Re: [Freesurfer] Ynt: linux data and macbook

2018-09-20 Thread Greve, Douglas N.,Ph.D. 
sorry, we need way more detail

On 9/20/18 11:59 PM, emre wrote:

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thalamus and hippocampus

Gönderen Outlook

Gönderen: Greve, Douglas N.,Ph.D. 
 adına 
freesurfer-boun...@nmr.mgh.harvard.edu
 

Gönderildi: 21 Eylül 2018 Cuma 00:15
Kime: freesurfer@nmr.mgh.harvard.edu
Konu: Re: [Freesurfer] linux data and macbook

what segmentation?

On 09/20/2018 12:53 PM, emre wrote:
>
> External Email - Use Caution
>
>
> hi freesurfer team,
>
> I analyzed the data at linux, this data i can use in macbook for
> segmantation?
> (linux only reconall -all, other analyze in macbook)
>
> Is it possible without problems?
>
>
> thanks, good luck
>
> Gönderen Outlook 
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Ynt: linux data and macbook

2018-09-20 Thread emre 
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thalamus and hippocampus

Gönderen Outlook

Gönderen: Greve, Douglas N.,Ph.D.  adına 
freesurfer-boun...@nmr.mgh.harvard.edu 
Gönderildi: 21 Eylül 2018 Cuma 00:15
Kime: freesurfer@nmr.mgh.harvard.edu
Konu: Re: [Freesurfer] linux data and macbook

what segmentation?

On 09/20/2018 12:53 PM, emre wrote:
>
> External Email - Use Caution
>
>
> hi freesurfer team,
>
> I analyzed the data at linux, this data i can use in macbook for
> segmantation?
> (linux only reconall -all, other analyze in macbook)
>
> Is it possible without problems?
>
>
> thanks, good luck
>
> Gönderen Outlook 
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] Dead Links to 3rd Party Libraries

2018-09-20 Thread Moon, Joseph Young-Joon 
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Hi,

I’m trying to build Freesurfer according to the instructions 
athttp://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page

However, the FTP link to prebuilt 3rd party libraries seems to be down. The 
directory “ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt” 
is no longer being hosted.

Please let me know if I misunderstood something!

Thanks,
Joseph Moon

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Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

2018-09-20 Thread Yendiki, Anastasia 
Hi Matt - I am asking about the raw diffusion images. You sent a screenshot of 
an FA map that looked truncated, with slices missing from the bottom of the 
brain (which explains why the error happened for the ILF, which would go 
through that missing part of the brain). Does dmri/dwi.nii.gz look like that?


Best,

a.y


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

Sent: Thursday, September 20, 2018 2:00:11 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault


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If you are referring to the T1 raw images, no they appear normal and the 
standard Freesurfer pipeline generates correct volumes.

If you are referring to the DTI raw images off the scanner, they also don't 
appear to have brain parts missing, although some appear more noisy and 
pixelated than others.

This is a mTBI subject with no other anatomical brain anomalies scanned with a 
Siemens 3T.




Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700



Do the raw images look like that too?

From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Matthew Grecsek 
mailto:m...@grecsek.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, September 19, 2018 at 4:07 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

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Yes, a part of the brain appears missing. See attached screenshot.

I did not use a configuration file, I simply accepted all defaults and kicked
off the process with -s and -i flags.


Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700

Hi Matt – It looks like some sort of registration issue. When you display the
FA map (dmri/dtifit_FA) and structural segmentation in diffusion space
(label/diff/aparc+aseg), do they look fine? Is there any part of the brain that
is cut off from any of the images? Also, can you attach your config file?
Thanks!

a.y
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[Freesurfer] segmentThalamicNuclei.sh do not produce .stats

2018-09-20 Thread stdp82 
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Hi list,

the segmentThalamicNuclei.sh do not produce thalamic-nuclei.lh.v10.T1.stats.

All the other files are produced (ThalamicNuclei.v10.T1.volumes.txt/mgz).

The segmentation viewed by freeview is fine.

Thanks.


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Re: [Freesurfer] linux data and macbook

2018-09-20 Thread Greve, Douglas N.,Ph.D. 
what segmentation?

On 09/20/2018 12:53 PM, emre wrote:
>
> External Email - Use Caution
>
>
> hi freesurfer team,
>
> I analyzed the data at linux, this data i can use in macbook for 
> segmantation?
> (linux only reconall -all, other analyze in macbook)
>
> Is it possible without problems?
>
>
> thanks, good luck
>
> Gönderen Outlook 
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] ERROR: no voxels found in segmentation- Outputs of segmentThalamicNuclei.sh in FS-FAST

2018-09-20 Thread stdp82 
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Hi I'm using as seed in FS-FAST the outputs of segmentThalamicNuclei.sh.

However when I run

fcseed-config -segid 8103 -fcname L_AV.dat -fsd rest -mean -cfg mean.L_AV.config
fcseed-sess -sf sessid -cfg mean.L_AV.config

 

this error occurs:

Voxel Volume is 36.3469 mm^3

Generating list of segmentation ids

Found 1 segmentations

Computing statistics for each segmentation

Reporting on 0 segmentations

Using PrintSegStat

Computing spatial average of each frame

ERROR: no voxels found in segmentation___
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Re: [Freesurfer] asegstats2table - env: python2: No such file or directory

2018-09-20 Thread ts+ml 
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> On September 20, 2018 at 9:12 PM std...@virgilio.it wrote:
> 
> 
> External Email - Use Caution
> 
> I'm using last version dev with MacOS High Sierra 10.13.6.
> 
> I have run, for each subject:
> 
> segmentThalamicNuclei.sh
> 
I don't know what python2 is used for, but the message says it's missing on 
your path. It should be installed by default under MacOS, maybe not named 
python2 though. I guess your options are:

1) symlink the python binary of your OS (find it by running `env python`) to 
python2
 or, most likely better,
2) install the most recent version of python 2 using homebrew or another 
package manager of your choice. If you use homebrew, it will automatically 
symlink python to python2.

> but when I run the command line "asegstats2table", I obtain:
> 
> 
> env: python2: No such file or directory
> 
> 
> Thanks
> 
> 
> Stefano___
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> 
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> at
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> properly
> dispose of the e-mail.

-- 
Tim Schäfer

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[Freesurfer] asegstats2table - env: python2: No such file or directory

2018-09-20 Thread stdp82 
External Email - Use Caution

I'm using last version dev with MacOS High Sierra 10.13.6.

I have run, for each subject:

segmentThalamicNuclei.sh

but when I run the command line "asegstats2table", I obtain:


env: python2: No such file or directory


Thanks


Stefano___
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Re: [Freesurfer] Reporting Cohen's D for a significant cluster

2018-09-20 Thread Maksimovskiy, Arkadiy 
Hi Bruce,
Thank you so much for the tip and the quick response.
For some reason, the position and Cohen’s D value do not change when I input 
the vertex and I think this might be due to an outdated Freeview version (2.0) 
that I am using.
I attempted to load the new one from this link: 
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
But I am getting an error: The requested URL 
/pub/dist/freesurfer/freeview/freeview_osx.tar.gz was not found on this server.
I was wondering if you have this file available at another location?
Thanks again,
arkadiy
--
Arkadiy L. Maksimovskiy, Ph.D.
Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School

--
Arkadiy L. Maksimovskiy, Ph.D.
Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School
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Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

2018-09-20 Thread Matthew Grecsek 
External Email - Use Caution

If you are referring to the T1 raw images, no they appear normal and the
standard Freesurfer pipeline generates correct volumes.

If you are referring to the DTI raw images off the scanner, they also don't
appear to have brain parts missing, although some appear more noisy and
pixelated than others.

This is a mTBI subject with no other anatomical brain anomalies scanned
with a Siemens 3T.



Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700



Do the raw images look like that too?

From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu
>>
 on behalf of Matthew Grecsek
mailto:m...@grecsek.com >>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu
>>
Date: Wednesday, September 19, 2018 at 4:07 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu
>>
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

External Email - Use Caution

Yes, a part of the brain appears missing. See attached screenshot.

I did not use a configuration file, I simply accepted all defaults and kicked
off the process with -s and -i flags.


Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700

Hi Matt – It looks like some sort of registration issue. When you display the
FA map (dmri/dtifit_FA) and structural segmentation in diffusion space
(label/diff/aparc+aseg), do they look fine? Is there any part of the brain that
is cut off from any of the images? Also, can you attach your config file?
Thanks!

a.y
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[Freesurfer] linux data and macbook

2018-09-20 Thread emre 
External Email - Use Caution

hi freesurfer team,

I analyzed the data at linux, this data i can use in macbook for segmantation?
(linux only reconall -all, other analyze in macbook)

Is it possible without problems?


thanks, good luck

Gönderen Outlook
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[Freesurfer] Clarification about .annot file format

2018-09-20 Thread paul mccarthy 
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Howdy,

There is a discussion regarding the .annot file format over at the nibabel
github repository, regarding the interpretation of the flag/alpha value:

https://github.com/nipy/nibabel/issues/649

If one wishes to create an .annot file with colours that have a
transparency value, how should it be stored in the file? By piecing
together the information from the freesurfer code [1,2], and Graham
Wideman's helpful notes [3], I came to the conclusion that alpha values
should be stored as 1-the actual value. But it would be great to get some
clarification on this from somebody who knows more than me

Thanks very much,

Paul McCarthy

[1]
https://github.com/freesurfer/freesurfer/blob/dev/matlab/read_annotation.m
[2]
https://github.com/freesurfer/freesurfer/blob/dev/matlab/write_annotation.m
[3]
https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles#Annotation
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Re: [Freesurfer] Reporting Cohen's D for a significant cluster

2018-09-20 Thread Bruce Fischl 

Hi Arkadiy

if you have the surface loaded you can always type a vertex number into 
the info field (that shows the current selected vertex) at the bottom of 
the freeview window. It will then jump to that vertex, and adjust the views 
accordingly


cheers
Bruce
On Thu, 20 Sep 2018, Maksimovskiy, Arkadiy wrote:



Update: It occurred to me that reporting it for the max verted might be the 
best idea. In this case,
might anyone know what is the best way to navigate the Freeview to a specific 
vertex number (is
there a place where I can input that number). Thanks again.

 

From: "Maksimovskiy, Arkadiy" 
Date: Thursday, September 20, 2018 at 10:56 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Reporting Cohen's D for a significant cluster

 

Dear Experts,

 

I was requested to report the Cohen’s D value for a significant cluster, which 
resulted from a
cortical thickness analysis. I was able to calculate it and open the resulting 
Cohen’s D mgh file in
Freeview, together with the file, indicating a significant cluster.

As expected, when I move the cursor within the significant cluster, Cohen’s D 
value changes with
every vertex. I was wondering if you might have any recommendations for which 
of the Cohen’s D
values to report, and how best to obtain that value?

 

Thank you for your help,

arkadiy

 

 

 

-- 

Arkadiy L. Maksimovskiy, Ph.D.

Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School


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[Freesurfer] Reporting Cohen's D for a significant cluster

2018-09-20 Thread Maksimovskiy, Arkadiy 
Dear Experts,

I was requested to report the Cohen’s D value for a significant cluster, which 
resulted from a cortical thickness analysis. I was able to calculate it and 
open the resulting Cohen’s D mgh file in Freeview, together with the file, 
indicating a significant cluster.
As expected, when I move the cursor within the significant cluster, Cohen’s D 
value changes with every vertex. I was wondering if you might have any 
recommendations for which of the Cohen’s D values to report, and how best to 
obtain that value?

Thank you for your help,
arkadiy



--
Arkadiy L. Maksimovskiy, Ph.D.
Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School
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Re: [Freesurfer] Troubles to determine the type of recon editing needed

2018-09-20 Thread Bruce Fischl 

Hi Matthieu

only recon2 will use it, but you can specify it for all of them
cheers
Bruce


On Wed, 19 Sep 2018, Matthieu Vanhoutte wrote:



External Email - Use Caution

Dear Bram,
According recon-all help "If a subject has enlarged ventricles due to atrophy, 
include the
-bigventricles
flag with the -autorecon2 stage in order to prevent surfaces extending into the 
ventricle regions.
The flag directly affects the binary mri_ca_register, and mris_make_surfaces 
indirectly via
aseg.presurf.mgz.

So doesn't this mean that we should only out the -bigventricles flag for the 
-autorecon2 stage of
recon-all ?

Best,
Matthieu

Le mer. 19 sept. 2018 à 15:17, Diamond, Bram Ryder  
a écrit :

  Yes - if you've used the -bigventricles flag, you should always include 
it with the
  recon-all command.


  Bram 


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on
behalf of Matthieu Vanhoutte 
Sent: Tuesday, September 18, 2018 12:45:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Troubles to determine the type of recon editing 
needed  

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Ok I will test it on normal subjects.
Do I have to put this -bigventricles flag on all recon-all commands following 
manual editing
of brainmask, white matter,...etc or just once at the first recon-all -all 
command ?

Best,
Matthieu

Le mar. 18 sept. 2018 à 18:03, Bruce Fischl  a 
écrit :
  I think it should be ok. It will be a bit slower, but shouldn't reduce
  accuracy I don't think. Try it and see
  Bruce
  On Tue, 18 Sep 2018, Matthieu
  Vanhoutte wrote:

  >
  > External Email - Use Caution
  >
  > Hi Bruce,
  >
  > Thanks, but in this case will recon-all with -bigventricles flag work 
well on
  normal patients
  > without big ventricles ?
  >
  > Best,
  > Matthieu
  >
  > 2018-09-18 15:56 GMT+00:00 Bruce Fischl :
  >       Hi Matthieu
  >
  >       yes, you will want to run all of your subjects with it
  >
  >       cheers
  >       Bruce
  >       On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:
  >
  >
  >             External Email - Use Caution
  >
  >             Dear Bram,
  >
  >             It looks like the -bigventricles flag fixed my problem with 
my
  specific
  >             subject. Not only, this took
  >             into account large ventricles but also corrected grey matter
  segmentation
  >             from extra Dura tissue
  >             that was erroneously segmented in GM.
  >
  >             I understand the first point of amelioration allowed by the 
flag but
  don't
  >             understand where the
  >             second point come from ?
  >
  >             If I used the -bigventricles flag for all my atrophied and 
large
  ventricles
  >             patients and not for my
  >             healthy patients, wouldn't it introduce a bias when further
  statistically
  >             comparing groups between
  >             them ?
  >
  >             Best,
  >             Matthieu
  >
  >             2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder
  :
  >                   If you haven't already, you may want to run the 
subject
  through
  >             recon-all with the
  >                   -bigventricles flag since it looks like the lateral 
ventricle
  was
  >             significantly
  >                   mislabeled in the aseg. If using the -bigventricles 
flag
  doesn't fix
  >             your problem, you
  >                   can edit the aseg.mgz manually by following the 
directions
  in this
  >             tutorial. Then run
  >                   the following command (again, substituting  
for your
  >             subject's id):
  >             recon-all -autorecon2-noaseg -autorecon3 -subjid 
  >
  >             I would try this before doing the wm.mgz edits I suggested 
in my
  previous
  >             email.
  >
  >             Best,
  >             Bram
  >
  
>___

  >             _
  >             From: freesurfer-boun...@nmr.mgh.harvard.edu
  >              on
  >             behalf of Diamond, Bram Ryder 
  >             Sent: Friday, September 14, 2018 11:07:42 AM
  >             To: matthieuvanhou...@gmail.com
  >             Cc: freesurfer@nmr.mgh.harvard.edu; 
astev...@nmr.mgh.harvard.edu
  >             Subject: [Freesurfer] Troubles to determine the type of 
recon
  editing needed
  >              
  >
  >             Hi Matthieu,
  >
  >

[Freesurfer] Error running recon-all

2018-09-20 Thread Mark Wagshul 
External Email - Use Caution

Hi.  I am getting the following error trying to run recon-all (with Version 
6.0), it is failing while running the routine mri_nu_correct.mni:

Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/local/lib64/perl5 
/usr/local/share/perl5 /usr/lib64/perl5/vendor_perl 
/usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at 
/public/apps/freesurfer/6.0.0/mni/bin/nu_correct line 37.

I am guessing that this has to do with the setup of the environment variables, 
but not sure what needs fixing.  Any advice would be much appreciated, thanks.

Mark

Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einstein.yu.edu

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information intended only for the named recipient(s). If you are not the 
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distribution, and or copying of this message is strictly prohibited. If you 
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] error with trac-all -prep

2018-09-20 Thread Vinny K 
External Email - Use Caution

Thanks Anastasia, I'll give this approach a try.

On Thu, Sep 20, 2018 at 8:31 AM Yendiki, Anastasia 
wrote:

> That's correct! You can source the setup script of whichever version you
> need to use.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Vinny K <
> vinit.k.srivast...@gmail.com>
> *Sent:* Thursday, September 20, 2018 8:25:31 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] error with trac-all -prep
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> Thanks for your reply.  I needed the dev version in order to utilize the
> new thalamic segmentation nuclei tool:
> http://freesurfer.net/fswiki/ThalamicNuclei
>
> I'll download the stable one as well and use that one for Tracula.
>
> I'm assuming I can have both the stable and dev versions installed and
> modify the .bashrc profile to point to the correct freesurfer version that
> I wish to use?
>
> Vinny
>
> On Thu, Sep 20, 2018 at 8:20 AM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Hi Vinny - Unless there was a specific reason why you were using a dev
> version (a feature that you needed and wasn't working in the stable one),
> please use the stable one in general.
>
>
> Best,
>
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Vinny K <
> vinit.k.srivast...@gmail.com>
> *Sent:* Thursday, September 20, 2018 6:57:02 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] error with trac-all -prep
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> A similar post had encountered a similar problem a while back:
>
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-July/046979.html
>
> Should I install the latest stable release of FreeSurfer and run only the
> trac-all -prep step using the stable FreeSurfer release?  Or should I
> repeat entire process starting with recon-all using the stable release?
>
> Thanks,
>
> Vinny
>
> On Wed, Sep 19, 2018 at 8:44 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Hi Vinny - This error is during the diffusion-to-structural registration.
> Can you send the entire log file (scripts/trac-all.log)?
>
> Best,
> a.y
>
> On Sep 19, 2018 8:39 PM, Vinny K  wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4.
>
> I get the following error when running the command: trac-all -prep -c
> dmrirc.
>
> Any help would be greatly appreciated.
>
> Thanks,
>
> Vinny
>
> /home/Vinit/freesurfer/subjects/diffusion/Subj1
> flirt.fsl -ref
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii
> -in
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii
> -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz
> -90 90 -verbose 0 -omat
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat
> -schedule /home/Vinit/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat0
> Wed Sep 19 20:29:11 DST 2018
> /home/Vinit/freesurfer/subjects/diffusion/Subj1
> flirt.fsl -ref
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii
> -in
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii
> -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz
> -90 90 -verbose 0 -omat
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat
> -init
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat
> -schedule /home/Vinit/freesurfer/bin/flirt.newdefault.20080811.sch
> terminate called after throwing an instance of 'NEWMAT::SingularException'
> Abort (core dumped)
> ERROR: flirt
> Linux LAPTOP-VTQVHSSF 4.4.0-17134-Microsoft #285-Microsoft Thu Aug 30
> 17:31:00 PST 2018 x86_64 x86_64 x86_64 GNU/Linux
>
> trac-preproc exited with ERRORS at Wed Sep 19 20:29:14 DST 2018
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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

Re: [Freesurfer] error with trac-all -prep

2018-09-20 Thread Yendiki, Anastasia 
That's correct! You can source the setup script of whichever version you need 
to use.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Vinny K 

Sent: Thursday, September 20, 2018 8:25:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error with trac-all -prep


External Email - Use Caution

Hi Anastasia,

Thanks for your reply.  I needed the dev version in order to utilize the new 
thalamic segmentation nuclei tool: http://freesurfer.net/fswiki/ThalamicNuclei

I'll download the stable one as well and use that one for Tracula.

I'm assuming I can have both the stable and dev versions installed and modify 
the .bashrc profile to point to the correct freesurfer version that I wish to 
use?

Vinny

On Thu, Sep 20, 2018 at 8:20 AM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Vinny - Unless there was a specific reason why you were using a dev version 
(a feature that you needed and wasn't working in the stable one), please use 
the stable one in general.


Best,

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Vinny K 
mailto:vinit.k.srivast...@gmail.com>>
Sent: Thursday, September 20, 2018 6:57:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error with trac-all -prep


External Email - Use Caution

Hi Anastasia,

A similar post had encountered a similar problem a while back:

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-July/046979.html

Should I install the latest stable release of FreeSurfer and run only the 
trac-all -prep step using the stable FreeSurfer release?  Or should I repeat 
entire process starting with recon-all using the stable release?

Thanks,

Vinny

On Wed, Sep 19, 2018 at 8:44 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Vinny - This error is during the diffusion-to-structural registration. Can 
you send the entire log file (scripts/trac-all.log)?

Best,
a.y

On Sep 19, 2018 8:39 PM, Vinny K 
mailto:vinit.k.srivast...@gmail.com>> wrote:

External Email - Use Caution

Hi,

I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4.

I get the following error when running the command: trac-all -prep -c dmrirc.

Any help would be greatly appreciated.

Thanks,

Vinny

/home/Vinit/freesurfer/subjects/diffusion/Subj1
flirt.fsl -ref 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii
 -in 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii
 -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz 
-90 90 -verbose 0 -omat 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat
 -schedule /home/Vinit/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat0
Wed Sep 19 20:29:11 DST 2018
/home/Vinit/freesurfer/subjects/diffusion/Subj1
flirt.fsl -ref 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii
 -in 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii
 -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz 
-90 90 -verbose 0 -omat 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat
 -init 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat
 -schedule /home/Vinit/freesurfer/bin/flirt.newdefault.20080811.sch
terminate called after throwing an instance of 'NEWMAT::SingularException'
Abort (core dumped)
ERROR: flirt
Linux LAPTOP-VTQVHSSF 4.4.0-17134-Microsoft #285-Microsoft Thu Aug 30 17:31:00 
PST 2018 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Sep 19 20:29:14 DST 2018
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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
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Re: [Freesurfer] error with trac-all -prep

2018-09-20 Thread Vinny K 
External Email - Use Caution

Hi Anastasia,

Thanks for your reply.  I needed the dev version in order to utilize the
new thalamic segmentation nuclei tool:
http://freesurfer.net/fswiki/ThalamicNuclei

I'll download the stable one as well and use that one for Tracula.

I'm assuming I can have both the stable and dev versions installed and
modify the .bashrc profile to point to the correct freesurfer version that
I wish to use?

Vinny

On Thu, Sep 20, 2018 at 8:20 AM Yendiki, Anastasia 
wrote:

> Hi Vinny - Unless there was a specific reason why you were using a dev
> version (a feature that you needed and wasn't working in the stable one),
> please use the stable one in general.
>
>
> Best,
>
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Vinny K <
> vinit.k.srivast...@gmail.com>
> *Sent:* Thursday, September 20, 2018 6:57:02 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] error with trac-all -prep
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> A similar post had encountered a similar problem a while back:
>
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-July/046979.html
>
> Should I install the latest stable release of FreeSurfer and run only the
> trac-all -prep step using the stable FreeSurfer release?  Or should I
> repeat entire process starting with recon-all using the stable release?
>
> Thanks,
>
> Vinny
>
> On Wed, Sep 19, 2018 at 8:44 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Hi Vinny - This error is during the diffusion-to-structural registration.
> Can you send the entire log file (scripts/trac-all.log)?
>
> Best,
> a.y
>
> On Sep 19, 2018 8:39 PM, Vinny K  wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4.
>
> I get the following error when running the command: trac-all -prep -c
> dmrirc.
>
> Any help would be greatly appreciated.
>
> Thanks,
>
> Vinny
>
> /home/Vinit/freesurfer/subjects/diffusion/Subj1
> flirt.fsl -ref
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii
> -in
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii
> -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz
> -90 90 -verbose 0 -omat
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat
> -schedule /home/Vinit/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat0
> Wed Sep 19 20:29:11 DST 2018
> /home/Vinit/freesurfer/subjects/diffusion/Subj1
> flirt.fsl -ref
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii
> -in
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii
> -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz
> -90 90 -verbose 0 -omat
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat
> -init
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat
> -schedule /home/Vinit/freesurfer/bin/flirt.newdefault.20080811.sch
> terminate called after throwing an instance of 'NEWMAT::SingularException'
> Abort (core dumped)
> ERROR: flirt
> Linux LAPTOP-VTQVHSSF 4.4.0-17134-Microsoft #285-Microsoft Thu Aug 30
> 17:31:00 PST 2018 x86_64 x86_64 x86_64 GNU/Linux
>
> trac-preproc exited with ERRORS at Wed Sep 19 20:29:14 DST 2018
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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

Re: [Freesurfer] error with trac-all -prep

2018-09-20 Thread Yendiki, Anastasia 
Hi Vinny - Unless there was a specific reason why you were using a dev version 
(a feature that you needed and wasn't working in the stable one), please use 
the stable one in general.


Best,

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Vinny K 

Sent: Thursday, September 20, 2018 6:57:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error with trac-all -prep


External Email - Use Caution

Hi Anastasia,

A similar post had encountered a similar problem a while back:

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-July/046979.html

Should I install the latest stable release of FreeSurfer and run only the 
trac-all -prep step using the stable FreeSurfer release?  Or should I repeat 
entire process starting with recon-all using the stable release?

Thanks,

Vinny

On Wed, Sep 19, 2018 at 8:44 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Vinny - This error is during the diffusion-to-structural registration. Can 
you send the entire log file (scripts/trac-all.log)?

Best,
a.y

On Sep 19, 2018 8:39 PM, Vinny K 
mailto:vinit.k.srivast...@gmail.com>> wrote:

External Email - Use Caution

Hi,

I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4.

I get the following error when running the command: trac-all -prep -c dmrirc.

Any help would be greatly appreciated.

Thanks,

Vinny

/home/Vinit/freesurfer/subjects/diffusion/Subj1
flirt.fsl -ref 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii
 -in 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii
 -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz 
-90 90 -verbose 0 -omat 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat
 -schedule /home/Vinit/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat0
Wed Sep 19 20:29:11 DST 2018
/home/Vinit/freesurfer/subjects/diffusion/Subj1
flirt.fsl -ref 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii
 -in 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii
 -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz 
-90 90 -verbose 0 -omat 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat
 -init 
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat
 -schedule /home/Vinit/freesurfer/bin/flirt.newdefault.20080811.sch
terminate called after throwing an instance of 'NEWMAT::SingularException'
Abort (core dumped)
ERROR: flirt
Linux LAPTOP-VTQVHSSF 4.4.0-17134-Microsoft #285-Microsoft Thu Aug 30 17:31:00 
PST 2018 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Sep 19 20:29:14 DST 2018
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Re: [Freesurfer] trac-all using nifti

2018-09-20 Thread Yendiki, Anastasia 
What is the trac-all command line that you run?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Heidi Emmanuel Foo 

Sent: Wednesday, September 19, 2018 11:06:09 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all using nifti


External Email - Use Caution

Hi Anastasia,

Nope, I don't actually get any output and/or log file.

Regards,
Heidi Foo



On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Heidi - The config file that you sent looked fine to me. What is the 
trac-all command line that you run, and do you get any other output (like a 
trac-all.log file)?


Best,

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Heidi Emmanuel Foo 
mailto:heidifo...@gmail.com>>
Sent: Monday, September 17, 2018 11:03:47 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all using nifti


External Email - Use Caution

Hi Anastasia,

It seems like I do. Could the problem be the config.txt?

Thanks!

Best Regards,
Heidi Foo

On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Heidi – Do you have write permission to create the output directory 
/data_int/heidi/forHeidi/Preprocessed?

a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Heidi Emmanuel Foo 
mailto:heidifo...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, September 17, 2018 at 12:55 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] trac-all using nifti


External Email - Use Caution

Hi Anastasia,

I am currently trying to run trac-all with my DWI data. I do not have the DICOM 
but only the Nifti files and I would like to use the same bval and bvec 
template for every subject. I created a configiration file as attached. 
However, I have the following error message:

: Command not found.
: Command not found.
set: Variable name must begin with a letter.
does not exist.DIR /data_int/heidi/forHeidi/Preprocessed

It would be great if you could advise me on what to do.

Thank you!

Best Regards,
Heidi Foo


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Re: [Freesurfer] error with trac-all -prep

2018-09-20 Thread Vinny K 
External Email - Use Caution

Hi Anastasia,

A similar post had encountered a similar problem a while back:

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-July/046979.html

Should I install the latest stable release of FreeSurfer and run only the
trac-all -prep step using the stable FreeSurfer release?  Or should I
repeat entire process starting with recon-all using the stable release?

Thanks,

Vinny

On Wed, Sep 19, 2018 at 8:44 PM Yendiki, Anastasia 
wrote:

> Hi Vinny - This error is during the diffusion-to-structural registration.
> Can you send the entire log file (scripts/trac-all.log)?
>
> Best,
> a.y
>
> On Sep 19, 2018 8:39 PM, Vinny K  wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4.
>
> I get the following error when running the command: trac-all -prep -c
> dmrirc.
>
> Any help would be greatly appreciated.
>
> Thanks,
>
> Vinny
>
> /home/Vinit/freesurfer/subjects/diffusion/Subj1
> flirt.fsl -ref
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii
> -in
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii
> -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz
> -90 90 -verbose 0 -omat
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat
> -schedule /home/Vinit/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat0
> Wed Sep 19 20:29:11 DST 2018
> /home/Vinit/freesurfer/subjects/diffusion/Subj1
> flirt.fsl -ref
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii
> -in
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii
> -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz
> -90 90 -verbose 0 -omat
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat
> -init
> /home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat
> -schedule /home/Vinit/freesurfer/bin/flirt.newdefault.20080811.sch
> terminate called after throwing an instance of 'NEWMAT::SingularException'
> Abort (core dumped)
> ERROR: flirt
> Linux LAPTOP-VTQVHSSF 4.4.0-17134-Microsoft #285-Microsoft Thu Aug 30
> 17:31:00 PST 2018 x86_64 x86_64 x86_64 GNU/Linux
>
> trac-preproc exited with ERRORS at Wed Sep 19 20:29:14 DST 2018
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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
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> contains patient information, please contact the Partners Compliance
> HelpLine at
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[Freesurfer] freeview automated screenshots using color wheel scale & qt library issues

2018-09-20 Thread Emil H.J. Nijhuis 
External Email - Use Caution

Hi,

I am attempting to generate automated screenshots with freeview version
3.July 2018 and I noticed that when applying the color wheel option for a
surface overlay the coloring would be wrongly applied and I would need to
enter the configuration window to fix/refresh the overlay coloring. Is
there any way to enforce a refresh for overlays using the command line?

Also is there a way to save/load custom color scales with the command line?

I tried to use the latest developmental freeview.bin, however it gives me
the error: version 'qt_5' not found; for 4 existing qt libraries which are
softlinked to a newer versions (qt 5.5) in my system.

Do you have any advice to achieve automated screenshots with freeview?

With kind regards,

 Emil Nijhuis
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[Freesurfer] mris_fill ERROR: dyld: lazy symbol binding failed:

2018-09-20 Thread 岡留敏樹 
External Email - Use Caution

Hello freesurfer experts, 
when trying to run ‘ft_prepare_mesh’ command from fieldtrip with MATLAB R2018a, 
I run into an error.

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

mris_fill -c -r 1 
/Users/okadometoshiki/Desktop/SubjectUCI29/freesurfer/surf/lh.pial 
/private/var/folders/cc/fv5fk09d3hj5g5kx7dg7pqq8gn/T/tp0a8d7856_136c_4156_bf73_d23f64bbf687_pial.filled.mgz:
 Aborted
reading filled volume...
gunzip: can't stat: 
/private/var/folders/cc/fv5fk09d3hj5g5kx7dg7pqq8gn/T/tp0a8d7856_136c_4156_bf73_d23f64bbf687_pial.filled.mgz
 
(/private/var/folders/cc/fv5fk09d3hj5g5kx7dg7pqq8gn/T/tp0a8d7856_136c_4156_bf73_d23f64bbf687_pial.filled.mgz.gz):
 No such file or directory
ERROR: problem reading fname

I’m running this on a iMac, macOS High Sierra 10.13.6, with 
freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c. 
From past archives, I think this is because of SIP. So I disabled SIP of OSX, 
but I run into same errors.
I tried different subjects, which caused similar errors. 
Any ideas would be greatly appreciated, thank you! 




Toshiki Okadome___
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