date:20190917

Re: [Freesurfer] mri_convert for Philips dicoms

2019-09-17 Thread Greve, Douglas N.,Ph.D.

Try dcm2niix (not part of FS, you'll have to download and install)

On 9/17/19 3:10 PM, Mun, Anna wrote:
> Dear FreeSurfer team,
>
> I am working with data sent to us from other research site. They use 
> Philips scanner and I can not run mri_convert on the dicoms. Is there 
> other way to mri_convert and reconstruct Philips dicoms.
>
> error log is:
>
> WARNING: tag SeriesNumber not found
> WARNING: tag image orientation not found
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 7
>
> break DICOMRead.c:5228
> Ref Series No = 0
> ERROR: bits = 0 not supported.
> Send email to freesurfer@nmr.mgh.harvard.edu
>
>
> Thank you in advance!
>
> Best,
> Anna
>
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[Freesurfer] mri_convert for Philips dicoms

2019-09-17 Thread Mun, Anna

Dear FreeSurfer team,

I am working with data sent to us from other research site. They use Philips 
scanner and I can not run mri_convert on the dicoms. Is there other way to 
mri_convert and reconstruct Philips dicoms.

error log is:
WARNING: tag SeriesNumber not found
WARNING: tag image orientation not found
ERROR: GetDICOMInfo(): dcmGetDWIParams() 7

break DICOMRead.c:5228
Ref Series No = 0
ERROR: bits = 0 not supported.
Send email to freesurfer@nmr.mgh.harvard.edu

Thank you in advance!

Best,
Anna
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Re: [Freesurfer] mris_sphere question

2019-09-17 Thread Lauricella, Michael

External Email - Use Caution

Hi Bruce,

Sometimes it completes. About 20% of the time I get this problem for anyone. I 
don't think it's specific to a certain subject.

Best,
Michael

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bruce Fischl
Sent: Tuesday, September 17, 2019 10:53 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mris_sphere question

hmmm, if you rerun does it complete?
On Tue, 17 Sep 2019, Lauricella,
Michael wrote:

>External Email - Use Caution
>
> Hi Bruce,
>
> No error message, just runs forever and eventually breaks my SSH connection 
> to the cloud I'm running it on. But when I do "-make all" afterwards it 
> starts a few steps before mris_spheres, so I have to redo and often crashes 
> again.
>
> Thank you for your help!
>
> Best,
> Michael
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Bruce Fischl
> Sent: Tuesday, September 17, 2019 10:16 AM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] mris_sphere question
>
> Hi Michael
>
> I think that is the last message that mris_sphere prints so I believe it has 
> finished. Does it exit with an error message or just keep running forever?
> Bruce
>
>
> On Tue, 17 Sep 2019, Lauricella, Michael wrote:
>
>>
>> External Email - Use Caution
>>
>> Dear Freesurfer Experts,
>>
>>  
>>
>> I’m fairly new to freesurfer, but have a set-up in which I have been 
>> able to run many successful recon-all runs. One problem that I have 
>> sometimes, maybe about 20% of the time, is that the run will freeze and 
>> crash at this step:
>>
>>  
>>
>> mris_sphere -rusage
>> /mnt/freesurfer_subjs/SUBJECT_ID/touch/rusage.mris_sphere.lh.dat 
>> -seed
>> 1234 ../surf/lh.inflated ../surf/lh.sphere
>>
>>  
>>
>> here’s the end of the logfile:
>>
>>  
>>
>> “== Number of threads available to mris_sphere for OpenMP = 2 ==
>>
>> scaling brain by 0.287...
>>
>> MRISunfold() max_passes = 1 ---
>>
>> tol=5.0e-01, sigma=0.0, host=mgt-i, nav=1024, nbrs=2, l_area=1.000,
>> l_dist=1.000
>>
>> using quadratic fit line minimization
>>
>> complete_dist_mat 0
>>
>> rms 0
>>
>> smooth_averages 0
>>
>> remove_neg 0
>>
>> ico_order 0
>>
>> which_surface 0
>>
>> target_radius 0.00
>>
>> nfields 0
>>
>> scale 1.00
>>
>> desired_rms_height -1.00
>>
>> momentum 0.90
>>
>> nbhd_size 7
>>
>> max_nbrs 8
>>
>> niterations 25
>>
>> nsurfaces 0
>>
>> SURFACES 3
>>
>> flags 0 (0)
>>
>> use curv 0
>>
>> no sulc 0
>>
>> no rigid align 0
>>
>> mris->nsize 2
>>
>> mris->hemisphere 0
>>
>> randomSeed 1234
>>
>>  
>>
>> 
>>
>>   mrisRemoveNegativeArea()
>>
>> pass 1: epoch 1 of 3 starting distance error %21.21
>>
>> pass 1: epoch 2 of 3 starting distance error %20.95
>>
>> unfolding complete - removing small folds...
>>
>> starting distance error %20.57
>>
>> removing remaining folds...
>>
>> final distance error %20.59
>>
>> MRISunfold() return, current seed 1234”
>>
>>  
>>
>>  
>>
>> Does anyone have any ideas why this might be happening? Maybe this is 
>> a computationally intensive step? If I run a few recon-alls 
>> concurrently it almost always crashes at this step.
>>
>>  
>>
>> The command I run is: recon-all  -all -openmp 2 -qcache 
>> -nuintensitycor-3T -s SUBJECT_ID -sd /mnt/freesurfer_subjs/
>>
>>  
>>
>> Thank you so much for your help!
>>
>>  
>>
>> Best,
>>
>> Michael
>>
>>
>>
>
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>
>

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Re: [Freesurfer] Recon-all on a cluster error

2019-09-17 Thread Lauricella, Michael

External Email - Use Caution

Hi Douglas,

Yes it does fine. On the cluster, this same error happens for all subjects.

Thank you for your help!

Best,
Michael

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Greve, Douglas N.,Ph.D.
Sent: Tuesday, September 17, 2019 10:50 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all on a cluster error

Does it run properly off the cluster for this data set?

On 9/17/19 1:45 PM, Lauricella, Michael wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Experts,
>
> I have a an error when running recon-all on a computing cluster. I've 
> checked the environment and so have some of my more knowledgeable 
> colleagues but we can't see anything wrong with the environment. I was 
> wondering if anyone else has experienced difficulties like the one 
> below when trying to run recon-all on a computing cluster and might 
> have some advice. Error of my run is below and the full log file is 
> attached. Thank you in advance for your help!
>
> "Iteration 1 Wed Aug  7 13:53:08 PDT 2019
>
> nu_correct -clobber ./tmp.mri_nu_correct.mni.18980/nu0.mnc
> ./tmp.mri_nu_correct.mni.18980/nu1.mnc -tmpdir 
> ./tmp.mri_nu_correct.mni.18980/0/ -iterations 1000 -distance 50
>
> [mlauricella@qb3-id115:/mnt/freesurfer_subjs/SUBJECT_ID/mri/]
> [2019-08-07 13:53:08] running:
>
> /mnt/neuroimaging/FreeSurfer/V6.0.0/mni/bin/nu_estimate_np_and_em
> -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 
> -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute 
> -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.18980/0/ 
> ./tmp.mri_nu_correct.mni.18980/nu0.mnc
> ./tmp.mri_nu_correct.mni.18980/nu1.imp
>
> Assertion failed at line 742 in file templates/CachedArray.cc
>
> nu_estimate_np_and_em: crashed while running volume_stats (termination
> status=256)
>
> nu_correct: crashed while running nu_estimate_np_and_em (termination
> status=256)
>
> ERROR: nu_correct
>
> Linux qb3-id115 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 
> UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s SUBJECT_ID exited with ERRORS at Wed Aug  7 13:53:09 PDT 
> 2019
>
> To report a problem, see
> https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.har
> vard.edu_fswiki_BugReporting&d=DwIF-g&c=iORugZls2LlYyCAZRB3XLg&r=LfvXl
> A0kIui4WmLLCYdWlZdLsYFY_HKuPRMZoERJi_o&m=lOOasQKo-5smKR_WagoWBOFxCVZA3
> 8xYpWHKJOqIVGU&s=hZ8c1_TEb9oDCsFUiTaioaVn7pRCbIkq9BrlyHA-jps&e=
>   >"
>
> Best,
>
> Michael
>
>
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> FxCVZA38xYpWHKJOqIVGU&s=RJ3pNp6iSv3KoImUDqKyKKlfJax1r3VtjF-gcSU_E60&e=


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Re: [Freesurfer] mris_sphere question

2019-09-17 Thread Bruce Fischl


hmmm, if you rerun does it complete?
On Tue, 17 Sep 2019, Lauricella, 
Michael wrote:



   External Email - Use Caution

Hi Bruce,

No error message, just runs forever and eventually breaks my SSH connection to the cloud 
I'm running it on. But when I do "-make all" afterwards it starts a few steps 
before mris_spheres, so I have to redo and often crashes again.

Thank you for your help!

Best,
Michael

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bruce Fischl
Sent: Tuesday, September 17, 2019 10:16 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mris_sphere question

Hi Michael

I think that is the last message that mris_sphere prints so I believe it has 
finished. Does it exit with an error message or just keep running forever?
Bruce


On Tue, 17 Sep 2019, Lauricella, Michael wrote:



External Email - Use Caution

Dear Freesurfer Experts,

 

I’m fairly new to freesurfer, but have a set-up in which I have been
able to run many successful recon-all runs. One problem that I have
sometimes, maybe about 20% of the time, is that the run will freeze and crash 
at this step:

 

mris_sphere -rusage
/mnt/freesurfer_subjs/SUBJECT_ID/touch/rusage.mris_sphere.lh.dat -seed
1234 ../surf/lh.inflated ../surf/lh.sphere

 

here’s the end of the logfile:

 

“== Number of threads available to mris_sphere for OpenMP = 2 ==

scaling brain by 0.287...

MRISunfold() max_passes = 1 ---

tol=5.0e-01, sigma=0.0, host=mgt-i, nav=1024, nbrs=2, l_area=1.000,
l_dist=1.000

using quadratic fit line minimization

complete_dist_mat 0

rms 0

smooth_averages 0

remove_neg 0

ico_order 0

which_surface 0

target_radius 0.00

nfields 0

scale 1.00

desired_rms_height -1.00

momentum 0.90

nbhd_size 7

max_nbrs 8

niterations 25

nsurfaces 0

SURFACES 3

flags 0 (0)

use curv 0

no sulc 0

no rigid align 0

mris->nsize 2

mris->hemisphere 0

randomSeed 1234

 



  mrisRemoveNegativeArea()

pass 1: epoch 1 of 3 starting distance error %21.21

pass 1: epoch 2 of 3 starting distance error %20.95

unfolding complete - removing small folds...

starting distance error %20.57

removing remaining folds...

final distance error %20.59

MRISunfold() return, current seed 1234”

 

 

Does anyone have any ideas why this might be happening? Maybe this is
a computationally intensive step? If I run a few recon-alls
concurrently it almost always crashes at this step.

 

The command I run is: recon-all  -all -openmp 2 -qcache
-nuintensitycor-3T -s SUBJECT_ID -sd /mnt/freesurfer_subjs/

 

Thank you so much for your help!

 

Best,

Michael





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Re: [Freesurfer] PET input file for mri_gtmpvc

2019-09-17 Thread Greve, Douglas N.,Ph.D.

I would use unstripped, but it probably won't make much difference. Just 
make sure that the registration is good.

On 9/17/19 1:48 PM, Jane Tseng wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I was wondering if there is any recommendation on the PET input file 
> for partial volume correction using mri_gtmpvc? Should I use a 
> non-skullstripped SUV or a skullstripped SUV? If a skullstripped SUV 
> can be used, would a tight (just aparc+aseg binarized) or a lenient 
> (e.g. aparc+aseg binarized and dilated by 2mm) mask be better? I am 
> interested in using the GTM regional values. Thank you for your help!
>
> Best wishes,
> Jane
>
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Re: [Freesurfer] Recon-all on a cluster error

2019-09-17 Thread Greve, Douglas N.,Ph.D.

Does it run properly off the cluster for this data set?

On 9/17/19 1:45 PM, Lauricella, Michael wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Experts,
>
> I have a an error when running recon-all on a computing cluster. I’ve 
> checked the environment and so have some of my more knowledgeable 
> colleagues but we can’t see anything wrong with the environment. I was 
> wondering if anyone else has experienced difficulties like the one 
> below when trying to run recon-all on a computing cluster and might 
> have some advice. Error of my run is below and the full log file is 
> attached. Thank you in advance for your help!
>
> “Iteration 1 Wed Aug  7 13:53:08 PDT 2019
>
> nu_correct -clobber ./tmp.mri_nu_correct.mni.18980/nu0.mnc 
> ./tmp.mri_nu_correct.mni.18980/nu1.mnc -tmpdir 
> ./tmp.mri_nu_correct.mni.18980/0/ -iterations 1000 -distance 50
>
> [mlauricella@qb3-id115:/mnt/freesurfer_subjs/SUBJECT_ID/mri/] 
> [2019-08-07 13:53:08] running:
>
> /mnt/neuroimaging/FreeSurfer/V6.0.0/mni/bin/nu_estimate_np_and_em 
> -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 
> -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute 
> -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.18980/0/ 
> ./tmp.mri_nu_correct.mni.18980/nu0.mnc 
> ./tmp.mri_nu_correct.mni.18980/nu1.imp
>
> Assertion failed at line 742 in file templates/CachedArray.cc
>
> nu_estimate_np_and_em: crashed while running volume_stats (termination 
> status=256)
>
> nu_correct: crashed while running nu_estimate_np_and_em (termination 
> status=256)
>
> ERROR: nu_correct
>
> Linux qb3-id115 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 
> UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s SUBJECT_ID exited with ERRORS at Wed Aug  7 13:53:09 PDT 2019
>
> To report a problem, see 
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
> ”
>
> Best,
>
> Michael
>
>
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[Freesurfer] PET input file for mri_gtmpvc

2019-09-17 Thread Jane Tseng

External Email - Use Caution

Dear Freesurfer experts,

I was wondering if there is any recommendation on the PET input file for
partial volume correction using mri_gtmpvc? Should I use a
non-skullstripped SUV or a skullstripped SUV? If a skullstripped SUV can be
used, would a tight (just aparc+aseg binarized) or a lenient (e.g.
aparc+aseg binarized and dilated by 2mm) mask be better? I am interested in
using the GTM regional values. Thank you for your help!

Best wishes,
Jane
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[Freesurfer] Recon-all on a cluster error

2019-09-17 Thread Lauricella, Michael

External Email - Use Caution

Dear Freesurfer Experts,

I have a an error when running recon-all on a computing cluster. I've checked 
the environment and so have some of my more knowledgeable colleagues but we 
can't see anything wrong with the environment. I was wondering if anyone else 
has experienced difficulties like the one below when trying to run recon-all on 
a computing cluster and might have some advice. Error of my run is below and 
the full log file is attached. Thank you in advance for your help!

"Iteration 1 Wed Aug  7 13:53:08 PDT 2019
nu_correct -clobber ./tmp.mri_nu_correct.mni.18980/nu0.mnc 
./tmp.mri_nu_correct.mni.18980/nu1.mnc -tmpdir 
./tmp.mri_nu_correct.mni.18980/0/ -iterations 1000 -distance 50
[mlauricella@qb3-id115:/mnt/freesurfer_subjs/SUBJECT_ID/mri/] [2019-08-07 
13:53:08] running:
  /mnt/neuroimaging/FreeSurfer/V6.0.0/mni/bin/nu_estimate_np_and_em -parzen 
-log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask 
-nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp 
-tmpdir ./tmp.mri_nu_correct.mni.18980/0/ 
./tmp.mri_nu_correct.mni.18980/nu0.mnc ./tmp.mri_nu_correct.mni.18980/nu1.imp

Assertion failed at line 742 in file templates/CachedArray.cc
nu_estimate_np_and_em: crashed while running volume_stats (termination 
status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)
ERROR: nu_correct
Linux qb3-id115 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 2019 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s SUBJECT_ID exited with ERRORS at Wed Aug  7 13:53:09 PDT 2019

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting";

Best,
Michael


cluster_error_recon-all.log
Description: cluster_error_recon-all.log
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Re: [Freesurfer] mris_sphere question

2019-09-17 Thread Lauricella, Michael

External Email - Use Caution

Hi Bruce,

No error message, just runs forever and eventually breaks my SSH connection to 
the cloud I'm running it on. But when I do "-make all" afterwards it starts a 
few steps before mris_spheres, so I have to redo and often crashes again.

Thank you for your help!

Best,
Michael

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bruce Fischl
Sent: Tuesday, September 17, 2019 10:16 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mris_sphere question

Hi Michael

I think that is the last message that mris_sphere prints so I believe it has 
finished. Does it exit with an error message or just keep running forever?
Bruce


On Tue, 17 Sep 2019, Lauricella, Michael wrote:

> 
> External Email - Use Caution
> 
> Dear Freesurfer Experts,
> 
>  
> 
> I’m fairly new to freesurfer, but have a set-up in which I have been 
> able to run many successful recon-all runs. One problem that I have 
> sometimes, maybe about 20% of the time, is that the run will freeze and crash 
> at this step:
> 
>  
> 
> mris_sphere -rusage
> /mnt/freesurfer_subjs/SUBJECT_ID/touch/rusage.mris_sphere.lh.dat -seed 
> 1234 ../surf/lh.inflated ../surf/lh.sphere
> 
>  
> 
> here’s the end of the logfile:
> 
>  
> 
> “== Number of threads available to mris_sphere for OpenMP = 2 ==
> 
> scaling brain by 0.287...
> 
> MRISunfold() max_passes = 1 ---
> 
> tol=5.0e-01, sigma=0.0, host=mgt-i, nav=1024, nbrs=2, l_area=1.000,
> l_dist=1.000
> 
> using quadratic fit line minimization
> 
> complete_dist_mat 0
> 
> rms 0
> 
> smooth_averages 0
> 
> remove_neg 0
> 
> ico_order 0
> 
> which_surface 0
> 
> target_radius 0.00
> 
> nfields 0
> 
> scale 1.00
> 
> desired_rms_height -1.00
> 
> momentum 0.90
> 
> nbhd_size 7
> 
> max_nbrs 8
> 
> niterations 25
> 
> nsurfaces 0
> 
> SURFACES 3
> 
> flags 0 (0)
> 
> use curv 0
> 
> no sulc 0
> 
> no rigid align 0
> 
> mris->nsize 2
> 
> mris->hemisphere 0
> 
> randomSeed 1234
> 
>  
> 
> 
> 
>   mrisRemoveNegativeArea()
> 
> pass 1: epoch 1 of 3 starting distance error %21.21
> 
> pass 1: epoch 2 of 3 starting distance error %20.95
> 
> unfolding complete - removing small folds...
> 
> starting distance error %20.57
> 
> removing remaining folds...
> 
> final distance error %20.59
> 
> MRISunfold() return, current seed 1234”
> 
>  
> 
>  
> 
> Does anyone have any ideas why this might be happening? Maybe this is 
> a computationally intensive step? If I run a few recon-alls 
> concurrently it almost always crashes at this step.
> 
>  
> 
> The command I run is: recon-all  -all -openmp 2 -qcache 
> -nuintensitycor-3T -s SUBJECT_ID -sd /mnt/freesurfer_subjs/
> 
>  
> 
> Thank you so much for your help!
> 
>  
> 
> Best,
> 
> Michael
> 
> 
>

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Re: [Freesurfer] mris_sphere question

2019-09-17 Thread Bruce Fischl


Hi Michael

I think that is the last message that mris_sphere prints so I believe it 
has finished. Does it exit with an error message or just keep running 
forever?

Bruce


On Tue, 17 Sep 2019, Lauricella, Michael wrote:



External Email - Use Caution

Dear Freesurfer Experts,

 

I’m fairly new to freesurfer, but have a set-up in which I have been able to
run many successful recon-all runs. One problem that I have sometimes, maybe
about 20% of the time, is that the run will freeze and crash at this step:

 

mris_sphere -rusage
/mnt/freesurfer_subjs/SUBJECT_ID/touch/rusage.mris_sphere.lh.dat -seed 1234
../surf/lh.inflated ../surf/lh.sphere

 

here’s the end of the logfile:

 

“== Number of threads available to mris_sphere for OpenMP = 2 ==

scaling brain by 0.287...

MRISunfold() max_passes = 1 ---

tol=5.0e-01, sigma=0.0, host=mgt-i, nav=1024, nbrs=2, l_area=1.000,
l_dist=1.000

using quadratic fit line minimization

complete_dist_mat 0

rms 0

smooth_averages 0

remove_neg 0

ico_order 0

which_surface 0

target_radius 0.00

nfields 0

scale 1.00

desired_rms_height -1.00

momentum 0.90

nbhd_size 7

max_nbrs 8

niterations 25

nsurfaces 0

SURFACES 3

flags 0 (0)

use curv 0

no sulc 0

no rigid align 0

mris->nsize 2

mris->hemisphere 0

randomSeed 1234

 



  mrisRemoveNegativeArea()

pass 1: epoch 1 of 3 starting distance error %21.21

pass 1: epoch 2 of 3 starting distance error %20.95

unfolding complete - removing small folds...

starting distance error %20.57

removing remaining folds...

final distance error %20.59

MRISunfold() return, current seed 1234”

 

 

Does anyone have any ideas why this might be happening? Maybe this is a
computationally intensive step? If I run a few recon-alls concurrently it
almost always crashes at this step.

 

The command I run is: recon-all  -all -openmp 2 -qcache -nuintensitycor-3T
-s SUBJECT_ID -sd /mnt/freesurfer_subjs/

 

Thank you so much for your help!

 

Best,

Michael


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[Freesurfer] mris_sphere question

2019-09-17 Thread Lauricella, Michael

External Email - Use Caution

Dear Freesurfer Experts,

I'm fairly new to freesurfer, but have a set-up in which I have been able to 
run many successful recon-all runs. One problem that I have sometimes, maybe 
about 20% of the time, is that the run will freeze and crash at this step:

mris_sphere -rusage 
/mnt/freesurfer_subjs/SUBJECT_ID/touch/rusage.mris_sphere.lh.dat -seed 1234 
../surf/lh.inflated ../surf/lh.sphere

here's the end of the logfile:

"== Number of threads available to mris_sphere for OpenMP = 2 ==
scaling brain by 0.287...
MRISunfold() max_passes = 1 ---
tol=5.0e-01, sigma=0.0, host=mgt-i, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.00
nfields 0
scale 1.00
desired_rms_height -1.00
momentum 0.90
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234


  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %21.21
pass 1: epoch 2 of 3 starting distance error %20.95
unfolding complete - removing small folds...
starting distance error %20.57
removing remaining folds...
final distance error %20.59
MRISunfold() return, current seed 1234"


Does anyone have any ideas why this might be happening? Maybe this is a 
computationally intensive step? If I run a few recon-alls concurrently it 
almost always crashes at this step.

The command I run is: recon-all  -all -openmp 2 -qcache -nuintensitycor-3T -s 
SUBJECT_ID -sd /mnt/freesurfer_subjs/

Thank you so much for your help!

Best,
Michael
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Re: [Freesurfer] Freeview error

2019-09-17 Thread Ruopeng Wang


Is your work disk full?

On 9/17/19 10:22 AM, Miguel Ángel Rivas Fernández wrote:


External Email - Use Caution


I tried in the command window where I started freeview but nothing 
happened. This is the output


miguel@miguel-VirtualBox:~$ ls 
/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz



El mar., 17 sept. 2019 a las 1:56, Ruopeng Wang 
(mailto:rpw...@nmr.mgh.harvard.edu>>) 
escribió:


Can you run the command in the command window that you start
freeview?

Ruopeng


On Sep 16, 2019, at 5:11 PM, Miguel Ángel Rivas Fernández
mailto:miguelrivasf...@gmail.com>> wrote:

External Email - Use Caution


Dear Ruopeng,

I put that command in the freeview command console and this is
the output

[FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
This is not a shell. Only freeview commands are supported. Type
'-h' for all the available commands.
 Best regards,

El lun., 16 sept. 2019 a las 22:58, Ruopeng Wang
(mailto:rpw...@nmr.mgh.harvard.edu>>) escribió:

If you run:

ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

What does it show?

Ruopeng

On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:


External Email - Use Caution

Dear Freesurfer devs,

I tried to open the brainmask.mgz file in freeview but I
obtained this error:


mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz,
-1): could not open file
MRIread failed: Unable to read from
/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz,
-1): could not open file

Any suggestion about what could be the problem?, maybe the
write permissons of the freesurfer folder?

I am using the
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
version that is installed in a Ubuntu 18.04 virtual machine.
It is very strange because few weeks ago everything it was
working correctly.

Thanks in advance.


Best regards,
-- 
*Miguel Ángel Rivas Fernández*


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-- 
*Miguel Ángel Rivas Fernández*

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--
*Miguel Ángel Rivas Fernández*

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Re: [Freesurfer] Freeview error

2019-09-17 Thread Miguel Ángel Rivas Fernández

External Email - Use Caution

I tried in the command window where I started freeview but nothing
happened. This is the output

miguel@miguel-VirtualBox:~$ ls
/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz



El mar., 17 sept. 2019 a las 1:56, Ruopeng Wang ()
escribió:

> Can you run the command in the command window that you start freeview?
>
> Ruopeng
>
> On Sep 16, 2019, at 5:11 PM, Miguel Ángel Rivas Fernández <
> miguelrivasf...@gmail.com> wrote:
>
> External Email - Use Caution
>
> Dear Ruopeng,
>
> I put that command in the freeview command console and this is the output
>
> [FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
> This is not a shell. Only freeview commands are supported. Type '-h' for
> all the available commands.
>
>
>
>  Best regards,
>
> El lun., 16 sept. 2019 a las 22:58, Ruopeng Wang (<
> rpw...@nmr.mgh.harvard.edu>) escribió:
>
>> If you run:
>>
>> ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
>>
>> What does it show?
>>
>> Ruopeng
>> On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:
>>
>> External Email - Use Caution
>> Dear Freesurfer devs,
>>
>> I tried to open the brainmask.mgz file in freeview but I obtained this
>> error:
>>
>>
>> mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could
>> not open file
>> MRIread failed: Unable to read from
>> /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
>> mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could
>> not open file
>>
>> Any suggestion about what could be the problem?, maybe the write
>> permissons of the freesurfer folder?
>>
>> I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>> version that is installed in a Ubuntu 18.04 virtual machine. It is very
>> strange because few weeks ago everything it was working correctly.
>>
>> Thanks in advance.
>>
>>
>> Best regards,
>> --
>> *Miguel Ángel Rivas Fernández*
>>
>> ___
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>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
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>
>
>
> --
> *Miguel Ángel Rivas Fernández*
> ___
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-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] Freeview error

Re: [Freesurfer] Freeview error

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