[Freesurfer] meanings of trac-all outputs

2022-04-22 Thread Zeng, Qi 
External Email - Use Caution

Hi experts,

Just want to check if dmri/dwi.nii.gz is the 4D dwi volumes after
correction for B0 inhomogeneities, eddy current, and head motion? and
dmri/nodif_brain_mask.nii.gz is the 3D ROI mask for the whole brain? and
dmri/bvals and dmri/bvecs are rotated bvals and rotated bvecs?
Thank you!

Best,
Qi
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Re: [Freesurfer] ERROR: Talairach failed!

2022-04-22 Thread Fritze, Stefan 
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Thanks for your reply! The command is:

tkregisterfv --s participant_name  --fstal
ERROR: cannot find participant_name/surf/lh.white

Best
Stefan



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. Greve 

Gesendet: Donnerstag, 21. April 2022 20:03:32
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] ERROR: Talairach failed!

Can you provide the tkregisterfv command line and the terminal output?

On 4/21/2022 3:37 AM, Fritze, Stefan wrote:

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Hello FreeSurfer Developers,

I'm attempting to compute recon-all -all -subjid XXX -qcache -3T, which works 
fine with most of my study participants, but for some of them I receive 
Talairach error (s. error message below):

I've searched the list and similar errors have been reported and there is a 
webpage dealing with this type of error (MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1nJqbXyvi0ZdnVubukLDfIIP6F5eP0uDJmJ85ZEE2-CfZyDP7fKdoHGk-l9icpFIAJlrAGT-PQ6Yk7_Kyne4FQ4g9kjxgcAsKFfqoahpUZj_STuGENyfXk_MhQNUM6KlGj2vQ_Nj8J9MNgEDQOG7b_avUc_Qx20yIWfgbmUSQMJJ7vF5mXJ4dH3uENAGs-NhjmNRvuoLo9pWEPCE_bS3nk8cq37eSNo3-3NAoQxf4CyXge3ZHd_tprndBtwoyMGu1QzgXkAoGpU1liYZC93alD87NWvE04tppkYrkQbTelT6KjW5Yb9WD8mfkBFg0TB0DRTH2598UNIfee2yunY8wOQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach_freeview).
 Yet, tkregisterfv produces also an error, even when I do not set the --surf 
orig flag (the surf folder of these participants is empty). Running the 
mritotal utility from the MNI toolset produces the same error. In one 
participant, the problem was solved when I converted the .nifti file to .mgz 
and started recon-all from there. But this did not help with the other 
participants. Including the -notal-check flag allows recon-all to complete, yet 
I do not know whether the results are trustworthy.

Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive 
attached the recon-all.log in case it's of any use.

1) FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
2) Platform: 54G7T63 Kernel: 5.0.0-32-generic x86_64 bits: 64 compiler: gcc v: 
7.4.0
   Desktop: MATE 1.22.2 wm: marco dm: LightDM Distro: Linux Mint 19.3 
Tricia
   base: Ubuntu 18.04 bionic
3) recon-all.log: see attached

Best wishes,


Stefan

#@# Talairach Failure Detection Fr 11. Mär 18:44:03 CET 2022


 talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
***FAILED*** (p=0.0321, pval=0.0034 < threshold=0.0050)
Command exited with non-zero status 1
@#@FSTIME  2022:03:11:18:44:03 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 100% M 
6312 F 0 R 247 W 0 c 0 w 1 I 0 O 0 L 83 1 60
@#@FSLOADPOST 2022:03:11:18:44:03 talairach_afd N 4 83 1 60

Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See:

http://secure-web.cisco.com/1UT1AAFsldR3wkUATYIjEYL_5proRYQNSNGyTJKVNntV131q733BTrj2ERp9j1sx_ZTmJ6m1ii08-Jornf4UaZNtx9z9STWU66ab0ZRezNjfHjPhkBk8Mkpll5hNSn7e02TvDumOnQQ867uveSad9BEooMLIIyw9oYxyu3bKPlLS6Qh-fMelrcPkwl_VGOtELnh0YKzS0zzfgOCvcW-xElF6BOF7hzl3qJkcqQoMGpdMGz8AvnD8n7umQcDySzH-0eE0uRorgYBBrc_K_Lh8M6VwpwdiqiC5L25pAIpaZw-CdK_fZlMr2xFlZa4LwttfvrbaiIURH0Pix3n0Uc3Ysmw/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach
ERROR: Talairach failed!




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[Freesurfer] TRACULA question

2022-04-22 Thread Gonzalo Rojas Costa 
External Email - Use Caution

Hi:

  Is it possible to use input diffusion files in MOSAIC IMA Siemens
file format directly? Or is it necessary to convert to nifti file
format first?

  Sincerely,


Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
https://secure-web.cisco.com/13PUT3U3zuLu0QBvcZiGdm18njGuoQr6dUsSQj9e5H3gOiFfFDIQfzquemma2IXSELZNdhFwGi3w3goGxGPnOUdDoh9pHJjjlEzyWgHhOvtSI1rWfiptKHRGKPqroO3HfU5LOzYece7gEBewcRdacnxbyoGkrInzayFlpCHDwMovVj2RsZXoAPA1TJD0c6qPpjpyNdRSfvWEQjlWFseO0XmY2GzERvEGLNZ2jVD7cFivFtsBZI6QKXubnoVYv7ZIhYdk8IDuEDnUGkM6aGN0fQdo0EfKqqQ5mvrA_-URQ1HAlx7fGFKcWaS-msf5JV3UYewMKh29ySoudmFsGrqP2Jg/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ
https://secure-web.cisco.com/1TdZ-Zm0eaCvN4RyCzzXuq6HNPTVfbbxwGyNTIGMGFiRfybDhlZfcJej5DuQlBFxYwDJwSO1NbZisBp1yVrq7nyw2kMBF6oos5kUwQY5n5PaU_F0e5FlhFPXN8jHJ9-2ZjvCR48B8WX_Z98dUDwJgPDp6W5J9Qx86YoNJpPWxzK2nlRZBUv4m4xJZ1yZl8bc-y_rLC_yBmefTddoYvHRgxm-Sx-sI3urGbmLlgo1GW0ejAy5O87MgIVb9l10EMEi9Scz6WXE-mZCKUDK68bg0_py0KqpFw23M8fQvUlt-KsNQxJKwM0xjpEwDF8JFFDEW1fwAuuxSsUuDnVYZUTIW-g/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2
https://secure-web.cisco.com/1lJu3jBI0nOfv9_IwBeCbcBNGA2K6pj5tSumDqMfk3ZItRd8BPyGam7Jzi5vwYgKSWZn_h3NHNpB-2LvnR0NG2dicPxcNLIMT9-kyIhxlIVn9KJDnI0UkMvvB_bwD35c9Wo8ZgYrmeeME-Xhopc25SP0b4uZ_ac8eyRU7siPGYplCIdV_wlbcpaf4QKngZ0GQ0OlKTSFA0kUvGppEUPh0dKLd1GGfVI7ta1xtDWAEeQDRZIJPDNENvLEMET8cajKIPIxhR0Pj9mFACW91chNeZqqgUH-RWTQD6lH1n-FqHFhQVN7buFLIgM89GsJppvGFD4sZGKjuTmnCpl4rS9rfaw/https%3A%2F%2Fcvn.fecyt.es%2F-0002-6228-2678
http://secure-web.cisco.com/1vs-E3PvUdSdie9Xm5LpQNiLpowx1KB-bnADkKZ76Vp4VANi--BPTBe90wM8SCdFK734_gIbmMr3PBFV4ZJOOJBA24RG16y2k3uomDr6zt-G7miVY8bETh1mVxRJXumLpmc3Yy3dH2PFE6uhzJNvuE5hUZqhTfQw-X7c4anBMhN_zYMez258yi_VwfB2Bz28yNTA0qClOp844_ELq3fX0tWSuBqUJmcCh8gyVYmA64LHU5lnFXwPdUjWzaoH9ZZ273niweURIdtncHPz5NN3wKifGl9r1dIbi8P9MG0Z64fjTArReR1NbSk-Z64E3_nvqJ-7Si7om181qm26Y05GJJQ/http%3A%2F%2Fwww.researcherid.com%2Frid%2FB-2036-2013
https://secure-web.cisco.com/1FM_I0dgNRRtoYqJmIXPdHgx__9woRyRSo5bnLSxgt51fCtFxOKP6SAvGDvzMdI6MlI8dr1A-GDLm7Ugbz4xQx_eBa-r6rF_KXZvcjQcG7c3HVqDBJ5Osza-xTwzP_JY8XT3vlujEpbz8lruWJRubpiv8DahDeUMtd6pNWEUHJagvmUDsyMHXbd1pm-XmpTmfa1RXkgkyaVwFfLwauPMJh4WFhchF7wz1ikJ8evtbLmu13H0jH_fCDLhFjkQlIHGSX4u1iiBtVtWcQQBc3tYacYBQNS-ly18qBzxa6Ebq21iyHPLMQ5lsZwvlRZoZl9d53xxdrTkwCPcwwkvO1szKIQ/https%3A%2F%2Fcl.linkedin.com%2Fin%2Fgonzalorojascosta

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Re: [Freesurfer] mri_segment_hypothalamic_subunits error

2022-04-22 Thread Douglas N. Greve 


From Benjamin Billot:
Yep, that’s just an out of memory issue for the GPU. He/she can use the 
cropping flag, or use the cpu flag.


On 4/18/2022 9:58 AM, Chen ZY wrote:


External Email - Use Caution

Dear FreeSurfer Developers,

I'm attempting to use the mri_segment_hypothalamic_subunits tool on 
subjects that have been analyzed with recon-all as described on the 
wiki page


(https://surfer.nmr.mgh.harvard.edu/fswiki/HypothalamicSubunits), but 
I received the following error when I run the 
mri_segment_hypothalamic_subunits


command (mri_segment_hypothalamic_subunits --s):

(tensorflow) brain@neurodebian:/usr/local/apps/freesurfer/subjects$ 
mri_segment_hypothalamic_subunits --s bert


using 1 thread

processing 1/1

*** Error in `/usr/local/apps/freesurfer/python/bin/python3': 
munmap_chunk(): invalid pointer: 0x7fa1707b3400 ***


Aborted

I would be appreciated if you can help me solve this problem.

Thank you very much!

Regrads,

发送自Windows 10 版邮件 
应用



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Re: [Freesurfer] recon-all error

2022-04-22 Thread Huang, Yujing 
Hi Rebecca,

I’m wondering if the dicom files are being recognized.

Can you run the following command with some dicom files in the directory?
mri_probedicom --i  --d filetype

(Replace  with full path to dicom file.)

Thanks.

Yujing

From: coope...@student.unimelb.edu.au 
Sent: Friday, April 22, 2022 1:34 AM
To: Huang, Yujing ; 'Freesurfer support list' 

Subject: RE: [Freesurfer] recon-all error


External Email - Use Caution
Dear Yujing,

Thank you for your reply.

  1.  Confirmed I am running Freesurfer 6.0.
  2.  I am running both commands from within the individual subject directory 
(ID=1003156). The parent folder contains several folders all labelled with 
different subject IDs, and within each contains the dicom directories.
  3.  I attempted this and received the error:

/Applications/freesurfer_v6/bin/dcmunpack -src 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/

-rwxr-xr-x  1 chesterk  admin  23759 Jun 14  2018 
/Applications/freesurfer_v6/bin/dcmunpack
---
---
Searching for matching files
Fri Apr 22 15:32:30 AEST 2022
Fri Apr 22 15:32:30 AEST 2022
Found 114 total files.
  Interrogating each and every one of them.
  Be patient.
If you have collected the data in the Martinos center, this
will run faster if you kill this job and re-run with -martinos
Except, with changes in the file naming (Oct 2012), this does
not work.
cat: /tmp/dcmdir-all.23294: No such file or directory
Found 0 unique series:
Patient: Undefined variable.

With thanks,
Rebecca



From: Huang, Yujing mailto:yhuan...@mgh.harvard.edu>>
Sent: Friday, 22 April 2022 4:19 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: coope...@student.unimelb.edu.au
Subject: RE: [Freesurfer] recon-all error

Hi Rebecca,

I’m trying to get more information to determine how it core dumped.


  1.  Can you confirm that you are running Freesurfer 6.0?
  2.  From which directory, did you run recon-all and dcmunpack?
  3.  Can you try dcmunpack by passing it full path to dicom directory?

Thanks.

Yujing


 Forwarded Message 
Subject:
[Freesurfer] recon-all error
Date:
Sun, 10 Apr 2022 07:01:30 +1000
From:
coope...@student.unimelb.edu.au
Reply-To:
Freesurfer support list 

To:
freesurfer@nmr.mgh.harvard.edu


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Dear FreeSurfer developers,

I’m attempting to run recon-all on a set of T1-weighted images acquired in the 
1980s-1990s and am having trouble with the recon-all pipeline. I have used the 
original dicom files in the recon-all using the command below.
Command: recon-all -s 1003156_dicom -i 
2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 -all
Error message:
/Applications/freesurfer_v6/bin/mri_convert: line 3:  8196 Segmentation fault: 
11  mri_convert.bin "$@"
The recon-all.log is also attached.

I’ve also explored using dcmunpack and obtain the following result:
Command: dcmunpack -src 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
Message:
cat: /tmp/dcmdir-all.89439: No such file or directory
Found 0 unique series:
Patient: Undefined variable.

Do you have any idea what might be the problem?

Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: Mac OS X 10.13.3
Recon-all.log: attached.

With warm regards,
Rebecca Cooper

The information in this e-mail is intended only for the person to whom it is 
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