Re: [Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz

[Chung, Yoonho]

I found out why it didn't work. One of the script that  bedpostx_postproc.sh 
calls is written in python2. I set my default to python3 and therefore caused 
the error in the last step. After I loaded python2 environment, i got the 
merged files and finished properly. Thanks for your help as always!


Yoon
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[Freesurfer] sulcus measurement from aparcstat2table

[tulu]

Dear FS expert

I use the aparcstat2table and generate the cortical volume/thickness. I have
a question regarding sulcus volume and thickness meaning.

For example, it generate lh_S_front_inf volume and thickness, which
represents as left inferior frontal sulcus. Did the volume represent as CSF
volume in this sulcus ? and what is the thickness of sulcus meaning ?

Thanks

JLH

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[Freesurfer] Recon-all GNU parallel Error. : Segmentation fault

[Dev vasu]

Dear Sir / madam,

I have tried running recon-all with GNU parallel and  i am incurring
following error kindly review the recon-all.log ( see below ).

Could you please let me know why such problem persists for me. Is it the
issue with memory space ?


Thanks
Vasudev


Calling the GNU parallel in terminal

" ls PAT*.nii.gz | sed 's/.nii.gz//' | parallel --jobs 5 recon-all -s {} -i
{}.nii.gz -all -qcache "





recon-all-log


Fr 2. Sep 17:59:48 CEST 2016
/media/vasudev/Daten/VBCT_results/PAT30
/usr/local/bin/freesurfer/bin/recon-all
-s PAT30 -i PAT30.nii.gz -all -qcache
subjid PAT30
setenv SUBJECTS_DIR /media/vasudev/Daten/VBCT_results
FREESURFER_HOME /usr/local/bin/freesurfer
Actual FREESURFER_HOME /usr/local/bin/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP
Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun
29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 64 kbytes
maxproc  15208
maxlocks unlimited
maxsignal15208
maxmessage   819200
maxnice  0
maxrtprio0
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:   39154323730516 184916  17476  21512 505448
-/+ buffers/cache:3203556 711876
Swap:0  0  0


program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
###
GCADIR /usr/local/bin/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/bin/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
###
/media/vasudev/Daten/VBCT_results/PAT30

 mri_convert /media/vasudev/Daten/VBCT/PAT30.nii.gz
/media/vasudev/Daten/VBCT_results/PAT30/mri/orig/001.mgz

Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun
29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s PAT30 exited with ERRORS at Fr 2. Sep 17:59:56 CEST 2016

To report a problem, see http://surfer.nmr.mgh.harvard.
edu/fswiki/BugReporting
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[Freesurfer] Recon-all GNU parallel Error. : Segmentation fault

[Dev vasu]

Dear Sir / madam,

I have tried running recon-all with GNU parallel and  i am incurring
following error kindly review the recon-all.log ( see below ).

Could you please let me know why such problem persists for me. Is it the
issue with memory space ?


Thanks
Vasudev


Calling the GNU parallel in terminal

" ls PAT*.nii.gz | sed 's/.nii.gz//' | parallel --jobs 5 recon-all -s {} -i
{}.nii.gz -all -qcache "





recon-all-log


Fr 2. Sep 17:59:48 CEST 2016
/media/vasudev/Daten/VBCT_results/PAT30
/usr/local/bin/freesurfer/bin/recon-all
-s PAT30 -i PAT30.nii.gz -all -qcache
subjid PAT30
setenv SUBJECTS_DIR /media/vasudev/Daten/VBCT_results
FREESURFER_HOME /usr/local/bin/freesurfer
Actual FREESURFER_HOME /usr/local/bin/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP
Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun
29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 64 kbytes
maxproc  15208
maxlocks unlimited
maxsignal15208
maxmessage   819200
maxnice  0
maxrtprio0
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:   39154323730516 184916  17476  21512 505448
-/+ buffers/cache:3203556 711876
Swap:0  0  0


program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
###
GCADIR /usr/local/bin/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/bin/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
###
/media/vasudev/Daten/VBCT_results/PAT30

 mri_convert /media/vasudev/Daten/VBCT/PAT30.nii.gz
/media/vasudev/Daten/VBCT_results/PAT30/mri/orig/001.mgz

Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun
29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s PAT30 exited with ERRORS at Fr 2. Sep 17:59:56 CEST 2016

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] white matter errors due to inhomogeneities (bright spots) in cortex

[Benjamin Baird]

Hi Bruce and Clara,

Thanks for your comments. Indeed the bright points are segmented as WM in
wm.mgz, however these errors do not occur only in a few places but in many
slices throughout the brain so manual edits will be quite extensive, which
is why we wanted to double check that there is no parameter tweak to recon
that might at least help some of these errors. But sounds like there's no
way to adjust the parameters of recon to mitigate this type of error? If
not we will move forward with manual edits to wm.mgz as you suggest. Thanks!

Best regards,
Ben

On Fri, Sep 2, 2016 at 8:36 AM, Clara Kühn  wrote:

> Hello Ben,
>
> I am no expert, I can only talk from my experience.
> I've had similar images in my data. Those might be blood vessels or dura
> that were included in the surface. If they are included in the surface on
> more than 5 slices and pretty well visible you could delete those voxels
> from the brainmask. From the looks of the attached screenshots however I
> wouldn't worry about the brainmask but rather remove a few voxels from the
> wm.mgz. Then you rerun the subject with the -wm flag and check again. If it
> is only on one or two slices, though, I wouldn't edit it at all. The
> surfaces are just not going to be perfect.
>
> Hope I could help.
> Clara
>
>
> - Ursprüngliche Mail -
> Von: "Benjamin Baird" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Donnerstag, 1. September 2016 21:56:58
> Betreff: [Freesurfer] white matter errors due to inhomogeneities (bright
>   spots) in cortex
>
> Dear Freesurfer experts,
>
> We are currently working with some scans that were collected on a GE 3T
> scanner. The goal is to analyze cortical thickness. The scans seem to be
> relatively high quality with the exception that there are what appear to be
> inhomogeneities in the intensity of the gray matter (appears too bright in
> places), which is causing the WM to extend/jump into cortex (see attached
> image). We're wondering if there are any parameter adjustments to recon
> that might help with this as the errors occur frequently enough that fixing
> them all manually will be fairly cumbersome. This type of error doesn’t
> seem to be discussed very much in the available information on freesurfer
> quality control as far as we’ve seen.
> Thanks in advance for any advice you might be able to offer.
>
> Best regards,
> Ben
>
>
>
>
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>
>
> 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 Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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dispose of the e-mail.

Re: [Freesurfer] white matter errors due to inhomogeneities (bright spots) in cortex

[Clara Kühn]

Hello Ben,

I am no expert, I can only talk from my experience. 
I've had similar images in my data. Those might be blood vessels or dura that 
were included in the surface. If they are included in the surface on more than 
5 slices and pretty well visible you could delete those voxels from the 
brainmask. From the looks of the attached screenshots however I wouldn't worry 
about the brainmask but rather remove a few voxels from the wm.mgz. Then you 
rerun the subject with the -wm flag and check again. If it is only on one or 
two slices, though, I wouldn't edit it at all. The surfaces are just not going 
to be perfect.

Hope I could help.
Clara


- Ursprüngliche Mail -
Von: "Benjamin Baird" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 1. September 2016 21:56:58
Betreff: [Freesurfer] white matter errors due to inhomogeneities (bright
spots) in cortex

Dear Freesurfer experts, 

We are currently working with some scans that were collected on a GE 3T 
scanner. The goal is to analyze cortical thickness. The scans seem to be 
relatively high quality with the exception that there are what appear to be 
inhomogeneities in the intensity of the gray matter (appears too bright in 
places), which is causing the WM to extend/jump into cortex (see attached 
image). We're wondering if there are any parameter adjustments to recon that 
might help with this as the errors occur frequently enough that fixing them all 
manually will be fairly cumbersome. This type of error doesn’t seem to be 
discussed very much in the available information on freesurfer quality control 
as far as we’ve seen. 
Thanks in advance for any advice you might be able to offer. 

Best regards, 
Ben 




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Re: [Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz

[Anastasia Yendiki]

Hi Yoon - It sounds like FSL's bedpostx postprocessing script 
failed. You can run it like this:


bedpostx_postproc.sh /path/to/your/subject/dmri

This script merges the results from all the slices. It's possible that 
something went wrong with the slices (you ran out disk space for example).

If the slice results are ok, this'll do it.

Best,
a.y

On Fri, 2 Sep 2016, Chung, Yoonho wrote:



Hi Anastasia,


trac-all -prep completed without error.

I thought trac-all -bedp starts and ends without any error but trac-all path
failed with these messages.


Loading BEDPOST parameter samples from */dmri.bedpostX
niiRead(): error opening file*/dmri.bedpostX/merged_ph1samples.nii.gz
ERROR: Could not read */dmri.bedpostX/merged_ph1samples.nii.gz
 

I looked at the dmri.bedpostX directory and all slices exist in
the dmri.bedpostX/diff_slices directory but realized the trac-all -bedp
phase did not create the 

merged samples in this directory.


I am currently runnning with 

FSL/5.0.6

Program versions:
$Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $
and freesurfer version 5.3


I looked through the mailing list to see if someone ran into a similar
problem but could not find a good solution. Do you have what may have caused
this? Any other files I would like to look into?


Thank you

Yoon


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[Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz

[Chung, Yoonho]

Hi Anastasia,


trac-all -prep completed without error.

I thought trac-all -bedp starts and ends without any error but trac-all path 
failed with these messages.


Loading BEDPOST parameter samples from */dmri.bedpostX
niiRead(): error opening file*/dmri.bedpostX/merged_ph1samples.nii.gz
ERROR: Could not read */dmri.bedpostX/merged_ph1samples.nii.gz


I looked at the dmri.bedpostX directory and all slices exist in the 
dmri.bedpostX/diff_slices directory but realized the trac-all -bedp phase did 
not create the

merged samples in this directory.


I am currently runnning with

FSL/5.0.6

Program versions:
$Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $
and freesurfer version 5.3


I looked through the mailing list to see if someone ran into a similar problem 
but could not find a good solution. Do you have what may have caused this? Any 
other files I would like to look into?


Thank you

Yoon
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