[Freesurfer] Setup & Configuration Error

2020-03-31 Thread Hossein Shooli 
External Email - Use Caution

Hello FreeSurfer Development Team,
I have just install the FreeSurfer
(freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c)
on my mac Catalina OS (10.15.2). The installation path was set as default
(/Application/freesurfer).
 Then, in the Setup & Configuration step I have faced some troubles that
I'm in need to fix it. In this step the first line " $> export
FREESURFER_HOME=/Applications/freesurfer" works properly. But when I typed
the " $> source $FREESURFER_HOME/SetUpFreeSurfer.sh ".
an error occurred as below:

Hosseins-MacBook-Pro:~ dhs$ > export
FREESURFER_HOME=/Applications/freesurfer

Hosseins-MacBook-Pro:~ dhs$ > source $FREESURFER_HOME/SetUpFreeSurfer.sh

/Applications/freesurfer/SetUpFreeSurfer.sh: line 14: return: can only
`return' from a function or sourced script

/Applications/freesurfer/SetUpFreeSurfer.sh: line 42: /FreeSurferEnv.sh: No
such file or directory

Hosseins-MacBook-Pro:~ dhs$


I have checked the mail archives but there no answer to my problem. Please
help me solve the issue and setup freesurfer successfully.


Bests regard

Hossein




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Re: [Freesurfer] kill recon-all programatically/remotely

2020-03-31 Thread Bruce Fischl 
ps aux | grep recon-all

To get the pid, then 

kill -9 pid

Or 

killall recon-all

If it is the only one running on that box

Cheers
Bruce

> On Mar 31, 2020, at 10:10 PM, Octavian Lie  wrote:
> 
> 
> External Email - Use Caution
> 
> Dear All, 
> 
> Is there a way to kill a  recon-all run on linux via ssh/putty. Ctrl+C is not 
> working, obviously, and it is not easy to figure out which process encodes 
> the recon-all runs with commands such as ps aux, top etc. One gross way may 
> be removing the subject directory all together midway, but not sure how this 
> affects FS, subsequent runs
> Thank you, 
> Octavian
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] kill recon-all programatically/remotely

2020-03-31 Thread Octavian Lie 
External Email - Use Caution

Dear All,

Is there a way to kill a  recon-all run on linux via ssh/putty. Ctrl+C is
not working, obviously, and it is not easy to figure out which process
encodes the recon-all runs with commands such as ps aux, top etc. One gross
way may be removing the subject directory all together midway, but not sure
how this affects FS, subsequent runs
Thank you,
Octavian
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Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}

2020-03-31 Thread fsbuild 
External Email - Use Caution

Hello Tristan,
Going back to that thread, I’d like to try the command you uploaded data for 
as freesurfer_data.tar.gz on a couple of Ubuntu systems, but either I’m 
looking in the wrong place or it’s not there anymore.  Is there a shared 
google drive link or something you point me to for a download link? 
> freeview -v brainmask.mgz T1.mgz -f lh.white:edgecolor=yellow 
> lh.pial:edgecolor=magenta rh.white:edgecolor=yellow 
rh.pial:edgecolor=magenta
> 
> We can also replicate the error by opening freeview and opening all the 
above 
> files sequentially through the GUI.

- R.

On Mar 31, 2020, at 13:41, TRISTAN J PAUTSCH  
wrote:External Email - Use 
CautionThanks for the reply, 
all.The issues I'm having are the same as they were in my prior thread, found 
here:https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63458.htmlI 
tried everything up to and including compiling everything from scratch 
(including FS itself, missing libs, PETSC, etc.). The main takeaway is 
that I pretty convincingly narrowed the issue down to PETSC+Ubuntu 18.04, the 
most pertinent details for that being in the following 
post:https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63702.htmlBack
 when I was active in that thread, I emailed the PETSC mailing list and got no 
response, and at the time I was pretty busy with other projects so I had to let 
it go for the time being; I maintained my old RHEL6 server so people could 
continue to use FS. Now with everyone in quarantine (and RHEL6 entering ELS 
this November), it's a decent time to look back into this issue. I 
wouldn't have reached back out to the FS list, however when I saw that a focus 
was being placed on Ubuntu (and that there was a working Ubuntu VM), I became 
hopeful that maybe this issue was 
resolved?TFrom: fsbu...@contbay.com Sent: Tuesday,
 March 31, 2020 3:57 
AMTo: freesurfer@nmr.mgh.harvard.edu Cc: ts...@rcmd.org ;
 TRISTAN J PAUTSCH Subject: Re: [Freesurfer] on 
Ubuntu (was FreeSurfer V 7.0 on Centos 8) We would also like to know about 
any issues you are seeing on Ubuntu.I think Ubuntu eliminated some jpeg/png 
packages from their repos.  Those can be downloaded and installed 
manually,e.g., libpng12-0_1.2.54-1ubuntu1.1_amd64.deb, 
libjpeg62_6b2-3_amd64.deb.  That is part of the reason we made an Ubuntu 
18 VM available with everything pre-installed.. The VM is essentially what 
has been used for the freesurfer course which runs mostly freeview commands 
with some mri* commands (though I believe a recon-all also works).  The VM 
is running binaries built on CentOS7 - as the reference platforms for 
freesurfer dev are currently CentOS and MacOS.  We are looking at making a 
.deb installer for freesurfer on Ubuntu though.There is some info on the wiki 
about packages required to compile the source on Ubuntu - but you don’t need 
all of these to run (even the CentOS) binaries.MailScanner has detected a 
possible fraud attempt from "surfer..nmr.mgh.harvard.edu" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements- R.On Mar 31, 
2020, at 02:50, Tim Schäfer  
wrote:   External Email - Use Caution 
   Hi Tristan,I'm about to setup a 
FreeSurfer installation on an Ubuntu system, and I wondered whether you could 
elaborate on the kind of issues you are experiencing.Best,Tim--Dr. Tim 
SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent 
Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, 
Goethe University Frankfurt am Main, GermanyOn March 30, 2020 at 11:01 PM 
TRISTAN J PAUTSCH  
wrote:   External Email - Use Caution 
   Is there going to be an "official" 
Ubuntu build this time around (as in, built and tested in Ubuntu) that isn't 
the VM? Both the current CentOS and the dev builds continue to have issues 
(even when compiled from scratch) on my Ubuntu 18.04 
servers.Thanks!TFrom: 
freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbu...@contbay.com 
Sent: Monday, March 30, 2020 9:40 AMTo: 
freesurfer@nmr.mgh.harvard.edu Cc: 
dr.minafak...@live.com Subject: Re: [Freesurfer] 
FreeSurfer V 7.0 on Centos 8   External 
Email - Use CautionHello Mina,I see from 
https://www.centosblog.com/centos-eol-dates/ that CentOS 6 will no longer be 
updated as of 11/2020, and similarly for CentOS 7 in 6/2024.  It looks 
like CentOS 8 was released around September of 2019.While we do not currently 
build/test on CentOS8, I am sure it will eventually be supported. 
  Given some users will continue to use CentOS 6 even after 11/2020 
and that many people have been running the freesurfer 6 release on CentOS6, 
then even th

Re: [Freesurfer] Reducing FreeSurfer recon-all time

2020-03-31 Thread Bruce Fischl 

Hi Xiaojiang

do you have multiple cores? If so, you can use -openmp 4  or something to 
reduce the recon time even on your linux box


cheers
Bruce
On Tue, 31 Mar 2020, Xiaojiang 
Yang wrote:




External Email - Use Caution

Freesurfer experts:

I know in my powerful Linux machine, recon-all needs about 10 hours to finish 
all computation. What
is the possible way I can use to greatly reduce this computation time from 10 
hours to, say 1-3
hours?

Is Sun Grid Engine (SGE), or GPU/CUDA, or any other technique, helpful?

Thank you!
Xiaojiang


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[Freesurfer] Reducing FreeSurfer recon-all time

2020-03-31 Thread Xiaojiang Yang 
External Email - Use Caution

Freesurfer experts:

I know in my powerful Linux machine, recon-all needs about 10 hours to
finish all computation. What is the possible way I can use to greatly
reduce this computation time from 10 hours to, say 1-3 hours?

Is Sun Grid Engine (SGE), or GPU/CUDA, or any other technique, helpful?

Thank you!
Xiaojiang
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Re: [Freesurfer] Hippocampal Subfield Segmentation Error

2020-03-31 Thread Iglesias Gonzalez, Juan E. 
Uuuummm this is a tough one. Any ideas, Andrew? Maybe updating java?


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of "Lab of Autism and 
Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" 

Reply-To: Freesurfer support list 
Date: Tuesday, March 31, 2020 at 17:59
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal Subfield Segmentation Error


External Email - Use Caution
Hello Eugenio,
No I wasn't! When I first tried to run the subfields I wasn't pointed to 
downloading a version of Java. I do have Java on the MAC I'm using, but the 
error "unable to start JVM because of a bad java option" still appears. Any 
other ideas on how to fix this?
Thanks,
Alex

On Mon, Mar 30, 2020 at 10:12 AM Iglesias Gonzalez, Juan E. 
mailto:jiglesiasgonza...@mgh.harvard.edu>> 
wrote:
HI Alex,
Were you pointed to downloading a version of Java when you first tried to run
the subfields? If so, did you follow the instructions?
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Lab of Autism and Developmental Neuroscience, Lab of Autism and 
Developmental Neuroscience" mailto:l...@email.gwu.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Saturday, March 28, 2020 at 02:07
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Hippocampal Subfield Segmentation Error


External Email - Use Caution
Dear Freesurfer experts,

Hope everyone is well! I'm unfortunately continuing to have errors running the 
hippocampal subfield segmentation. Apparently it's being caused by issues with 
the java.opts files. I tried removing it (as recommended by a link someone set 
me from the Matlab help website), but it made no difference. Please find my 
code and error message below:







CCASPH-A1900447:3003 ajobsaid$ recon-all -s Sub_42 -hippocampal-subfields-T1

Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

INFO: SUBJECTS_DIR is /Applications/freesurfer/BAP/3003

Actual FREESURFER_HOME /Applications/freesurfer

-rw-rw-r--  1 ajobsaid  wheel  859204 Mar 24 12:59 
/Applications/freesurfer/BAP/3003/Sub_42/scripts/recon-all.log

Darwin 
CCASPH-A1900447.cloud.ccas.gwu.edu 
18.7.0 Darwin Kernel Version 18.7.0: Thu Jan 23 06:52:12 PST 2020; 
root:xnu-4903.278.25~1/RELEASE_X86_64 x86_64

#

#@# Hippocampal Subfields processing (T1 only) left Tue Mar 24 15:09:44 EDT 2020

\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 
/Applications/freesurfer Sub_42 /Applications/freesurfer/BAP/3003 left \n

See log file: 
/Applications/freesurfer/BAP/3003/Sub_42/scripts/hippocampal-subfields-T1.log

--

Setting up environment variables

---

DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:

Warning: application is running on a locale different from the original 
platform locale.

JavaVM: Failed to load JVM: 
/Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib

JavaVM FATAL: Failed to load the jvm library.

2020-03-24 15:09:45.262 segmentSubjectT1_autoEstimateAlveusML[66267:3452922] 
This process is attempting to exclude an item from Time Machine by path without 
administrator privileges. This is not supported.

2020-03-24 15:09:45.263 segmentSubjectT1_autoEstimateAlveusML[66267:3452922] 
This process is attempting to exclude an item from Time Machine by path without 
administrator privileges. This is not supported.

2020-03-24 15:09:45.263 segmentSubjectT1_autoEstimateAlveusML[66267:3452922] 
This process is attempting to exclude an item from Time Machine by path without 
administrator privileges. This is not supported.

2020-03-24 15:09:45.264 segmentSubjectT1_autoEstimateAlveusML[66267:3452922] 
This process is attempting to exclude an item from Time Machine by path without 
administrator privileges. This is not supported.

2020-03-24 15:09:45.264 segmentSubjectT1_autoEstimateAlveusML[66267:3452922] 
This process is attempting to exclude an item from Time Machine by path without 
administrator privileges. This is not supported.

2020-03-24 15:09:45.264 segmentSubjectT1_autoEstimateAlveusML[66267:3452922] 
This process is attempting to exclude an item from Time Machine by path without 
administrator privileges. This is not supported.

2020-03-24 15:09:45.265 segmentSubjectT1_autoEstimateAlveusML[66267:3452922] 
This process is attempting to exclude an item from Time Machine by path without 
administrator privilege

Re: [Freesurfer] Hippocampal Subfield Segmentation Error

2020-03-31 Thread Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 
External Email - Use Caution

Hello Eugenio,
No I wasn't! When I first tried to run the subfields I wasn't pointed to
downloading a version of Java. I do have Java on the MAC I'm using, but the
error "unable to start JVM because of a bad java option" still appears. Any
other ideas on how to fix this?
Thanks,
Alex

On Mon, Mar 30, 2020 at 10:12 AM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:

> HI Alex,
>
> Were you pointed to downloading a version of Java when you first tried to
> run
>
> the subfields? If so, did you follow the instructions?
>
> Cheers,
>
> /Eugenio
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Lab of
> Autism and Developmental Neuroscience, Lab of Autism and Developmental
> Neuroscience" 
> *Reply-To: *Freesurfer support list 
> *Date: *Saturday, March 28, 2020 at 02:07
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Hippocampal Subfield Segmentation Error
>
>
>
> *External Email - Use Caution*
>
> Dear Freesurfer experts,
>
>
>
> Hope everyone is well! I'm unfortunately continuing to have errors running
> the hippocampal subfield segmentation. Apparently it's being caused by
> issues with the java.opts files. I tried removing it (as recommended by a
> link someone set me from the Matlab help website), but it made no
> difference. Please find my code and error message below:
>
>
>
>
>
>
>
> CCASPH-A1900447:3003 ajobsaid$ recon-all -s Sub_42
> -hippocampal-subfields-T1
>
> Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>
> Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>
> INFO: SUBJECTS_DIR is /Applications/freesurfer/BAP/3003
>
> Actual FREESURFER_HOME /Applications/freesurfer
>
> -rw-rw-r--  1 ajobsaid  wheel  859204 Mar 24 12:59
> /Applications/freesurfer/BAP/3003/Sub_42/scripts/recon-all.log
>
> Darwin CCASPH-A1900447.cloud.ccas.gwu.edu 18.7.0 Darwin Kernel Version
> 18.7.0: Thu Jan 23 06:52:12 PST 2020; root:xnu-4903.278.25~1/RELEASE_X86_64
> x86_64
>
> #
>
> #@# Hippocampal Subfields processing (T1 only) left Tue Mar 24 15:09:44
> EDT 2020
>
> \n /Applications/freesurfer/bin/segmentSF_T1.sh
> /Applications/freesurfer/MCRv80 /Applications/freesurfer Sub_42
> /Applications/freesurfer/BAP/3003 left \n
>
> See log file:
> /Applications/freesurfer/BAP/3003/Sub_42/scripts/hippocampal-subfields-T1.log
>
> --
>
> Setting up environment variables
>
> ---
>
> DYLD_LIBRARY_PATH is
> .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:
>
> Warning: application is running on a locale different from the original
> platform locale.
>
> JavaVM: Failed to load JVM:
> /Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib
>
> JavaVM FATAL: Failed to load the jvm library.
>
> 2020-03-24 15:09:45.262
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.263
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.263
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.264
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.264
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.264
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.265
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.265
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.265
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This i

Re: [Freesurfer] Problem with version of mri_surfcluster provided with fspalm

2020-03-31 Thread Syam Gadde 
External Email - Use Caution

Just to update, I found another version of mri_surfcluster that you (Doug) 
linked from the archives, with a build date of April 3, 2019, and that 
apparently worked just fine.  I'm not sure where I got the one I downloaded.  
Sorry for the red herrings!

-syam


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Syam Gadde 

Sent: Friday, March 27, 2020 12:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Problem with version of mri_surfcluster provided with 
fspalm

External Email - Use Caution

This is the actual command that fails:

mri_surfcluster --in rh.50to50.glmdir//con_nonpos/sig.mgh --mask 
rh.50to50.glmdir//mask.mgh --cwsig 
rh.50to50.glmdir//con_nonpos/--perm-resid.sig.cluster.mgh --sum 
rh.50to50.glmdir//con_nonpos/--perm-resid.sig.cluster.summary --ocn 
rh.50to50.glmdir//con_nonpos/--perm-resid.sig.ocn.mgh --annot aparc 
--cwpvalthresh .05 --o rh.50to50.glmdir//con_nonpos/--perm-resid.sig.masked.mgh 
--no-fixmni --csd rh.50to50.glmdir//csd/--perm-resid.j001-con_nonpos.csd 
--csdpdf rh.50to50.glmdir//con_nonpos/--perm-resid.pdf.dat --vwsig 
rh.50to50.glmdir//con_nonpos/--perm-resid.sig.voxel.mgh --vwsigmax 
rh.50to50.glmdir//con_nonpos/--perm-resid.sig.voxel.max.dat --oannot 
rh.50to50.glmdir//con_nonpos/--perm-resid.sig.ocn.annot --surf white

Output is:

Creating CDFs from CSD files
csd->threshsign = 0
thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $
hemi   = rh
srcid  = rh.50to50.glmdir//con_nonpos/sig.mgh
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = abs
thmin  = 3
thmax  = -1
fdr= -1
minarea= 0
xfmfile= talairach.xfm
nth = -1
outid= rh.50to50.glmdir//con_nonpos/--perm-resid.sig.masked.mgh MGH
ocnid= rh.50to50.glmdir//con_nonpos/--perm-resid.sig.ocn.mgh MGH
sumfile  = rh.50to50.glmdir//con_nonpos/--perm-resid.sig.cluster.summary
subjectsdir= /usr/local/packages/freesurfer_v6.0.0/subjects
FixMNI = 0
Found 149926 vertices in mask
Found 149926 vertices in mask
Found 149926 points in clabel.
- XFM matrix (RAS2RAS) ---
/usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/mri/transforms/talairach.xfm

 1.0   0.0   0.0   0.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;
MRISread(^Y$<91>^?): could not open file

Reading source surface 
/usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/rh.white
No such file or directory
mri_surfcluster: could not read surface 
/usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/rh.white
No such file or directory

When I removed the --vwsigmax option and ran the old version, it runs to 
completion, and the following line:

MRISread(^Y$<91>^?): could not open file

does not show up in the output.

-syam


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Syam Gadde 

Sent: Friday, March 27, 2020 11:17 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Problem with version of mri_surfcluster provided with 
fspalm

External Email - Use Caution

Actually I was just sending an example command to demonstrate the same error.  
I'll see if I can get the actual command fspalm was running.

-syam


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

Sent: Friday, March 27, 2020 10:43 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Problem with version of mri_surfcluster provided with 
fspalm

Hi Syam, it looks like fspalm is not creating the correct command line
for mri_surfcluster (the --in should be an output of palm, not the
fsaverage surface). Can you send the full terminal output?
doug


On 3/25/2020 9:13 AM, Syam Gadde wrote:
>  External Email - Use Caution
>
> Hi,
>
> We have a user trying to use fspalm.  I followed all the directions to 
> install, but are getting an error with the new mri_surfcluster that we were 
> asked to download with fspalm.  Here is the dummy command I ran to replicate 
> the error:
>
> mri_surfcluster --thmin 0 --subject fsaverage --hemi lh --in 
> /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white
>
> and the end of its output:
>
> <...>
> subjectsdir= /usr/local/packages/freesurfer_v6.0.0/subjects
> FixMNI = 1
> - XFM matrix (RAS2RAS) ---
> /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/mri/transforms/talairach.xfm
>   1.0   0.0   0.0   0.0;
>   0.0   1.0   0.0   0.0;
>   0.0   0.0   1.0   0.0;
>   0.0   0.0   0.0   1.0;
> 
> Reading source surf

Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}

2020-03-31 Thread TRISTAN J PAUTSCH 
External Email - Use Caution

Thanks for the reply, all.

The issues I'm having are the same as they were in my prior thread, found here:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63458.html

I tried everything up to and including compiling everything from scratch 
(including FS itself, missing libs, PETSC, etc.). The main takeaway is that I 
pretty convincingly narrowed the issue down to PETSC+Ubuntu 18.04, the most 
pertinent details for that being in the following post:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63702.html

Back when I was active in that thread, I emailed the PETSC mailing list and got 
no response, and at the time I was pretty busy with other projects so I had to 
let it go for the time being; I maintained my old RHEL6 server so people could 
continue to use FS. Now with everyone in quarantine (and RHEL6 entering ELS 
this November), it's a decent time to look back into this issue.

I wouldn't have reached back out to the FS list, however when I saw that a 
focus was being placed on Ubuntu (and that there was a working Ubuntu VM), I 
became hopeful that maybe this issue was resolved?

T

From: fsbu...@contbay.com 
Sent: Tuesday, March 31, 2020 3:57 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: ts...@rcmd.org ; TRISTAN J PAUTSCH 
Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8)

We would also like to know about any issues you are seeing on Ubuntu.

I think Ubuntu eliminated some jpeg/png packages from their repos.  Those can 
be downloaded and installed manually,e.g., 
libpng12-0_1.2.54-1ubuntu1.1_amd64.deb, libjpeg62_6b2-3_amd64.deb.  That is 
part of the reason we made an Ubuntu 18 VM available with everything 
pre-installed.

The VM is essentially what has been used for the freesurfer course which runs 
mostly freeview commands with some mri* commands (though I believe a recon-all 
also works).  The VM is running binaries built on CentOS7 - as the reference 
platforms for freesurfer dev are currently CentOS and MacOS.  We are looking at 
making a .deb installer for freesurfer on Ubuntu though.

There is some info on the wiki about packages required to compile the source on 
Ubuntu - but you don’t need all of these to run (even the CentOS) binaries.

https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements

- R.

On Mar 31, 2020, at 02:50, Tim Schäfer  wrote:

   External Email - Use Caution

Hi Tristan,

I'm about to setup a FreeSurfer installation on an Ubuntu system, and I 
wondered whether you could elaborate on the kind of issues you are experiencing.

Best,

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany


On March 30, 2020 at 11:01 PM TRISTAN J PAUTSCH  wrote:


   External Email - Use Caution

Is there going to be an "official" Ubuntu build this time around (as in, built 
and tested in Ubuntu) that isn't the VM? Both the current CentOS and the dev 
builds continue to have issues (even when compiled from scratch) on my Ubuntu 
18.04 servers.

Thanks!
T


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbu...@contbay.com 

Sent: Monday, March 30, 2020 9:40 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: dr.minafak...@live.com 
Subject: Re: [Freesurfer] FreeSurfer V 7.0 on Centos 8


   External Email - Use Caution

Hello Mina,

I see from https://www.centosblog.com/centos-eol-dates/ that CentOS 6 will no 
longer be updated as of 11/2020, and similarly for CentOS 7 in 6/2024.  It 
looks like CentOS 8 was released around September of 2019.

While we do not currently build/test on CentOS8, I am sure it will eventually 
be supported.   Given some users will continue to use CentOS 6 even after 
11/2020 and that many people have been running the freesurfer 6 release on 
CentOS6, then even the upcoming freesurfer 7 release is targeting CentOS6, 
CentOS7 and Ubuntu linux (as well as Mac OS).

There is also currently an Ubuntu 18 VM with freesurfer 6 and the beta release 
of freesurfer 7 pre-installed which you can find here, 
https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67

- R.

On Mar 30, 2020, at 08:52, Mina Rizkallah  wrote:

   External Email - Use Caution
Greetings FreeSurfer team,

I recently upgraded by workstation from Centos 7 to 8.1 as the support for 
centos  7 will be over soon.

I tried installing freesurfer version 7.0 beta 1 but failed due to some 
unresolved dependencies (tried on a  virtual centos 7 and worked fine) !!

so, when will there be support for centos 8, thank you

Best regards
Mina
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Re: [Freesurfer] Using freeview to view (and edit?) talairach registrations

2020-03-31 Thread Ruopeng Wang 
You can go to menu Tools -> Transform Volume to adjust the registration and 
save it as a lta registration file. Then run lta_convert to convert it to xfm:

lta_convert --inlta foo.lta --outmni foo.xfm

> On Mar 31, 2020, at 1:06 PM, Rachel Hoel  > wrote:
> 
> External Email - Use Caution
> 
> 
> Hi Ruopeng,
> 
> I entered the full path for the transformation file, and this is what I’m 
> seeing in freeview (screenshot attached). Is it possible to edit the 
> talairach registrations in freeview similar to how they could be edited in 
> tkmedit, or can freeview only be used for looking at talairach registrations?
> 
> Thanks again,
> Rachel
> 
> 
> 
> 
> 

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Re: [Freesurfer] Issue with tkregister command

2020-03-31 Thread Douglas N. Greve 


I think this is a bug. Can you try this version?
https://gate.nmr.mgh.harvard.edu/safelinks/greve/reg-feat2anat
copy it to $FREESURFER_HOME/bin
and run
chmod a+x $FREESURFER_HOME/bin/reg-feat2anat



On 3/31/2020 11:46 AM, Tiffany Bell wrote:


External Email - Use Caution

Hello

I am trying to transform a free surfer segmentation to functional 
space using reg-feat2anat but I get the error


tkregister2_cmdl_cmdl: Command not found.


I am running freesufer on linux through a virtual machine. See below 
for the full command and output. Any help would be greatly appreciated.


reg-feat2anat --feat LTFI_FEAT_PE_FB_R1/LTFI_02.feat --subject LTFI_02
FeatDir is LTFI_FEAT_PE_FB_R1/LTFI_02.feat
template volume is LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz
log file is 
LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/reg-feat2anat.log

Thu 26 Mar 17:17:56 GMT 2020
/storage/gold/cinn/2013/neuroade/LTFI_Analysis
/usr/local/freesurfer7/freesurfer/bin/reg-feat2anat
--feat LTFI_FEAT_PE_FB_R1/LTFI_02.feat --subject LTFI_02
Linux neurodebian-1022 4.4.0-165-generic #193-Ubuntu SMP Tue Sep 17 
17:42:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

example_func ras_good_flag 1
---
Initializing exf2anat with header
tkregister2_cmdl_cmdl --targ 
/storage/gold/cinn/2013/neuroade/LTFI_Analysis/Freesurfer_output/LTFI_02/mri/brainmask.mgz 
--mov LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz --reg 
LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/anat2exf.register.dat.init 
--fslregout 
LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/exf2anat.init.fsl.mat 
--regheader --noedit

tkregister2_cmdl_cmdl: Command not found.

Many Thanks

Tiffany


--

Tiffany Bell, PhD

Postdoctoral Associate
Cumming School of Medicine
*University of Calgary*
*AlbertaChildren’sHospital*
2888 Shaganappi Trail, NW Calgary, AB T3B 6A8

(E) tiffany.b...@ucalgary.ca 
(T) 403-955-2970

www.kidsmigraine.info 



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[Freesurfer] Issue with tkregister command

2020-03-31 Thread Tiffany Bell 
External Email - Use Caution

Hello

I am trying to transform a free surfer segmentation to functional space using 
reg-feat2anat but I get the error

tkregister2_cmdl_cmdl: Command not found.


I am running freesufer on linux through a virtual machine. See below for the 
full command and output. Any help would be greatly appreciated.

reg-feat2anat --feat LTFI_FEAT_PE_FB_R1/LTFI_02.feat --subject LTFI_02
FeatDir is LTFI_FEAT_PE_FB_R1/LTFI_02.feat
template volume is LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz
log file is LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/reg-feat2anat.log
Thu 26 Mar 17:17:56 GMT 2020
/storage/gold/cinn/2013/neuroade/LTFI_Analysis
/usr/local/freesurfer7/freesurfer/bin/reg-feat2anat
--feat LTFI_FEAT_PE_FB_R1/LTFI_02.feat --subject LTFI_02
Linux neurodebian-1022 4.4.0-165-generic #193-Ubuntu SMP Tue Sep 17 17:42:52 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
example_func ras_good_flag 1
---
Initializing exf2anat with header
tkregister2_cmdl_cmdl --targ 
/storage/gold/cinn/2013/neuroade/LTFI_Analysis/Freesurfer_output/LTFI_02/mri/brainmask.mgz
 --mov LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz --reg 
LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/anat2exf.register.dat.init 
--fslregout 
LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/exf2anat.init.fsl.mat 
--regheader --noedit
tkregister2_cmdl_cmdl: Command not found.

Many Thanks

Tiffany


--

Tiffany Bell, PhD

Postdoctoral Associate
Cumming School of Medicine
University of Calgary
Alberta Children’s Hospital
2888 Shaganappi Trail, NW Calgary, AB T3B 6A8

(E) tiffany.b...@ucalgary.ca
(T) 403-955-2970

www.kidsmigraine.info


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Re: [Freesurfer] Using freeview to view (and edit?) talairach registrations

2020-03-31 Thread Ruopeng Wang 
Hi Rachel,

You need to enter the full path of the transformation file or relative one like 
/mri/...

Best,
Ruopeng

> On Mar 31, 2020, at 12:20 AM, Rachel Hoel  wrote:
> 
> External Email - Use Caution
> Dear Freesurfer Developers,
> 
> I'm working with v6.0 on OS Catalina 10.15 and I'm trying to use freeview to 
> check talairach registrations - I've always used tkmedit, so I am running 
> into some issues with the command line for viewing the transform.
> 
> When I run the following command: 
>   freeview -v /mri/T1.mgz \
> /mri/brainmask.mgz:reg=/mri/transforms/talairach.xfm
>  I get the following errors:
> 
> regio_read_mincxfm: No such file or directory
> ERROR: could not read /mri/transforms/talairach.xfm
> ERROR: could not read /mri/transforms/talairach.xfm
> 
> Thanks in advance!
> 
> Rachel
> 
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> 
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Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}

2020-03-31 Thread fsbuild 
External Email - Use Caution

We would also like to know about any issues you are seeing on Ubuntu..

I think Ubuntu eliminated some jpeg/png packages from their repos.  Those 
can be downloaded and installed manually,e.g., 
libpng12-0_1.2.54-1ubuntu1.1_amd64.deb, libjpeg62_6b2-3_amd64.deb.  That 
is part of the reason we made an Ubuntu 18 VM available with everything 
pre-installed. 
The VM is essentially what has been used for the freesurfer course which runs 
mostly freeview commands with some mri* commands (though I believe a recon-all 
also works).  The VM is running binaries built on CentOS7 - as the 
reference platforms for freesurfer dev are currently CentOS and MacOS.  We 
are looking at making a .deb installer for freesurfer on Ubuntu though.
There is some info on the wiki about packages required to compile the source on 
Ubuntu - but you don’t need all of these to run (even the CentOS) binaries.
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements
- R.

On Mar 31, 2020, at 02:50, Tim Schäfer  
wrote:   External Email - Use Caution 
   Hi Tristan,I'm about to setup a 
FreeSurfer installation on an Ubuntu system, and I wondered whether you could 
elaborate on the kind of issues you are experiencing.Best,Tim--Dr. Tim 
SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent 
Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, 
Goethe University Frankfurt am Main, GermanyOn March 30, 2020 at 11:01 PM 
TRISTAN J PAUTSCH  
wrote:   External Email - Use Caution 
   Is there going to be an "official" 
Ubuntu build this time around (as in, built and tested in Ubuntu) that isn't 
the VM? Both the current CentOS and the dev builds continue to have issues 
(even when compiled from scratch) on my Ubuntu 18.04 
servers.Thanks!TFrom: 
freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbu...@contbay.com 
Sent: Monday, March 30, 2020 9:40 AMTo: 
freesurfer@nmr.mgh.harvard.edu Cc: 
dr.minafak...@live.com Subject: Re: [Freesurfer] 
FreeSurfer V 7.0 on Centos 8   External 
Email - Use CautionHello Mina,I see from 
https://www.centosblog.com/centos-eol-dates/ that CentOS 6 will no longer be 
updated as of 11/2020, and similarly for CentOS 7 in 6/2024.  It looks 
like CentOS 8 was released around September of 2019.While we do not currently 
build/test on CentOS8, I am sure it will eventually be supported. 
  Given some users will continue to use CentOS 6 even after 11/2020 
and that many people have been running the freesurfer 6 release on CentOS6, 
then even the upcoming freesurfer 7 release is targeting CentOS6, CentOS7 and 
Ubuntu linux (as well as Mac OS).There is also currently an Ubuntu 18 VM with 
freesurfer 6 and the beta release of freesurfer 7 pre-installed which you can 
find here, https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67- R.On Mar 30, 2020, 
at 08:52, Mina Rizkallah  
wrote:   External Email - Use 
CautionGreetings FreeSurfer team,I recently upgraded by workstation from Centos 
7 to 8.1 as the support for centos  7 will be over soon.I tried installing 
freesurfer version 7.0 beta 1 but failed due to some unresolved dependencies 
(tried on a  virtual centos 7 and worked fine) !!so, when will there be 
support for centos 8, thank youBest 
regardsMina___Freesurfer mailing 
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