.img 
-overlay-reg register.datAnd got this error:Tcl_Init failed: Can't 
find a usable init.tcl in the following 
directories:/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4This
 probably means that Tcl wasn't installed properly.Tk_Init failed: 
invalid command name "tcl_findLibrary"Tix_Init failed: Can't find a usable Tix 
Init.tcl in the following 
directories:./library./tix8.1./library./tix8.1/usr/pubsw/packages/tcltktixblt/current/lib/tix8.1How
 can I fix this 
error?Thanks,Rachel___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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.

[Freesurfer] Tksurfer Error

2022-06-29 Thread Rachel Wagner 
External Email - Use Caution

Hello,

I am attempting to paint my spm functional data onto freesurfer’s anatomical 
image.

I ran this code: tksurfer bert lh inflated -overlay updated.img -overlay-reg 
register.dat

And got this 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.

Tk_Init failed: invalid command name "tcl_findLibrary"
Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories:
./library
./tix8.1
./library
./tix8.1
/usr/pubsw/packages/tcltktixblt/current/lib/tix8.1


How can I fix this error?

Thanks,
Rachel
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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.

[Freesurfer] Fwd: Pass code to expand archive for VirtualBox

2022-06-29 Thread Cody Slater 
External Email - Use Caution

Hello,

I am following the instructions to install the VirtualBox for Freesurfer
7.2.0 and would like access to the code for expanding the archive.

Regards,

Cody Slater
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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.

[Freesurfer] mri_concat killed

2022-06-29 Thread Benjamin Deck 
External Email - Use Caution

Hi there,

I am attempting to concat a number of volume files that are filled cortical
ribbons from a series of label files.

My workflow is to take the following steps:
*Convert overlay file to label file*
 mri_vol2label --i
${inDir}/Indi_Matched_ROIs/${net}/${sub}/${hemi}.${netMaskName}_native.mgh \
--id 1 \
--l
${inDir}/Indi_Matched_ROIs/${net}/${sub}/${hemi}.${netMaskName}_native.label
\
--surf ${sub} ${hemi} white \
--dilate 2
  mri_label2label --srclabel
${inDir}/Indi_Matched_ROIs/${net}/${sub}/${hemi}.${netMaskName}_native.label
\
--s ${sub} \
--hemi ${hemi} \
--trglabel
/${subDir}/${sub}/label/li2019/${hemi}.${netMaskName}_native.label \
--regmethod surface

*Convert label to volume *
  mri_label2vol --label
/${subDir}/${sub}/label/li2019/${hemi}.${netMaskName}_native.label \
  --identity \
  --fill-ribbon \
  --subject ${sub} \
  --hemi ${hemi} \
  --o /${subDir}/${sub}/mri/li2019_vols/${hemi}.${netMaskName}_native.mgz

*Finally concatenate the vols together*

mri_concat --f rois.txt  --o yeo2011_nat.mgz --sum
ninputs = 104
Checking inputs
nframestot = 104
Allocing output
Done allocing
Killed

Not sure why this is being killed.

OS: WSL2 Ubuntu
FS version:   freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b

Thanks for your help!

-- 
*Benjamin L. Deck*
*Doctoral Student*
*Applied Cognitive and Brain Sciences*
*Department of Psychological and Brain Sciences*
*Drexel University*


Virus-free.
http://secure-web.cisco.com/1YLbrDWxmBkdEGq0tv_IFuOJQDM7x0wCDq8h35ylt8kjv2AQI2LHEJmsZdtdtNAuFcmGZ82vP1vRN2T8ViR1K1rkciL6Un6xImaVWTXMUxC2YSjOluyxvT82lvK3Ml8b_FsZLxJo15rnsjyiRqZlqK9bNkv9Hol_6N4Tsb86EUfOn5oc5Bg9mA9l-P9PWYFipUvW3eZhgR1ZEp_YUKOBni1WmaucHlW3FEeOSjf0oTtP-GCE6fdWnJtfBycPqY73ANPqKBD44ICZB7AOG0kdEtf8XUFkEcOeQ_viEPXuQpf2VckajLznbCoGGrmoMQYKM_pr9vrG-QRL61hamc9H8ng/http%3A%2F%2Fwww.avast.com

<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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] trac-all -prep -c ERROR

2022-06-29 Thread Yendiki, Anastasia 
Any chance that part of the left CST is truncated in this one subject? E.g., if 
the top part of the brain was outside the field of view?

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Salar Dini, Elaheh 

Sent: Wednesday, June 29, 2022 11:38 AM
To: Freesurfer support list 
Subject: [Freesurfer] trac-all -prep -c ERROR


External Email - Use Caution

Dear experts,

I am running TRACULA for 90 subjects. Exceptionally, for one of the subjects, I 
get the following error in -prep step:

((INFO: Distances between consecutive points in test subject's space are 10 13 
12 13 13 12
WARN: Could not find satisfactory control point fit - try 17034
Writing output files to 
/home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_*
Writing spline volume to 
/home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_cpts_7.nii.gz
Segmentation fault (core dumped)
Linux tauruspet.med.yale.edu 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Wed Jun 29 10:31:11 EDT 2022))

I am attaching the log file as well: MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://drive.google.com/file/d/1pgEmkMtk4UoELpGR2bU_Vac-2BDr-eNy/view?usp=sharing
 On a quick look, aparc+aseg seems to be properly done. Will you please help me 
to troubleshoot this if possible?

Thank you,
Ela
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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.

[Freesurfer] trac-all -prep -c ERROR

2022-06-29 Thread Salar Dini, Elaheh 
External Email - Use Caution

Dear experts,

I am running TRACULA for 90 subjects. Exceptionally, for one of the subjects, I 
get the following error in -prep step:

((INFO: Distances between consecutive points in test subject's space are 10 13 
12 13 13 12
WARN: Could not find satisfactory control point fit - try 17034
Writing output files to 
/home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_*
Writing spline volume to 
/home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_cpts_7.nii.gz
Segmentation fault (core dumped)
Linux tauruspet.med.yale.edu 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Wed Jun 29 10:31:11 EDT 2022))

I am attaching the log file as well: 
https://secure-web.cisco.com/1SmnY7WYnV1XRZV1hzFK0-fljtz5hTgSEDuVurOZOZqB22zXjeNXjwoJmMg8m0rebhhkBgEG85lX60uQdweaszlFaJK0aAf6k-tDqRHPeCrz3HbLV22IVyX0RGrImMTcUBc_63gMzWjWK9eyH69Bjr8g1UyxZXFkNJ3OsWaVuwX97x0BWhtcbbrQ_LY-JCZgpxP_XA6lSuz7dbq1KXKfR7hYJkRBpmu-dwHdY2yz8QubiCBLB8q20-RD8dv0uLOM-aXyamfQOU9KFfOAuT1t9aehuseGannHIdY4Fq30y2JAnFZ42owKAg-cUAjR6_wDxWve_BGI77yzfLgDi7CusPY_0vml2btWwy8N3p1xjaHs/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1pgEmkMtk4UoELpGR2bU_Vac-2BDr-eNy%2Fview%3Fusp%3Dsharing
 On a quick look, aparc+aseg seems to be properly done. Will you please help me 
to troubleshoot this if possible?

Thank you,
Ela
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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.