Re: [Freesurfer] recon-all error

2022-04-23 Thread Huang, Yujing 
Hi Rebecca,

Thank you for the information.

I'm wondering if you would like to try converting those dicom using dcm2niix to 
.nii, and then feed .nii to recon-all pipeline.

You can download dcm2niix here:
https://github.com/rordenlab/dcm2niix

I use the following command to do conversion: dcm2niix -o  -f 
"%s_%p" 

Please note that  needs to be specified as last parameter.  '-f <>' 
specifies output file name format - "%s_%p" will have series no + protocol as 
prefix.

Hope these helps.

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
coope...@student.unimelb.edu.au 
Sent: Saturday, April 23, 2022 2:44 AM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] recon-all error


External Email - Use Caution

Hi Yujing,



I guess not. This is the output:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 
mri_probedicom --i 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem



Entering IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256)



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem



I also ran straight to the dicom files themselves, with the same response:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 
mri_probedicom --i 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 is not a dicom file or some other problem



Entering IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)

Opening 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 as part10

DCM_FILEOPENFAILED

   20092 DCM failed to open file: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 in DCM_OpenFile

Opening as littleendian

DCM_FILEOPENFAILED

Opening as bigendian

DCM_FILEOPENFAILED

Opening as format conversion

DCM_ILLEGALOPTION

Leaving IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 is not a dicom file or some other problem



Thank you,



Rebecca





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: Friday, 22 April 2022 11:11 PM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] recon-all error



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 
mailto:coope...@student.unimelb.edu.au>>
Sent: Friday, April 22, 2022 1:34 AM
To: Huang, Yujing mailto:yhuan...@mgh.harvard.edu>>; 
'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: RE: [Freesurfer] recon-all error



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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...@

Re: [Freesurfer] ERROR: Talairach failed!

2022-04-23 Thread Douglas N. Greve 

Try adding --no-surfs

On 4/22/2022 11:38 AM, Fritze, Stefan wrote:


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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 computerecon-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://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_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:

*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

ERROR: Talairach failed!


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[Freesurfer] pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z

2022-04-23 Thread Peng, Shichun 
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Could you please send me the pass code to unzip the file?

Thanks,
Shichun

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