[Freesurfer] Hippocampal overestimation 5.3 vs 6.0

[Dawn C. Matthews]

Eugenio and Freesurfer team,

 

Many thanks for responding to these questions. My question relates to 
hippocampal volume overestimation. I believe that a European team recently 
evaluated the performance of hippocampus segmentation using different automated 
segmentation methods including Freesurfer on more than 400 scans from several 
previous studies, and found that Freesurfer and FSL-FIRST may include tissue 
that is not part of the hippocampus. Liedlgruger et al, “Variability Issues in 
Automated Hippocampal Segmentation”, 2017, also reported that Freesurfer 
overestimated volumes vs. other methods tested. I wondered if version 6.0 
addresses the overestimation issue?  It appeared that the FS 6.0 release web 
page figure (which showed the hippocampal portion of an MRI at left, the 5.3 
subfield segmentation in the middle, and the 6.0 subfield segmentation at 
right) showed that a portion of gray tissue superior to hippocampus was 
included in the 5.3 segmentation but not in the 6.0 version – was that an 
example of 5.3 overinclusion, addressed in 6.0?

 

Thank you again for your help and for the team’s continued advances.

 

Dawn

 

 

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Re: [Freesurfer] LME mass univariate model

[Martin Reuter]

Hi Bronwyn, 

I think years-between-scans should be years-from-baseline-scans . You may need 
to compute that if what you have is really years between neighbouring scans.

1. Usually people use intercept and maybe years-from-baseline as random 
effects. I would not include too many random effects, as it each adds a lot of 
free parameters and you need a lot of data to fit all that in a meaningful way. 
Which of your columns are random effects can be passed lme_fit_FS(X,[1 
2],Y(:,1)+Y(:,2),ni);
for example has column 1 and 2 as random effects. 

2. You can do a model comparison as described on our wiki 
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels 
 

You run the more complex model first (do the EM init and maybe RgGrow and RgW 
fit) and then the simple one (only the EMinit and  RgW fit) and do a likelihodd 
ratio test.  An example is on the above wiki.

Best ,Martin 





> On 27 Feb 2017, at 04:16, Bronwyn Overs  wrote:
> 
> Dear mailing list,
> 
> I am trying to run a LME model using the matlab tools, but I’m unsure how to 
> specify the model we wish to run. We have a qdec file that contains the 
> following columns:
> fsid, fsid-abse, years between scans, age at baseline, gender, group
> 
> We want to specify a model where we can examine four interaction terms 
> (years*age, years*group, age*group, years*age*group), as well as random 
> effects for the intercept, years and age. My questions are:
> 1. How do we specify a model that will include the random effects we want?
> 2. How do we compare our full model (3 random effects) with a model excluding 
> the random effect for age?
> 
> Kind regards,
> Bronwyn Overs
> Research Assistant
> 
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
> 
> neura.edu.au  
>   
>  
> 
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[Freesurfer] panning Freeview on MacBook Pro

[me]

Hi,

How do I pan on Freeview on a Mac please? Mine is an El Capitan, MacBook 
Pro (Early 2011).

On 
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewGeneralUsage/FreeviewNavigation
it reads:
You can pan across the data, which is especially useful when zoomed in. 
To do so while in Navigate mode navigate.gif , Voxel Edit mode 
voxel_edit.gif , or Recon Edit mode recon_edit.gif click and hold the 
scroll button on the mouse while moving the image. Alternatively, you 
can use the arrow keys on the keyboard. When using the arrow keys, know 
that when you scroll up, down, right or left, the actual label moves 
around, not the screen.

I have tried the touchpad, with and without cmd, alt, fn, shift, ctrl... 
Also tried the arrow keys.

Thanks,
mary
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Re: [Freesurfer] panning Freeview on MacBook Pro

[Ruopeng Wang]

If you have middle mouse button defined, use middle button. Otherwise, Shift + 
Left Button should do it.

Best,
Ruopeng

> On Mar 3, 2017, at 9:51 AM, m...@marychin.org wrote:
> 
> Hi,
> 
> How do I pan on Freeview on a Mac please? Mine is an El Capitan, MacBook 
> Pro (Early 2011).
> 
> On 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewGeneralUsage/FreeviewNavigation
> it reads:
> You can pan across the data, which is especially useful when zoomed in. 
> To do so while in Navigate mode navigate.gif , Voxel Edit mode 
> voxel_edit.gif , or Recon Edit mode recon_edit.gif click and hold the 
> scroll button on the mouse while moving the image. Alternatively, you 
> can use the arrow keys on the keyboard. When using the arrow keys, know 
> that when you scroll up, down, right or left, the actual label moves 
> around, not the screen.
> 
> I have tried the touchpad, with and without cmd, alt, fn, shift, ctrl... 
> Also tried the arrow keys.
> 
> Thanks,
> mary
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> 


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Re: [Freesurfer] panning Freeview on MacBook Pro

[Ruopeng Wang]

Sorry, that appears to only work with 3D view. On 2D view you’ll have to use 
Cmd + arrow keys to pan. I’ll fix it in future update.

> On Mar 3, 2017, at 9:58 AM, Ruopeng Wang  wrote:
> 
> If you have middle mouse button defined, use middle button. Otherwise, Shift 
> + Left Button should do it.
> 
> Best,
> Ruopeng
> 
>> On Mar 3, 2017, at 9:51 AM, m...@marychin.org wrote:
>> 
>> Hi,
>> 
>> How do I pan on Freeview on a Mac please? Mine is an El Capitan, MacBook 
>> Pro (Early 2011).
>> 
>> On 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewGeneralUsage/FreeviewNavigation
>> it reads:
>> You can pan across the data, which is especially useful when zoomed in. 
>> To do so while in Navigate mode navigate.gif , Voxel Edit mode 
>> voxel_edit.gif , or Recon Edit mode recon_edit.gif click and hold the 
>> scroll button on the mouse while moving the image. Alternatively, you 
>> can use the arrow keys on the keyboard. When using the arrow keys, know 
>> that when you scroll up, down, right or left, the actual label moves 
>> around, not the screen.
>> 
>> I have tried the touchpad, with and without cmd, alt, fn, shift, ctrl... 
>> Also tried the arrow keys.
>> 
>> Thanks,
>> mary
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
> 
> 
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Re: [Freesurfer] FreeSurfer v6.0 in an AWS cloud configuration (hipposubfield/brainstem failures)

[randrews]

Thanks Antonin,We had suspected as much.  For those who might want to use NITRC-CE (FS v6.0 via their AWS service in the future), please note that our initial (and memory-insufficient) "instance" was "c3.large" .  As you can see in the table below, we should have paid more attention to the guidance regarding memory from the installation instructions.  Since "c3.xlarge had only 7.5 GB memory, we opted for the next tier, "c3.2xlarge".For for this initial benchmark, we used an ADNI subject (N3-corrected, downloaded from ADNI/LONI as *.nii), and the run completed in toto and took 9.038 hrs.Much appreciated,-RandyInstance Types MatrixInstance TypevCPUMemory (GiB) Storage (GB)Networking PerformancePhysical ProcessorClock Speed (GHz)Intel AVX†Intel AVX2†Intel TurboEBS OPTEnhanced Networking†c3.large23.752 x 16 SSDModerateIntel Xeon E5-2680 v22.8Yes-Yes-Yesc3.xlarge47.52 x 40 SSDModerateIntel Xeon E5-2680 v22.8Yes-YesYesYesc3.2xlarge8152 x 80 SSDHighIntel Xeon E5-2680 v22.8Yes-YesYesYes Re: [Freesurfer] FreeSurfer v6.0 in an AWS cloud configuration (hipposubfield/brainstem failures)Antonin Skoch Thu, 02 Mar 2017 09:15:57 -0800   Dear Randy, from the log file you provided it seems that both of your jobs exited on the insufficient RAM. You should check your available RAM resources. brainstem-structures: std::bad_alloc hippocampal subfiels: Out of memory. Regards, AntoninRandolph D. Andrews, MSStaff Scientist | ADM Diagnostics, LLCphone +1 847 978 5007 | randr...@admdx.com


 Original Message 
Subject: FreeSurfer v6.0 in an AWS cloud configuration
(hipposubfield/brainstem failures)
From: 
Date: Thu, March 02, 2017 9:18 am
To: freesurfer@nmr.mgh.harvard.edu

Hello FreeSurfer Experts/Community,I am currently working with NITRC (as a novice user) to build and investigate the operability of FreeSurfer v6.0 in their Computational Environment (NITRC-CE).We have been able to get a "recon-all" run to work, but we are failing to get the sub-calls -hippocampal-subfields-T1(see link earlier in thread)-brainstem-structures(see link earlier in thread)... to run correctly / run to completion.  We are aware that Matlab Runtime needed to be installed, and a partial completion is a testament to that.However, they seem to choke near the end, and it would be good to get some insight as to why.  To wit, I am pasting the last dozen or so lines from each (see below) in the hopes we might get a tip or a comment from this forum.For this exercise, we used an ADNI subject (N3-corrected, downloaded from ADNI/LONI as *.nii)The syntax/command I used was:recon-all -s ADNI_003_S_2374_m00 \-i $SUBJECTS_DIR/ADNI_003_S_2374__MRI_m00__EMCI-EMCI__20110506__S108554_I235638.nii \-all -hippocampal-subfields-T1 -brainstem-structures I'm simply not sure if there's something wrong with my syntax or if there is something else we're missing.  Any help would be greatly appreciated, and I can pass on what is shared to my developer (and so that eventually everyone might begin to have a vetted version of v6.0 using NITRC-CE if they wish in the future)-RandyFrom:/scripts/brainstem-structures ___<<>>Resolution level 3 iteration 3 deformation iterations 8Did one deformation step of max. 1.6685e-05 voxels in 8.485 secondsminLogLikelihoodTimesPrior = 7.5772e+06Resolution level 3 iteration 3 deformation iterations 9Did one deformation step of max. 5.3959e-05 voxels in 3.4185 secondsminLogLikelihoodTimesPrior = 7.5772e+06Resolution level 3 iteration 3 deformation iterations 10Did one deformation step of max. 0 voxels in 6.782 secondsminLogLikelihoodTimesPrior = 7.5772e+06maximalDeformation is too small; stoppingFitting mesh to image data mask took 919.7675 secondsnumberOfLabels: 21Rasterizing mesh...here: 21here2: 21doneError using kvlGEMSMatlabstd::bad_allocError in kvlRasterizeAtlasMesh (line 11)Error in segmentSubject (line 1151) __<<>>From:/scripts/hippocampal-subfields-T1___<<>>  Making alveus map to reduced label 3--Making Left-Lateral-Ventricle map to reduced label 4--Making hippocampal-fissure map to reduced label 5--Making Left-Pallidum map to reduced label 6--Making Left-Putamen map to reduced label 7--Making Left-Caudate map to reduced label 8--Making Left-Thalamus-Proper map to reduced label 9--Making Left-choroid-plexus map to reduced label 10--Making Left-VentralDC map to reduced label 11--Making Left-Accumbens-area map to reduced label 12--Making Unknown map to reduced label 13Computing hyperparameters for estimation of Gaussian parametersEstimating typical intensit

Re: [Freesurfer] Hippocampal overestimation 5.3 vs 6.0

[Iglesias Gonzalez, Eugenio]

Dear Dawn.
We have observed that the hippocampal volumes obtained from the subfield module 
are ~10% smaller than those from the main recon-all stream - but, in any case, 
very highly correlated.
I believe that the discrepancy is due to the smaller voxel size in the 
analysis, and due to the fact that the subfield module does not include the 
alveus in the segmentation.
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 3 Mar 2017, at 13:15, Dawn C. Matthews 
mailto:dmatth...@admdx.com>> wrote:

Eugenio and Freesurfer team,

Many thanks for responding to these questions. My question relates to 
hippocampal volume overestimation. I believe that a European team recently 
evaluated the performance of hippocampus segmentation using different automated 
segmentation methods including Freesurfer on more than 400 scans from several 
previous studies, and found that Freesurfer and FSL-FIRST may include tissue 
that is not part of the hippocampus. Liedlgruger et al, “Variability Issues in 
Automated Hippocampal Segmentation”, 2017, also reported that Freesurfer 
overestimated volumes vs. other methods tested. I wondered if version 6.0 
addresses the overestimation issue?  It appeared that the FS 6.0 release web 
page figure (which showed the hippocampal portion of an MRI at left, the 5.3 
subfield segmentation in the middle, and the 6.0 subfield segmentation at 
right) showed that a portion of gray tissue superior to hippocampus was 
included in the 5.3 segmentation but not in the 6.0 version – was that an 
example of 5.3 overinclusion, addressed in 6.0?

Thank you again for your help and for the team’s continued advances.

Dawn


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Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding

[Z K]

I could be wrong, but I dont think it has anything to do with the 
installation location. Can you upload your subject folder so I can take 
a look?

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


On 03/03/2017 09:11 AM, Daniela wrote:
> I second the problem found in this thread:
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51917.html
>
> I recently downloaded FreeSurfer v. 6 on a macOS 10.12. To work around
> the System Integrity Protection issue, I installed my freesurfer folder
> in a local "Documents" folder instead of in Applications and that seemed
> to allow me to keep System Integrity Protection enabled while running
> FreeSurfer commands.
>
> Last night I ran recon-all on the same subject simultaneously, one using
> the -parallel tag and the other without it. This morning I see that only
> the one with the -parallel tag exited with errors and it seems to be
> this same "lazy symbol" error (see attached for recon-all error log).
>
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Users/Ajay/Documents/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> I can try running with System Integrity Protection off to see if that
> will make the -parallel tag work... any other thoughts?
>
>
> Thanks,
> Daniela
>
>
>
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[Freesurfer] transform a custom segmentation to native space

[Gabor Perlaki]

Dear all,

We've segmented some brain regions on orig.mgz using another program (this
custom segmentation is called our_segmentation.mgz). Is it possible to
transform this segmentation into the original native anatomical space using
the following command?

mri_label2vol --seg our_segmentation.mgz --temp rawavg.mgz --o
our_segmentation-in-rawavg.mgz --regheader aseg.mgz


Could somebody verify, that the above command is OK or not?

Best,
Gabor

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Re: [Freesurfer] recon-all exited with error.

[Z K]

Im looking into this now, but I think their might be a bug when using 
the -parallel flag on Mac platforms. I should have a fix shortly. I will 
let you know.

On 03/03/2017 12:10 PM, miracle ozzoude wrote:
> Thanks Antonin. I also have different error when running another
> subject. Recon fails in the smooth stage of recon-all (please see the
> attached screenshot). How can i fix this?
> Best,
> Paul
>
>
> On Thu, Mar 2, 2017 at 7:19 PM, Antonin Skoch  > wrote:
>
> Dear Paul,
>
> yes, this is the modification of FREESURFER_HOME you need to do
> (using setenv command if you are using tcsh).
>
> Regards,
>
> Antonin
>
>
> Hey Antonin,
> Thank you. hence, the right path should be "setenv FREESURFER_HOME
> /opt/freesurfer-6.0.0/freesurfer "
> Best,
> Paul.
>
> On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch  > wrote:
>
> > Dear Paul,
> >
> > the slash problem prevents to properly create symbolic link to 
> fsaverage in
> > your SUBJECTS_DIR.
> >
> > Then, the mri_label2label could not find the fsaverage label file since
> > symbolic link for fsaverage does not exist, hence produces the 
> error.log you
> > are attaching.
> >
> > Regards,
> >
> > Antonin
> >
> >
> > Thanks Antonin. Also, I got this error.log file in my label folder. Do 
> you
> > think it is due to the slash problem?
> > Best,
> > Paul
> >
> > On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch  > wrote:
> >
> > > Dear Paul,
> > >
> > > I suppose the clue is following messages from your recon-all.log file:
> > >
> > > FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/
> > >
> > > and
> > >
> > >  cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln 
> -s
> > > /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd -
> > >
> > > ln: failed to create symbolic link './fsaverage': File exists
> > >
> > > The problem is that your FREESURFER_HOME contains slash in the end. 
> Remove
> > > it
> > > and rerun relevant part of recon-all. It should work then.
> > >
> > > Antonin
> > >
> > >
> > >
> > >
> > > Hello Freesurfer,
> > > I was running recon-all in steps (recon-all -autorecon1, recon-all
> > > -autorecon2, and recon-all - -T2 /T2 volume  -T2pial autorecon3). 
> However,
> > > it exited with error during the BA_exvivo labels part of autorecon3 
> (please
> > > see attached recon-all.log file). Please, how can I fix it? Thanks
> > > Best,
> > > Paul
>
>
>
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> addressed. If you believe this e-mail was sent to you in error and
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> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] recon-all exited with error.

[miracle ozzoude]

Thanks. Z K
Best,
Paul

On Fri, Mar 3, 2017 at 12:14 PM, Z K  wrote:

> Im looking into this now, but I think their might be a bug when using
> the -parallel flag on Mac platforms. I should have a fix shortly. I will
> let you know.
>
> On 03/03/2017 12:10 PM, miracle ozzoude wrote:
> > Thanks Antonin. I also have different error when running another
> > subject. Recon fails in the smooth stage of recon-all (please see the
> > attached screenshot). How can i fix this?
> > Best,
> > Paul
> >
> >
> > On Thu, Mar 2, 2017 at 7:19 PM, Antonin Skoch  > > wrote:
> >
> > Dear Paul,
> >
> > yes, this is the modification of FREESURFER_HOME you need to do
> > (using setenv command if you are using tcsh).
> >
> > Regards,
> >
> > Antonin
> >
> >
> > Hey Antonin,
> > Thank you. hence, the right path should be "setenv FREESURFER_HOME
> > /opt/freesurfer-6.0.0/freesurfer "
> > Best,
> > Paul.
> >
> > On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch  a...@ikem.cz>> wrote:
> >
> > > Dear Paul,
> > >
> > > the slash problem prevents to properly create symbolic link to
> fsaverage in
> > > your SUBJECTS_DIR.
> > >
> > > Then, the mri_label2label could not find the fsaverage label file
> since
> > > symbolic link for fsaverage does not exist, hence produces the
> error.log you
> > > are attaching.
> > >
> > > Regards,
> > >
> > > Antonin
> > >
> > >
> > > Thanks Antonin. Also, I got this error.log file in my label
> folder. Do you
> > > think it is due to the slash problem?
> > > Best,
> > > Paul
> > >
> > > On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch  > wrote:
> > >
> > > > Dear Paul,
> > > >
> > > > I suppose the clue is following messages from your recon-all.log
> file:
> > > >
> > > > FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/
> > > >
> > > > and
> > > >
> > > >  cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326;
> ln -s
> > > > /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd -
> > > >
> > > > ln: failed to create symbolic link './fsaverage': File exists
> > > >
> > > > The problem is that your FREESURFER_HOME contains slash in the
> end. Remove
> > > > it
> > > > and rerun relevant part of recon-all. It should work then.
> > > >
> > > > Antonin
> > > >
> > > >
> > > >
> > > >
> > > > Hello Freesurfer,
> > > > I was running recon-all in steps (recon-all -autorecon1,
> recon-all
> > > > -autorecon2, and recon-all - -T2 /T2 volume  -T2pial
> autorecon3). However,
> > > > it exited with error during the BA_exvivo labels part of
> autorecon3 (please
> > > > see attached recon-all.log file). Please, how can I fix it?
> Thanks
> > > > Best,
> > > > Paul
> >
> >
> >
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> >
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[Freesurfer] Reslice image

[John Anderson]

Dear experts:
I have nifti file with 96 slices. I want to re-slice it to form nifti file with 
200 slice. Are there any tools in Freesurfer that can help to achieve this?

Many thanks for any suggestion

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Re: [Freesurfer] ACPC alignment before or after running on Freesurfer?

[dg wakeman]

Also, re-slicing already acquired data will introduce blurring into
the data you input to FreeSurfer, which may hurt reconstruction.

hth
d

On Wed, Mar 1, 2017 at 10:30 AM, Bruce Fischl
 wrote:
> Hi Kristine
>
> no, it doesn't. Randy Buckner did a small study on this and found no
> detectable effect
>
> cheers
> Bruce
> On Tue, 28 Feb 2017, Lee Subin Kristine wrote:
>
>> Dear Freesurfer team,
>> This may sound like a bit of a small question, but I could not find any
>> exact answer elsewhere.
>>
>> Does the exact orientation of the input image have much effect on the
>> accuracy of the segmentation in Freesurfer?
>> It seems that some people apply ACPC alignment to the output of Freesurfer,
>> so I am confused as to which order would be optimal.
>>
>>
>> Thank you in advance,
>> Kristine
>>
>>
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[Freesurfer] Resting State group comparison procedure

[Bailin, Emma]

Hello,

I'm currently doing a resting state functional connectivity analysis. I have 
two groups and my ultimate goal is to compare the resting state network of 
group 1 to that of group 2.

What is the standard procedure for comparing resting state connectivity across 
groups?

I've followed the directions on the FsFast Functional Connectivity Walkthrough 
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough)
 and after the isxconcat-sess, I did mri_glmfit --y ces.nii.gz -wls pcc.nii.gz 
-surface fsaverage lh -glmdir [my/group1.directory.wls} -nii.gz, for each 
group. This got me the mean for both groups individually. I'm now stuck on how 
to proceed to compare across my groups. Using mri_glmfit creates the problem of 
trying to pre-process each group without a variable for -measure, and I'm not 
sure if using the -iv flag with the ces.nii.gz or pcc.nii.gz is going to give 
me what I need.

Thank you.

--Emma Bailin

Emma Bailin
Research Coordinator
Laboratory for Visual Neuroplasticity
Schepens Eye Research Institute
Mass. Eye and Ear Infirmary
Harvard Medical School
emma_bai...@meei.harvard.edu
(617)-573-3794



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[Freesurfer] preproc-sess - Cannot allocate memory

[Peled, Noam]

Hey all,
I'm running preproc-sess, and getting the following error:
...
Reading in mov rest/tmp.bbregister.28405/template.nii
Reading in ref .../mri/brainmask.mgz
Reading in and applying refmask .../mri/aparc+aseg.mgz
Cannot allocate memory

I checked, and the aparc+aseg.mgz file is ok (I can read it with nibabel)

I'm using the FreeSurfer dev version 
(freesurfer-Linux-centos6_x86_64-dev-20161215-dd925e2) on a
32GB CentOs7 machine, so I don't think I'm really out of memory.

Thanks,
Noam
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Re: [Freesurfer] mri_vol2surf

[Redwan Maatoug]

Hi Douglas,

Thank you for your help,

So I still can't convert my volumetric file to a surface file and I don't
know what I am doing wrong.

My nifti volumetric file looks like : 1. screenshot
As you said, i have first registered the volumetric file
 using bbregister.
 I have used this command line :
tkregister2 --mov segment_7.nii --reg register7.dat --surf
 (knowing that segment_7.nii is my volumetric file which looks like
1.screenshot).
With this command line, my output is this file : 2.screenshot (attached).

Am I satisfied with this file ? if not what can I do to improve the result
and the matching ?

And after that, I have tried to convert my volumetric file to surface file
with this command line :

mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o
./segment_7-lh.nii --float2int round

But with this command when I load the file with freeview it does not work
and with tkregister the file is empty.

Or this one :

mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o
./segment_7-lh.w --out_type paint --float2int tkregister

But with this command I have the following warning :
Warning: all vertex values are zero

Thank you by advance for your precious help,
Have a nice day,
Redwan


On 2 March 2017 at 10:07, Redwan Maatoug  wrote:

> Hi Douglas,
>
> Thank you for your help,
>
> So I still can't convert my volumetric file to a surface file and I don't
> know what I am doing wrong.
>
> My nifti volumetric file looks like : 1. screenshot
> As you said, i have first registered the volumetric file
>  using bbregister.
>  I have used this command line :
> tkregister2 --mov segment_7.nii --reg register7.dat --surf
>  (knowing that segment_7.nii is my volumetric file which looks like
> 1.screenshot).
> With this command line, my output is this file : 2.screenshot (attached).
>
> Am I satisfied with this file ? if not what can I do to improve the result
> and the matching ?
>
> And after that, I have tried to convert my volumetric file to surface file
> with this command line :
>
> mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o
> ./segment_7-lh.nii --float2int round
>
> But with this command when I load the file with freeview it does not work
> and with tkregister the file is empty.
>
> Or this one :
>
> mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o
> ./segment_7-lh.w --out_type paint --float2int tkregister
>
> But with this command I have this warning :
> Warning: all vertex values are zero
>
> Thank you by advance for your precious help,
> Have a nice day,
> Redwan
>
> On 1 March 2017 at 07:31, Douglas Greve  wrote:
>
>> Hi Redwan,
>>
>> You'll need to register your volume to an FS-analyzed data set (probably
>> using bbregister). Then apply mri_vol2surf (run with --help to get examples)
>>
>> doug
>>
>> On 2/28/17 5:17 PM, Redwan Maatoug wrote:
>>
>> Hi all !
>>
>> I would like to convert my files : volumetrics nifti files to surfaces
>> files.
>> My volumetrics nifti files come from an Atlas and I would like to convert
>> them to surfaces files (i need the surfaces files).
>>
>> Could you please tell me the process because I have tried many things
>> like :
>>
>> mri_vol2surf --src pathwaytomyfile --hemi lh --float2int round --out
>> thepathwayIwantToputmySurfaceFileAfterConversion
>>
>> And it did not work.
>>
>> Thank you for your help,
>> Redwan
>>
>>
>>
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Re: [Freesurfer] threshold method used to obtain *exvivo.thresh.labels

[Antonin Skoch]

Dear experts,

concerning my question regarding thresholding method of entorhinal and 
perirhinal labels, I looked at

Augustinack JC et al, Predicting the location of human perirhinal  cortex, 
Brodmann's area 35, from MRI, Neuroimage 2013 Jan 1;64:32-42.

where I found the text:

For each label, the vertices were ordered from most probable least probable), 
then thresholded so that the surface area of each predicted entorhinal cortex 
or perirhinal cortex label matched the average surface area of the ex vivo 
labels.

So, if I understand it correctly, at least for the entorhinal and perirhinal 
*thresh labels, the threshold has been found individually for each label and 
hemisphere separately, so that the area of the label in the fsaverage space 
match average surface area of the corresponding ex-vivo labels? 
Therefore, no restriction for overlap of perirhinal and entorhinal labels was 
applied in the thresholding? I found that in the right hemisphere the 
rh.entorhinal_thresh.label almost completely overlaps with 
lh.entorhinal_thresh.label.

But, for generating custom aparc+aseg I need non-overlapping labels. I 
attempted to resolve the issue by using 

mris_label2annot --s fsaverage --l fsaverage/label/lh.entorhinal_exvivo.label 
--l fsaverage/label/lh.perirhinal_exvivo.label --hemi lh --ctab 
entorhinal_perirhinal.annot.ctab --maxstatwinner --thresh 0.4 --a 
entorhinal_perirhinal_thresh_0.4

i.e. using --maxstatswinner and --thresh 0.4 which gives non-overlapping labels 
with shapes approximately similar to the original 
entorhinal_exvivo.thresh.label and perirhinal_exvivo.thresh.label, but it 
probably violates the condition of similar area extent.

Could you please comment on if my used method is acceptable, or suggest better 
method how to achieve non-overlaping entorhinal and perirhinal labels for the 
purpose of generating custom aparc+aseg from them?

Regards,

Antonin Skoch

Dear experts,

Could you please provide me the information how exactly the 
*_exvivo.thresh.labels have been thresholded?According to this post, 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32542.html
.thresh labels are thresholded to pick the most likely vertices that give a 
label that is 
the right surface area.But how they are thresholded in the boundary of the 
region where the unthresholded labels do not overlap? There must be additional 
threshold applied:
For example for BA45 there is no further BA label towards frontal pole, but the 
BA45_exvivo.thresh.label is also restricted in this region wrt 
BA45_exvivo.label.

I have further question concerning used thresholding method of 
perirhinal_exvivo.thresh and entorhinal_exvivo.thresh labels. It seems that 
this method is not applied here since looking at them at the fsaverage surface, 
they are overlapping. And also *rhinal_exvivo.labels are much more extending to 
the adjacent regions than *rhinal_exvivo.thresh.labels. What method is applied 
here?

My main objective to obtain annotation with the vertices properly assigned to 
perirhinal_exvivo and entorhinal_exvivo to supply this annotation to 
mri_aparc2aseg to assign ribbon voxels to that parcellation. I think I could 
use mris_label2annot --maxstatswinner with unthresholded entorhinal and 
perirhinal labels to assign vertices to most probable label, but I would need 
to further threshold the labels by correct value to obtain results similar in 
extent to thresh.labels.

For perirhinal, it seems that the additional threshold is 0.4 (what is 
rationale for this value?), for entorhinal it seems also around 0.4 but could 
not find any particular threshold to obtain the exact shape of label 
corresponding to entorhinal_exvivo.thresh.

Thank you in advance for clarification.

Regards,

Antonin Skoch

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