[Freesurfer] error in hippocampal subfields and nuclei of amygdala segmentation

[오진영]

External Email - Use Caution

Dear freesurfer experts,

I'm trying to run segmentation of hippocampal subfields and nuclei of
amygdala with segmentHA_T1.sh command.
I already run segmentation of hippocampal subfields and nuclei of amygdala
several times, however, after segment nuclei of amygdala in left hemisphere
and before segment nuclei of amygdala in right hemisphere, there appears
same error "MATLAB is exiting because of fatal error" and hippocampal
subfields segmentation stops.
Ignoring and Trying the same command few more times, I can make it to
segment subfields of amygdala, but I am still wondering if I can run
segmentHA_T1.sh without any error.

Following is the repeated error with the few lines:

#

#@# Hippocampal Subfields processing (T1) right 2018년 10월 30일 화요일 14시 07분
17초 KST

--

Setting up environment variables

---

DYLD_LIBRARY_PATH is
.:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64:/Applications/freesurfer/lib/gcc/lib:

PostVMInit failed to initialize com.mathworks.mwswing.MJStartupForDesktop




   Segmentation violation detected at Tue Oct 30 14:07:20 2018




Configuration:

  Crash Decoding : Disabled

  Current Visual : Quartz

  Default Encoding   : US-ASCII

  MATLAB Architecture: maci64

  MATLAB Root: /Applications/freesurfer/MCRv84

  MATLAB Version : 8.4.0.150421 (R2014b)

  Operating System   : Darwin 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun
21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64

  Processor ID   : x86 Family 6 Model 158 Stepping 9, GenuineIntel

  Software OpenGL: 0

  Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java
HotSpot(TM) 64-Bit Server VM mixed mode

  Window System  : Quartz


Fault Count: 2



Abnormal termination:

Segmentation violation


Register State (from fault):

  RAX = 7fafcba4f000  RBX = 7fafcba4f000

  RCX = 7cdf72d0  RDX = 000111cba97e

  RSP = 7fafcba4f000  RBP = 9b630cdf72d0

  RSI = 7fafcdb8a9b0  RDI = 


   R8 = 7fafcc2dc270   R9 = 7fafcba4f000

  R10 = 00011bd1f76a  R11 = 

  R12 = 7cdf7330  R13 = 000111b083c7

  R14 = 7cdf73a0  R15 = 00011bd1f777


  RIP = 000116ca6f40  RFL = 7fafcc2dc270


   CS = 9b6300305bc3   FS = 00011bd1f76a   GS = 7fafcba4f1e8


Stack Trace (from fault):

[  0] 0x000105f76e64
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00028260
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052

[  1] 0x000105f7aa2a
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00043562
_ZN2fl4test17terminate_handledEv+0906

[  2] 0x000105f7a477
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00042103
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119

[  3] 0x00010d041b7a
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00387962
_Z32mnRunPathDependentInitializationv+3146

[  4] 0x00010d041e58
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00388696
_Z32mnRunPathDependentInitializationv+3880

[  5] 0x00010d03f733
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00378675
mnFatalSignalHandler+0275

[  6] 0x7fff74b75f5a
/usr/lib/system/libsystem_platform.dylib+8026
_sigtramp+0026

[  7] 0x000111b096f8
/Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568
_ZN23JNI_ArgumentPusherVaArg7iterateEy+

[  8] 0x000111af9d67
/Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679
jni_GetMethodID+0126

[  9] 0x0001104dd271
/Applications/freesurfer/MCRv84//bin/maci64/libmwjmi.dylib+00160369
_Z12mljGetMethodP7_jclassPKcS2_+0049

[ 10] 0x00011b57a366
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00598886
_ZN2ui14JavaScreenData20getPrimaryScreenRectEv+0150

[ 11] 0x00011b57fef4
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00622324
_ZN10ScreenImpl13getScreenSizeEv+0036

[ 12] 0x00011b57e2e2
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00615138
_ZNK2ui24RootScreenAndPointerImpl13getScreenSizeEv+0018

[ 13] 0x00011b582f58
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00634712
_ZN2ui4Root17getScreenSizeImplEPN4mcos11COSPropInfoEPNS1_9COSClientEPNS1_12COSInterfaceE+0040

[ 14] 0x00011b9b9d13
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+05053715
_ZN7hgutils6StubPIIN2ui4RootENS_15PropertyStorageIN8graphics8datatype8PositionENS_6NoModeENS_21NoSerializableStorage8getValueEPN4mcos12COSInterfaceE+0099

[ 

Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file {Disarmed}

[Chen Guoyang (IMH)]

External Email - Use Caution

Hi Martin,

Thanks for the input! It worked perfectly.

A follow up question:

I understand that for T1 hippocampal subfield segmentation, Freesurfer has a 
longitudinal module for it (segmentHA_T1.long.sh)

Does freesurfer have a longitudinal module for T1+T2 hippocampal segmentations?

If such a module is not available, will just like to consult you guys whether 
are our current processing steps appropriate for longitudinal comparisons:

1.   Run the longitudinal pipeline (FSv6.0) across all our subjects and 
each of their timepoints, example:

recon-all -long Subject1_timepoint1 Subject1_base

recon-all -long Subject1_timepoint2 Subject1_base

2.   Run segmentHA_T2.sh across each longitudinal scan of each of our 
subjects, example:
segmentHA_T2.sh Subject1_timepoint1 Subject1_timepoint1.long.Subject1_base 
Subject1_timepoint1_T2.nii T2 1
segmentHA_T2.sh Subject1_timepoint2 Subject1_timepoint2.long.Subject1_base 
Subject1_timepoint2_T2.nii T2 1

Thanks!

Yours Sincerely,
Guoyang

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter
Sent: Saturday, 27 October, 2018 4:59 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform 
file

Hi,

Looks like the input is a multi frame image. Should only be single frame.

Best Martin

On 26. Oct 2018, at 13:52, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

It seems like a problem with mri_robust_register.
Martin, any ideas?

--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College London
http://www.jeiglesias.com



From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Chen Guoyang (IMH)" 
mailto:guoyang_c...@imh.com.sg>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, 26 October 2018 at 11:35
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file

External Email - Use Caution
Dear Freesurfer experts,

I am currently attempting to include an additional T2 MRI scan in the 
segmentation of our T1 scan. The freesurfer version that I'm using is the 
freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa (developmental version).

However, I ran into this issue, ERROR: cannot find transform file. I've pasted 
the output below.

Will like your advices for the this matter.

Thanks!

Sincerely,
Guoyang

OS Darwin
Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct  4 
00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64
--

#
#@# Hippocampal Subfields processing (T1+T2) left Fri Oct 26 17:50:06 +08 2018
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer_Dev_26Sep18/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//bin/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_26Sep18/lib/gcc/lib:
Registering norm.mgz to additional volume
/Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register: only pass single 
frame MRI target /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii.

/Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register --mov 
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/norm.mgz
 --maskmov 
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//wholeBrainMask.mgz
 --dst /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii --lta 
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta
 --noinit --cost NMI -nosym >/dev/null: Signal 127
ERROR: cannot find transform file 
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta
gunzip: can't stat: 
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz
 
(/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz.gz):
 No such file or directory
ERROR: problem reading fname
SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)



Error in myMRIread>myMRIread_aux (line 92)



Error in myMRIread (line 63)



Error in segmentSubjectT1T2_autoEstimateAlveusML (line 207)



MATLAB:badSwitchExpression
Darwin newfeis-iMac.local 16.7.0 

Re: [Freesurfer] Segmentation fault

[fsbuild]

External Email - Use Caution

​Hello Jon,

Looks like you are already running with -debug and -allowcoredump option, and 
the shell limits do not look like they are too small to allow the coredump to 
be written. I don't know offhand if that coredump option causes a file to 
be written somewhere, but I will try and find out if there is a location for it.

When the program exits you could try looking at the end of the system log to 
see if their is any info logged there, e.g.,

$ tail -50 /var/log/syslog

- and look for events that match the timestamp of when the program ran/stopped 
running.

If you can reproduce running a trac* command from the terminal that causes the 
crash, then you could try running that same command with gdb, e.g.,

$ gdb /usr/local/freesurfer/bin/trac-all-debug -allowcoredump -path 
-c /data/Abeona/648TT/run_648TT_path.txt

 gdb will output some text then at the gdb prompt type run...

(gdb) run

 then wait for the program to stop and try to get the backtrace with the 
back trace command 

(gdb) bt full

 which may yield some more info about the crash .

On Oct 29, 2018, at 16:59, Whitney, Jon jon.whit...@ert.com 
wrote:External Email - Use 
CautionI got someone to help 
me, and based on what they told me the trac-all.log is where the debug 
information gets stored (I tried using -x +x in my bash command script and it 
only gave me upper level debugging information), so I have attached the 
trac-all.log file. I also was able to get help from someone who was able 
to save the core dump for when the system crashed, but it is extremely large 
(1.7GB). I can upload the core dump file if that would be helpful. I 
watched the system resources while the program ran, and I noticed that the 
memory usage only got up to 4% while the CPU usage was 100%, so I don't think 
I'm running out of memory. We looked at the core dump file, and my linux 
expert friend suggested that it may be a memory overflow error because it 
references memory at 0x000etc.image.pngunfortunately, without the 
source code to help us interpret the core dump, I don't think I can provide 
much more in the way of specific information. Please let me know if 
there's somewhere I can upload the core dump if you want to look at it.Thanks!
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Re: [Freesurfer] Cortical Parcellation: ROIs not covering gray matter in depth direction

[Bruce Fischl]

Hi Yixin

check to see if the lh.pial and rh.pial surfaces are accurate.

cheers
Bruce
On Mon, 29 
Oct 2018, Yixin Ma wrote:




External Email - Use Caution

Hi,
I’m writing to ask about cortical parcellation (Desikan-Killiany and 
Destrieux), which do not work
well on my recent anatomical scan (a new anatomical scan sequence that gives 
better grey and white
matter contrast). I’m writing to ask if you know what is causing this artifact 
(ROIs are not
covering all gray matter in depth direction) and from which step should I start 
to debug. Thank you
for your help.

Best regards,

Yixin Ma

Screen Shot 2018-10-29 at 12.19.43 PM.png

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Re: [Freesurfer] resampling data onto cortical surface

[Bruce Fischl]

Hi Greg,

yes, that sounds correct
cheers
Bruce
On Mon, 29 Oct 2018, GREGORY R KIRK wrote:



External Email - Use Caution

there is some misunderstanding ? I said to resample onto the cortical surface 
not

into a volume


you say Use --s subject instead of --reg (run mri_vol2vol with --help to get
more info). but this is not mri_vol2surf mri_vol2surf does not have --s as an 
option.



the volume is already in registration with orig.mgz for the subject so i can't 
use --reg
register.dat

I need to use an identity transformation somehow.


i tried mri_vol2surf --mov vout.mgz  --regheader 311140 --hemi lh --o R1.mgz

and that seemed to work, is this correct ?


greg


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of
Greve, Douglas N.,Ph.D. 
Sent: Monday, October 22, 2018 11:58:51 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] resampling data onto cortical surface  
Use --s subject instead of --reg (run mri_vol2vol with --help to get
more info).
btw, if you have multi echo data, you are probably measuring R2*, not R1.

On 10/22/2018 12:55 PM, GREGORY R KIRK wrote:
>
> External Email - Use Caution
>
>
> I have R1 values that I want to resample onto the cortical surface.
> The R1 values were computed from a multi echo
>
> T1 sequence that was also used to create the T1 weighted image that
> was used in recon-all to produce the cortical surface reconstructions
>
> and thus is inherently in registration to the 001.mgz that was used to
> start recon. There will be a difference in orientation in the volume
>
> in that orig.mgz is in coronal and in the .mgz format.
>
>
> I was thinking that if I run the first step of recon-all it should
> give me an volume named orig.mgz that is in registration to the
> freesurfer space
>
> for the subject ... or else some call to mri_convert reslice_as or
> whatever is used in the recon-all script to convert 001.mgz to orig.mgz
>
>
>
>
> then my problem is to get a file with the resampling of the R1 onto
> the cortical surface withR1 values at each vertex.
>
>
> when i work with fmri data I run bbregister and get the transformation
> from the epi volume to the freesurfer space and then use
>
> mri_vol2surf --mov sig.nii \to resample the data onto the cortical surface
>  --reg bb.register.dat \
>  --projfrac 0.5 --interp nearest \
>  --hemi lh --o lh.sig.mgh
>
> to resample the epi data onto the cortical surface. however in this case the 
R1 data
> is already in perfect registration to the T1 other than the reorientation and 
reslicing
> done to prepare the orig.mgz volume.
>
> so can someone tell me what is the proper way to cook this goose
>
> Greg
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] freeview libpng12.so.0 error

[fsbuild]

External Email - Use Caution

​Hello Ashesh,

You need to install the "gdebi" command on your Ubuntu machine.

Then download and install the libpng12 package from,
http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb

Then install that package with the gdebi command,
$ sudo gdebi libpng12-0_1.2.54-1ubuntu1_amd64.deb



On Oct 29, 2018, at 14:43, Thaker, Ashesh A ashesh.tha...@ucdenver.edu 
wrote:External Email - Use 
CautionDear FreeSurfer Team,I'm 
running FreeSurfer on a 64-bit Linux machine running Ubuntu 18.04 LTS. Here is 
my config:ashesh@ashesh-gpu:~$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Setting up 
environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME 
/usr/local/freesurferFSFAST_HOME 
/usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR 
/usr/local/freesurfer/subjectsMNI_DIR
 
/usr/local/freesurfer/mniFSL_DIR
 /usr/local/fslI have this error running freeview:ashesh@ashesh-gpu:~$ 
freeviewfreeview.bin: error while loading shared libraries: libpng12.so.0: 
cannot open shared object file: No such file or directoryI have installed 
libjpeg62-dev but still get the same error.Any thoughts?Thanks,AsheshAshesh 
Thaker, MD| Assistant ProfessorSchool of Medicine, Department of 
RadiologyUniversity of Colorado Anschutz Medical Campus
720 848 6568 
(office)|ashesh.tha...@ucdenver.edu

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[Freesurfer] freeview libpng12.so.0 error

[Thaker, Ashesh A]

External Email - Use Caution

Dear FreeSurfer Team,


I'm running FreeSurfer on a 64-bit Linux machine running Ubuntu 18.04 LTS. Here 
is my config:


ashesh@ashesh-gpu:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl

I have this error running freeview:


ashesh@ashesh-gpu:~$ freeview
freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open 
shared object file: No such file or directory


I have installed libjpeg62-dev but still get the same error.


Any thoughts?


Thanks,

Ashesh



Ashesh Thaker, MD | Assistant Professor

School of Medicine, Department of Radiology

University of Colorado Anschutz Medical Campus


720 848 6568 (office) | ashesh.tha...@ucdenver.edu








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Re: [Freesurfer] resampling data onto cortical surface

[GREGORY R KIRK]

External Email - Use Caution

there is some misunderstanding ? I said to resample onto the cortical surface 
not

into a volume


you say Use --s subject instead of --reg (run mri_vol2vol with --help to get
more info). but this is not mri_vol2surf mri_vol2surf does not have --s as an 
option.



the volume is already in registration with orig.mgz for the subject so i can't 
use --reg register.dat

I need to use an identity transformation somehow.


i tried mri_vol2surf --mov vout.mgz  --regheader 311140 --hemi lh --o R1.mgz

and that seemed to work, is this correct ?


greg


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Greve, Douglas N.,Ph.D. 

Sent: Monday, October 22, 2018 11:58:51 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] resampling data onto cortical surface

Use --s subject instead of --reg (run mri_vol2vol with --help to get
more info).
btw, if you have multi echo data, you are probably measuring R2*, not R1.

On 10/22/2018 12:55 PM, GREGORY R KIRK wrote:
>
> External Email - Use Caution
>
>
> I have R1 values that I want to resample onto the cortical surface.
> The R1 values were computed from a multi echo
>
> T1 sequence that was also used to create the T1 weighted image that
> was used in recon-all to produce the cortical surface reconstructions
>
> and thus is inherently in registration to the 001.mgz that was used to
> start recon. There will be a difference in orientation in the volume
>
> in that orig.mgz is in coronal and in the .mgz format.
>
>
> I was thinking that if I run the first step of recon-all it should
> give me an volume named orig.mgz that is in registration to the
> freesurfer space
>
> for the subject ... or else some call to mri_convert reslice_as or
> whatever is used in the recon-all script to convert 001.mgz to orig.mgz
>
>
>
>
> then my problem is to get a file with the resampling of the R1 onto
> the cortical surface withR1 values at each vertex.
>
>
> when i work with fmri data I run bbregister and get the transformation
> from the epi volume to the freesurfer space and then use
>
> mri_vol2surf --mov sig.nii \to resample the data onto the cortical surface
>  --reg bb.register.dat \
>  --projfrac 0.5 --interp nearest \
>  --hemi lh --o lh.sig.mgh
>
> to resample the epi data onto the cortical surface. however in this case the 
> R1 data
> is already in perfect registration to the T1 other than the reorientation and 
> reslicing
> done to prepare the orig.mgz volume.
>
> so can someone tell me what is the proper way to cook this goose
>
> Greg
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Freeview coordinates

[Bruce Fischl]

glad to hear it
Bruce
On Mon, 29 Oct 2018, k3...@free.fr wrote:


   External Email - Use Caution

Hi Ruopen and Bruce,

indeed I fixed the transform multiplication and now I am able to get the good 
coordinates.
Thanks for your help!

Best,
Florent

- Mail original -
De: "Ruopeng Wang" 
À: freesurfer@nmr.mgh.harvard.edu
Envoyé: Vendredi 26 Octobre 2018 19:08:28
Objet: Re: [Freesurfer] Freeview coordinates




Hi Florent,

I'm not sure how you got -152, 73, -66. If you apply the matrix to (152, 66, 
73, 1), you should get

-24, -55, 62

Which matches what is shown in freeview.

Best,
Ruopeng


On 10/26/2018 12:06 PM, k3...@free.fr wrote:




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Hi Bruce,


Thanks for the tip.
When I run the command on 'lh.white' surface for example, I don't get an affine 
transform but a simpler one:


vox2ras-tk:
-1 0 0 128
0 0 1 -128
0 -1 0 128
0 0 0 1


So when I apply this transform to a pixel position (152, 66, 73) here is the 
result I get:
-152, 73, -66


But the expected result provided in Freeview as TkRegRAS T1 is:
-23.61, -55.02, 61.25


Which obviously involving an affine transform.


Did I miss something?
Thanks


Cheers,
Florent



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Re: [Freesurfer] Freeview coordinates

[k3ops]

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Hi Ruopen and Bruce,

indeed I fixed the transform multiplication and now I am able to get the good 
coordinates.
Thanks for your help!

Best,
Florent

- Mail original -
De: "Ruopeng Wang" 
À: freesurfer@nmr.mgh.harvard.edu
Envoyé: Vendredi 26 Octobre 2018 19:08:28
Objet: Re: [Freesurfer] Freeview coordinates




Hi Florent, 

I'm not sure how you got -152, 73, -66. If you apply the matrix to (152, 66, 
73, 1), you should get 

-24, -55, 62 

Which matches what is shown in freeview. 

Best, 
Ruopeng 


On 10/26/2018 12:06 PM, k3...@free.fr wrote: 




External Email - Use Caution 
Hi Bruce, 


Thanks for the tip. 
When I run the command on 'lh.white' surface for example, I don't get an affine 
transform but a simpler one: 


vox2ras-tk: 
-1 0 0 128 
0 0 1 -128 
0 -1 0 128 
0 0 0 1 


So when I apply this transform to a pixel position (152, 66, 73) here is the 
result I get: 
-152, 73, -66 


But the expected result provided in Freeview as TkRegRAS T1 is: 
-23.61, -55.02, 61.25 


Which obviously involving an affine transform. 


Did I miss something? 
Thanks 


Cheers, 
Florent 



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Re: [Freesurfer] cavum septum pellucidum

[Bruce Fischl]

Hi Sarah

can you upload your subject processed with both version? There isn't 
anything explicit we have done that would change the 5th ventricle 
segmentation as far as I know.


5.2 was an orphan version, so hopefully we can sort this out and you can 
stop using it

cheers
Bruce


On Mon, 
29 Oct 2018, Keedy, Sarah [PSY] wrote:




HI, wondering if there are thoughts on this question I posted a week ago?  
Repeated here:

I’m comparing output of Freesurfer5.2 to 6 on the same set of brains. The “5th 
ventricle” (Cavum
septum pellucidum) is not being detected by 6. I had eyeballed the output from 
5.2 and convinced
myself it was reasonably well detecting this developmentally abnormal finding 
pretty well.  I am
wondering what changed in version 6, if anything, that could explain this? 

 

 

 

Sarah K. Keedy, Ph.D.

Assistant Professor, Psychiatry and Behavioral Neuroscience

Director, Cognition Emotion Neuroscience Lab (CENSL)

Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior

University of Chicago

ph (773) 834-7178

 


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[Freesurfer] cavum septum pellucidum

[Keedy, Sarah [PSY]]

External Email - Use Caution

HI, wondering if there are thoughts on this question I posted a week ago?  
Repeated here:
I'm comparing output of Freesurfer5.2 to 6 on the same set of brains. The "5th 
ventricle" (Cavum septum pellucidum) is not being detected by 6. I had 
eyeballed the output from 5.2 and convinced myself it was reasonably well 
detecting this developmentally abnormal finding pretty well.  I am wondering 
what changed in version 6, if anything, that could explain this?



Sarah K. Keedy, Ph.D.
Assistant Professor, Psychiatry and Behavioral Neuroscience
Director, Cognition Emotion Neuroscience Lab (CENSL)
Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior
University of Chicago
ph (773) 834-7178

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[Freesurfer] Research Opportunity

[Nillo, Ryan Michael R]

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UCSF, Dept. of Radiology & Biomedical Imaging is seeking a Postdoctoral Scholar 
for The Laboratory for Precision Neuroimaging


We are seeking a postdoctoral candidate with a strong background in genetics 
human imaging and a desire to use a multi-disciplinary approach to pursue 
neurodegenerative and neurodevelopment research. The candidate should have a 
strong statistical/computational background with experience with data analytic 
tools such as Matlab, R, and PLINK and potentially, MRI image analysis tools 
such as Freesurfer, FSL, and SPM. Applicants should have a Ph.D. or M.D. degree 
with less than five years of postdoctoral experience. Highly motivated 
individuals with a record of productive research are encouraged to apply. The 
position is available starting immediately.

Salary is commensurate with qualifications and experience.


Job Requirements:

1.CV/NIH biosketch (must contain previous research experience)

2.Cover Letter - Short statement on why you are interested in this position and 
how this position will help you achieve your career goals

3.Three references


If interested please contact Dr. Leo Sugrue at 
leo.sug...@ucsf.edu



Ryan M Nillo

Staff Research Associate I

UCSF Department of Radiology and Biomedical Imaging
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Re: [Freesurfer] cluster failing on HCP freesurfer script

[Sanchez, Juan (NYSPI)]

External Email - Use Caution

Thanks Matt

The Environment script actually sets up:

freesurfer-Darwin-lion-stable-pub-v5.3.0-HCP




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Glasser, Matthew 

Sent: Friday, October 26, 2018 5:39:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] cluster failing on HCP freesurfer script


ATTENTION: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.


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That seems like an old version to me.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Sanchez, Juan (NYSPI)" 
mailto:juan.sanc...@nyspi.columbia.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, October 26, 2018 at 3:43 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] cluster failing on HCP freesurfer script


External Email - Use Caution

Thanks for the reply Matt


freesurfer-i386-apple-darwin11.4.2-stable5-20130514


The scripts run fine outside of condor. So it must be how condor is selecting 
the freesurfer

The Environment is set up correclty




From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Friday, October 26, 2018 4:26:13 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] cluster failing on HCP freesurfer script


ATTENTION: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.


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What version of FreeSurfer are you using?  Is the FreeSurfer environment set up 
correctly?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Sanchez, Juan (NYSPI)" 
mailto:juan.sanc...@nyspi.columbia.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, October 26, 2018 at 3:12 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] cluster failing on HCP freesurfer script


External Email - Use Caution

Dear community,

My group is using the latest version of condor clustering to process our data 
on OS X.

We have a bash script that calls freesurfer to run our HCP pipelines. I can run 
the script to completion when running it locally on each of the clustered 
machines, however when submitting the job I get the following error

Can’t locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup 
module) (@INC contains: 
/Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 
/Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 
/Network/Library/Perl/5.18/darwin-thread-multi-2level 
/Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 
/System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 
/System/Library/Perl/Extras/5.18/darwin-thread-multi-2level 
/System/Library/Perl/Extras/5.18 .) at 
/Applications/freesurfer/mni/bin/nu_correct line 37.
BEGIN failed--compilation aborted at 
/Applications/freesurfer/mni/bin/nu_correct line 37.
(standard_in) 2: comparison in expression

 Can anyone suggest a solution?
Thanks
J






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Re: [Freesurfer] mris_apply_reg failing for area/volume

[Bruce Fischl]

Hi James

can you verify that the various files (e.g. 
/cluster/projects/p23/projects/Memory_Project/James/AgeSym/long_recons_FXhemi/010_NDev/1000409_02_10_02_11.long.base_1000409_11/surf/rh.area)


are intact by loading them into freeview? For the area file you will of 
course have to load it as an overlay not as a surface (since it isn't a 
surface)


cheers
Bruce
On Mon, 29 Oct 2018, James Michael Roe wrote:



External Email - Use Caution


​Dear freesurfer experts

 

I’m running the following commands to register RH area and volume files per sub 
to both hemispheres
of a symmetrical template following Xhemi routines. 

The commands have already worked for many subs, but are failing to write the 
target file for a
number of others (and all run fine without the –-jac flag)


#right to left

mris_apply_reg \

--src $SUBJECTS_DIR/$sub/surf/rh.area \

--trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \

--streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg
$SUBJECTS_DIR/${template}/surf/lh.sphere.reg \

--jac

 

#right to right

mris_apply_reg \

--src $SUBJECTS_DIR/$sub/surf/rh.area \

--trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \

--streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg
$SUBJECTS_DIR/${template}/surf/rh.sphere.reg \

--jac

 


The error is not template-specific as the output is the same using fsaverage_sym

Attached is the log file.

 

Thanks in advance!

 


​- James

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Re: [Freesurfer] subfield normalization vs. covarying for whole hippocampal volume

[Iglesias Gonzalez, Eugenio]

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Dear Lauren,
This is a very interesting question!
Site harmonization matters aside (there’s a vast literature on it), whether you 
correct by ICV or whole hippocampal volume essentially answers to different 
questions:
- ICV: you’re asking whether there’s an effect of X on subfield Y.
- whole hippo volume: you’re asking whether X has an effect on the fraction of 
hippocampal volume attributed to Y.
Both questions are interesting; it depends on what you’re trying to answer.
Of course, if you’re correcting by whole hippocampal volume, then don’t correct 
by ICV…
I hope this helps!
/Eugenio

--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College London
http://www.jeiglesias.com



From:  on behalf of Lauren Salminen 

Reply-To: Freesurfer support list 
Date: Friday, 26 October 2018 at 22:40
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] subfield normalization vs. covarying for whole 
hippocampal volume


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Hello,

I’m working on a multi-site hippocampal subfields project (FSv. 6) and am 
wondering if it is “better” to normalize subfield volumes by dividing each 
subfield by whole hippocampal volume, or covary for hippocampal volume as an 
independent predictor variable in the regression models.

Ultimately the goal is to determine the degree that each subfield may be 
uniquely associated with my target predictor variable, and we would like to 
know if this effect can be observed independent of potential differences in the 
whole hippocampus.  Traditionally we have covaried for whole hippocampal 
volume, but I’ve found more interesting effects by normalizing each subfield to 
their hippocampal volume.

Any guidance is appreciated.

Thank you!



Lauren E. Salminen, Ph.D.
Imaging Genetics Center
Stevens Neuroimaging and Informatics Institute
Keck School of Medicine
University of Southern California
http://igc.ini.usc.edu/



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[Freesurfer] mris_apply_reg failing for area/volume

[James Michael Roe]

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?

Dear freesurfer experts



I'm running the following commands to register RH area and volume files per sub 
to both hemispheres of a symmetrical template following Xhemi routines.

The commands have already worked for many subs, but are failing to write the 
target file for a number of others (and all run fine without the --jac flag)

#right to left

mris_apply_reg \

--src $SUBJECTS_DIR/$sub/surf/rh.area \

--trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \

--streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg 
$SUBJECTS_DIR/${template}/surf/lh.sphere.reg \

--jac



#right to right

mris_apply_reg \

--src $SUBJECTS_DIR/$sub/surf/rh.area \

--trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \

--streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg 
$SUBJECTS_DIR/${template}/surf/rh.sphere.reg \

--jac




The error is not template-specific as the output is the same using fsaverage_sym

Attached is the log file.



Thanks in advance!




?- James


subexample_slurm.log
Description: subexample_slurm.log
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