Re: [Freesurfer] problem using recon-all

2019-02-13 Thread Shachar Gal 
External Email - Use Caution

Hey Douglas,
A couple of question about the patch
In order to use it, I need to download the regular Freesurfer version-6, and 
replace only the scripts that are in the patch? (i.e Make_average_surface, 
recon_all, conf2hires, longmc)
Which recon-all to use? The one under the hcp sub folder?

Thanks!
Shachar

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Fix topology correcting defect

2019-02-13 Thread Milene Bürger 
External Email - Use CautionHi Freesurfers,
 

I tried to run the recon-all command for several subjects of my study. It worked out for all of them except for one. This one froze at fixing topology „Correcting defect“ 11 out of 140 defects. 

I looked for advises in the mailing list but I can’t find any major problems in the images that Freesurfer processed so far. The last correct file that I can open in freeview, is filled.mgz (the skull and cerebellum are properly removed and it shows the two hemispheres with 127 for rh and 255 for lh). I can’t find the file "filled-pretess255.mgz“ which should be the output, but I do have the files lh.orig.nofix and rh.orig.nofix for example. I tried to look at these files, but freeview can't open them (failed to load MRI) so that I can’t see if there are topological defects to correct as you described on one of the FsTutorials. I already tried to run only the autorecon2 command, but the same freezing problem appeared at one point. I also tried to only use the mri_pretess command with different options, but it didn’t work.

 

I copied you the fix topology and what I tried with mri_pretess. I use freesurfer version 6.0.1.

 

Thanks a lot!

 

Milène

 



 mris_fix_topology -rusage /data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Versuch_Pretess/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -g 1234 FJ_20170425_T1_Versuch_Pretess lh 

reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*
Topology Correction Parameters
retessellation mode:           genetic search
number of patches/generation : 10
number of generations :        10
surface mri loglikelihood coefficient :         1.0
volume mri loglikelihood coefficient :          10.0
normal dot loglikelihood coefficient :          1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :                             2
eliminate vertices during search :              1
initial patch selection :                       1
select all defect vertices :                    0
ordering dependant retessellation:              0
use precomputed edge table :                    0
smooth retessellated patch :                    2
match retessellated patch :                     1
verbose mode :                                  0

*
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
before topology correction, eno=-666 (nv=184736, nf=370804, ne=556206, g=334)
using quasi-homeomorphic spherical map to tessellate cortical surface...
 


Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
92297 ambiguous faces found in tessellation
segmenting defects...
151 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 3 into 2
      -merging segment 32 into 12
      -merging segment 94 into 12
      -merging segment 45 into 36
      -merging segment 53 into 37
      -merging segment 62 into 60
      -merging segment 81 into 70
      -merging segment 88 into 70
      -merging segment 144 into 132
      -merging segment 141 into 138
      -merging segment 150 into 147

140 defects to be corrected 
0 vertices coincident
reading input surface /data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Versuch_Pretess/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.3516  (-4.6758)
      -vertex     loglikelihood: -6.1930  (-3.0965)
      -normal dot loglikelihood: -3.5442  (-3.5442)
      -quad curv  loglikelihood: -6.0556  (-3.0278)
      Total Loglikelihood : -25.1443

 

CORRECTING DEFECT 0 (vertices=9329, convex hull=1902, v0=235)
XL defect detected...
After retessellation of defect 0 (v0=235), euler #=-122 (135106,396534,261306) : difference with theory (-137) = -15 

CORRECTING DEFECT 1 (vertices=47, convex hull=87, v0=788)
After retessellation of defect 1 (v0=788), euler #=-121 (135129,396640,261390) : difference with theory (-136) = -15 

CORRECTING DEFECT 2 (vertices=1438, convex hull=465, v0=1311)
XL defect detected...
After retessellation of defect 2 (v0=1311), euler #=-119 (135552,398142,262471) : difference with theory (-135) = -16 

CORRECTING DEFECT 3 (vertices=24, convex hull=64, v0=9358)
After retessellation of defect 3 (v0=9358), euler #=-118 (135563,398202,262521) : difference with theory (-134) = -16 

CORRECTING DEFECT 4 (vertices=35, convex hull=54, v0=11845)
After retessellation of def

[Freesurfer] talairach.m3z question

2019-02-13 Thread Tim Schäfer 
External Email - Use Caution

Dear FreeSurfer experts,

I have 2 questions on the talairach.m3z file generated by recon-all.

1) What exactly does it contain? I read its the displacement field for a 
non-linear transform from native space to some freesurfer space. But from which 
input file (or space) to which other one does it transform?

2) What's the file format? Is there a spec somewhere?

Thanks,

-- 
Tim

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] problem using recon-all

2019-02-13 Thread Shachar Gal 
External Email - Use Caution

ok, so I tried doing what I mentioned above (I used the hcp recon-all
version), and when trying to run the FreeSurfer Pipeline, I received this
error:

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

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

any thoughts?

thanks,
Shachar



On Wed, 13 Feb 2019 at 10:21, Shachar Gal  wrote:

> Hey Douglas,
> A couple of question about the patch
> In order to use it, I need to download the regular Freesurfer version-6,
> and replace only the scripts that are in the patch? (i.e
> Make_average_surface, recon_all, conf2hires, longmc)
> Which recon-all to use? The one under the hcp sub folder?
>
> Thanks!
> Shachar
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] problem using recon-all

2019-02-13 Thread Tim Schäfer 
External Email - Use Caution

The release notes mention this message:

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

under 'Known issues' and recommend you run 'sudo -E fs_update'.


> On February 13, 2019 at 1:45 PM Shachar Gal  wrote:
> 
> 
> External Email - Use Caution
> 
> ok, so I tried doing what I mentioned above (I used the hcp recon-all
> version), and when trying to run the FreeSurfer Pipeline, I received this
> error:
> 
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
> 
> dyld: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
> 
> any thoughts?
> 
> thanks,
> Shachar
> 
> 
> 
> On Wed, 13 Feb 2019 at 10:21, Shachar Gal  wrote:
> 
> > Hey Douglas,
> > A couple of question about the patch
> > In order to use it, I need to download the regular Freesurfer version-6,
> > and replace only the scripts that are in the patch? (i.e
> > Make_average_surface, recon_all, conf2hires, longmc)
> > Which recon-all to use? The one under the hcp sub folder?
> >
> > Thanks!
> > Shachar
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Tim

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] problem using recon-all

2019-02-13 Thread Tim Schäfer 
External Email - Use Caution

That being said, this did not help in my case. I had to disable System 
Integrity Protection.

> On February 13, 2019 at 2:08 PM Tim Schäfer  wrote:
> 
> 
> External Email - Use Caution
> 
> The release notes mention this message:
> 
>   https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
> 
> under 'Known issues' and recommend you run 'sudo -E fs_update'.
> 
> 
> > On February 13, 2019 at 1:45 PM Shachar Gal  wrote:
> > 
> > 
> > External Email - Use Caution
> > 
> > ok, so I tried doing what I mentioned above (I used the hcp recon-all
> > version), and when trying to run the FreeSurfer Pipeline, I received this
> > error:
> > 
> > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
> >   Referenced from:
> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
> >   Expected in: /usr/lib/libSystem.B.dylib
> > 
> > dyld: Symbol not found: ___emutls_get_address
> >   Referenced from:
> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
> >   Expected in: /usr/lib/libSystem.B.dylib
> > 
> > any thoughts?
> > 
> > thanks,
> > Shachar
> > 
> > 
> > 
> > On Wed, 13 Feb 2019 at 10:21, Shachar Gal  wrote:
> > 
> > > Hey Douglas,
> > > A couple of question about the patch
> > > In order to use it, I need to download the regular Freesurfer version-6,
> > > and replace only the scripts that are in the patch? (i.e
> > > Make_average_surface, recon_all, conf2hires, longmc)
> > > Which recon-all to use? The one under the hcp sub folder?
> > >
> > > Thanks!
> > > Shachar
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Tim
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>

-- 
Tim

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] problem using recon-all

2019-02-13 Thread Shachar Gal 
External Email - Use Caution

Hey Tim,

I tried to run the “-E fs_update”, and got this message:

rsync -zbrlv --progress --suffix=.1550066275_bak 
rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/*
 /Applications/freesurfer
receiving file list ... 
rsync: change_dir 
"/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in 
pub) failed: No such file or directory (2)
0 files to consider

sent 4 bytes  received 9 bytes  8.67 bytes/sec
total size is 0  speedup is 0.00
rsync error: some files could not be transferred (code 23) at 
/BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52.200.1/rsync/main.c(1404)
 [receiver=2.6.9]


Does the indicate I should disable SIP, or is it a different issue?

Thanks,
Shachar___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] problem using recon-all

2019-02-13 Thread Shachar Gal 
External Email - Use Caution

I am not sure that the issue is with the SIP, because the message says this
- *"freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c"* does not exist in the
patches directory, and in fact, it does not exist here -
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/
any ideas where this patch needs to come from?

thanks,
Shachar

On Wed, 13 Feb 2019 at 16:09, Shachar Gal  wrote:

> Hey Tim,
>
> I tried to run the “-E fs_update”, and got this message:
>
> rsync -zbrlv --progress --suffix=.1550066275_bak
> rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/*
> /Applications/freesurfer
> receiving file list ...
> rsync: change_dir
> "/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c"
> (in pub) failed: No such file or directory (2)
> 0 files to consider
>
> sent 4 bytes  received 9 bytes  8.67 bytes/sec
> total size is 0  speedup is 0.00
> rsync error: some files could not be transferred (code 23) at
> /BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52.200.1/rsync/main.c(1404)
> [receiver=2.6.9]
>
>
> Does the indicate I should disable SIP, or is it a different issue?
>
> Thanks,
> Shachar
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Postdoctoral position (EEG-MRI) available at NORMENT (Oslo, Norway)

2019-02-13 Thread Kjetil Nordbø Jørgensen 
External Email - Use Caution

Dear FreeSurfer users!

A three-year position as postdoctoral fellow is now available at the Norwegian 
Centre for Mental Disorders Research (NORMENT) in Oslo, Norway. 

NORMENT is a Center of Excellence (CoE) funded by the Research Council of 
Norway. The main purpose of the research is to disentangle and characterize the 
neurobiological, genetic, psychological and environmental factors contributing 
to the development of severe mental disorders. Within this context, the 
postdoctoral fellow is expected to focus on the relationships between 
MRI-derived measures of brain myelination and EEG-derived electrophysiological 
measures in connection to psychotic symptomatology.

More information about the position can be found here:
https://www.jobbnorge.no/ledige-stillinger/stilling/163184/postdoctoral-research-fellowship

We welcome applicants! Please note the short deadline, February 17th.

Kind regards,
Kjetil Nordbø Jørgensen, PhD
Postdoctoral fellow and clinical psychologist 
Diakonhjemmet Hospital and the Norwegian Centre for Mental Disorders Research 
(NORMENT)
Oslo, Norway


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Different aseg and aparc stats with Freesurfer 5.3 and 6.0

2019-02-13 Thread Bruce Fischl 

Hi Ranila

the different versions contain slightly different algorithms, so why 
would you expect them to be the same? With 20 subjects you may be at the 
edge of having enough power to see a significant effect.


cheers
Bruce
On Wed, 13 Feb 
2019, Ranila Bhoyroo wrote:




External Email - Use Caution

Hello Experts,

 

I was working with some data pre-processed using freesurfer v5.3 - i think this 
was done on linux.
Recently I pre-processed the dataset using v6.0 on an imac. I extracted 
cortical thickness and
surface area from both hemispheres. The data is different for each version. 
What worries me is that
I am correlating the neural metrics with some behavioral data and this gives me 
different results.
My sample size is only 20.

 

Some advice would be very helpful.

 

Thanks.

 

Cheers, 

Ranila 


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] MRISalloc error during automatic reconstruction

2019-02-13 Thread Bruce Fischl 

Hi Julia

I think you only have about 1.5G free memory at the beinning of 
running recon-all, which is not enough for this subject. It looks like some 
other process is using another 2G, which might be enough if you can free it 
up. In general though you probably want a machine with more ram


cheers
Bruce


On Wed, 13 Feb 
2019, Julia Ströhlein wrote:



   External Email - Use Caution

Hi,
of course.

Julia

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 12. Februar 2019 16:12
An: Freesurfer support list 
Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction

Hi Julia

can you send us the recon-all.log file?

cheers
Bruce
On Tue, 12 Feb 2019,
Julia Ströhlein wrote:



External Email - Use Caution

Dear experts,

while running one of my subjects, I got this error:

 

MRISalloc(732595, 480): could not allocate vertices

Cannot allocate memory

Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10

20:41:14 UTC 2012 i686 i686 i386 GNU/Linux

 

recon-all -s P_04 exited with ERRORS at Mon Feb  4 16:40:03 EST 2019

 

Do you know what went wrong and how I can fix this?

Best regards,

Julia

 

 

Unbenannt

 



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Fix topology correcting defect

2019-02-13 Thread Bruce Fischl 

Hi Milène

a couple of things. First, to view a surface in freeview you have to 
specify that it is a surface with -f before the surface file name. So, 
from the mri dir you could do:


freeview -v norm.mgz -f ../surf/lh.orig.nofix ../surf/lh.inflated.nofix

Second, how long did you wait? Big defects take a long time. You should 
definitely look at your inflated and orig surfaces though to make sure that 
some dramatic isn't wrong (like skull attached, or hemispheres not 
separated) as your defect is probably too large to be an ordinary one that 
the topo fixer will correct successfully.


cheers
Bruce

On Wed, 13 Feb 2019, "Milene Bürger" wrote:



External Email - Use Caution

Hi Freesurfers,  
I tried to run the recon-all command for several subjects of my study. It 
worked out for all of them
except for one. This one froze at fixing topology „Correcting defect“ 11 out of 
140 defects. 
I looked for advises in the mailing list but I can’t find any major problems in 
the images that
Freesurfer processed so far. The last correct file that I can open in freeview, 
is filled.mgz (the
skull and cerebellum are properly removed and it shows the two hemispheres with 
127 for rh and 255
for lh). I can’t find the file "filled-pretess255.mgz“ which should be the 
output, but I do have the
files lh.orig.nofix and rh.orig.nofix for example. I tried to look at these 
files, but freeview
can't open them (failed to load MRI) so that I can’t see if there are 
topological defects to correct
as you described on one of the FsTutorials. I already tried to run only the 
autorecon2 command, but
the same freezing problem appeared at one point. I also tried to only use the 
mri_pretess command
with different options, but it didn’t work.
 
I copied you the fix topology and what I tried with mri_pretess. I use 
freesurfer version 6.0.1.
 
Thanks a lot!
 
Milène
 
 mris_fix_topology 
-rusage/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Versu
ch_Pretess/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -g 
1234
FJ_20170425_T1_Versuch_Pretess lh 
reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234
*
Topology Correction Parameters
retessellation mode:           genetic search
number of patches/generation : 10
number of generations :        10
surface mri loglikelihood coefficient :         1.0
volume mri loglikelihood coefficient :          10.0
normal dot loglikelihood coefficient :          1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :                             2
eliminate vertices during search :              1
initial patch selection :                       1
select all defect vertices :                    0
ordering dependant retessellation:              0
use precomputed edge table :                    0
smooth retessellated patch :                    2
match retessellated patch :                     1
verbose mode :                                  0
*
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
before topology correction, eno=-666 (nv=184736, nf=370804, ne=556206, g=334)
using quasi-homeomorphic spherical map to tessellate cortical surface...
 
Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
92297 ambiguous faces found in tessellation
segmenting defects...
151 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 3 into 2
      -merging segment 32 into 12
      -merging segment 94 into 12
      -merging segment 45 into 36
      -merging segment 53 into 37
      -merging segment 62 into 60
      -merging segment 81 into 70
      -merging segment 88 into 70
      -merging segment 144 into 132
      -merging segment 141 into 138
      -merging segment 150 into 147
140 defects to be corrected 
0 vertices coincident
reading input 
surface/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Versu
ch_Pretess/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.3516  (-4.6758)
      -vertex     loglikelihood: -6.1930  (-3.0965)
      -normal dot loglikelihood: -3.5442  (-3.5442)
      -quad curv  loglikelihood: -6.0556  (-3.0278)
      Total Loglikelihood : -25.1443
 
CORRECTING DEFECT 0 (vertices=9329, convex hull=1902, v0=235)
XL defect detected...
After retessellation of defect 0 (v0=235), euler #=-122 (135106,396534,261306) 
: difference with
theory (-137)

[Freesurfer] neuroimaging quality control survey

2019-02-13 Thread Remi gau 
External Email - Use Caution

Hello all,

Forward this here as it seems relevant to this mailing list. Do not hesitate to 
circulate this on your institute mailing lists, and ask your collaborators and 
friends.

Thanks

Remi

The neuroimaging quality control (niQC) special interest group (SIG) aims to 
standardize and develop best practices for niQC and Quality Assurance (QA). 
Learn more here: tinyurl.com/WeNeedNiQC


We invite you to fill this survey, to help us to get a sense of various types 
of QC/QA that is done in the neuroimaging community. We would like you to cover 
the "full life-cycle" of neuroimaging research, including but not limited to 
data collection, preprocessing, intermediate outputs and final results. We 
request you to provide details into the various QC/QA processes you conduct in 
your projects. We plan to analyze all the responses from the community to 
identify the challenges our community is facing, consolidate and review 
existing research, develop protocols, compile manuals, improve tools, and make 
recommendations for best practices.


Fill the survey: https://tinyurl.com/niQC-HighLevel-Survey-2019


Find out more about joining this effort to standardize neuroimaging QC here: 
https://groups.google.com/d/forum/niqc


This survey is fully anonymous and we do not track anything. We plan to 
publicly release your input, in its raw form as well as in various forms of 
aggregate summaries. In addition to the aforementioned uses, your response will 
be used for anything else the group would consider necessary in the future to 
advance its mission. Your participation is voluntary and you can withdraw from 
this survey anytime.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] problem using recon-all

2019-02-13 Thread Hoopes, Andrew 
Hi Shachar, the patch will not fix this. You’ll probably need to disable SIP - 
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
 - which prevents access to libraries in /usr. This bug has been fixed in the 
dev version.

best
Andrew


From:  on behalf of Shachar Gal 

Reply-To: FS Help 
Date: Wednesday, February 13, 2019 at 9:24 AM
To: "ts...@rcmd.org" 
Cc: FS Help , Ido Tavor 
Subject: Re: [Freesurfer] problem using recon-all


External Email - Use Caution
I am not sure that the issue is with the SIP, because the message says this - 
"freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" does not exist in the patches 
directory, and in fact, it does not exist here - 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/
any ideas where this patch needs to come from?

thanks,
Shachar

On Wed, 13 Feb 2019 at 16:09, Shachar Gal 
mailto:gal.shac...@gmail.com>> wrote:
Hey Tim,

I tried to run the “-E fs_update”, and got this message:

rsync -zbrlv --progress --suffix=.1550066275_bak 
rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/*
 /Applications/freesurfer
receiving file list ...
rsync: change_dir 
"/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in 
pub) failed: No such file or directory (2)
0 files to consider

sent 4 bytes  received 9 bytes  8.67 bytes/sec
total size is 0  speedup is 0.00
rsync error: some files could not be transferred (code 23) at 
/BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52.200.1/rsync/main.c(1404)
 [receiver=2.6.9]




Does the indicate I should disable SIP, or is it a different issue?

Thanks,
Shachar
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] FreeSurfer Registration Error

2019-02-13 Thread Peng Wang 
External Email - Use Caution

Whatever I filled the form I got "Spammer. Go away!" message. Please help!
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Missing files after recon-all

2019-02-13 Thread Zhi Li 
External Email - Use Caution

Hello FreeSurfer experts,

I am trying recon-all in a SGE cluster. However, the size of of the results
was smaller than that executed in a local CentOs system. I did not found
error in the recon-all log file which ended with "recon-all -s sub001
finished without error". But when I used QAtools, it reported:

 Checking if all files exist...FAILED
 (read ../a003/scripts/recon_checker.log)
 ERROR: Subject a003 missing output file
../mri/transforms/talairach.m3z.inv.x.mgz
 ERROR: Subject a003 missing output file
../mri/transforms/talairach.m3z.inv.y.mgz
 ERROR: Subject a003 missing output file
../mri/transforms/talairach.m3z.inv.z.mgz
 ERROR: Subject a003 missing output file ../mri/nu_noneck.mgz
 ERROR: Subject a003 missing output file ../label/lh.BA1.label
 ERROR: Subject a003 missing output file ../label/lh.BA2.label
 ERROR: Subject a003 missing output file ../label/lh.BA3a.label
 ERROR: Subject a003 missing output file ../label/lh.BA3b.label
 ERROR: Subject a003 missing output file ../label/lh.BA4a.label
 ERROR: Subject a003 missing output file ../label/lh.BA4p.label
 ERROR: Subject a003 missing output file ../label/lh.BA6.label
 ERROR: Subject a003 missing output file ../label/lh.BA44.label
 ERROR: Subject a003 missing output file ../label/lh.BA45.label
 ERROR: Subject a003 missing output file ../label/lh.V1.label
 ERROR: Subject a003 missing output file ../label/lh.V2.label
 ERROR: Subject a003 missing output file ../label/lh.MT.label
 ERROR: Subject a003 missing output file ../label/lh.BA.annot
 ERROR: Subject a003 missing output file ../stats/lh.BA.stats
 ERROR: Subject a003 missing output file ../label/rh.BA1.label
 ERROR: Subject a003 missing output file ../label/rh.BA2.label
 ERROR: Subject a003 missing output file ../label/rh.BA3a.label
 ERROR: Subject a003 missing output file ../label/rh.BA3b.label
 ERROR: Subject a003 missing output file ../label/rh.BA4a.label
 ERROR: Subject a003 missing output file ../label/rh.BA4p.label
 ERROR: Subject a003 missing output file ../label/rh.BA6.label
 ERROR: Subject a003 missing output file ../label/rh.BA44.label
 ERROR: Subject a003 missing output file ../label/rh.BA45.label
 ERROR: Subject a003 missing output file ../label/rh.V1.label
 ERROR: Subject a003 missing output file ../label/rh.V2.label
 ERROR: Subject a003 missing output file ../label/rh.MT.label
 ERROR: Subject a003 missing output file ../label/rh.BA.annot
 ERROR: Subject a003 missing output file ../label/BA.ctab
 ERROR: Subject a003 missing output file ../stats/rh.BA.stats
 ERROR: Subject a003 missing output file
../stats/lh.entorhinal_exvivo.stats
 ERROR: Subject a003 missing output file
../stats/rh.entorhinal_exvivo.stats

In addition, the QA results were black. But if I apply QATools on these
results in a local CentOs system, the results seemed normal. Should this QA
problem be caused by X11? I did not install FSL in the SGE cluster, would
this be the problem of missing files after recon-all? Any suggestions would
be appreciated.

Thanks and best wishes,

Lizhi
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] FreeSurfer Registration Error

2019-02-13 Thread Hoopes, Andrew 
Hi, what are you trying to register for? A wiki account?
Andrew


From:  on behalf of Peng Wang 

Reply-To: FS Help 
Date: Wednesday, February 13, 2019 at 12:54 PM
To: FS Help 
Subject: [Freesurfer] FreeSurfer Registration Error


External Email - Use Caution
Whatever I filled the form I got "Spammer. Go away!" message. Please help!
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] FreeSurfer Registration Error

2019-02-13 Thread Peng Wang 
External Email - Use Caution

The freesurfer license.

https://surfer.nmr.mgh.harvard.edu/registration.html


On Wed, Feb 13, 2019 at 1:38 PM Hoopes, Andrew 
wrote:

> Hi, what are you trying to register for? A wiki account?
>
> Andrew
>
>
>
>
>
> *From: * on behalf of Peng Wang <
> pen...@gmail.com>
> *Reply-To: *FS Help 
> *Date: *Wednesday, February 13, 2019 at 12:54 PM
> *To: *FS Help 
> *Subject: *[Freesurfer] FreeSurfer Registration Error
>
>
>
> *External Email - Use Caution*
>
> Whatever I filled the form I got "Spammer. Go away!" message. Please help!
> ___
> 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

[Freesurfer] Registrations with freesurfer voxel space and posterior map of thalamic nuclei segmentation results

2019-02-13 Thread Sherry Shen 
External Email - Use Caution

Hello Freesurfer Developers,


I got the posterior map of thalamic nuclei segmentation by setting the 
environment parameter:

export WRITE_POSTERIORS=1

I found the posterior map is of different dimension.


In my case, posterior map is of [173, 117,116] dimension with 0.5mm voxel 
resolution. However, the segmentation label ThalamicNuclei.v10.T1 is of 
[187,117,112] 0.5mm and ThalamicNuclei.v10.T1.FSvoxelSpace is of [256,256,256] 
1mm. How can I align posterior map with the other two?


Thank you,

Sherry
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] dt_recon issue

2019-02-13 Thread Daniel Davidson Callow 
External Email - Use Caution

Hello,

I am trying to run dt_recon on my dti data using the following script.

dt_recon --debug --i
Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm --s
${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon



with the following error


echo "ERROR: cannot find $InputVol"

echo ERROR: cannot find
Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm

ERROR: cannot find
Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm

goto error_exit ;


the DICOM files are named image01.dcm through image65.dcm


These were 64 gradient images acquired on a SIEMENS scanner with 1 bo
image. Any advice on how I should structure this command would be greatly
appreciated!


*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
dcal...@umd.edu 
443-254-6298
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] dt_recon issue

2019-02-13 Thread fsbuild 
External Email - Use Caution

Hello Daniel.
It looks like you need a slash in front of Volumes for the path after —I/Volumes
- R.

On Feb 13, 2019, at 14:44, Daniel Davidson Callow  
wrote:External Email - Use 
CautionHello,I am trying to run 
dt_recon on my dti data using the following script.dt_recon --debug --i 
Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm --s 
${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtreconwith the following 
errorecho "ERROR: cannot find $InputVol"echo ERROR: cannot find 
Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcmERROR: cannot 
find Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcmgoto 
error_exit ;the DICOM files are 
named image01.dcm through image65.dcmThese were 64 
gradient images acquired on a SIEMENS scanner with 1 bo image. Any advice on 
how I should structure this command would be greatly appreciated!Daniel 
CallowPhD Student, Neuroscience and Cognitive ScienceExercise 
for Brain Health LabUniversity of Maryland, College 
Parkdcallow@umd.edu443-254-6298___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://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

[Freesurfer] License Registration Error "Spammer, go away!"

2019-02-13 Thread Peng Wang 
External Email - Use Caution

Please help!

Repost with a better title.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] License Registration Error "Spammer, go away!"

2019-02-13 Thread Greve, Douglas N.,Ph.D. 
it would be helpful if you were to tell us exactly what you were doing 
(eg, URL, which text box, etc)

On 2/13/19 3:49 PM, Peng Wang wrote:
>
> External Email - Use Caution
>
> Please help!
>
> Repost with a better title.
>
> ___
> 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

Re: [Freesurfer] License Registration Error "Spammer, go away!"

2019-02-13 Thread Hoopes, Andrew 
Are you using some sort of form auto-fill plugin when you're accessing the 
registration page? Our spam filter checks if a hidden parameter has been 
supplied. If there's a way for you to turn auto-fill off temporarily - I would 
try that first. Let me know how that goes.

best
Andrew


On 2/13/19, 4:08 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Greve, Douglas N.,Ph.D."  wrote:

it would be helpful if you were to tell us exactly what you were doing 
(eg, URL, which text box, etc)

On 2/13/19 3:49 PM, Peng Wang wrote:
>
> External Email - Use Caution
>
> Please help!
>
> Repost with a better title.
>
> ___
> 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


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] dt_recon issue

2019-02-13 Thread Daniel Davidson Callow 
External Email - Use Caution

Thanks for pointing that out! Unfortunately after making the change

dt_recon --debug --i
/Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm --s
${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon


I still get the error.


./dt_recon.sh

mkdir: tutorial_data: File exists

mkdir: diffusion_recons: File exists

subj =  AES101 , cond =  Ex

mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: File exists

set echo = 1 ;

breaksw

breaksw

end

end

while ( $#argv != 0 )

while ( 6 != 0 )


set flag = $argv[1] ; shift ;

set flag = --i

shift


switch ( $flag )

switch ( --i )

if ( $#argv < 1 ) goto arg1err ;

if ( 5 < 1 ) goto arg1err

set InputVol = "$argv[1]" ; shift ;

set InputVol =
Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm

shift

if ( ! -e "$InputVol" ) then

if ( ! -e Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
) then

echo "ERROR: cannot find $InputVol"

echo ERROR: cannot find
Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm

ERROR: cannot find
Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm

goto error_exit ;

goto error_exit

uname -a | tee -a $LF

uname -a

tee -a

Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10
20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64

echo "" | & tee -a $LF

tee -a

echo


echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF

tee -a

echo dt_recon exited with ERRORS at `date`

date

dt_recon exited with ERRORS at Wed Feb 13 17:12:30 EST 2019

echo "" | & tee -a $LF

tee -a

echo


exit 1 ;

exit 1


Again the DICOM files are named image01.dcm through image65.dcm. These
were 64 gradient images acquired on a SIEMENS scanner with 1 bo image. I
assume there is an issue with how I am naming the input volumes for
dt_recon. Any advice on how I should structure this command would be
greatly appreciated!


Thanks,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
dcal...@umd.edu 
443-254-6298
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


On Wed, Feb 13, 2019 at 3:04 PM fsbuild  wrote:

> Hello Daniel.
>
> It looks like you need a slash in front of Volumes for the path after —I
> /Volumes
>
> - R.
>
> On Feb 13, 2019, at 14:44, Daniel Davidson Callow  wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am trying to run dt_recon on my dti data using the following script.
>
> dt_recon --debug --i
> Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm
> --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
>
>
> with the following error
>
> echo "ERROR: cannot find $InputVol"
> echo ERROR: cannot find
> Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> ERROR: cannot find
> Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> goto error_exit ;
>
> the DICOM files are named image01.dcm through image65.dcm
>
> These were 64 gradient images acquired on a SIEMENS scanner with 1 bo
> image. Any advice on how I should structure this command would be greatly
> appreciated!
>
> *Daniel Callow*
> *PhD Student, Neuroscience and Cognitive Science*
> Exercise for Brain Health Lab
> University of Maryland, College Park
> dcal...@umd.edu 
> 443-254-6298
>
> ___
> 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

Re: [Freesurfer] dt_recon issue

2019-02-13 Thread Greve, Douglas N.,Ph.D. 
can you send the command line without the variables?


On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
>
> External Email - Use Caution
>
> Thanks for pointing that out! Unfortunately after making the change
>
> dt_recon --debug --i 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm 
> --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
>
>
> I still get the error.
>
>
> ./dt_recon.sh
>
> mkdir: tutorial_data: File exists
>
> mkdir: diffusion_recons: File exists
>
> subj =AES101 , cond =Ex
>
> mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: File 
> exists
>
> set echo = 1 ;
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 6 != 0 )
>
>
> set flag = $argv[1] ; shift ;
>
> set flag = --i
>
> shift
>
>
> switch ( $flag )
>
> switch ( --i )
>
> if ( $#argv < 1 ) goto arg1err ;
>
> if ( 5 < 1 ) goto arg1err
>
> set InputVol = "$argv[1]" ; shift ;
>
> set InputVol = 
> Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
>
> shift
>
> if ( ! -e "$InputVol" ) then
>
> if ( ! -e 
> Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm ) then
>
> echo "ERROR: cannot find $InputVol"
>
> echo ERROR: cannot find 
> Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
>
> ERROR: cannot find 
> Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
>
> goto error_exit ;
>
> goto error_exit
>
> uname -a | tee -a $LF
>
> uname -a
>
> tee -a
>
> Darwin hlhp-105.umd.edu  16.7.0 Darwin Kernel 
> Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; 
> root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
>
> echo "" | & tee -a $LF
>
> tee -a
>
> echo
>
>
> echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF
>
> tee -a
>
> echo dt_recon exited with ERRORS at `date`
>
> date
>
> dt_recon exited with ERRORS at Wed Feb 13 17:12:30 EST 2019
>
> echo "" | & tee -a $LF
>
> tee -a
>
> echo
>
>
> exit 1 ;
>
> exit 1
>
>
> Again the DICOM files are named image01.dcm through 
> image65.dcm. These were 64 gradient images acquired on a SIEMENS 
> scanner with 1 bo image. I assume there is an issue with how I am 
> naming the input volumes for dt_recon. Any advice on how I should 
> structure this command would be greatly appreciated!
>
>
> Thanks,
>
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> dcal...@umd.edu 
> 443-254-6298
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> _ddcc2...@gmail.com _
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 3:04 PM fsbuild  > wrote:
>
> Hello Daniel.
>
> It looks like you need a slash in front of Volumes for the path
> after —I
> /Volumes
>
> - R.
>
>> On Feb 13, 2019, at 14:44, Daniel Davidson Callow
>> mailto:dcal...@umd.edu>> wrote:
>>
>> External Email - Use Caution
>>
>>
>> Hello,
>>
>> I am trying to run dt_recon on my dti data using the following
>> script.
>>
>> dt_recon --debug --i
>> Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm
>> --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
>>
>>
>> with the following error
>>
>> echo "ERROR: cannot find $InputVol"
>> echo ERROR: cannot find
>> Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
>> ERROR: cannot find
>> Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
>> goto error_exit ;
>>
>> the DICOM files are named image01.dcm through image65.dcm
>>
>> These were 64 gradient images acquired on a SIEMENS scanner with
>> 1 bo image. Any advice on how I should structure this command
>> would be greatly appreciated!
>>
>> *Daniel Callow*
>> /PhD Student, Neuroscience and Cognitive Science/
>> Exercise for Brain Health Lab
>> University of Maryland, College Park
>> dcal...@umd.edu 
>> 443-254-6298
>>
>> ___
>> 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


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] dt_recon issue

2019-02-13 Thread Daniel Callow 
External Email - Use Caution

Is this what you mean by no variables??

dt_recon --debug --i
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon

*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> can you send the command line without the variables?
>
>
> On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
> >
> > External Email - Use Caution
> >
> > Thanks for pointing that out! Unfortunately after making the change
> >
> > dt_recon --debug --i
> > /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm
> > --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
> >
> >
> > I still get the error.
> >
> >
> > ./dt_recon.sh
> >
> > mkdir: tutorial_data: File exists
> >
> > mkdir: diffusion_recons: File exists
> >
> > subj =AES101 , cond =Ex
> >
> > mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: File
> > exists
> >
> > set echo = 1 ;
> >
> > breaksw
> >
> > breaksw
> >
> > end
> >
> > end
> >
> > while ( $#argv != 0 )
> >
> > while ( 6 != 0 )
> >
> >
> > set flag = $argv[1] ; shift ;
> >
> > set flag = --i
> >
> > shift
> >
> >
> > switch ( $flag )
> >
> > switch ( --i )
> >
> > if ( $#argv < 1 ) goto arg1err ;
> >
> > if ( 5 < 1 ) goto arg1err
> >
> > set InputVol = "$argv[1]" ; shift ;
> >
> > set InputVol =
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > shift
> >
> > if ( ! -e "$InputVol" ) then
> >
> > if ( ! -e
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm ) then
> >
> > echo "ERROR: cannot find $InputVol"
> >
> > echo ERROR: cannot find
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > ERROR: cannot find
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > goto error_exit ;
> >
> > goto error_exit
> >
> > uname -a | tee -a $LF
> >
> > uname -a
> >
> > tee -a
> >
> > Darwin hlhp-105.umd.edu  16.7.0 Darwin Kernel
> > Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018;
> > root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
> >
> > echo "" | & tee -a $LF
> >
> > tee -a
> >
> > echo
> >
> >
> > echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF
> >
> > tee -a
> >
> > echo dt_recon exited with ERRORS at `date`
> >
> > date
> >
> > dt_recon exited with ERRORS at Wed Feb 13 17:12:30 EST 2019
> >
> > echo "" | & tee -a $LF
> >
> > tee -a
> >
> > echo
> >
> >
> > exit 1 ;
> >
> > exit 1
> >
> >
> > Again the DICOM files are named image01.dcm through
> > image65.dcm. These were 64 gradient images acquired on a SIEMENS
> > scanner with 1 bo image. I assume there is an issue with how I am
> > naming the input volumes for dt_recon. Any advice on how I should
> > structure this command would be greatly appreciated!
> >
> >
> > Thanks,
> >
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > dcal...@umd.edu 
> > 443-254-6298
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > _ddcc2...@gmail.com _
> > 443-254-6298
> >
> >
> > On Wed, Feb 13, 2019 at 3:04 PM fsbuild  > > wrote:
> >
> > Hello Daniel.
> >
> > It looks like you need a slash in front of Volumes for the path
> > after —I
> > /Volumes
> >
> > - R.
> >
> >> On Feb 13, 2019, at 14:44, Daniel Davidson Callow
> >> mailto:dcal...@umd.edu>> wrote:
> >>
> >> External Email - Use Caution
> >>
> >>
> >> Hello,
> >>
> >> I am trying to run dt_recon on my dti data using the following
> >> script.
> >>
> >> dt_recon --debug --i
> >>
>  Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm
> >> --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
> >>
> >>
> >> with the following error
> >>
> >> echo "ERROR: cannot find $InputVol"
> >> echo ERROR: cannot find
> >> Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >> ERROR: cannot find
> >> Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >> goto error_exit ;
> >>
> >> the DICOM files are named image01.dcm through image65.dcm
> >>
> >> These were 64 gradient images acquired on a SIEMENS scanner with
> >> 1 bo image. Any advice on how I should structure this command
> >> would be greatly appreciated!
> >>
> >> *Daniel Callow*
> >> /PhD Student, Neuroscience and Cognitive Science/
> >> Exercise for Brain Health Lab
> >> University of Maryland, College Park
> >> dcal...@umd.edu

Re: [Freesurfer] dt_recon issue

2019-02-13 Thread Daniel Callow 
External Email - Use Caution

The error output that accompanies the command.


administrator% dt_recon --debug --i
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon

set echo = 1 ;

breaksw

breaksw

end

end

while ( $#argv != 0 )

while ( 6 != 0 )


set flag = $argv[1] ; shift ;

set flag = --i

shift


switch ( $flag )

switch ( --i )

if ( $#argv < 1 ) goto arg1err ;

if ( 5 < 1 ) goto arg1err

set InputVol = "$argv[1]" ; shift ;

set InputVol =
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm

shift

if ( ! -e "$InputVol" ) then

if ( ! -e /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
) then

echo "ERROR: cannot find $InputVol"

echo ERROR: cannot find
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm

ERROR: cannot find
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm

goto error_exit ;

goto error_exit

uname -a | tee -a $LF

uname -a

tee -a

Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10
20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64

echo "" | & tee -a $LF

tee -a

echo


echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF

tee -a

echo dt_recon exited with ERRORS at `date`

date

dt_recon exited with ERRORS at Wed Feb 13 18:26:16 EST 2019

echo "" | & tee -a $LF

tee -a

echo


exit 1 ;
exit 1


*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow  wrote:

>
> Is this what you mean by no variables??
>
> dt_recon --debug --i
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
> AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
>
> *Daniel Callow*
> *PhD Student, Neuroscience and Cognitive Science*
> Exercise for Brain Health Lab
> University of Maryland, College Park
> *ddcc2...@gmail.com *
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> can you send the command line without the variables?
>>
>>
>> On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Thanks for pointing that out! Unfortunately after making the change
>> >
>> > dt_recon --debug --i
>> > /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm
>> > --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
>> >
>> >
>> > I still get the error.
>> >
>> >
>> > ./dt_recon.sh
>> >
>> > mkdir: tutorial_data: File exists
>> >
>> > mkdir: diffusion_recons: File exists
>> >
>> > subj =AES101 , cond =Ex
>> >
>> > mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: File
>> > exists
>> >
>> > set echo = 1 ;
>> >
>> > breaksw
>> >
>> > breaksw
>> >
>> > end
>> >
>> > end
>> >
>> > while ( $#argv != 0 )
>> >
>> > while ( 6 != 0 )
>> >
>> >
>> > set flag = $argv[1] ; shift ;
>> >
>> > set flag = --i
>> >
>> > shift
>> >
>> >
>> > switch ( $flag )
>> >
>> > switch ( --i )
>> >
>> > if ( $#argv < 1 ) goto arg1err ;
>> >
>> > if ( 5 < 1 ) goto arg1err
>> >
>> > set InputVol = "$argv[1]" ; shift ;
>> >
>> > set InputVol =
>> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
>> >
>> > shift
>> >
>> > if ( ! -e "$InputVol" ) then
>> >
>> > if ( ! -e
>> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm ) then
>> >
>> > echo "ERROR: cannot find $InputVol"
>> >
>> > echo ERROR: cannot find
>> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
>> >
>> > ERROR: cannot find
>> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
>> >
>> > goto error_exit ;
>> >
>> > goto error_exit
>> >
>> > uname -a | tee -a $LF
>> >
>> > uname -a
>> >
>> > tee -a
>> >
>> > Darwin hlhp-105.umd.edu  16.7.0 Darwin Kernel
>> > Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018;
>> > root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
>> >
>> > echo "" | & tee -a $LF
>> >
>> > tee -a
>> >
>> > echo
>> >
>> >
>> > echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF
>> >
>> > tee -a
>> >
>> > echo dt_recon exited with ERRORS at `date`
>> >
>> > date
>> >
>> > dt_recon exited with ERRORS at Wed Feb 13 17:12:30 EST 2019
>> >
>> > echo "" | & tee -a $LF
>> >
>> > tee -a
>> >
>> > echo
>> >
>> >
>> > exit 1 ;
>> >
>> > exit 1
>> >
>> >
>> > Again the DICOM files are named image01.dcm through
>> > image65.dcm. These were 64 gradient images acquired on a SIEMENS
>> > scanner with 1 bo image. I assume there is an issue with how I am
>> > naming the input volumes for dt_recon. Any advice on how I should
>> > structure this command would be greatly appreciated!
>> >
>> >
>> > Thanks,
>> >
>> > *Daniel Callow*
>> > /PhD Student, Neuroscience and Cognitive Science/
>> > Exercise for Brain Health Lab
>> > University of Maryland, College Park
>> > dcal...@umd.edu

Re: [Freesurfer] dt_recon issue

2019-02-13 Thread Greve, Douglas N.,Ph.D. 
Yes. Can you run it with --debug with the slash in front of "Volumes"?

On 2/13/19 6:25 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
>
> Is this what you mean by no variables??
>
> dt_recon --debug --i 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s 
> AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
>
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> _ddcc2...@gmail.com _
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> can you send the command line without the variables?
>
>
> On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
> >
> > External Email - Use Caution
> >
> > Thanks for pointing that out! Unfortunately after making the change
> >
> > dt_recon --debug --i
> >
> /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm
>
> > --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
> >
> >
> > I still get the error.
> >
> >
> > ./dt_recon.sh
> >
> > mkdir: tutorial_data: File exists
> >
> > mkdir: diffusion_recons: File exists
> >
> > subj =AES101 , cond =Ex
> >
> > mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex:
> File
> > exists
> >
> > set echo = 1 ;
> >
> > breaksw
> >
> > breaksw
> >
> > end
> >
> > end
> >
> > while ( $#argv != 0 )
> >
> > while ( 6 != 0 )
> >
> >
> > set flag = $argv[1] ; shift ;
> >
> > set flag = --i
> >
> > shift
> >
> >
> > switch ( $flag )
> >
> > switch ( --i )
> >
> > if ( $#argv < 1 ) goto arg1err ;
> >
> > if ( 5 < 1 ) goto arg1err
> >
> > set InputVol = "$argv[1]" ; shift ;
> >
> > set InputVol =
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > shift
> >
> > if ( ! -e "$InputVol" ) then
> >
> > if ( ! -e
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> ) then
> >
> > echo "ERROR: cannot find $InputVol"
> >
> > echo ERROR: cannot find
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > ERROR: cannot find
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > goto error_exit ;
> >
> > goto error_exit
> >
> > uname -a | tee -a $LF
> >
> > uname -a
> >
> > tee -a
> >
> > Darwin hlhp-105.umd.edu 
>  16.7.0 Darwin Kernel
> > Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018;
> > root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
> >
> > echo "" | & tee -a $LF
> >
> > tee -a
> >
> > echo
> >
> >
> > echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF
> >
> > tee -a
> >
> > echo dt_recon exited with ERRORS at `date`
> >
> > date
> >
> > dt_recon exited with ERRORS at Wed Feb 13 17:12:30 EST 2019
> >
> > echo "" | & tee -a $LF
> >
> > tee -a
> >
> > echo
> >
> >
> > exit 1 ;
> >
> > exit 1
> >
> >
> > Again the DICOM files are named image01.dcm through
> > image65.dcm. These were 64 gradient images acquired on a
> SIEMENS
> > scanner with 1 bo image. I assume there is an issue with how I am
> > naming the input volumes for dt_recon. Any advice on how I should
> > structure this command would be greatly appreciated!
> >
> >
> > Thanks,
> >
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > dcal...@umd.edu 
> >
> > 443-254-6298
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > _ddcc2...@gmail.com 
> >_
> > 443-254-6298
> >
> >
> > On Wed, Feb 13, 2019 at 3:04 PM fsbuild  
> > >> wrote:
> >
> >     Hello Daniel.
> >
> >     It looks like you need a slash in front of Volumes for the path
> >     after —I
> >     /Volumes
> >
> >     - R.
> >
> >>     On Feb 13, 2019, at 14:44, Daniel Davidson Callow
> >>     mailto:dcal...@umd.edu>
> >> wrote:
> >>
> >>     External Email - Use Caution
> >>
>

Re: [Freesurfer] dt_recon issue

2019-02-13 Thread Greve, Douglas N.,Ph.D. 
what happens when you run

ls -l /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm

On 2/13/19 6:27 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> The error output that accompanies the command.
>
>
> administrator% dt_recon --debug --i 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s 
> AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
>
> set echo = 1 ;
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 6 != 0 )
>
>
> set flag = $argv[1] ; shift ;
>
> set flag = --i
>
> shift
>
>
> switch ( $flag )
>
> switch ( --i )
>
> if ( $#argv < 1 ) goto arg1err ;
>
> if ( 5 < 1 ) goto arg1err
>
> set InputVol = "$argv[1]" ; shift ;
>
> set InputVol = 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
>
> shift
>
> if ( ! -e "$InputVol" ) then
>
> if ( ! -e 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm ) then
>
> echo "ERROR: cannot find $InputVol"
>
> echo ERROR: cannot find 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
>
> ERROR: cannot find 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
>
> goto error_exit ;
>
> goto error_exit
>
> uname -a | tee -a $LF
>
> uname -a
>
> tee -a
>
> Darwin hlhp-105.umd.edu  16.7.0 Darwin Kernel 
> Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; 
> root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
>
> echo "" | & tee -a $LF
>
> tee -a
>
> echo
>
>
> echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF
>
> tee -a
>
> echo dt_recon exited with ERRORS at `date`
>
> date
>
> dt_recon exited with ERRORS at Wed Feb 13 18:26:16 EST 2019
>
> echo "" | & tee -a $LF
>
> tee -a
>
> echo
>
>
> exit 1 ;
>
> exit 1
> *
> *
> *
> *
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> _ddcc2...@gmail.com _
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow  > wrote:
>
>
> Is this what you mean by no variables??
>
> dt_recon --debug --i
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
>
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> _ddcc2...@gmail.com _
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> can you send the command line without the variables?
>
>
> On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
> >
> > External Email - Use Caution
> >
> > Thanks for pointing that out! Unfortunately after making the
> change
> >
> > dt_recon --debug --i
> >
> 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm
>
> > --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
> >
> >
> > I still get the error.
> >
> >
> > ./dt_recon.sh
> >
> > mkdir: tutorial_data: File exists
> >
> > mkdir: diffusion_recons: File exists
> >
> > subj =AES101 , cond =Ex
> >
> > mkdir:
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: File
> > exists
> >
> > set echo = 1 ;
> >
> > breaksw
> >
> > breaksw
> >
> > end
> >
> > end
> >
> > while ( $#argv != 0 )
> >
> > while ( 6 != 0 )
> >
> >
> > set flag = $argv[1] ; shift ;
> >
> > set flag = --i
> >
> > shift
> >
> >
> > switch ( $flag )
> >
> > switch ( --i )
> >
> > if ( $#argv < 1 ) goto arg1err ;
> >
> > if ( 5 < 1 ) goto arg1err
> >
> > set InputVol = "$argv[1]" ; shift ;
> >
> > set InputVol =
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > shift
> >
> > if ( ! -e "$InputVol" ) then
> >
> > if ( ! -e
> >
> Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> ) then
> >
> > echo "ERROR: cannot find $InputVol"
> >
> > echo ERROR: cannot find
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > ERROR: cannot find
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > goto error_exit ;
> >
> > goto error_exit
> >
> > uname -a | tee -a $LF
> >
> > uname -a
> >
> > t

Re: [Freesurfer] dt_recon issue

2019-02-13 Thread Daniel Callow 
External Email - Use Caution

Here it is.


[hlhp-105:DANIEL/scripts/dti_freesurfer] administrator% dt_recon --debug
--i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon

set echo = 1 ;

breaksw

breaksw

end

end

while ( $#argv != 0 )

while ( 6 != 0 )


set flag = $argv[1] ; shift ;

set flag = --i

shift


switch ( $flag )

switch ( --i )

if ( $#argv < 1 ) goto arg1err ;

if ( 5 < 1 ) goto arg1err

set InputVol = "$argv[1]" ; shift ;

set InputVol =
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm

shift

if ( ! -e "$InputVol" ) then

if ( ! -e /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
) then

echo "ERROR: cannot find $InputVol"

echo ERROR: cannot find
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm

ERROR: cannot find
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm

goto error_exit ;

goto error_exit

uname -a | tee -a $LF

uname -a

tee -a

Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10
20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64

echo "" | & tee -a $LF

tee -a

echo


echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF

tee -a

echo dt_recon exited with ERRORS at `date`

date

dt_recon exited with ERRORS at Wed Feb 13 18:44:07 EST 2019

echo "" | & tee -a $LF

tee -a

echo


exit 1 ;

exit 1
[hlhp-105:DANIEL/scripts/dti_freesurfer] administrator% *aniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


On Wed, Feb 13, 2019 at 6:31 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> what happens when you run
>
> ls -l /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
>
> On 2/13/19 6:27 PM, Daniel Callow wrote:
> >
> > External Email - Use Caution
> >
> > The error output that accompanies the command.
> >
> >
> > administrator% dt_recon --debug --i
> > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
> > AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
> >
> > set echo = 1 ;
> >
> > breaksw
> >
> > breaksw
> >
> > end
> >
> > end
> >
> > while ( $#argv != 0 )
> >
> > while ( 6 != 0 )
> >
> >
> > set flag = $argv[1] ; shift ;
> >
> > set flag = --i
> >
> > shift
> >
> >
> > switch ( $flag )
> >
> > switch ( --i )
> >
> > if ( $#argv < 1 ) goto arg1err ;
> >
> > if ( 5 < 1 ) goto arg1err
> >
> > set InputVol = "$argv[1]" ; shift ;
> >
> > set InputVol =
> > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > shift
> >
> > if ( ! -e "$InputVol" ) then
> >
> > if ( ! -e
> > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm ) then
> >
> > echo "ERROR: cannot find $InputVol"
> >
> > echo ERROR: cannot find
> > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > ERROR: cannot find
> > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > goto error_exit ;
> >
> > goto error_exit
> >
> > uname -a | tee -a $LF
> >
> > uname -a
> >
> > tee -a
> >
> > Darwin hlhp-105.umd.edu  16.7.0 Darwin Kernel
> > Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018;
> > root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
> >
> > echo "" | & tee -a $LF
> >
> > tee -a
> >
> > echo
> >
> >
> > echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF
> >
> > tee -a
> >
> > echo dt_recon exited with ERRORS at `date`
> >
> > date
> >
> > dt_recon exited with ERRORS at Wed Feb 13 18:26:16 EST 2019
> >
> > echo "" | & tee -a $LF
> >
> > tee -a
> >
> > echo
> >
> >
> > exit 1 ;
> >
> > exit 1
> > *
> > *
> > *
> > *
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > _ddcc2...@gmail.com _
> > 443-254-6298
> >
> >
> > On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow  > > wrote:
> >
> >
> > Is this what you mean by no variables??
> >
> > dt_recon --debug --i
> > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> > --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
> >
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > _ddcc2...@gmail.com _
> > 443-254-6298
> >
> >
> > On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > can you send the command line without the variables?
> >
> >
> > On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Thanks for pointing that out! Unfortunately after making the
> > change
> > >
> > > dt_recon --debug -