date:20190715

Re: [Freesurfer] Viewing Uncorrected Significance Map in Freeview

2019-07-15 Thread Greve, Douglas N.,Ph.D.

Try changing the thresholds (via the Configure button). When it first loads, 
the thresholds are set very low. When they get changed to your values (4,5), 
then there is nothing left and it looks like a blank brain.

On 7/6/2019 9:38 AM, Marie Hill wrote:

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Hi everyone,


I have just finished running glmfit. When I try to load the significance maps 
in freeview, they appear to load for a moment and then disappear, just showing 
the brain volume without any highlighted areas of significance. Does anyone 
have any idea why this could be?


I ran the command: freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.g4v1.glmdir/bipolar-vs-schizophrenia/sig.mgh:overlay_threshold=4,5
 -viewport 3d


Kindest Regards,


Marie



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Re: [Freesurfer] How to Divide the Surface Parcellations of the Brain

2019-07-15 Thread Greve, Douglas N.,Ph.D.

Can you use mris_divide_parcellation

On 7/8/2019 1:27 PM, Mahshid Fouladivanda wrote:

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Dear Bruce,

All the outputs are .nii and .gii
I do not know if it is possible to convert it to the annotation!
By the way, what is needed for creation of the annotation file? I mean what 
information, it needs?

Regards
Mahshid




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Re: [Freesurfer] make_average_subject error: could not load norm volume from (null)

2019-07-15 Thread Greve, Douglas N.,Ph.D.

I think it is crashing outside of make_average_surface and make_average_volume, 
so the log files are not telling me what is going on. Can you capture the full 
terminal output? Also, you can try it with two subjects so that it runs faster  
(but it might not crash).

On 7/10/2019 5:39 AM, Mads Jensen wrote:

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Thank you very much for spending time on this!

I have attached the make_average_volume.log and make_average_surface.log files.

Den man. 8. jul. 2019 kl. 16.44 skrev Greve, Douglas N.,Ph.D.
:



Can you send the full terminal output of make_average_subject? There should 
also be some log files (make_average_volume.log and make_average_surface.log) 
in the average subject that would be helpful

On 7/4/2019 4:36 AM, Mads Jensen wrote:

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HI FreeSurfer Developers,

I'm attempting to create an average subject make_average_subject but I
get the error message the following error when I run the
make_average_command:

Loading aseg from REMOVED-PATH/avg_elder/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from (null)

Linux 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:53:28 UTC 2018
x86_64 x86_64 x86_64 GNU/Linux

I cannot find anything similar on the mailing list. I hope anyone have
any thoughts on how to trouble-shoot this one? Also, Ive attached the
recon-all.log in case it's of any use.

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu 16.04.4 LTS
3) uname -a: Linux hyades02 4.4.0-130-generic #156-Ubuntu SMP Thu Jun
14 08:53:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached


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Re: [Freesurfer] A Question Regarding Topology Correction

2019-07-15 Thread Greve, Douglas N.,Ph.D.

It does not sound like something we can do, though I don't entirely follow 
everything that you wrote

On 7/10/2019 11:07 PM, Maedeh Khalilian wrote:

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Dear FreeSurfer experts,
I know that FreeSurfer does segmentation, surface reconstruction and topology 
correction through its routine pipeline using "recon-all" . However, I have 
some T2w brain MR images and I have done the segmentation and extracted WM, GM, 
and CSF with my own algorithm. Now I need to remove back to back (i.e. a part 
of topology correction) which is caused in sulci due to the segmentation. In 
other word, after doing my segmentation, I wanna open the closed concavities in 
CSF that were open originally.
Now I wanna know if I can do the topology correction using FreeSurfer while I 
have done the segmentation by myself? I would be grateful if you could help me 
with that.
Best,
Maedeh



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Re: [Freesurfer] optseq2 parameters setup

2019-07-15 Thread Greve, Douglas N.,Ph.D.



On 7/15/2019 12:50 PM, Tugce Duran wrote:

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Hi Dr. Greve,

I am interested in designing the Face Name Associative Memory Exam (FNAME) fMRI 
task for our study.
There are 80 face-name pairs that we will use and the duration can be between 
3.5 and 4.75 secs.  I have used the following command:
optseq2 --ntp 200 --tr 2 --psdwin 0 32 2  --ev facename 4 80  --nkeep 3 --o 
trial2 --tnullmin 0 --tnullmax 6 --nsearch 1
Total scan time appx 6-7 mins.

Q1: For NULL, why do we have only 2 sec and 4 sec jitters? Can we change the 
variety amount of the jitters? Are more jitters good or bad (instead of just 
having 2 secs and 4 secs, let’s say we get 0.25, 1, 2, 3 and 4 secs) ?
It always makes the NULL durations a integer multiple of the dPSD. You set this 
to 2 (--psdwin 0 32 2). If you are assuming the shape to the hemodyamic 
response (eg, the canonical SPM HRF), then it won't matter much if you decrease 
it to 1 or less). The benefit of jitter in that case depends more on the 
psychology than the signal processing.

Q2: For the event design I am interested in above, what would be the “best” 
parameters used?
Usually, you set the total time for the NULL to be equal to that of a stimulus 
type. In this case, you have one stimulus type presented for a total of 320 sec 
(4*80), so you could set the scan duration to be 320*2=640sec=10min 40sec. That 
would be optimum for testing your stimulus against baseline, but that is 
probably not what you are planning to do.

Trial2-001.par:
0.14.000   1.  facename
  4.14.000   1.  facename
  8.14.000   1.  facename
12.02.000   1.  NULL
14.14.000   1.  facename
18.14.000   1.  facename
22.14.000   1.  facename
26.14.000   1.  facename
30.14.000   1.  facename
34.14.000   1.  facename
38.14.000   1.  facename
42.04.000   1.  NULL
46.14.000   1.  facename
50.14.000   1.  facename
54.14.000   1.  facename
58.14.000   1.  facename
62.14.000   1.  facename
66.14.000   1.  facename
70.14.000   1.  facename
74.02.000   1.  NULL
76.14.000   1.  facename
80.02.000   1.  NULL
82.14.000   1.  facename
.
.
.
.

372.04.000   1.  NULL
376.14.000   1.  facename
380.14.000   1.  facename
384.14.000   1.  facename
388.14.000   1.  facename
392.14.000   1.  facename
396.14.000   1.  facename

Thank you in advance!

Tugce



Tugce Duran
Graduate Student, Biomedical Sciences MS Program
Neuroscience Concentration | Section on Gerontology & Geriatric Medicine, WFSM
[2color]
Graduate Programs in Biomedical Sciences
525 Vine Street, Suite 150, Winston-Salem, NC 27101
• 317-893-9100 | • tdu...@wakehealth.edu | 
|[Image result for linked 
in]linkedin.com/in/tugceduran/
The information contained in this message is privileged and confidential 
information intended for the sole use of the addressee. If the reader of this 
message is not the intended recipient, or the employee or agent responsible for 
delivering it to the intended recipient, you are hereby notified that any 
dissemination, distribution or copying of this communication is strictly 
prohibited. If you have received this message in error, please notify the 
person listed above immediately by e-mail, and delete the original message and 
attachments.


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Re: [Freesurfer] Question about coordinates in Freesurfer

2019-07-15 Thread Greve, Douglas N.,Ph.D.

For question 1, try this 
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
You did not say which MNI space you were dealing with (we use mni305, not 152).

On 7/15/2019 12:02 PM, Zhi Li wrote:

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Thank you very much, Tim. Any idea for the 1st question?

Thanks and best wishes,

Lizhi

On Sat, 13 Jul 2019 at 09:18, Tim Schäfer 
mailto:ts%2...@rcmd.org>> wrote:
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Dear Lizhi,

on your 2nd question: a rough explanation is on the FS Wiki at [1], but I found 
this website [2] easier to follow as it has some example images.

Regarding space, I think they are all in native space. You can run `mri_info` 
on them to get detailed information.

[1] https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
[2] http://www.grahamwideman.com/gw/brain/fs/fsunderstanding/fssampleimages.htm

Best,

Tim

> On July 12, 2019 at 9:30 PM Zhi Li 
> mailto:lizhi.ps...@gmail.com>> wrote:
>
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> Now I have an annotation file in fsaverage space and a MNI voxel coordinate
> of one subject. May I ask how could I know if this coordinate is in one
> parcel of the annotation file? There are many coordinates that I cannot
> check it one by one in Freeview. In addition, if this is a native image
> coordinate how could I check whether it is in a parcel then?
>
> An additional question is whether the spaces of all the files in folder
> "mri" generated by recon-all are native individual space? What do the files
> 'orig.mgz', norm.mgz'', 'brainmask.mgz', 'brain.mgz' and 'T1.mgz' refer to?
> They are very similar to each other, with skull-stripped or not. Is there
> any document on it I could reference?
>
> Looking forward to your kind suggestions,
>
> Many thanks and best regards,
>
> Lizhi
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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[Freesurfer] freeview

2019-07-15 Thread Juan Rivas

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I try again with fortran, uploaded it again, and now I get this message:
jcrn12@jcrn12-VirtualBox:~$ freeview
This application failed to start because it could not find or load the Qt
platform plugin "xcb"
in "".

Reinstalling the application may fix this problem.
Aborted (core dumped)

Best regards,
JC.
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[Freesurfer] Fwd: freeview

2019-07-15 Thread Juan Rivas

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libgfortran.so.3. No found.
I día the fortran step as you indicated yo me.
Thanks again,
JC.

-- Mensaje reenviado -
De: fsbuild 
Fecha: El lun, 15 de jul. de 2019 a las 17:09
Asunto: Re: [Freesurfer] freeview
Para: 
Cc: 


Did you try,

$ ldd /usr/local/freesurfer/bin/freeview | grep not

?

- R.

On Jul 12, 2019, at 08:42, Juan Rivas  wrote:

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It looks like freeview is in: jcrn12@jcrn12-VirtualBox:~$
/usr/local/freesurfer/bin/freeview
But when I try to use it, I can not do it, because: jcrn12@jcrn12-VirtualBox:~$
ldd freeview | grep not
ldd: ./freeview: No such file or directory.
Thank you for your help,
JC.
-- Forwarded message -
De: Juan Rivas 
Date: vie., 12 jul. 2019 a las 6:57
Subject: freeview
To: 


That is what happened:
$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
$ bash
jcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
JC.
-- Forwarded message -
De: fsbuild 
Date: lun., 15 jul. 2019 a las 14:19
Subject: Re: [Freesurfer] Freeview
To: 
Cc: 


Hello JC,

Try this to see what libs are missing,

$ ldd /usr/local/bin/freeview | grep not

- R.

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Re: [Freesurfer] freeview

2019-07-15 Thread fsbuild

External Email - Use Caution

Did you try,

$ ldd /usr/local/freesurfer/bin/freeview | grep not

?
- R.
On Jul 12, 2019, at 08:42, Juan Rivas  
wrote:External Email - Use 
CautionIt looks like freeview 
is in: jcrn12@jcrn12-VirtualBox:~$ /usr/local/freesurfer/bin/freeviewBut when I 
try to use it, I can not do it, because: jcrn12@jcrn12-VirtualBox:~$ ldd 
freeview | grep notldd: ./freeview: No such file or directory.Thank you for 
your help,JC.-- Forwarded message -De: Juan 
Rivas Date: vie., 12 jul. 2019 a las 6:57Subject: 
freeviewTo: That is what happened:$ ldd 
/usr/local/bin/freeview | grep notldd: /usr/local/bin/freeview: No such file or 
directory$ bashjcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep 
notldd: /usr/local/bin/freeview: No such file or directoryJC.-- 
Forwarded message 
-De: fsbuild Date: lun., 15 jul. 
2019 a las 14:19Subject: Re: [Freesurfer] FreeviewTo: 
Cc: Hello JC,Try 
this to see what libs are missing,$ ldd /usr/local/bin/freeview | grep not- 
R.___Freesurfer mailing 
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[Freesurfer] Fwd: freeview

2019-07-15 Thread Juan Rivas

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It looks like freeview is in: jcrn12@jcrn12-VirtualBox:~$
/usr/local/freesurfer/bin/freeview
But when I try to use it, I can not do it, because: jcrn12@jcrn12-VirtualBox:~$
ldd freeview | grep not
ldd: ./freeview: No such file or directory.
Thank you for your help,
JC.
-- Forwarded message -
De: Juan Rivas 
Date: vie., 12 jul. 2019 a las 6:57
Subject: freeview
To: 


That is what happened:
$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
$ bash
jcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
JC.
-- Forwarded message -
De: fsbuild 
Date: lun., 15 jul. 2019 a las 14:19
Subject: Re: [Freesurfer] Freeview
To: 
Cc: 


Hello JC,

Try this to see what libs are missing,

$ ldd /usr/local/bin/freeview | grep not

- R.
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Re: [Freesurfer] Fwd: Fwd: Freeview

2019-07-15 Thread Bruce Fischl


you need to run:

ldd /usr/local/freesurfer/bin/freeview | grep not

cheers
Bruce
On Fri, 12 Jul 2019, Juan 
Rivas wrote:




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It does not work:jcrn12@jcrn12-VirtualBox:/usr/local/bin$ which freeview
/usr/local/freesurfer/bin/freeview
jcrn12@jcrn12-VirtualBox:/usr/local/bin$ ldd freeview | grep not
ldd: ./freeview: No such file or directory

JC
-- Forwarded message -
De: fsbuild 
Date: lun., 15 jul. 2019 a las 15:19
Subject: Re: [Freesurfer] Fwd: Freeview
To: 
Cc: 


Sorry - from your previous mail, I mistakenly thought “which freeview”
returned /usr/local/bin/freeview.
If you can reproduce what you did before to run freeview from the command
line where it tells you that it was not finding libgfortran, then “which
freeview” will likely tell you where the binary is.  You should have already
set FREESURFER_HOME to point to the freesurfer  installation and then did
the source of the shell init file (SetUpFreeSurfer.sh for bash or sh,
SetUpFreeSurfer.csh for csh).  See the wiki page here under setup 
andconfiguration, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
  That should have put freeview in your PATH so that “which freeview” works.

What you want to do is to cd into the directory where the freeview binary
lives and run ldd on it.  If “which freeview” returned
/usr/local/bin/freeview then you could “cd /usr/local/bin” and from there
directly run “ldd freeview | grep not”.

- R. 

  On Jul 12, 2019, at 07:32, Juan Rivas  wrote:

External Email - Use Caution


That is what happened:
$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
$ bash
jcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
JC.
-- Forwarded message -
De: fsbuild 
Date: lun., 15 jul. 2019 a las 14:19
Subject: Re: [Freesurfer] Freeview
To: 
Cc: 


Hello JC,
Try this to see what libs are missing,

$ ldd /usr/local/bin/freeview | grep not

- R.
  On Jul 12, 2019, at 06:19, Juan Rivas 
  wrote:

External Email - Use Caution


Hi, thank you for your help. 
I tried again and once again it did not work. I am using Ubuntu
18
This is the message I get:

$ freeview
sh: 8: freeview: not found
$  which freeview                  
$ /usr/local/bin/freeview
sh: 10: /usr/local/bin/freeview: not found
$ which ldd
/usr/bin/ldd
$ ldd `which freeview` | grep not
ldd: missing file arguments
Try `ldd --help' for more information.

Thank you very much,
JC.

El lun., 15 jul. 2019 a las 12:50, fsbuild
() escribió:
  Hello Juan,
For CentOS try:
$ sudo yum install gcc-gfortran.x86_64
… if that does not work then,
$ sudo yum install libgfortran.x86_64

For Ubuntu,
$sudo apt-get install gfortran

One thing you might want to try first is to run the “ldd”
command on the freeview binary to see all/any libraries
that are missing

This should return the path to freeview, e.g.,
/usr/local/bin/freeview, though your path may differ.
$ which freeview
/usr/local/bin/freeview

- then check you have the ldd command, 
$ which ldd
/usr/bin/ldd

If the above returned paths for freeview and ldd, then run
the ldd command followed by the grep command to see what
libraries are missing.  Prior to doing the install of
libgfortran above, it should list libgfortran is missing.

$ ldd `which freeview` | grep not

Also it would be good to know what linux you are running,
e.g., CentOS 7, Ubuntu 18, etc.

- R.

  On Jul 15, 2019, at 12:39, Juan Rivas
   wrote:

External Email - Use Caution




-- Forwarded message -
De: Juan Rivas 
Date: vie., 12 jul. 2019 a las 3:02
Subject: Re: [Freesurfer] Freeview
To: fsbuild 


Hi, thank you for your answer.I did what you
recommended to me, and I get this message:freeview:
error while loading shared libraries:
libgfortran.so.3: cannot open shared object file: No
such file or directory.
What could be the next step?
JC.

El lun., 15 jul. 2019 a las 9:57, fsbuild
() escribió:
  Hello JC,
Your machine could be missing the qt5
libraries/files.

On Ubuntu linux you can try installing them
with,
$ sudo apt-get install qt5-default
qtcreator libqt5x11extras5-dev

On CentOS linux,
$ sudo yum install qt-create qt-config.x86_64
$ sudo yum install qt5-qtx11extras.x86_64
qt5-qtx11extras-devel...x86_64

- R.

  On Jul 12, 2019, at 02:28, Juan
  Rivas  wrote:

External Email - Use
Caution


Hello, I am trying to use freeview, but
everytime I try I get this
message:freeview: error while loading
shared libraries: libQt5Widgets.so.5:
cannot open shared object file: No such
file or directory.
How can I fix it?
Thanks a lot,
JC.
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[Freesurfer] Fwd: Fwd: Freeview

2019-07-15 Thread Juan Rivas

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It does not work:
jcrn12@jcrn12-VirtualBox:/usr/local/bin$ which freeview
/usr/local/freesurfer/bin/freeview
jcrn12@jcrn12-VirtualBox:/usr/local/bin$ ldd freeview | grep not
ldd: ./freeview: No such file or directory

JC
-- Forwarded message -
De: fsbuild 
Date: lun., 15 jul. 2019 a las 15:19
Subject: Re: [Freesurfer] Fwd: Freeview
To: 
Cc: 


Sorry - from your previous mail, I mistakenly thought “which freeview”
returned /usr/local/bin/freeview.

If you can reproduce what you did before to run freeview from the command
line where it tells you that it was not finding libgfortran, then “which
freeview” will likely tell you where the binary is.  You should have
already set FREESURFER_HOME to point to the freesurfer  installation and
then did the source of the shell init file (SetUpFreeSurfer.sh for bash or
sh, SetUpFreeSurfer.csh for csh).  See the wiki page here under setup and
configuration, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
That should have put freeview in your PATH so that “which freeview” works.

What you want to do is to cd into the directory where the freeview binary
lives and run ldd on it.  If “which freeview” returned
/usr/local/bin/freeview then you could “cd /usr/local/bin” and from there
directly run “ldd freeview | grep not”.

- R.

On Jul 12, 2019, at 07:32, Juan Rivas  wrote:

External Email - Use Caution

That is what happened:
$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
$ bash
jcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
JC.
-- Forwarded message -
De: fsbuild 
Date: lun., 15 jul. 2019 a las 14:19
Subject: Re: [Freesurfer] Freeview
To: 
Cc: 


Hello JC,

Try this to see what libs are missing,

$ ldd /usr/local/bin/freeview | grep not

- R.

On Jul 12, 2019, at 06:19, Juan Rivas  wrote:

External Email - Use Caution

Hi, thank you for your help.
I tried again and once again it did not work. I am using Ubuntu 18
This is the message I get:

$ freeview
sh: 8: freeview: not found
$  which freeview
$ /usr/local/bin/freeview
sh: 10: /usr/local/bin/freeview: not found
$ which ldd
/usr/bin/ldd
$ ldd `which freeview` | grep not
ldd: missing file arguments
Try `ldd --help' for more information.

Thank you very much,
JC.

El lun., 15 jul. 2019 a las 12:50, fsbuild () escribió:

> Hello Juan,
>
> For CentOS try:
> $ sudo yum install gcc-gfortran.x86_64
> … if that does not work then,
> $ sudo yum install libgfortran.x86_64
>
> For Ubuntu,
> $sudo apt-get install gfortran
>
> One thing you might want to try first is to run the “ldd” command on the
> freeview binary to see all/any libraries that are missing
>
> This should return the path to freeview, e.g., /usr/local/bin/freeview,
> though your path may differ.
> $ which freeview
> /usr/local/bin/freeview
>
> - then check you have the ldd command,
> $ which ldd
> /usr/bin/ldd
>
> If the above returned paths for freeview and ldd, then run the ldd command
> followed by the grep command to see what libraries are missing.  Prior to
> doing the install of libgfortran above, it should list libgfortran is
> missing.
>
> $ ldd `which freeview` | grep not
>
> Also it would be good to know what linux you are running, e.g., CentOS 7,
> Ubuntu 18, etc.
>
> - R.
>
> On Jul 15, 2019, at 12:39, Juan Rivas  wrote:
>
> External Email - Use Caution
>
>
>
> -- Forwarded message -
> De: Juan Rivas 
> Date: vie., 12 jul. 2019 a las 3:02
> Subject: Re: [Freesurfer] Freeview
> To: fsbuild 
>
>
> Hi, thank you for your answer.
> I did what you recommended to me, and I get this message:
> freeview: error while loading shared libraries: libgfortran.so.3: cannot
> open shared object file: No such file or directory.
> What could be the next step?
> JC.
>
> El lun., 15 jul. 2019 a las 9:57, fsbuild ()
> escribió:
>
>> Hello JC,
>>
>> Your machine could be missing the qt5 libraries/files.
>>
>> On Ubuntu linux you can try installing them with,
>> $ sudo apt-get install qt5-default qtcreator libqt5x11extras5-dev
>>
>> On CentOS linux,
>> $ sudo yum install qt-create qt-config.x86_64
>> $ sudo yum install qt5-qtx11extras.x86_64 qt5-qtx11extras-devel...x86_64
>>
>> - R.
>>
>> On Jul 12, 2019, at 02:28, Juan Rivas > > wrote:
>>
>> External Email - Use Caution
>>
>> Hello, I am trying to use freeview, but everytime I try I get this
>> message:
>> freeview: error while loading shared libraries: libQt5Widgets.so.5:
>> cannot open shared object file: No such file or directory.
>> How can I fix it?
>> Thanks a lot,
>> JC.
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>

Re: [Freesurfer] Fwd: Freeview

2019-07-15 Thread fsbuild

External Email - Use Caution

Sorry - from your previous mail, I mistakenly thought “which freeview” returned 
/usr/local/bin/freeview.
If you can reproduce what you did before to run freeview from the command line 
where it tells you that it was not finding libgfortran, then “which freeview” 
will likely tell you where the binary is.  You should have already set 
FREESURFER_HOME to point to the freesurfer  installation and then did the 
source of the shell init file (SetUpFreeSurfer.sh for bash or sh, 
SetUpFreeSurfer.csh for csh).  See the wiki page here under setup and 
configuration, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall ;
 That should have put freeview in your PATH so that “which freeview” works.
What you want to do is to cd into the directory where the freeview binary lives 
and run ldd on it.  If “which freeview” returned /usr/local/bin/freeview 
then you could “cd /usr/local/bin” and from there directly run “ldd freeview | 
grep not”.
- R. 
On Jul 12, 2019, at 07:32, Juan Rivas  
wrote:External Email - Use 
CautionThat is what happened:$ 
ldd /usr/local/bin/freeview | grep notldd: /usr/local/bin/freeview: No such 
file or directory$ bashjcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview 
| grep notldd: /usr/local/bin/freeview: No such file or directoryJC.-- 
Forwarded message 
-De: fsbuild Date: lun., 15 jul. 
2019 a las 14:19Subject: Re: [Freesurfer] FreeviewTo: 
Cc: Hello JC,Try 
this to see what libs are missing,$ ldd /usr/local/bin/freeview | grep not- 
R.On Jul 12, 2019, at 06:19, Juan Rivas  
wrote:External Email - Use 
CautionHi, thank you for your 
help. I tried again and once again it did not work. I am using Ubuntu 
18This is the message I get:$ freeviewsh: 8: freeview: not found$  which 
freeview                  $ 
/usr/local/bin/freeviewsh: 10: /usr/local/bin/freeview: not found$ which 
ldd/usr/bin/ldd$ ldd `which freeview` | grep notldd: missing file argumentsTry 
`ldd --help' for more information.Thank you very much,JC.El lun., 15 jul. 2019 
a las 12:50, fsbuild () escribió:Hello Juan,For 
CentOS try:$ sudo yum install gcc-gfortran.x86_64… if that does not work then,$ 
sudo yum install libgfortran.x86_64For Ubuntu,$sudo apt-get install gfortranOne 
thing you might want to try first is to run the “ldd” command on the freeview 
binary to see all/any libraries that are missingThis should return the path 
to freeview, e.g., /usr/local/bin/freeview, though your path may differ.$ which 
freeview/usr/local/bin/freeview- then check you have the ldd command, $ 
which ldd/usr/bin/lddIf the above returned paths for freeview and ldd, then run 
the ldd command followed by the grep command to see what libraries are 
missing.  Prior to doing the install of libgfortran above, it should list 
libgfortran is missing.$ ldd `which freeview` | grep notAlso it would be good 
to know what linux you are running, e.g., CentOS 7, Ubuntu 18, etc.- R.On Jul 
15, 2019, at 12:39, Juan Rivas  
wrote:External Email - Use 
Caution-- Forwarded 
message -De: Juan Rivas Date: vie., 
12 jul. 2019 a las 3:02Subject: Re: [Freesurfer] FreeviewTo: fsbuild 
Hi, thank you for your answer.I did what you 
recommended to me, and I get this message:freeview: error while loading shared 
libraries: libgfortran.so.3: cannot open shared object file: No such file or 
directory.What could be the next step?JC.El lun., 15 jul. 2019 a las 9:57, 
fsbuild () escribió:Hello JC,Your machine could be 
missing the qt5 libraries/files.On Ubuntu linux you can try installing them 
with,$ sudo apt-get install qt5-default 
qtcreator libqt5x11extras5-devOn CentOS linux,$ sudo yum install 
qt-create qt-config.x86_64$ sudo yum install qt5-qtx11extras.x86_64 
qt5-qtx11extras-devel..x86_64- R.On Jul 12, 2019, at 02:28, Juan Rivas 
 
wrote:External Email - Use 
CautionHello, I am trying to 
use freeview, but everytime I try I get this message:freeview: error while 
loading shared libraries: libQt5Widgets.so.5: cannot open shared object file: 
No such file or directory.How can I fix it?Thanks a 
lot,JC.___Freesurfer mailing 
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 mailing 
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 mailing 
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 mailing 
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[Freesurfer] freeview

2019-07-15 Thread Juan Rivas

External Email - Use Caution

That is what happened:
$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
$ bash
jcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
JC.
-- Forwarded message -
De: fsbuild 
Date: lun., 15 jul. 2019 a las 14:19
Subject: Re: [Freesurfer] Freeview
To: 
Cc: 


Hello JC,

Try this to see what libs are missing,

$ ldd /usr/local/bin/freeview | grep not

- R.
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[Freesurfer] Fwd: Freeview

2019-07-15 Thread Juan Rivas

External Email - Use Caution

That is what happened:
$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
$ bash
jcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep not
ldd: /usr/local/bin/freeview: No such file or directory
JC.
-- Forwarded message -
De: fsbuild 
Date: lun., 15 jul. 2019 a las 14:19
Subject: Re: [Freesurfer] Freeview
To: 
Cc: 


Hello JC,

Try this to see what libs are missing,

$ ldd /usr/local/bin/freeview | grep not

- R.

On Jul 12, 2019, at 06:19, Juan Rivas  wrote:

External Email - Use Caution

Hi, thank you for your help.
I tried again and once again it did not work. I am using Ubuntu 18
This is the message I get:

$ freeview
sh: 8: freeview: not found
$  which freeview
$ /usr/local/bin/freeview
sh: 10: /usr/local/bin/freeview: not found
$ which ldd
/usr/bin/ldd
$ ldd `which freeview` | grep not
ldd: missing file arguments
Try `ldd --help' for more information.

Thank you very much,
JC.

El lun., 15 jul. 2019 a las 12:50, fsbuild () escribió:

> Hello Juan,
>
> For CentOS try:
> $ sudo yum install gcc-gfortran.x86_64
> … if that does not work then,
> $ sudo yum install libgfortran.x86_64
>
> For Ubuntu,
> $sudo apt-get install gfortran
>
> One thing you might want to try first is to run the “ldd” command on the
> freeview binary to see all/any libraries that are missing
>
> This should return the path to freeview, e.g., /usr/local/bin/freeview,
> though your path may differ.
> $ which freeview
> /usr/local/bin/freeview
>
> - then check you have the ldd command,
> $ which ldd
> /usr/bin/ldd
>
> If the above returned paths for freeview and ldd, then run the ldd command
> followed by the grep command to see what libraries are missing.  Prior to
> doing the install of libgfortran above, it should list libgfortran is
> missing.
>
> $ ldd `which freeview` | grep not
>
> Also it would be good to know what linux you are running, e.g., CentOS 7,
> Ubuntu 18, etc.
>
> - R.
>
> On Jul 15, 2019, at 12:39, Juan Rivas  wrote:
>
> External Email - Use Caution
>
>
>
> -- Forwarded message -
> De: Juan Rivas 
> Date: vie., 12 jul. 2019 a las 3:02
> Subject: Re: [Freesurfer] Freeview
> To: fsbuild 
>
>
> Hi, thank you for your answer.
> I did what you recommended to me, and I get this message:
> freeview: error while loading shared libraries: libgfortran.so.3: cannot
> open shared object file: No such file or directory.
> What could be the next step?
> JC.
>
> El lun., 15 jul. 2019 a las 9:57, fsbuild ()
> escribió:
>
>> Hello JC,
>>
>> Your machine could be missing the qt5 libraries/files.
>>
>> On Ubuntu linux you can try installing them with,
>> $ sudo apt-get install qt5-default qtcreator libqt5x11extras5-dev
>>
>> On CentOS linux,
>> $ sudo yum install qt-create qt-config.x86_64
>> $ sudo yum install qt5-qtx11extras.x86_64 qt5-qtx11extras-devel..x86_64
>>
>> - R.
>>
>> On Jul 12, 2019, at 02:28, Juan Rivas  wrote:
>>
>> External Email - Use Caution
>>
>> Hello, I am trying to use freeview, but everytime I try I get this
>> message:
>> freeview: error while loading shared libraries: libQt5Widgets.so.5:
>> cannot open shared object file: No such file or directory.
>> How can I fix it?
>> Thanks a lot,
>> JC.
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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[Freesurfer] optseq2 parameters setup

2019-07-15 Thread Tugce Duran

External Email - Use Caution

Hi Dr. Greve,

I am interested in designing the Face Name Associative Memory Exam (FNAME) fMRI 
task for our study.
There are 80 face-name pairs that we will use and the duration can be between 
3.5 and 4.75 secs.  I have used the following command:
optseq2 --ntp 200 --tr 2 --psdwin 0 32 2  --ev facename 4 80  --nkeep 3 --o 
trial2 --tnullmin 0 --tnullmax 6 --nsearch 1
Total scan time appx 6-7 mins.

Q1: For NULL, why do we have only 2 sec and 4 sec jitters? Can we change the 
variety amount of the jitters? Are more jitters good or bad (instead of just 
having 2 secs and 4 secs, let's say we get 0.25, 1, 2, 3 and 4 secs) ?

Q2: For the event design I am interested in above, what would be the "best" 
parameters used?

Trial2-001.par:
0.14.000   1.  facename
  4.14.000   1.  facename
  8.14.000   1.  facename
12.02.000   1.  NULL
14.14.000   1.  facename
18.14.000   1.  facename
22.14.000   1.  facename
26.14.000   1.  facename
30.14.000   1.  facename
34.14.000   1.  facename
38.14.000   1.  facename
42.04.000   1.  NULL
46.14.000   1.  facename
50.14.000   1.  facename
54.14.000   1.  facename
58.14.000   1.  facename
62.14.000   1.  facename
66.14.000   1.  facename
70.14.000   1.  facename
74.02.000   1.  NULL
76.14.000   1.  facename
80.02.000   1.  NULL
82.14.000   1.  facename
.
.
.
.

372.04.000   1.  NULL
376.14.000   1.  facename
380.14.000   1.  facename
384.14.000   1.  facename
388.14.000   1.  facename
392.14.000   1.  facename
396.14.000   1.  facename

Thank you in advance!

Tugce



Tugce Duran
Graduate Student, Biomedical Sciences MS Program
Neuroscience Concentration | Section on Gerontology & Geriatric Medicine, WFSM
[2color]
Graduate Programs in Biomedical Sciences
525 Vine Street, Suite 150, Winston-Salem, NC 27101
* 317-893-9100 | * tdu...@wakehealth.edu | 
|[Image result for linked 
in]linkedin.com/in/tugceduran/
The information contained in this message is privileged and confidential 
information intended for the sole use of the addressee. If the reader of this 
message is not the intended recipient, or the employee or agent responsible for 
delivering it to the intended recipient, you are hereby notified that any 
dissemination, distribution or copying of this communication is strictly 
prohibited. If you have received this message in error, please notify the 
person listed above immediately by e-mail, and delete the original message and 
attachments.

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Re: [Freesurfer] Freeview

2019-07-15 Thread fsbuild

External Email - Use Caution

Hello JC,
Try this to see what libs are missing,

$ ldd /usr/local/bin/freeview | grep not

- R.
On Jul 12, 2019, at 06:19, Juan Rivas  
wrote:External Email - Use 
CautionHi, thank you for your 
help. I tried again and once again it did not work. I am using Ubuntu 
18This is the message I get:$ freeviewsh: 8: freeview: not found$  which 
freeview                  $ 
/usr/local/bin/freeviewsh: 10: /usr/local/bin/freeview: not found$ which 
ldd/usr/bin/ldd$ ldd `which freeview` | grep notldd: missing file argumentsTry 
`ldd --help' for more information.Thank you very much,JC.El lun., 15 jul. 2019 
a las 12:50, fsbuild () escribió:Hello Juan,For 
CentOS try:$ sudo yum install gcc-gfortran.x86_64… if that does not work then,$ 
sudo yum install libgfortran.x86_64For Ubuntu,$sudo apt-get install gfortranOne 
thing you might want to try first is to run the “ldd” command on the freeview 
binary to see all/any libraries that are missingThis should return the path 
to freeview, e.g., /usr/local/bin/freeview, though your path may differ.$ which 
freeview/usr/local/bin/freeview- then check you have the ldd command, $ 
which ldd/usr/bin/lddIf the above returned paths for freeview and ldd, then run 
the ldd command followed by the grep command to see what libraries are 
missing.  Prior to doing the install of libgfortran above, it should list 
libgfortran is missing.$ ldd `which freeview` | grep notAlso it would be good 
to know what linux you are running, e.g., CentOS 7, Ubuntu 18, etc.- R.On Jul 
15, 2019, at 12:39, Juan Rivas  
wrote:External Email - Use 
Caution-- Forwarded 
message -De: Juan Rivas Date: vie., 
12 jul. 2019 a las 3:02Subject: Re: [Freesurfer] FreeviewTo: fsbuild 
Hi, thank you for your answer.I did what you 
recommended to me, and I get this message:freeview: error while loading shared 
libraries: libgfortran.so.3: cannot open shared object file: No such file or 
directory.What could be the next step?JC.El lun., 15 jul. 2019 a las 9:57, 
fsbuild () escribió:Hello JC,Your machine could be 
missing the qt5 libraries/files.On Ubuntu linux you can try installing them 
with,$ sudo apt-get install qt5-default 
qtcreator libqt5x11extras5-devOn CentOS linux,$ sudo yum install 
qt-create qt-config.x86_64$ sudo yum install qt5-qtx11extras.x86_64 
qt5-qtx11extras-devel..x86_64- R.On Jul 12, 2019, at 02:28, Juan Rivas 
 
wrote:External Email - Use 
CautionHello, I am trying to 
use freeview, but everytime I try I get this message:freeview: error while 
loading shared libraries: libQt5Widgets.so.5: cannot open shared object file: 
No such file or directory.How can I fix it?Thanks a 
lot,JC.___Freesurfer mailing 
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 mailing 
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Re: [Freesurfer] general installation and configuration questions (new user!)

2019-07-15 Thread fsbuild

External Email - Use Caution

Hello Robin,
I believe folks use the freesurfer binary archive expanded/installed on file 
servers that are remotely mounted, e.g., thru NFS, so everyone can share a 
common installation.  IT/dev-ops can implement that in different ways, 
e.g., maybe the freesurfer installation actually lives on a fast RAID/redundant 
file system over NFS, etc.  But you ultimately need to set FREESURFER_HOME 
in your shell environment point to wherever freesurfer is installed which could 
be a remote mount point on your local computers file system.  Hopefully a 
remote mount point to the freesurfer installation (via NFS) is standardized to 
be the same path for everyone on their local machines.
Fast disks and fast filesystems can always help with speeding up read/writes of 
data.  SSD storage hanging off the latest PCIe buss designs should 
outperform hard drives. Users often have a local disk in their machine to 
process data (preferably not the same disk as the boot partition is on). 
 Or maybe IT has some available storage over NFS for users to process 
their data, though read/writes over NFS are going to be slower than working off 
a local disk (with or w/o -openmp).   You could use soft links to point to 
different parts of the data if you wanted to physically re-locate pieces of it, 
but any paths thru soft links should make it look like there is a single tree 
with the data.

- R.

On Jul 15, 2019, at 05:06, Robin Warne  
wrote:External Email - Use 
CautionHi folks, I am new 
to the Freesurfer world and I have a couple of questions about installing the 
application, specifically around the 10Gb “footprint” of data, after unpacking 
the archive file. So I have run through the installation and configuration 
steps outlined on the Wiki page, which is great, by the way!  Running 
through the steps first time around went without a hitch but the conversion of 
the sample data took many hours.  If I have to run that conversion again, 
I will try the recon-all with “ -openmp { some appropriate value } “ 
to try and speed it up. I’m guessing that the sample data is occupying a 
large part of the 10Gb disk space “footprint” so is it appropriate to remove 
it, without breaking anything?  If we wanted to install Freesurfer on to a 
server, for multiple users to access, is that possible?  Somewhere like 
‘/usr/local’, as described in the Wiki? Thanks in advance, for any 
guidance anyone can offer. Robin Warne,University of Kent 
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[Freesurfer] Freeview

2019-07-15 Thread Juan Rivas

External Email - Use Caution

Hi, thank you for your help.
I tried again and once again it did not work. I am using Ubuntu 18
This is the message I get:

$ freeview
sh: 8: freeview: not found
$  which freeview
$ /usr/local/bin/freeview
sh: 10: /usr/local/bin/freeview: not found
$ which ldd
/usr/bin/ldd
$ ldd `which freeview` | grep not
ldd: missing file arguments
Try `ldd --help' for more information.

Thank you very much,
JC.

El lun., 15 jul. 2019 a las 12:50, fsbuild () escribió:

> Hello Juan,
>
> For CentOS try:
> $ sudo yum install gcc-gfortran.x86_64
> … if that does not work then,
> $ sudo yum install libgfortran.x86_64
>
> For Ubuntu,
> $sudo apt-get install gfortran
>
> One thing you might want to try first is to run the “ldd” command on the
> freeview binary to see all/any libraries that are missing
>
> This should return the path to freeview, e.g., /usr/local/bin/freeview,
> though your path may differ.
> $ which freeview
> /usr/local/bin/freeview
>
> - then check you have the ldd command,
> $ which ldd
> /usr/bin/ldd
>
> If the above returned paths for freeview and ldd, then run the ldd command
> followed by the grep command to see what libraries are missing.  Prior to
> doing the install of libgfortran above, it should list libgfortran is
> missing.
>
> $ ldd `which freeview` | grep not
>
> Also it would be good to know what linux you are running, e.g., CentOS 7,
> Ubuntu 18, etc.
>
> - R.
>
> On Jul 15, 2019, at 12:39, Juan Rivas  wrote:
>
> External Email - Use Caution
>
>
>
> -- Forwarded message -
> De: Juan Rivas 
> Date: vie., 12 jul. 2019 a las 3:02
> Subject: Re: [Freesurfer] Freeview
> To: fsbuild 
>
>
> Hi, thank you for your answer.
> I did what you recommended to me, and I get this message:
> freeview: error while loading shared libraries: libgfortran.so.3: cannot
> open shared object file: No such file or directory.
> What could be the next step?
> JC.
>
> El lun., 15 jul. 2019 a las 9:57, fsbuild ()
> escribió:
>
>> Hello JC,
>>
>> Your machine could be missing the qt5 libraries/files.
>>
>> On Ubuntu linux you can try installing them with,
>> $ sudo apt-get install qt5-default qtcreator libqt5x11extras5-dev
>>
>> On CentOS linux,
>> $ sudo yum install qt-create qt-config.x86_64
>> $ sudo yum install qt5-qtx11extras.x86_64 qt5-qtx11extras-devel..x86_64
>>
>> - R.
>>
>> On Jul 12, 2019, at 02:28, Juan Rivas  wrote:
>>
>> External Email - Use Caution
>>
>> Hello, I am trying to use freeview, but everytime I try I get this
>> message:
>> freeview: error while loading shared libraries: libQt5Widgets.so.5:
>> cannot open shared object file: No such file or directory.
>> How can I fix it?
>> Thanks a lot,
>> JC.
>> ___
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>>
>>
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Re: [Freesurfer] Freeview

2019-07-15 Thread fsbuild

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Hello Juan,
For CentOS try:$ sudo yum install gcc-gfortran.x86_64… if that does not work 
then,$ sudo yum install libgfortran.x86_64
For Ubuntu,$sudo apt-get install gfortran
One thing you might want to try first is to run the “ldd” command on the 
freeview binary to see all/any libraries that are missing

This should return the path to freeview, e.g., /usr/local/bin/freeview, though 
your path may differ.
$ which freeview/usr/local/bin/freeview
- then check you have the ldd command, $ which ldd/usr/bin/ldd
If the above returned paths for freeview and ldd, then run the ldd command 
followed by the grep command to see what libraries are missing..  Prior to 
doing the install of libgfortran above, it should list libgfortran is missing.
$ ldd `which freeview` | grep not
Also it would be good to know what linux you are running, e.g., CentOS 7, 
Ubuntu 18, etc.
- R.
On Jul 15, 2019, at 12:39, Juan Rivas  
wrote:External Email - Use 
Caution-- Forwarded 
message -De: Juan Rivas Date: vie., 
12 jul. 2019 a las 3:02Subject: Re: [Freesurfer] FreeviewTo: fsbuild 
Hi, thank you for your answer.I did what you 
recommended to me, and I get this message:freeview: error while loading shared 
libraries: libgfortran.so.3: cannot open shared object file: No such file or 
directory.What could be the next step?JC.El lun., 15 jul. 2019 a las 9:57, 
fsbuild () escribió:Hello JC,Your machine could be 
missing the qt5 libraries/files.On Ubuntu linux you can try installing them 
with,$ sudo apt-get install qt5-default 
qtcreator libqt5x11extras5-devOn CentOS linux,$ sudo yum install 
qt-create qt-config.x86_64$ sudo yum install qt5-qtx11extras.x86_64 
qt5-qtx11extras-devel.x86_64- R.On Jul 12, 2019, at 02:28, Juan Rivas 
 
wrote:External Email - Use 
CautionHello, I am trying to 
use freeview, but everytime I try I get this message:freeview: error while 
loading shared libraries: libQt5Widgets.so.5: cannot open shared object file: 
No such file or directory.How can I fix it?Thanks a 
lot,JC.___Freesurfer mailing 
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 mailing 
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[Freesurfer] Freeview

2019-07-15 Thread Juan Rivas

External Email - Use Caution

-- Forwarded message -
De: Juan Rivas 
Date: vie., 12 jul. 2019 a las 3:02
Subject: Re: [Freesurfer] Freeview
To: fsbuild 


Hi, thank you for your answer.
I did what you recommended to me, and I get this message:
freeview: error while loading shared libraries: libgfortran.so.3: cannot
open shared object file: No such file or directory.
What could be the next step?
JC.

El lun., 15 jul. 2019 a las 9:57, fsbuild () escribió:

> Hello JC,
>
> Your machine could be missing the qt5 libraries/files.
>
> On Ubuntu linux you can try installing them with,
> $ sudo apt-get install qt5-default qtcreator libqt5x11extras5-dev
>
> On CentOS linux,
> $ sudo yum install qt-create qt-config.x86_64
> $ sudo yum install qt5-qtx11extras.x86_64 qt5-qtx11extras-devel.x86_64
>
> - R.
>
> On Jul 12, 2019, at 02:28, Juan Rivas  wrote:
>
> External Email - Use Caution
>
> Hello, I am trying to use freeview, but everytime I try I get this message:
> freeview: error while loading shared libraries: libQt5Widgets.so.5: cannot
> open shared object file: No such file or directory.
> How can I fix it?
> Thanks a lot,
> JC.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] Question about coordinates in Freesurfer

2019-07-15 Thread Zhi Li

External Email - Use Caution

Thank you very much, Tim. Any idea for the 1st question?

Thanks and best wishes,

Lizhi

On Sat, 13 Jul 2019 at 09:18, Tim Schäfer  wrote:

> External Email - Use Caution
>
> Dear Lizhi,
>
> on your 2nd question: a rough explanation is on the FS Wiki at [1], but I
> found this website [2] easier to follow as it has some example images.
>
> Regarding space, I think they are all in native space. You can run
> `mri_info` on them to get detailed information.
>
> [1] https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
> [2]
> http://www.grahamwideman.com/gw/brain/fs/fsunderstanding/fssampleimages.htm
>
> Best,
>
> Tim
>
> > On July 12, 2019 at 9:30 PM Zhi Li  wrote:
> >
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts,
> >
> > Now I have an annotation file in fsaverage space and a MNI voxel
> coordinate
> > of one subject. May I ask how could I know if this coordinate is in one
> > parcel of the annotation file? There are many coordinates that I cannot
> > check it one by one in Freeview. In addition, if this is a native image
> > coordinate how could I check whether it is in a parcel then?
> >
> > An additional question is whether the spaces of all the files in folder
> > "mri" generated by recon-all are native individual space? What do the
> files
> > 'orig.mgz', norm.mgz'', 'brainmask.mgz', 'brain.mgz' and 'T1.mgz' refer
> to?
> > They are very similar to each other, with skull-stripped or not. Is there
> > any document on it I could reference?
> >
> > Looking forward to your kind suggestions,
> >
> > Many thanks and best regards,
> >
> > Lizhi
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
>
> ___
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Re: [Freesurfer] Freeview

2019-07-15 Thread fsbuild

External Email - Use Caution

Hello JC,
Your machine could be missing the qt5 libraries/files.

On Ubuntu linux you can try installing them with,$ sudo apt-get install 
qt5-default qtcreator libqt5x11extras5-dev
On CentOS linux,$ sudo yum install qt-create qt-config.x86_64$ sudo 
yum install qt5-qtx11extras.x86_64 qt5-qtx11extras-devel.x86_64
- R..

On Jul 12, 2019, at 02:28, Juan Rivas  
wrote:External Email - Use 
CautionHello, I am trying to 
use freeview, but everytime I try I get this message:freeview: error while 
loading shared libraries: libQt5Widgets.so.5: cannot open shared object file: 
No such file or directory.How can I fix it?Thanks a 
lot,JC.___Freesurfer mailing 
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[Freesurfer] Freeview

2019-07-15 Thread Juan Rivas

External Email - Use Caution

Hello, I am trying to use freeview, but everytime I try I get this message:
freeview: error while loading shared libraries: libQt5Widgets.so.5: cannot
open shared object file: No such file or directory.
How can I fix it?
Thanks a lot,
JC.
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[Freesurfer] MRI Technologist Job Posting at The Ohio State University

2019-07-15 Thread Prakash Lab

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Hello,

The Center for Cognitive and Behavioral Brain Imaging (CCBBI) at The Ohio
State University is seeking to hire a Magnetic Resonance Imaging (MRI)
Technologist. Please see attached document for full description.

Best Regards,
The Clinical Neuroscience Laboratory

[image: The Ohio State University]
The Clinical Neuroscience Laboratory Department of Psychology
74 Psychology Building, 1835 Neil Avenue, Columbus, OH 43210
614-292-9568 Office
r...@clinicalneurosciencelab.com www.clinicalneurolab.org

Confidentiality Notice: This email transmission (including any documents,
files or attachments) is for the sole use of the intended recipient(s) and
may contain confidential and privileged information.  If you are not the
intended recipient, you are hereby notified that any disclosure, copying or
distribution, or any use of the enclosed or attached information is
strictly prohibited.  If you have received this transmission in error,
please notify me immediately by return email and delete all materials
without reading, copying, saving or printing them.


MRI Technologist CCBBI-PRAKASH.pdf
Description: Adobe PDF document
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Re: [Freesurfer] Create no-skull brain with gray matter mask

2019-07-15 Thread Greve, Douglas N.,Ph.D.

The ribbon.mgz file should be about the same (but for both hemis)

On 7/15/2019 9:36 AM, Bruce Fischl wrote:
Hi Marina

if you have a pial surface you can use mris_fill to fill the interior then use 
that as a mask

cheers
Bruce


On Mon, 15 Jul 2019, Marina Fernández wrote:


External Email - Use Caution

Dear experts,

I need to get a no-skull brain. The automated no-skull brain has many errors
and I was thinking that I could create it taking into account the gray
matter mask (we segment manually, so the mask is accurate) in such a way
that everything outside the gray matter mask is eliminated and everything
inside is maintained.

Do you know how can I create it?

Any idea will be welcome. Thank you very much.

Best regards,

Marina.






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Re: [Freesurfer] CSF mask

2019-07-15 Thread Greve, Douglas N.,Ph.D.

that or see here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

On 7/15/2019 9:39 AM, Bruce Fischl wrote:
you can do this with mri_convert:

mri_convert -rl native_volume.mgz -rt nearest apas+head.mgz apas+head.native.mgz


cheers
Bruce

On Mon, 15 Jul 2019, Laboratorio de Neurociencia Funcional wrote:


External Email - Use Caution

Thank you, Doug. The voxel resolution of the apas+head.mgz file is 1mm3.
Would it be possible to obtain the same file but with the native resolution?

Best,
Jose

El lun., 15 jul. 2019 a las 6:01, Greve, Douglas N.,Ph.D.
() escribió:
  You can try running gtmseg. You will not want its final output,
  but along the way it will  produce a file called apas+head.mgz,
  and this will have a semi-good segmentation of extracerebral
  CSF.


  On 7/12/2019 12:14 PM, Laboratorio de Neurociencia Funcional
  wrote:

  External Email - Use Caution

Dear Freesurfer experts,

Is there any way to obtain a CSF mask in Freesurfer similar to that obtained
 with the SPM segmentation (see attached file)? I would need that the CSF ma
sk contains not only the cerebral ventricles but also the extracerebral CSF.

Any help with this would be greatly appreciated.

Best regards, Jose

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Re: [Freesurfer] CSF mask

2019-07-15 Thread Bruce Fischl


you can do this with mri_convert:

mri_convert -rl native_volume.mgz -rt nearest apas+head.mgz apas+head.native.mgz


cheers
Bruce

On Mon, 15 Jul 
2019, Laboratorio de 
Neurociencia Funcional wrote:




External Email - Use Caution

Thank you, Doug. The voxel resolution of the apas+head.mgz file is 1mm3.
Would it be possible to obtain the same file but with the native resolution?

Best,
Jose

El lun., 15 jul. 2019 a las 6:01, Greve, Douglas N.,Ph.D.
() escribió:
  You can try running gtmseg. You will not want its final output,
  but along the way it will  produce a file called apas+head.mgz,
  and this will have a semi-good segmentation of extracerebral
  CSF.


  On 7/12/2019 12:14 PM, Laboratorio de Neurociencia Funcional
  wrote:

  External Email - Use Caution

Dear Freesurfer experts,

Is there any way to obtain a CSF mask in Freesurfer similar to that obtained
 with the SPM segmentation (see attached file)? I would need that the CSF ma
sk contains not only the cerebral ventricles but also the extracerebral CSF.

Any help with this would be greatly appreciated.

Best regards, Jose 



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Re: [Freesurfer] Create no-skull brain with gray matter mask

2019-07-15 Thread Bruce Fischl


Hi Marina

if you have a pial surface you can use mris_fill to fill the interior then 
use that as a mask


cheers
Bruce


On Mon, 15 Jul 2019, Marina Fernández wrote:



External Email - Use Caution

Dear experts,

I need to get a no-skull brain. The automated no-skull brain has many errors
and I was thinking that I could create it taking into account the gray
matter mask (we segment manually, so the mask is accurate) in such a way
that everything outside the gray matter mask is eliminated and everything
inside is maintained.

Do you know how can I create it?

Any idea will be welcome. Thank you very much.

Best regards,

Marina.


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Re: [Freesurfer] CSF mask

2019-07-15 Thread Laboratorio de Neurociencia Funcional

External Email - Use Caution

Thank you, Doug. The voxel resolution of the apas+head.mgz file is 1mm3.
Would it be possible to obtain the same file but with the native resolution?

Best,
Jose

El lun., 15 jul. 2019 a las 6:01, Greve, Douglas N.,Ph.D. (<
dgr...@mgh.harvard.edu>) escribió:

> You can try running gtmseg. You will not want its final output, but along
> the way it will  produce a file called apas+head.mgz, and this will have a
> semi-good segmentation of extracerebral CSF.
>
>
> On 7/12/2019 12:14 PM, Laboratorio de Neurociencia Funcional wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> Is there any way to obtain a CSF mask in Freesurfer similar to that obtained 
> with the SPM segmentation (see attached file)? I would need that the CSF mask 
> contains not only the cerebral ventricles but also the extracerebral CSF.
>
> Any help with this would be greatly appreciated.
>
> Best regards, Jose
>
>
>
> ___
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>
>
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[Freesurfer] general installation and configuration questions (new user!)

2019-07-15 Thread Robin Warne

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Hi folks,

I am new to the Freesurfer world and I have a couple of questions about 
installing the application, specifically around the 10Gb "footprint" of data, 
after unpacking the archive file.

So I have run through the installation and configuration steps outlined on the 
Wiki page, which is great, by the way!  Running through the steps first time 
around went without a hitch but the conversion of the sample data took many 
hours.  If I have to run that conversion again, I will try the recon-all with " 
-openmp { some appropriate value } " to try and speed it up.

I'm guessing that the sample data is occupying a large part of the 10Gb disk 
space "footprint" so is it appropriate to remove it, without breaking anything? 
 If we wanted to install Freesurfer on to a server, for multiple users to 
access, is that possible?  Somewhere like '/usr/local', as described in the 
Wiki?

Thanks in advance, for any guidance anyone can offer.

Robin Warne,
University of Kent (U.K.)

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[Freesurfer] Create no-skull brain with gray matter mask

2019-07-15 Thread Marina Fernández

External Email - Use Caution

Dear experts,

I need to get a no-skull brain. The automated no-skull brain has many
errors and I was thinking that I could create it taking into account the
gray matter mask (we segment manually, so the mask is accurate) in such a
way that everything outside the gray matter mask is eliminated and
everything inside is maintained.

Do you know how can I create it?

Any idea will be welcome. Thank you very much.

Best regards,

Marina.
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Re: [Freesurfer] Viewing Uncorrected Significance Map in Freeview

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Re: [Freesurfer] optseq2 parameters setup

Re: [Freesurfer] Question about coordinates in Freesurfer

[Freesurfer] freeview

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Re: [Freesurfer] freeview

[Freesurfer] Fwd: freeview

Re: [Freesurfer] Fwd: Fwd: Freeview

[Freesurfer] Fwd: Fwd: Freeview

Re: [Freesurfer] Fwd: Freeview

[Freesurfer] freeview

[Freesurfer] Fwd: Freeview

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Re: [Freesurfer] Freeview

Re: [Freesurfer] general installation and configuration questions (new user!)

[Freesurfer] Freeview

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[Freesurfer] Freeview

Re: [Freesurfer] Question about coordinates in Freesurfer

Re: [Freesurfer] Freeview

[Freesurfer] Freeview

[Freesurfer] MRI Technologist Job Posting at The Ohio State University

Re: [Freesurfer] Create no-skull brain with gray matter mask

Re: [Freesurfer] CSF mask

Re: [Freesurfer] CSF mask

Re: [Freesurfer] Create no-skull brain with gray matter mask

Re: [Freesurfer] CSF mask

[Freesurfer] general installation and configuration questions (new user!)

[Freesurfer] Create no-skull brain with gray matter mask

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