Ah, thank you Anastasia! I'm glad it's that straightforward.

Best,
John
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edu>
Sent: Tuesday, September 21, 2021 12:00 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Freesurfer Digest, Vol 211, Issue 32
 
Send Freesurfer mailing list submissions to
        freesurfer@nmr.mgh.harvard.edu

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When replying, please edit your Subject line so it is more specific
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Today's Topics:

   1. Tcl_Init error on Ubuntu (Kevin Nguyen)
   2. Brainstem segmentation (Erik O'Hanlon)
   3. Re: Tcl_Init error on Ubuntu (fsbuild)
   4. Re: TRACULA mri_convert error (Yendiki, Anastasia)


----------------------------------------------------------------------

Message: 1
Date: Mon, 20 Sep 2021 18:35:47 +0200
From: Kevin Nguyen <kevin.nguyen0196@gmail.com>
Subject: [Freesurfer] Tcl_Init error on Ubuntu
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <6ccc849b-5e1c-5cd3-a53b-030b2838858c@gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hey FreeSurfer community!

I am running into a problem when trying to use the command "qdec --table
$SUBJECTS_DIR/cross.qdec.table.dat" on my data. The following error
message is shown:

"""
Tcl_Init error: Can't find a usable init.tcl in the following directories:
 ???? /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4
/home/kevin/freesurfer/lib/tcl8.4 /home/kevin/lib/tcl8.4
/home/kevin/freesurfer/library /home/kevin/library
/home/kevin/tcl8.4.6/library /home/tcl8.4.6/library
/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4



This probably means that Tcl wasn't installed properly.

Error initializing Tcl.

"""



I suppose there are version issues between the FreeSurfer version of Tcl
(8.4.6?) and my own version (8.6). I would very much appreciate any help
with that error:) Also, I am very new to Unix and FreeSurfer. I am
running the latest FreeSurfer version as well as Ubuntu 20.04.3 LTS.


Thanks in advance for your help!


Best,

Kevin

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Message: 2
Date: Mon, 20 Sep 2021 16:43:41 +0000
From: "Erik O'Hanlon" <OHANLOER@tcd.ie>
Subject: [Freesurfer] Brainstem segmentation
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <DB9PR02MB6571C1A751B0E59B18848A08B7A09@DB9PR02MB6571.eurprd02.prod.outlook.com>
       
Content-Type: text/plain; charset="iso-8859-1"

        External Email - Use Caution       

Dear Experts,

We hope to acquire some multishell dwi and structural data to investigate tracts passing through the Locus Coeruleus (LC) and we want to apply the brainstem segmentation to our structural data to obtain subject specific LC masks.
Is it possible to feed multispectral data into the brainstem segmentation ?
Is it possible to acquire a high res volume capturing the LC in greater detail and co-register that to the whole brain T1 (T2 or FLAIR ) to further assist in the delineation of the LC roi and quantification of the LC volume?
If it's possible to use an additional small volume like this, do I need to pre-process it using recon-all and what is the optimal way to co-register the small volume to the whole brain T1 to assist in the mask generation?

Any guidance is very much appreciated.

Best regards and thanks,

Erik




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Message: 3
Date: Mon, 20 Sep 2021 21:34:14 +0200
From: fsbuild <fsbuild@contbay.com>
Subject: Re: [Freesurfer] Tcl_Init error on Ubuntu
To: freesurfer@nmr.mgh.harvard.edu
Cc: kevin.nguyen0196@gmail.com
Message-ID: <1632166454.6148e236efa47@trashmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hello Kevin,
There are some previous postings on the freesurfer mail list archive,https://secure-web.cisco.com/1I_RCjLRTernteRhPGRN9r5086M5fnUaoFjoQyKzJCggnm09G9D3F_M4YV90J_yw5AhFlP-KlHa6h2hvGRBzCaZAPWJaTYm-vafaSfkl9hmEljS5sTGAQ-Tane5Clu5nlKdFFoJdlHJfe0COO-1IsnaaebSPByf3l-Q9xJGkeBMkyQC7GARe_C71RwrPznSYsExzJow8d2KUrRihm1Xfr0VrmoG9CIj2nhA_e3y0Yq_ItEcFSJ9uXgjiCCcL9qpUkdeIlix4N49a6DmPQcbvBww/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmaillist.html%26nbsp;
- that indicate qdec has been deprecated in favor of using other commands, e.g.,
https://secure-web.cisco.com/1qNHXP51Xhk1P62kV5_cYpUz-ZHahoX-I5CEwnuolSL1_js3EP08cn89bwM5B7wQYgKi5XwnFdTnhxVnNcRt4KxAQfMYYprnw1slDmTiD8ymtF4FBoSPFw125S2cK-lertNm7nD-9WseftGN4e98Rdo_epKD9QbJiG3Z0BY7MAGWQ4_UZcOinrES9rCkpH3Mqn9DoHrRnIfSZPhw0edVlktiWgXmQZBNylMX0lh3UgLi68J7gF1Ijr2EpgNI9KS8pUS7IqZ9I-FtQTb4nY1RqcA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg70829.html
https://secure-web.cisco.com/1w9jy6AiKEdpXbkrum37AWzbX77n1pb8O2JI19ZzOfOrZU_qZTm6FNWOxNuy_Z8Lx1EgMqTpu0a9DEAB3Y6O1kt4NaGV2N4sD4JiRJMoUzMO1r_cE7JjWjAUgUpGhNQAVqwHb7FXFEvQ-N57oACoD-rRJB7NF8zFJSUWEZN0ITsQsiRk9DnQ2N5JhfdpTW4B21LcOmoQnMpm2Wfp9Qiwp9v3koJsjbp765tVDLzIQS7cHy6nGzwaup8USIl4miTrrTlmQlpYemgQCidRtc01USQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg70546.html
- R.


On Sep 20, 2021, at 12:35, Kevin Nguyen &lt;kevin.nguyen0196@gmail.com&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hey FreeSurfer community!I am running into a problem when trying to use the command "qdec --table&nbsp;$SUBJECTS_DIR/cross.qdec.table.dat" on my data. The following error&nbsp;message is shown:"""Tcl_Init error: Can't find a usable init.tcl in the following directories:&nbsp;&nbsp;&nbsp;&nbsp; /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4&nbsp;/home/kevin/freesurfer/lib/tcl8.4 /home/kevin/lib/tcl8.4&nbsp;/home/kevin/freesurfer/library /home/kevin/library&nbsp;/home/kevin/tcl8.4.6/library /home/tcl8.4.6/library&nbsp;/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4This probably means that Tcl wasn't installed properly.Error initializing Tcl.&nbsp;"""I suppose there are version issues between the FreeSurfer version of Tcl&nbsp;(8.4.6?) and my own version (8.6). I would very much
  appreciate any help&nbsp;with that error:) Also, I am very new to Unix and FreeSurfer. I am&nbsp;running the latest FreeSurfer version as well as Ubuntu 20.04.3 LTS.Thanks in advance for your help!Best,Kevin_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 4
Date: Mon, 20 Sep 2021 20:30:46 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA mri_convert error
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <MN2PR04MB68166B18256888483A13C1E88AA09@MN2PR04MB6816.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="us-ascii"

Hi John - You're using a config file set up for the new TRACULA (in FS 7.2) and running an older version of TRACULA (from FS 6.0). You won't be able to take advantage of all the new TRACULA features with this old version. It's OK if your T1's were run through FS 6.0, you can still process your DWIs with the new version of TRACULA.

Best,
Anastasia.
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Jacoby, John <JJACOBY@mgh.harvard.edu>
Sent: Thursday, September 16, 2021 2:16 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA mri_convert error

Hi all,

I'm running TRACULA preprocessing in FreeSurfer 6.0 and have run into an error. It looks like it might be caused by TRACULA calling mri_convert with the input as the whole DICOM root directory, as opposed to an individual file. I'm not sure what's going wrong that leads to that happening though. I'll paste my command, error file, config file, and log file below. Thank you for any help!

Best,
John

Command:
trac-all -prep -c /autofs/cluster/bang/TAW_New/scripts/resources/tracula_test_config.txt

trac-all.error:
------------------------------
SUBJECT 180515_4PR00065
DATE Thu Sep 16 13:30:13 EDT 2021
USER jj1006
HOST erso.nmr.mgh.harvard.edu
PROCESSOR x86_64
OS Linux
Linux erso.nmr.mgh.harvard.edu 4.18.0-310.el8.x86_64 #1 SMP Tue Jun 8 00:24:50 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
$Id: trac-preproc,v 1.54.2.2 2016/12/27 16:47:14 zkaufman Exp $
/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/trac-preproc
PWD /autofs/cluster/bang/TAW_New/scripts/resources
CMD mri_convert /autofs/cluster/bang/TAW_New/data/ /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/b0mag.nii.gz

Config File:
setenv SUBJECTS_DIR /autofs/cluster/bang/TAW_New/recons/default

set dtroot = /autofs/cluster/bang/TAW_New/tracula

set dcmroot = /autofs/cluster/bang/TAW_New/data

set epifactor = 128

set echospacing = 0.69

set dob0 = 2

set interreg = 4

set subjlist = ( 180515_4PR00065 180515_4PR00065 )

set dcmlist = ( 180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512252089486946407 180515_4PR00065/DICOMs/031_dMRI_dir98_PA/MR.1.3.12.2.1107.5.2.43.67026.2018051512284637673973138 )

set pedir = ( AP PA )

trac-all.log:
Thu Sep 16 13:13:39 EDT 2021
/autofs/cluster/bang/TAW_New/scripts/resources
/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/trac-all
-prep -c /autofs/cluster/bang/TAW_New/scripts/resources/tracula_test_config.txt
Subject 180515_4PR00065
SUBJECTS_DIR /autofs/cluster/bang/TAW_New/recons/default
FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
jj1006
erso.nmr.mgh.harvard.edu
Linux erso.nmr.mgh.harvard.edu 4.18.0-310.el8.x86_64 #1 SMP Tue Jun 8 00:24:50 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    unlimited
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  131070
memorylocked 64 kbytes
maxproc      62634
maxlocks     unlimited
maxsignal    62634
maxmessage   819200
maxnice      0
maxrtprio    0
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:       16101348     5617832     4625196      263964     5858320     9883424
Swap:      16777212        4388    16772824

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/09/16-17:13:39-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: jj1006  Machine: erso.nmr.mgh.harvard.edu  Platform: Linux  PlatformVersion: 4.18.0-310.el8.x86_64  CompilerName: GCC  CompilerVersion: 40400
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/09/16-17:13:39-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: jj1006  Machine: erso.nmr.mgh.harvard.edu  Platform: Linux  PlatformVersion: 4.18.0-310.el8.x86_64  CompilerName: GCC  CompilerVersion: 40400
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/09/16-17:13:40-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: jj1006  Machine: erso.nmr.mgh.harvard.edu  Platform: Linux  PlatformVersion: 4.18.0-310.el8.x86_64  CompilerName: GCC  CompilerVersion: 40400
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/09/16-17:13:40-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: jj1006  Machine: erso.nmr.mgh.harvard.edu  Platform: Linux  PlatformVersion: 4.18.0-310.el8.x86_64  CompilerName: GCC  CompilerVersion: 40400
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/09/16-17:13:40-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: jj1006  Machine: erso.nmr.mgh.harvard.edu  Platform: Linux  PlatformVersion: 4.18.0-310.el8.x86_64  CompilerName: GCC  CompilerVersion: 40400
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/09/16-17:13:41-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: jj1006  Machine: erso.nmr.mgh.harvard.edu  Platform: Linux  PlatformVersion: 4.18.0-310.el8.x86_64  CompilerName: GCC  CompilerVersion: 40400
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/09/16-17:13:41-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: jj1006  Machine: erso.nmr.mgh.harvard.edu  Platform: Linux  PlatformVersion: 4.18.0-310.el8.x86_64  CompilerName: GCC  CompilerVersion: 40400


New invocation of trac-preproc


jj1006
erso.nmr.mgh.harvard.edu
Linux erso.nmr.mgh.harvard.edu 4.18.0-310.el8.x86_64 #1 SMP Tue Jun 8 00:24:50 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    unlimited
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  131070
memorylocked 64 kbytes
maxproc      62634
maxlocks     unlimited
maxsignal    62634
maxmessage   819200
maxnice      0
maxrtprio    0
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:       16101348     5661112     4556004      263964     5884232     9840152
Swap:      16777212        4388    16772824

#-------------------------------------
/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/trac-preproc
#-------------------------------------
#@# Image corrections Thu Sep 16 13:13:41 EDT 2021
mri_convert --bvec-voxel /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512252089486946407 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512252089486946407 /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512252089486946407...
Getting Series No
INFO: Found 101 files in /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP
INFO: Scanning for Series Number 28
Scanning Directory
INFO: found 99 files in series
INFO: loading series header info.

RunNo = 27
WARNING: Run 1 appears to be truncated
  Files Found: 99, Files Expected (lRep+1): 1
FileName /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512220971428016067
Identification
NumarisVer        syngo MR E11
ScannerModel      Prisma_fit
PatientName       180515_4PR00065
Date and time
StudyDate         20180515
StudyTime         114840.347000
SeriesTime        122239.413000
AcqTime           122131.110000
Acquisition parameters
PulseSeq          ep_b5#1
Protocol          dMRI_dir98_AP
PhEncDir          COL
EchoNo            1
FlipAngle         78
EchoTime          89.2
InversionTime     -1
RepetitionTime    3230
PhEncFOV          210
ReadoutFOV        210
Image information
RunNo             27
SeriesNo          28
ImageNo           1
NImageRows        1400
NImageCols        1400
NFrames           99
SliceArraylSize   92
IsMosaic          1
ImgPos            1002.7822 1063.1628 325.3363
VolRes              1.5000   1.5000   1.5000
VolDim            140      140       92
Vc                 -0.9990  -0.0444  -0.0029
Vr                  0.0426  -0.9342  -0.3543
Vs                  0.0130  -0.3541   0.9351
VolCenter           0.0000   0.0000   0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (140 140  92), nframes = 99, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR E11
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 3230, TR = 3230 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   1.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;

FileName /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512220971428016067
Identification
NumarisVer        syngo MR E11
ScannerModel      Prisma_fit
PatientName       180515_4PR00065
Date and time
StudyDate         20180515
StudyTime         114840.347000
SeriesTime        122239.413000
AcqTime           122131.110000
Acquisition parameters
PulseSeq          ep_b5#1
Protocol          dMRI_dir98_AP
PhEncDir          COL
EchoNo            1
FlipAngle         78
EchoTime          89.2
InversionTime     -1
RepetitionTime    3230
PhEncFOV          210
ReadoutFOV        210
Image information
RunNo             27
SeriesNo          28
ImageNo           1
NImageRows        1400
NImageCols        1400
NFrames           99
SliceArraylSize   92
IsMosaic          1
ImgPos             98.9473 138.4093 -12.2484
VolRes              1.5000   1.5000   1.5000
VolDim            140      140       92
Vc                 -0.9990  -0.0444  -0.0029
Vr                  0.0426  -0.9342  -0.3543
Vs                  0.0130  -0.3541   0.9351
VolCenter          -0.5800  11.2260  14.7653
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 1
sagrev = 0, correv =0, trarev = 0
Vs = 0.0130269 -0.3541 0.935117
INFO: no Siemens slice order reversal detected (good!).
TR=3230.00, TE=89.20, TI=-1.00, flip angle=78.00
i_ras = (-0.999009, -0.0444233, -0.00290475)
j_ras = (0.0425695, -0.934152, -0.354328)
k_ras = (0.0130269, -0.3541, 0.935117)
writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.nii.gz...
Saving bvals and bvecs
mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.voxel_space.bvecs /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.bvecs
mri_probedicom --i /autofs/cluster/bang/TAW_New/data/180515_4PR00065/DICOMs/028_dMRI_dir98_AP/MR.1.3.12.2.1107.5.2.43.67026.2018051512252089486946407 > /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dcminfo.dat
mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.bvecs
mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvals.tmp /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.bvals
orientLAS /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 3.375
mri_convert -oni 140 -onj 140 -onk 92 -oid -0.999009 -0.0444233 -0.00290475 -ojd -0.0425695 0.934152 0.354328 -okd 0.0130269 -0.3541 0.935117 -oc -0.643818 12.6272 15.2968 -rt nearest /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 140 -onj 140 -onk 92 -oid -0.999009 -0.0444233 -0.00290475 -ojd -0.0425695 0.934152 0.354328 -okd 0.0130269 -0.3541 0.935117 -oc -0.643818 12.6272 15.2968 -rt nearest /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.nii.gz
normalizing out_i_direction: (-0.999009, -0.0444233, -0.00290475) -> (-0.999009, -0.0444233, -0.00290475)
normalizing out_j_direction: (-0.0425695, 0.934152, 0.354328) -> (-0.0425695, 0.934152, 0.354328)
normalizing out_k_direction: (0.0130269, -0.3541, 0.935117) -> (0.0130269, -0.3541, 0.935117)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.nii.gz...
TR=3230.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999009, -0.0444233, -0.00290475)
j_ras = (0.0425695, -0.934152, -0.354328)
k_ras = (0.0130269, -0.3541, 0.935117)
Reslicing using nearest
writing to /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.nii.gz...
INFO: found /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.bvals, copying
INFO: found /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig.bvecs, converting to LAS
mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.bvecs /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs
mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.bvals /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvals
eddy_correct /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_orig_las.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi.nii.gz 0
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0000
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0001
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0002
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0003
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0004
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0005
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0006
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0007
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0008
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0009
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0010
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0011
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0012
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0013
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0014
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0015
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0016
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0017
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0018
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0019
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0020
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0021
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0022
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0023
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0024
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0025
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0026
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0027
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0028
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0029
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0030
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0031
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0032
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0033
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0034
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0035
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0036
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0037
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0038
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0039
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0040
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0041
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0042
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0043
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0044
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0045
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0046
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0047
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0048
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0049
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0050
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0051
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0052
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0053
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0054
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0055
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0056
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0057
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0058
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0059
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0060
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0061
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0062
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0063
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0064
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0065
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0066
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0067
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0068
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0069
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0070
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0071
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0072
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0073
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0074
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0075
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0076
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0077
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0078
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0079
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0080
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0081
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0082
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0083
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0084
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0085
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0086
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0087
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0088
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0089
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0090
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0091
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0092
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0093
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0094
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0095
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0096
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0097
processing /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_tmp0098
mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs.norot
xfmrot /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi.ecclog /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs.norot /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/bvecs
mv -f /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi.nii.gz /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/dwi_eddy.nii.gz
mri_convert /autofs/cluster/bang/TAW_New/data/ /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/b0mag.nii.gz
mri_convert.bin /autofs/cluster/bang/TAW_New/data/ /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/b0mag.nii.gz
corRead(): can't open file /autofs/cluster/bang/TAW_New/data/COR-.info
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /autofs/cluster/bang/TAW_New/data/...
Linux erso.nmr.mgh.harvard.edu 4.18.0-310.el8.x86_64 #1 SMP Tue Jun 8 00:24:50 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Thu Sep 16 13:30:13 EDT 2021
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End of Freesurfer Digest, Vol 211, Issue 32
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