Re: [Freesurfer] QAtools for Freesurfer version6?

[Dicamillo, Robert]

Hello Seonjoo,

Could you send along a link to what you ran/tweaked for “QA tools” on 
freesurfer ?

- rob

On Oct 4, 2018, at 8:31 PM, Lee, Seonjoo 
mailto:sl3...@cumc.columbia.edu>> wrote:


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I tired to use QA tools for freesurfer version6, but did not have much success. 
Is anyone know how to tweak QA tools for freesurfer version 6?
Thank you.
-Seonjoo Lee
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[Freesurfer] QAtools for Freesurfer version6?

[Lee, Seonjoo]

External Email - Use Caution

I tired to use QA tools for freesurfer version6, but did not have much success. 
Is anyone know how to tweak QA tools for freesurfer version 6?
Thank you.
-Seonjoo Lee
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Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks!
Did you check whether the T2 and the T1 were correctly registered? You can 
check out the animated gif under mri/transforms in the subject’s directory.
Cheers,
/E

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Pradeep 

Reply-To: Freesurfer support list 
Date: Thursday, 4 October 2018 at 19:21
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal segmentation with an additional scan 
ERROR kvlGEMSMatlab


External Email - Use Caution
I have tried this for two subjects and got the same error.

Thanks,
Pradeep

On Thu, Oct 4, 2018 at 11:14 AM Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution
Dear Pradeep,
Did you get this error on several subjects, or only one?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Pradeep mailto:tprad...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 4 October 2018 at 19:12
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Hippocampal segmentation with an additional scan ERROR 
kvlGEMSMatlab


External Email - Use Caution
Hello,

I am trying to run the hippocampal segmentation with an additional Hi-res scan 
using the following command

recon-all -s  -hippocampal-subfields-T2   
and got the following error


Error using kvlGEMSMatlab
/autofs/cluster/koen/eugenio/InsightToolkit-4.9.1/Modules/Core/Common/include/itkImageConstIterator.h:211:
itk::ERROR: Region ImageRegion (0x7f67011c5dd0)
  Dimension: 3
  Index: [0, 845, 0]
  Size: [105, 18446744073709550952, 20]
 is outside of buffered region ImageRegion (0x7f6573ca8bb8)
  Dimension: 3
  Index: [0, 0, 0]
  Size: [526, 181, 526]

Error in kvlReadCroppedImage (line 11)
Error in segmentSubjectT2_autoEstimateAlveusML (line 838)
Started at Thu Oct 4 09:35:38 MST 2018
Ended   at Thu Oct 4 09:57:35 MST 2018
#@#%# recon-all-run-time-hours 0.366
recon-all -s subject_id finished without error at Thu Oct  4 09:57:36 MST 2018
done


I came across a similar error in the forums and using the most recent version 
seem to have worked for some, but it did not help in my case.

Freesurfer version I am using
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a

with matlab run time from 2012b as suggested
I have also tried to use 2014b runtime which exited right away.

Thank you for your help,
Pradeep





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Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

[Pradeep]

External Email - Use Caution

I have tried this for two subjects and got the same error.

Thanks,
Pradeep

On Thu, Oct 4, 2018 at 11:14 AM Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> External Email - Use Caution
>
> Dear Pradeep,
>
> Did you get this error on several subjects, or only one?
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of Pradeep <
> tprad...@gmail.com>
> *Reply-To: *Freesurfer support list 
> *Date: *Thursday, 4 October 2018 at 19:12
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] Hippocampal segmentation with an additional scan
> ERROR kvlGEMSMatlab
>
>
>
> *External Email - Use Caution*
>
> Hello,
>
>
>
> I am trying to run the hippocampal segmentation with an additional Hi-res
> scan using the following command
>
> recon-all -s  -hippocampal-subfields-T2  additional scan>  
>
> and got the following error
>
>
>
>
>
> Error using kvlGEMSMatlab
>
>
> /autofs/cluster/koen/eugenio/InsightToolkit-4.9.1/Modules/Core/Common/include/itkImageConstIterator.h:211:
>
> itk::ERROR: Region ImageRegion (0x7f67011c5dd0)
>
>   Dimension: 3
>
>   Index: [0, 845, 0]
>
>   Size: [105, 18446744073709550952, 20]
>
>  is outside of buffered region ImageRegion (0x7f6573ca8bb8)
>
>   Dimension: 3
>
>   Index: [0, 0, 0]
>
>   Size: [526, 181, 526]
>
>
>
> Error in kvlReadCroppedImage (line 11)
>
> Error in segmentSubjectT2_autoEstimateAlveusML (line 838)
>
> Started at Thu Oct 4 09:35:38 MST 2018
>
> Ended   at Thu Oct 4 09:57:35 MST 2018
>
> #@#%# recon-all-run-time-hours 0.366
>
> recon-all -s subject_id finished without error at Thu Oct  4 09:57:36 MST
> 2018
>
> done
>
>
>
>
>
> I came across a similar error in the forums and using the most recent
> version seem to have worked for some, but it did not help in my case.
>
>
>
> Freesurfer version I am using
>
> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
>
> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
>
>
>
> with matlab run time from 2012b as suggested
>
> I have also tried to use 2014b runtime which exited right away.
>
>
>
> Thank you for your help,
>
> Pradeep
>
>
>
>
>
>
>
>
>
>
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Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Pradeep,
Did you get this error on several subjects, or only one?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Pradeep 

Reply-To: Freesurfer support list 
Date: Thursday, 4 October 2018 at 19:12
To: Freesurfer support list 
Subject: [Freesurfer] Hippocampal segmentation with an additional scan ERROR 
kvlGEMSMatlab


External Email - Use Caution
Hello,

I am trying to run the hippocampal segmentation with an additional Hi-res scan 
using the following command

recon-all -s  -hippocampal-subfields-T2   
and got the following error


Error using kvlGEMSMatlab
/autofs/cluster/koen/eugenio/InsightToolkit-4.9.1/Modules/Core/Common/include/itkImageConstIterator.h:211:
itk::ERROR: Region ImageRegion (0x7f67011c5dd0)
  Dimension: 3
  Index: [0, 845, 0]
  Size: [105, 18446744073709550952, 20]
 is outside of buffered region ImageRegion (0x7f6573ca8bb8)
  Dimension: 3
  Index: [0, 0, 0]
  Size: [526, 181, 526]

Error in kvlReadCroppedImage (line 11)
Error in segmentSubjectT2_autoEstimateAlveusML (line 838)
Started at Thu Oct 4 09:35:38 MST 2018
Ended   at Thu Oct 4 09:57:35 MST 2018
#@#%# recon-all-run-time-hours 0.366
recon-all -s subject_id finished without error at Thu Oct  4 09:57:36 MST 2018
done


I came across a similar error in the forums and using the most recent version 
seem to have worked for some, but it did not help in my case.

Freesurfer version I am using
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a

with matlab run time from 2012b as suggested
I have also tried to use 2014b runtime which exited right away.

Thank you for your help,
Pradeep





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[Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

[Pradeep]

External Email - Use Caution

Hello,

I am trying to run the hippocampal segmentation with an additional Hi-res
scan using the following command

recon-all -s  -hippocampal-subfields-T2   

and got the following error


Error using kvlGEMSMatlab
/autofs/cluster/koen/eugenio/InsightToolkit-4.9.1/Modules/Core/Common/include/itkImageConstIterator.h:211:
itk::ERROR: Region ImageRegion (0x7f67011c5dd0)
  Dimension: 3
  Index: [0, 845, 0]
  Size: [105, 18446744073709550952, 20]
 is outside of buffered region ImageRegion (0x7f6573ca8bb8)
  Dimension: 3
  Index: [0, 0, 0]
  Size: [526, 181, 526]

Error in kvlReadCroppedImage (line 11)
Error in segmentSubjectT2_autoEstimateAlveusML (line 838)
Started at Thu Oct 4 09:35:38 MST 2018
Ended   at Thu Oct 4 09:57:35 MST 2018
#@#%# recon-all-run-time-hours 0.366
recon-all -s subject_id finished without error at Thu Oct  4 09:57:36 MST
2018
done


I came across a similar error in the forums and using the most recent
version seem to have worked for some, but it did not help in my case.

Freesurfer version I am using
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a

with matlab run time from 2012b as suggested
I have also tried to use 2014b runtime which exited right away.

Thank you for your help,
Pradeep
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Re: [Freesurfer] Mac OS free surfer instalation (Vasile, Eduard)

[Dicamillo, Robert]

Sure - or if you want to let us know your office number, I could stop by as 
well.

- rob

> On Oct 4, 2018, at 12:10 PM, Vasile, Eduard  wrote:
> 
> Hi Rob, 
> 
> I have matlab installed on my laptop. I am based in South Central, 149, is 
> there anywhere I can come to talk to you guys? I am in need of the software.
> 
> Kind regards
> Eduard
> 
> On 10/4/18, 12:00 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> freesurfer-requ...@nmr.mgh.harvard.edu" 
>  freesurfer-requ...@nmr.mgh.harvard.edu> wrote:
> 
> Mac OS free surfer instalation (Vasile, Eduard)
> 
> 
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] Mac OS free surfer instalation (Vasile, Eduard)

[Vasile, Eduard]

Hi Rob, 

I have matlab installed on my laptop. I am based in South Central, 149, is 
there anywhere I can come to talk to you guys? I am in need of the software.

Kind regards
Eduard

On 10/4/18, 12:00 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
freesurfer-requ...@nmr.mgh.harvard.edu"  wrote:

 Mac OS free surfer instalation (Vasile, Eduard)


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Re: [Freesurfer] mri_surf2surf --mapmethod nnf not working?

[Viessmann, Olivia M.]

Ok, thanks, that was very helpful. It was the surf2surf_nnfr() call that made 
me suspicious. And as you say, when run without specifying —mapmethod (sets the 
map method to nnfr in default) it gives out the surf2surf:Reverse Loop 
statement.
Thanks
Olivia

On 3 Oct 2018, at 23:31, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:

Are you worried about where it says "Using surf2surf_nnfr()"? There is actually 
one one function that performs both kinds of mapping. In this case, it is not 
doing the reverse loop. You can reassure yourself by running it with nnfr and 
see that it prints out "Surf2Surf: Reverse Loop" (which does not appear with 
nnf)



On 10/3/18 7:05 PM, Viessmann, Olivia M. wrote:
Hello,

I am using mri_surf2surf and would like to use the vertex map method nnf 
("neighest neighbor, forward only") which according to the --help description 
exists and avoids multiple source vertices to be mapped and averaged onto a 
single target vertex (crucial to my analysis here). However, when I run this 
the output suggests that it is running the nnfr (neighest-neighbor forward and 
reverse) method.
Is this a bug or am I misinterpreting the console output?

This is the command and output:

/usr/local/freesurfer/dev/bin/mri_surf2surf --srcsubject 994273 --sval 
994273/Results/Orientations/lh_SSangle_depth00_rfMRI_REST1_LR.mgz --trgsubject 
fsaverage --mapmethod nnf --o lh_SSangle_depth00_rfMRI_REST1_LR_inFSAv.mgz 
--hemi lh

sysname  Linux
machine  x86_64
user omv4
srcsubject = 994273
srcval = 994273/Results/Orientations/lh_SSangle_depth00_rfMRI_REST1_LR.mgz
srctype=
trgsubject = fsaverage
trgval = lh_SSangle_depth00_rfMRI_REST1_LR_inFSAv.mgz
trgtype=
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg 
/cluster/olivia/Data/994273/T1w/994273/surf/lh.sphere.reg
Loading source data
Reading target surface reg 
/cluster/olivia/Data/994273/T1w/fsaverage/surf/lh.sphere.reg
Done
Using surf2surf_nnfr()
Mapping Source Volume onto Source Subject Surface
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (163842)
Surf2Surf: Dividing by number of hits (163842)
INFO: nSrcLost = 26240
nTrg121 = 163842, nTrgMulti = 0, MnTrgMultiHits = 0
nSrc121 = 78298, nSrcLost = 26240, nSrcMulti = 62974, MnSrcMultiHits = 1.3584
Saving target data
Saving to lh_SSangle_depth00_rfMRI_REST1_LR_inFSAv.mgz



I'd appreciate any suggestions.
Thanks
Olivia





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[Freesurfer] Problem with new tool on thalamus segmentation

[stdp82]

External Email - Use Caution

I'm reposting my questions that I have done some week ago because without your 
helpfulness is impossible to go ahead with my analysis.

1- I have installed dev version.
I have run the segmentThalamicNuclei.sh but .stats file has been not
produced in any subjects.

I have also try to re-run recon-all but without success.


2 - I have used FS-FAST previously.
However, when I use the thalami segmentation as seed

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

I obtain the error listed below:

Voxel Volume is 36.3469 mm^3

Generating list of segmentation ids

Found 1 segmentations

Computing statistics for each segmentation

Reporting on 0 segmentations

Using PrintSegStat

Computing spatial average of each frame

ERROR: no voxels found in segmentation


Please could you give me can help?

Thanks


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