[Freesurfer] Mapping left to right for fsaverage 5 (ico5)

[Davide Tabarelli]

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Dear all,

I have a question about left-right sphere based co-registration.

I have a scalar quantity defined on the fsaverage5 ico5 surfaces and I would 
like to map left to right hemisphere.

I’ve computed left_right registered spheres by running following commands in 
the fsaverage5 folder:

mris_curvature -w lh.white
mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated
mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right 
rh.sphere.left_right
mris_curvature -w rh.white
mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated
mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right 
rh.sphere.left_right

As far as I understood, the lh.sphere.left_right contains the lh mesh warped to 
be consistent with the anatomical landmarks on rh.
Thus in mapping or interpolating, I have to use vertices in 
lh.sphere.left_right and map/interpolate them to rh.sphere.

Is that correct? There is a better way to do that?

Moreover I cannot find information about the “thresh” and “distances” arguments 
in mris_left_right_register help. Maybe those options are not fine for the 
fsaverage ico5 ?

Thank you all in advance.

D.

—
Davide Tabarelli, Ph.D.
Center for Mind Brain Sciences (CIMeC)
University of Trento,
Via delle Regole, 101
38123 Mattarello (TN)
Italy





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[Freesurfer] orig.mgz versus T1.mgz

[C.P.E. Rollins]

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Thanks Bruce. Will the orig.mgz file be different from the raw data in 
any significant way?

Thanks again,
Colleen

 Original Message 
Subject: orig.mgz versus T1.mgz
Date: 2018-04-30 11:54
 From: "C.P.E. Rollins" 
To: Freesurfer 

Dear Freesurfer developers,

A collaborator shared with me Freesurfer outputs, but I would like to 
some analyses requiring the scans in NIFTI format. I understand 
mri_convert should do the trick for this, though I was wondering whether 
I should use "orig.mgz" or "T1.mgz" to convert back to the original T1 
NIFTI files.

Many thanks,
Colleen

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[Freesurfer] aseg labels in nii | FreeSurfer to other software

[Otília]

External Email - Use Caution

 

Hi to all FS users!

Sorry in advance if I'm _cross-posting_ but
after searching and trying some stuff I still can't figure out how to do
this.

After all the processing in FS I would like to evaluate the
labels (from each participant) in other software (aseg labels). I
imagine I would need to binarize the label of each subject as masks or
volumes, in .nii or some more common file type.

Do someone know how to
do that?

Any help would be very much appreciated! Thank you!

Best
regards,

Otília
 



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[Freesurfer] Two year postdoc in Cambridge UK

[Anne-Laura Van Harmelen]

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Dear Colleagues,

I would like to draw your attention to a postdoc vacancy in Cambridge on the MQ 
funded 
HOPES
 
project.

The MQ HOPES role is a two year post available from May 2018. The candidate 
will be part of a large collaborative effort (The HOPES project) that aims to 
elucidate neurobiological mechanisms and behavioural phenotypes that underlie 
risk for STBs during adolescence, a critical period of development when STBs 
emerge. HOPES is a consortia of researchers across the world including Yale and 
Orygen (Melbourne), and is led by the University of Cambridge. The candidate 
will work together with researchers from those institutions to examine the 
neural underpinnings of adolescent suicide behaviour.

The candidate will investigate the neurobiological underpinnings of youth STBs 
(suicidal thoughts and behaviours). This will include pooling existing large, 
cross-sectional and longitudinal international neuroimaging datasets of youth 
with a range of psychiatric disorders to investigate a model that integrates 
brain structure and functioning as well as cognitive and social environmental 
factors to predict current and future STBs. The candidate will use multivariate 
statistics (such as Structural equation modelling) to do so.

Candidates should have a PhD or equivalent, in a related subject such as 
Neuroscience, Psychology, Psychiatry or otherwise relevant subject areas or be 
very close to completion/award of same prior to their appointment to the post. 
The funds for this post are available for two years in the first instance. The 
advert can be found here

Very best,
Anne-Laura van Harmelen
av...@cam.ac.uk



Dr Anne-Laura van Harmelen
Royal Society Dorothy Hodgkin Fellow
Senior Research Associate
Department of Psychiatry
University of Cambridge

18b Trumpington road
Cambridge, CB2 8AH
+44 (0)1223-465245

www.annelauravanharmelen.com
@DrAnneLaura


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Re: [Freesurfer] orig.mgz versus T1.mgz

[C.P.E. Rollins]

External Email - Use Caution

Just to clarify, by that I mean would the NIFTI converted from orig.mgz 
(with mri_convert) be different than the NIFTI produced by dcm2niix from 
the raw DICOMs?

Thanks,
Colleen

 Original Message 
Subject: orig.mgz versus T1.mgz
Date: 2018-05-02 10:24
 From: "C.P.E. Rollins" 
To: Freesurfer 

Thanks Bruce. Will the orig.mgz file be different from the raw data in 
any significant way?

Thanks again,
Colleen

 Original Message 
Subject: orig.mgz versus T1.mgz
Date: 2018-04-30 11:54
 From: "C.P.E. Rollins" 
To: Freesurfer 

Dear Freesurfer developers,

A collaborator shared with me Freesurfer outputs, but I would like to 
some analyses requiring the scans in NIFTI format. I understand 
mri_convert should do the trick for this, though I was wondering whether 
I should use "orig.mgz" or "T1.mgz" to convert back to the original T1 
NIFTI files.

Many thanks,
Colleen

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Re: [Freesurfer] orig.mgz versus T1.mgz

[Douglas Greve]

The orig.mgz is closer to the raw data than T1.mgz, but it will be 
different in a number of ways. First, it will be 256^3, 1mm voxel size 
regardless of the dimensions of the raw data. Second, it will be 8 bits 
(0-255) with some rescaling.


On 5/2/18 7:43 AM, C.P.E. Rollins wrote:
>  External Email - Use Caution
>
> Just to clarify, by that I mean would the NIFTI converted from orig.mgz
> (with mri_convert) be different than the NIFTI produced by dcm2niix from
> the raw DICOMs?
>
> Thanks,
> Colleen
>
>  Original Message 
> Subject: orig.mgz versus T1.mgz
> Date: 2018-05-02 10:24
>   From: "C.P.E. Rollins" 
> To: Freesurfer 
>
> Thanks Bruce. Will the orig.mgz file be different from the raw data in
> any significant way?
>
> Thanks again,
> Colleen
>
>  Original Message 
> Subject: orig.mgz versus T1.mgz
> Date: 2018-04-30 11:54
>   From: "C.P.E. Rollins" 
> To: Freesurfer 
>
> Dear Freesurfer developers,
>
> A collaborator shared with me Freesurfer outputs, but I would like to
> some analyses requiring the scans in NIFTI format. I understand
> mri_convert should do the trick for this, though I was wondering whether
> I should use "orig.mgz" or "T1.mgz" to convert back to the original T1
> NIFTI files.
>
> Many thanks,
> Colleen
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] aseg labels in nii | FreeSurfer to other software

[Douglas Greve]

If you just need the aseg in nii.gz format, then you can

mri_convert aseg.mgz aseg.nii.gz

If you need a particular seg in its own file, then you can

mri_binarize --i aseg.mgz --match 17 --o left-hippo.nii.gz

where 17 is from $FREESURFER_HOME/FreeSurferColorLUT.txt


On 5/2/18 5:47 AM, Otília wrote:



Hi to all FS users!

Sorry in advance if I'm/cross-posting/  but after searching and trying some 
stuff I still can't figure out how to do this.

After all the processing in FS I would like to evaluate the labels (from each 
participant) in other software (aseg labels). I imagine I would need to 
binarize the label of each subject as masks or volumes, in .nii or some more 
common file type.

Do someone know how to do that?

Any help would be very much appreciated! Thank you!

Best regards,

Otília





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Re: [Freesurfer] freesurfer selxavg3-sess error

[Francesca Strappini]

External Email - Use Caution

Hi, sorry, maybe my last email got lost. Is there anything I can try to fix
this problem with selxavg3-sess?

Thanks!
Best
Francesca

2018-04-24 20:35 GMT+03:00 Francesca Strappini :

> Thank you for the reply!
> I deleted the contrasts and run this command line:
>
> selxavg3-sess -a FF-MonkeyCassis.sm03.rh -s MonkeyCassis-FF -no-con-ok
>
>
> --- matlab output 
> MATLAB is selecting SOFTWARE OPENGL rendering.
>
> < M A T L A B (R) >
>   Copyright 1984-2016 The MathWorks, Inc.
>R2016b (9.1.0.441655) 64-bit (glnxa64)
>  September 7, 2016
>
>
> To get started, type one of these: helpwin, helpdesk, or demo.
> For product information, visit www.mathworks.com.
>
> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> >> /usr/local/freesurfer/matlab/MRIread.m
> >> >> >> starting fast_selxavg3b
>
>
> #@# MonkeyCassis-FF ###
> /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
> -
> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
> -
> outtop = /usr/local/freesurfer/fsfast/Monkeys
> Extension format = nii.gz
> INFO: key nSliceGroups unrecognized, line 11, skipping
> Subscripted assignment dimension mismatch.
>
> Error in fast_ldpar4 (line 97)
>   par4(nthrow,1) = tonset;
>
> Error in flac_customize (line 121)
> [par partype] = fast_ldpar4(parpath);
>
> Error in fast_selxavg3b (line 129)
> flac0 = flac_customize(flac0);
>
> >> --
> ERROR: fast_selxavg3() failed\n
>
>
> 2018-04-24 20:27 GMT+03:00 Douglas Greve :
>
>> Try deleting the contrasts (.mat files) and rerunning
>>
>> On 4/24/18 5:48 AM, Francesca Strappini wrote:
>>
>>
>> Dear FreeSurfer experts,
>>
>> I'm trying to analyze some monkey functional data. I got this error
>> message with selxavg3-sess.
>>
>> I run the following commands:
>>
>> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast ON-vs-OFF -a
>> 1 -c 0
>> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast ON-vs-OFF -a
>> 1 -c 0
>> preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s MonkeyCassis-FF -fsd
>> bold -per-session
>> selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF
>>
>>
>> --- matlab output 
>> MATLAB is selecting SOFTWARE OPENGL rendering.
>>
>> < M A T L A B (R) >
>>   Copyright 1984-2016 The MathWorks, Inc.
>>R2016b (9.1.0.441655) 64-bit (glnxa64)
>>  September 7, 2016
>>
>>
>> To get started, type one of these: helpwin, helpdesk, or demo.
>> For product information, visit www.mathworks.com.
>>
>> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
>> >> /usr/local/freesurfer/matlab/MRIread.m
>> >> >> >> starting fast_selxavg3b
>>
>>
>> #@# MonkeyCassis-FF ###
>> /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
>> -
>> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
>> -
>> outtop = /usr/local/freesurfer/fsfast/Monkeys
>> Extension format = nii.gz
>> INFO: key nSliceGroups unrecognized, line 11, skipping
>>  1 ON-vs-OFF.mat
>> Subscripted assignment dimension mismatch.
>>
>> Error in fast_ldpar4 (line 97)
>>   par4(nthrow,1) = tonset;
>>
>> Error in flac_customize (line 121)
>> [par partype] = fast_ldpar4(parpath);
>>
>> Error in fast_selxavg3b (line 129)
>> flac0 = flac_customize(flac0);
>>
>> >> --
>> ERROR: fast_selxavg3() failed\n
>>
>> Thank you!
>> Best
>>
>> Francesca
>>
>> --
>> Francesca Strappini, Ph.D.
>> Neurobiology Department
>> Weizmann Institute of Science
>> 234 Herzl Street, Rehovot 7610001 Israel
>> Tel.: +972 58 444 2584
>> E-mail: francesca.strapp...@weizmann.ac.il
>>
>>
>> ___
>> 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
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Instit

Re: [Freesurfer] problem using mri_vol2label for subcortical regions

[Lucia Billeci]

External Email - Use Caution

Dear Brouce,

thanks again.
I would like exactly how to set mri_vol2label for subcortical regions as the 
way I used give me all the values of the first column equal to -1. This is a 
problem when I want to obtain obtain the centroid of the ROI using 
mri_surfcluster as I get an empty file. 

Hope Doug can help me.

Thanks 
Lucia

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

Dr. Lucia Billeci, PhD
Institute of Clinical Physiology (IFC) National Research Council (CNR)
via Moruzzi 1, 56124, Pisa, Italy
e-mail: lucia.bill...@ifc.cnr.it
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 




> On 2 May 2018, at 16:01, Bruce Fischl  wrote:
> 
> Hi Lucia
> 
> can you cc the list so others can answer? You can't get a surface-based label 
> for a subcortical region as they aren't on (or close) to the surrface. I 
> think mri_vol2label is the right binary to create a volumetric ROI for each 
> one, but Doug will know
> cheers
> Bruce
> 
> On Wed, 2 May 2018, Lucia Billeci wrote:
> 
>> External Email - Use Caution
>> Dear Bruce,
>> thanks for your answer.
>> I would like to obtain .label file for each subcortical  region. I have 
>> tried the commands I
>> reported in the previous messages but probably they are not correct. Could 
>> you please indicate me
>> the correct way to have the .label file for subcortical regions? I am not 
>> sure if
>> using mri_vol2label is the right way or maybe there is another strategy.
>> Thanks
>> regards
>> Lucia
>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>> Dr. Lucia Billeci, PhD
>> Institute of Clinical Physiology (IFC) National Research Council (CNR)
>> via Moruzzi 1, 56124, Pisa, Italy
>> e-mail: lucia.bill...@ifc.cnr.it
>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
>> 
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.

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[Freesurfer] Fw: Query regarding creation of atlas directly from probabilistic information

[Mageshwar Selvakumar]

External Email - Use Caution

Dear Everyone,

A kind reminder. I'm unable to look beyond this step and am really looking for 
some help. I would like to know if we can use the probabilistic information 
directly on mri_train

Thank you,


Kind regards

Mageshwar Selvakumar, M.Sc

Department of Pharmakologische Bildgebung und Bildanalyse

Friedrich Alexander Universität Erlangen Nürnberg


Office: Fahrstr. 17, 91054 Erlangen

Phone: + 49-9131-8522898



From: Mageshwar Selvakumar 
Sent: Monday, April 23, 2018 10:36 AM
To: freesurfer@nmr.mgh.harvard.edu; Bruce Fischl
Subject: Query regarding creation of atlas directly from probabilistic 
information

Dear All and Bruce,

This mail is on top of the query I had a couple of weeks back where I 
misinterpreted that I had binary mask of each structure as individual nifti 
volume files but on closer look, the nifti files had the probability that the 
structure is present at that certain location. On looking into the freesurfer 
website, I came across this documentation of creation of Atlas, 
https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceLabelAtlas
SurfaceLabelAtlas - Free Surfer 
Wiki
Overview. This document provides an overview of two related topics: How the 
FreeSurfer pipeline automatically labels a subject's regions (producing an 
annotation file) by comparing the subject's curvature data to an "atlas" 
("gcs") file.
surfer.nmr.mgh.harvard.edu

 In this documentation the process is done by looping through N subjects to get 
the probability information, and these subjects are registered to the 
registration template derived from average of reference templates. I would like 
to know if I could use these probability information directly and since the 
atlas information is already in the MNI152 space, can I use the registration 
template which is already available with freesurfer, and if yes, can someone 
guide me on which registration files I must use.

Secondly, I tried using mri_vol2surf and tried to convert the volume data to a 
surface data before creating labels, but on doing so I had errors when creating 
labels from the surface files.
To convert into volume I ran the below code:


*mri_vol2surf --mov ID076_LL_PHGa_l_HvOx_prob.mgz  --ref 
ID076_LL_PHGa_l_HvOx_prob.mgz  --out ID076_LL_PHGa_l_HvOx_prob_surf.mgz  --hemi 
lh --mni152reg --projdist-max -2 0 .1 --reshape --interp nearest*

Then I to convert this surface file into label I ran


*mri_cor2label --i ID080_CPuP_l_HvOx_prob_surf.mgz --l area1.label --id 076*

And I got the error


*Found 0 label voxels

ERROR: found no voxels matching id 76*

But the process runs fine if I run the mri_cor2label on the volume file. It 
would be nice if someone can help me out on where I'm going wrong here.

Thank you,


Kind regards

Mageshwar Selvakumar, M.Sc

Department of Pharmakologische Bildgebung und Bildanalyse

Friedrich Alexander Universität Erlangen Nürnberg


Office: Fahrstr. 17, 91054 Erlangen

Phone: + 49-9131-8522898

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Re: [Freesurfer] problem using mri_vol2label for subcortical regions

[Bruce Fischl]

Hi Lucia

the first column being -1 means that it is not mapped to the surface, so 
is correct in your (subcortical) case. Try loading the label as an ROI in 
freeview and see if it is correct


cheers
Bruce
On Wed, 2 May 2018, Lucia Billeci wrote:



External Email - Use Caution

Dear Brouce,


thanks again.
I would like exactly how to set mri_vol2label for subcortical regions as the 
way I used
give me all the values of the first column equal to -1. This is a problem when 
I want
to obtain obtain the centroid of the ROI using mri_surfcluster as I get an 
empty file. 

Hope Doug can help me.

Thanks 
Lucia

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

Dr. Lucia Billeci, PhD
Institute of Clinical Physiology (IFC) National Research Council (CNR)
via Moruzzi 1, 56124, Pisa, Italy
e-mail: lucia.bill...@ifc.cnr.it
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 




  On 2 May 2018, at 16:01, Bruce Fischl  wrote:

Hi Lucia

can you cc the list so others can answer? You can't get a surface-based label 
for
a subcortical region as they aren't on (or close) to the surrface. I think
mri_vol2label is the right binary to create a volumetric ROI for each one, but
Doug will know
cheers
Bruce

On Wed, 2 May 2018, Lucia Billeci wrote:

  External Email - Use Caution
  Dear Bruce,
  thanks for your answer.
  I would like to obtain .label file for each subcortical  region. I
  have tried the commands I
  reported in the previous messages but probably they are not correct.
  Could you please indicate me
  the correct way to have the .label file for subcortical regions? I am
  not sure if
  using mri_vol2label is the right way or maybe there is another
  strategy.
  Thanks
  regards
  Lucia
  _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
  Dr. Lucia Billeci, PhD
  Institute of Clinical Physiology (IFC) National Research Council
  (CNR)
  via Moruzzi 1, 56124, Pisa, Italy
  e-mail: lucia.bill...@ifc.cnr.it
  _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 



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[Freesurfer] Starting with Neuroimaging

[Lan Naoyuki]

External Email - Use Caution

Hello Freesurfer experts,

I am a junior in Computer Science, and am planning to join a neuroimaging
lab in the summer. As far as I know, one of the projects that the lab is
interested in is structural MRI analyses of bovine brains, and they would
like to modify the pipeline of Freesurfer to achieve this.

I have little to no experience with neuroimaging, and would like to prepare
myself better before joining. My question is: is there any good resources
(online courses, videos, reading, etc...) that can give me a high level
picture of the analysis process? Or how to start getting into neuroimaging
from a Computer Science perspective in general?

Thank you for taking time to consider my questions. I apologize if they are
too trivial.

Best,

Lan
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Re: [Freesurfer] Starting with Neuroimaging

[Fernanda Hansen P. de Moraes]

External Email - Use Caution

HI!
The FreeSurfer Tutorials (http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials)
give a good overview of how FreeSurfer works and each step of the analysis.

Good luck and welcome!

Fernanda

On Wed, May 2, 2018 at 12:09 PM Lan Naoyuki  wrote:

> External Email - Use Caution
>
> Hello Freesurfer experts,
>
> I am a junior in Computer Science, and am planning to join a neuroimaging
> lab in the summer. As far as I know, one of the projects that the lab is
> interested in is structural MRI analyses of bovine brains, and they would
> like to modify the pipeline of Freesurfer to achieve this.
>
> I have little to no experience with neuroimaging, and would like to
> prepare myself better before joining. My question is: is there any good
> resources (online courses, videos, reading, etc...) that can give me a high
> level picture of the analysis process? Or how to start getting into
> neuroimaging from a Computer Science perspective in general?
>
> Thank you for taking time to consider my questions. I apologize if they
> are too trivial.
>
> Best,
>
> Lan
> ___
> Freesurfer mailing list
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
-- 
Fernanda Hansen P. de Moraes
Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz
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Re: [Freesurfer] problem using mri_vol2label for subcortical regions

[Lucia Billeci]

External Email - Use Caution

Dear Bruce,

the ROI appears correct in freeview. However I have a problem in the following 
step, i.e. obtain the centroid of the ROi.

I used the following command:

mri_surfcluster --in 
/Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel 
./tests_label/sub/lh.amygdala.label --sum ./tests_label/sum/sum.lh.amygdala 
--centroid --thmin 0 --hemi lh --subject fsaverage —nofixmni  

However it doesn’t work for subcortical label files (it works with cortical 
ones). I have the following output and the command doesn’t produce the file 
sum.lh.amygdala:

thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $
hemi   = lh
srcid  = /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness 
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = abs
thmin  = 0
thmax  = -1
fdr= -1
minarea= 0
xfmfile= talairach.xfm
clabelfile = ./tests_label/sub/lh.amygdala.label
clabelinv  = 0
nth = -1
sumfile  = ./tests_label/sum/sum.lh.amygdala
subjectsdir= /Applications/freesurfer/subjects
FixMNI = 0
Loading clabel ./tests_label/sub/lh.amygdala.label.
Found 1941 points in clabel.
- XFM matrix (RAS2RAS) ---
/Applications/freesurfer/subjects/fsaverage/mri/transforms/talairach.xfm
 1.0   0.0   0.0   0.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;

Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white
Done reading source surface
Computing metric properties
Loading source values
/Applications/freesurfer/bin/mri_surfcluster: line 3:  2828 Bus error: 10   
mri_surfcluster.bin "$@"

Maybe because lh.thickness is only for cortical regions? In this case, how can 
I obtain centroids of subcortical ROIs?

Thanks
Regards
Lucia


_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

Dr. Lucia Billeci, PhD
Institute of Clinical Physiology (IFC) National Research Council (CNR)
via Moruzzi 1, 56124, Pisa, Italy
e-mail: lucia.bill...@ifc.cnr.it
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 




> On 2 May 2018, at 17:05, Bruce Fischl  wrote:
> 
> Hi Lucia
> 
> the first column being -1 means that it is not mapped to the surface, so is 
> correct in your (subcortical) case. Try loading the label as an ROI in 
> freeview and see if it is correct
> 
> cheers
> Bruce
> On Wed, 2 May 2018, Lucia Billeci wrote:
> 
>> External Email - Use Caution
>> Dear Brouce,
>> thanks again.
>> I would like exactly how to set mri_vol2label for subcortical regions as the 
>> way I used
>> give me all the values of the first column equal to -1. This is a problem 
>> when I want
>> to obtain obtain the centroid of the ROI using mri_surfcluster as I get an 
>> empty file. 
>> Hope Doug can help me.
>> Thanks 
>> Lucia
>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>> Dr. Lucia Billeci, PhD
>> Institute of Clinical Physiology (IFC) National Research Council (CNR)
>> via Moruzzi 1, 56124, Pisa, Italy
>> e-mail: lucia.bill...@ifc.cnr.it
>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
>> 
>>  On 2 May 2018, at 16:01, Bruce Fischl  
>> wrote:
>> Hi Lucia
>> can you cc the list so others can answer? You can't get a surface-based 
>> label for
>> a subcortical region as they aren't on (or close) to the surrface. I think
>> mri_vol2label is the right binary to create a volumetric ROI for each one, 
>> but
>> Doug will know
>> cheers
>> Bruce
>> On Wed, 2 May 2018, Lucia Billeci wrote:
>> 
>>  External Email - Use Caution
>>  Dear Bruce,
>>  thanks for your answer.
>>  I would like to obtain .label file for each subcortical  region. I
>>  have tried the commands I
>>  reported in the previous messages but probably they are not correct.
>>  Could you please indicate me
>>  the correct way to have the .label file for subcortical regions? I am
>>  not sure if
>>  using mri_vol2label is the right way or maybe there is another
>>  strategy.
>>  Thanks
>>  regards
>>  Lucia
>>  _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>>  Dr. Lucia Billeci, PhD
>>  Institute of Clinical Physiology (IFC) National Research Council
>>  (CNR)
>>  via Moruzzi 1, 56124, Pisa, Italy
>>  e-mail: lucia.bill...@ifc.cnr.it
>>  _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properl

Re: [Freesurfer] Starting with Neuroimaging

[Bruce Fischl]

Hi Lan

we have tutorials on our wiki with associated data that you could try going 
through


cheers
Bruce
On Wed, 2 May 2018, Lan Naoyuki wrote:



External Email - Use Caution

Hello Freesurfer experts,
I am a junior in Computer Science, and am planning to join a neuroimaging lab 
in the summer. As far as I know, one of the
projects that the lab is interested in is structural MRI analyses of bovine 
brains, and they would like to modify the pipeline
of Freesurfer to achieve this. 

I have little to no experience with neuroimaging, and would like to prepare 
myself better before joining. My question is: is
there any good resources (online courses, videos, reading, etc...) that can 
give me a high level picture of the analysis
process? Or how to start getting into neuroimaging from a Computer Science 
perspective in general?

Thank you for taking time to consider my questions. I apologize if they are too 
trivial. 

Best,

Lan

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[Freesurfer] Differences in aseg.stats automatic results

[Fernanda Hansen P. de Moraes]

External Email - Use Caution

Good afternoon,

I've got two types of aseg.stats results from the file automatically
created from the regular script (recon-all -all). I am especially
interested in the SupraTentorialVolNotVent.

Here goes two examples:















































*Title Segmentation Statistics # # generating_program mri_segstats#
cvs_version $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $#
cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray
--in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv
--surf-wm-vol --surf-ctx-vol --totalgray --ctab
/usr/local/freesurfer/ASegStatsLUT.txt --subject SUBJ123 # sysname Linux#
hostname rachael.localdomain# machine x86_64# user fernanda.hansen#
anatomy_type volume# # SUBJECTS_DIR
/dados1/PROJETOS/PRJ1513_GIRIFICACAO_CONTROLES/03_PROCS/PREPROC_DATA/3DT1_ALZ_FOLLOWS/DICOM_PARA_RECONVERSAO2NII/SEG#
subjectname SUBJ123# Measure lhCortex, lhCortexVol, Left hemisphere
cortical gray matter volume, 211672.093308, mm^3# Measure rhCortex,
rhCortexVol, Right hemisphere cortical gray matter volume, 216185.270458,
mm^3# Measure Cortex, CortexVol, Total cortical gray matter volume,
427857.363767, mm^3# Measure lhCorticalWhiteMatter,
lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume,
227845.296875, mm^3# Measure rhCorticalWhiteMatter,
rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume,
227386.531250, mm^3# Measure CorticalWhiteMatter, CorticalWhiteMatterVol,
Total cortical white matter volume, 455231.828125, mm^3# Measure
SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 171469.00,
mm^3# Measure TotalGray, TotalGrayVol, Total gray matter volume,
599326.363767, mm^3# Measure SupraTentorial, SupraTentorialVol,
Supratentorial volume, 1050908.034545, mm^3# Measure IntraCranialVol, ICV,
Intracranial Volume, 1734351.873615, mm^3# SegVolFile mri/aseg.mgz Title
Segmentation Statistics # # generating_program mri_segstats# cvs_version
$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $# cmdline
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz
--empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in
mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv
--surf-wm-vol --surf-ctx-vol --totalgray --ctab
/usr/local/freesurfer/ASegStatsLUT.txt --subject SUBJ123 # sysname Linux#
hostname rachael.localdomain# machine x86_64# user fernanda.hansen#
anatomy_type volume# # SUBJECTS_DIR
/dados1/PROJETOS/PRJ1513_GIRIFICACAO_CONTROLES/03_PROCS/PREPROC_DATA/3DT1_ALZ_FOLLOWS/DICOM_PARA_RECONVERSAO2NII/SEG#
subjectname SUBJ123# Measure lhCortex, lhCortexVol, Left hemisphere
cortical gray matter volume, 211672.093308, mm^3# Measure rhCortex,
rhCortexVol, Right hemisphere cortical gray matter volume, 216185.270458,
mm^3# Measure Cortex, CortexVol, Total cortical gray matter volume,
427857.363767, mm^3# Measure lhCorticalWhiteMatter,
lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume,
227845.296875, mm^3# Measure rhCorticalWhiteMatter,
rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume,
227386.531250, mm^3# Measure CorticalWhiteMatter, CorticalWhiteMatterVol,
Total cortical white matter volume, 455231.828125, mm^3# Measure
SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 171469.00,
mm^3# Measure TotalGray, TotalGrayVol, Total gray matter volume,
599326.363767, mm^3# Measure SupraTentorial, SupraTentorialVol,
Supratentorial volume, 1050908.034545, mm^3# Measure IntraCranialVol, ICV,
Intracranial Volume, 1734351.873615, mm^3# SegVolFile mri/aseg.mgz*


and




































*Title Segmentation Statistics # # generating_program mri_segstats#
cvs_version $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $#
cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg
--excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol
--surf-ctx-vol --totalgray --euler --ctab
/usr/local/freesurfer/ASegStatsLUT.txt --subject PRI018 # sysname Linux#
hostname deckard.localdomain# machine x86_64# user fernanda.hansen#
anatomy_type volume# # SUBJECTS_DIR
/dados1/PROJETOS/PRJ1513_GIRIFICACAO_CONTROLES/03_PROCS/PREPROC_DATA/3DT1_ALZ_FOLLOWS#
subjectname PRI018# Measure BrainSeg, BrainSegVol, Brain Segmentation
Volume, 939020.00, mm^3# Measure BrainSegNotVent, BrainSegVolNotVent,
Brain Segmentation Volume Without Ventricles, 903909.00, mm^3# Measure
BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume
Without Ventricles from Surf, 903725.881149, mm^3# Measure lhCortex,
lhCortexVol, Left hemisphere cortical gray matter volume, 194350.327731,
mm^3# Measure rhCortex, rhCortexVol, Rig

[Freesurfer] mri_vol2surf warning

[Rachel Bencic]

External Email - Use Caution

Hello FreeSurfer Developers,



I'm attempting to resample beta weights generated from AFNI’s 3dDeconvolve
command to individual subjects’ cortical surfaces. Prior to running
3dDeconvolve, I ran bbregister to coregister subjects’ (unwarped)
functional data to their T1 anatomical scans and to generate a registration
file to be used in the mri_vol2surf command.



However, I get the following warning when I run the mri_vol2surf command:



WARNING: the voxel resolution in the source volume (3.75, 3.75, 3.75)
differs from that listed in the registration file (3.75, 3.75, 5)



I've searched the list and came across a potentially similar case from Apr.
26, 2011 (SUBJECT: (no subject), AUTHOR: Kevin Bickart), which included the
following advice:



Hi Kevin, you can ignore that warning. The values in the registration

file are not correct.



doug



I thought I would reach out to inquire as to whether this is still the case
(i.e., that this warning can be ignored) or if it might be a more serious
issue? I will add that mri_vol2surf did appear to run successfully (i.e.,
it did not error out) and provided a .mgh file as output.



In case it is helpful, as a next step I plan to convert the .mgh file to an
ASCII file to extract the time series. Ultimately, I plan to run graph
analyses on the time series data.



Any feedback you have would be greatly appreciated.



Rachel



1) FreeSurfer version: freesurfer_6.0_x86_64

2) Platform: OSX High Sierra



Here is my command:

mri_vol2surf --mov ../betaEPI/ Betas_EPIpreproc.nii --srcreg
../bbregistration.dat --hemi lh --projfrac 0.5 --o ./lh.1.mgh



mris_convert -c ./lh.1.mgh $parc_dir/${1}/surf/lh.white ../lh_ascii/lh.1.asc





And the full output:

srcvol = ../betaEPI/Betas_EPIpreproc.nii

srcreg = ../bbregistration.dat

srcregold = 0

srcwarp unspecified

surf = white

hemi = lh

ProjFrac = 0.5

thickness = thickness

reshape = 0

interp = nearest

float2int = round

GetProjMax = 0

INFO: float2int code = 0

Done loading volume

INFO: This REGISTER_DAT transform is valid only for volumes between  COR
types with c_(r,a,s) = 0.

Input reg is register.dat

WARNING: the voxel resolution in the source volume (3.75,3.75,3.75) differs

 from that listed in the registration file (3.75,3.75,5)

 original matrix ---

 0.99988  -0.00997   0.01155  -0.43638;

-0.01472  -0.43023   0.90260   22.14351;

 0.00403   0.90266   0.43033   34.58801;

 0.0   0.0   0.0   1.0;

 original matrix ---

Reading surface /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.white

Done reading source surface

Reading thickness
/Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.thickness

Done

Mapping Source Volume onto Source Subject Surface

 1 0.5 0.5 0.5

using old

Done mapping volume to surface

Number of source voxels hit = 8657

Writing to ./lh.1.mgh

Dim: 146930 1 1

srcvol = ../betaEPI/Betas_EPIpreproc.nii

srcreg = ../bbregistration.dat

srcregold = 0

srcwarp unspecified

surf = white

hemi = rh

ProjFrac = 0.5

thickness = thickness

reshape = 0

interp = nearest

float2int = round

GetProjMax = 0

INFO: float2int code = 0

Done loading volume

INFO: This REGISTER_DAT transform is valid only for volumes between  COR
types with c_(r,a,s) = 0.

Input reg is register.dat

WARNING: the voxel resolution in the source volume (3.75,3.75,3.75) differs

 from that listed in the registration file (3.75,3.75,5)

 original matrix ---

 0.99988  -0.00997   0.01155  -0.43638;

-0.01472  -0.43023   0.90260   22.14351;

 0.00403   0.90266   0.43033   34.58801;

 0.0   0.0   0.0   1.0;

 original matrix ---

Reading surface /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.white

Done reading source surface

Reading thickness
/Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.thickness

Done

Mapping Source Volume onto Source Subject Surface

 1 0.5 0.5 0.5

using old

Done mapping volume to surface

Number of source voxels hit = 8681

Writing to ./rh.1.mgh

Dim: 148618 1 1
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[Freesurfer] kvlGEMSMatlab error: search direction is not a descent direction

[Wayne Su]

External Email - Use Caution

Hello FreeSurfer Developers,
> 
> I'm attempting to run longitudinal segmentation of hippocampal subfields by
> using the development version of FreeSurfer, but for some of my subjects I get
> the following error:
>  
> ***
>  Global iteration 3
> ***
>  
>* Estimating subject-specific atlas *
> L-BFGS
> Verbose: 0
> MaximalDeformationStopCriterion: 1e-10
> LineSearchMaximalDeformationIntervalStopCriterion: 1e-10
> MaximumNumberOfIterations: 1000
> BFGS-MaximumMemoryLength: 12
> Subject atlas deformation, step 1 of 400
> Did one deformation step of max. 0.38685 voxels in 7.733 seconds
> 
> minLogLikelihoodTimesPrior =
> 
>1.0297e+05
> 
> Subject atlas deformation, step 2 of 400
> Error using kvlGEMSMatlab
> /autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/kvlAtlasMe
> shDeformationOptimizer.cxx:327:
> itk::ERROR: AtlasMeshDeformationLBFGSOptimizer(0x2b53b9427df0): search
> direction is not a descent direction!
> 
> Error in kvlStepOptimizer (line 11)
> Error in SegmentSubfieldsT1Longitudinal (line 1169)
> 
> 
> Does anyone have any thoughts on how to trouble-shoot this one?
> 
> 1) FreeSurfer version: freesurfer-x86_64-unknown-linux-gnu-dev-20180426
> 2) Platform: CentOS Linux release 7.4.1708 (Core)
> 3) uname -a: Linux bcmhari-hpc12 3.10.0-327.el7.x86_64 #1 SMP Thu Nov 19
> 22:10:57 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
> 
> 
> 
> Thanks,
> Wayne

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Re: [Freesurfer] Starting with Neuroimaging

[Lan Naoyuki]

External Email - Use Caution

Hi Fernanda and Bruce,

Thank you for your prompt replies! I will look into them.

Best,

Lan

On Wed, May 2, 2018 at 11:14 AM, Bruce Fischl 
wrote:

> Hi Lan
>
> we have tutorials on our wiki with associated data that you could try
> going through
>
> cheers
> Bruce
> On Wed, 2 May 2018, Lan Naoyuki wrote:
>
>
>> External Email - Use Caution
>>
>> Hello Freesurfer experts,
>> I am a junior in Computer Science, and am planning to join a neuroimaging
>> lab in the summer. As far as I know, one of the
>> projects that the lab is interested in is structural MRI analyses of
>> bovine brains, and they would like to modify the pipeline
>> of Freesurfer to achieve this.
>>
>> I have little to no experience with neuroimaging, and would like to
>> prepare myself better before joining. My question is: is
>> there any good resources (online courses, videos, reading, etc...) that
>> can give me a high level picture of the analysis
>> process? Or how to start getting into neuroimaging from a Computer
>> Science perspective in general?
>>
>> Thank you for taking time to consider my questions. I apologize if they
>> are too trivial.
>>
>> Best,
>>
>> Lan
>>
>>
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>
>
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> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] problem using mri_vol2label for subcortical regions

[Douglas N. Greve]

mri_surfcluster only works for surfaces (that's what the "surf" in the 
name means). If you want the centroid of a volume ROI use 
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids


On 05/02/2018 12:08 PM, Lucia Billeci wrote:
>
>
> Dear Bruce,
>
> the ROI appears correct in freeview. However I have a problem in the 
> following step, i.e. obtain the centroid of the ROi.
>
> I used the following command:
>
> mri_surfcluster --in 
> /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel 
> ./tests_label/sub/lh.amygdala.label --sum 
> ./tests_label/sum/sum.lh.amygdala --centroid --thmin 0 --hemi lh 
> --subject fsaverage —nofixmni
>
> However it doesn’t work for subcortical label files (it works with 
> cortical ones). I have the following output and the command doesn’t 
> produce the file sum.lh.amygdala:
>
> thsign = abs, id = 0
> version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman 
> Exp $
> hemi           = lh
> srcid          = 
> /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness
> srcsubjid      = fsaverage
> srcsurf        = white
> srcframe       = 0
> thsign         = abs
> thmin          = 0
> thmax          = -1
> fdr            = -1
> minarea        = 0
> xfmfile        = talairach.xfm
> clabelfile     = ./tests_label/sub/lh.amygdala.label
> clabelinv      = 0
> nth         = -1
> sumfile  = ./tests_label/sum/sum.lh.amygdala
> subjectsdir    = /Applications/freesurfer/subjects
> FixMNI = 0
> Loading clabel ./tests_label/sub/lh.amygdala.label.
> Found 1941 points in clabel.
> - XFM matrix (RAS2RAS) ---
> /Applications/freesurfer/subjects/fsaverage/mri/transforms/talairach.xfm
>  1.0   0.0   0.0   0.0;
>  0.0   1.0   0.0   0.0;
>  0.0   0.0   1.0   0.0;
>  0.0   0.0   0.0   1.0;
> 
> Reading source surface 
> /Applications/freesurfer/subjects/fsaverage/surf/lh.white
> Done reading source surface
> Computing metric properties
> Loading source values
> /Applications/freesurfer/bin/mri_surfcluster: line 3:  2828 Bus error: 
> 10           mri_surfcluster.bin "$@"
>
> Maybe because lh.thickness is only for cortical regions? In this case, 
> how can I obtain centroids of subcortical ROIs?
>
> Thanks
> Regards
> Lucia
>
>
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> Dr. Lucia Billeci, PhD
> Institute of Clinical Physiology (IFC) National Research Council (CNR)
> via Moruzzi 1, 56124, Pisa, Italy
> e-mail: lucia.bill...@ifc.cnr.it 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
>
>
>
>> On 2 May 2018, at 17:05, Bruce Fischl > > wrote:
>>
>> Hi Lucia
>>
>> the first column being -1 means that it is not mapped to the surface, 
>> so is correct in your (subcortical) case. Try loading the label as an 
>> ROI in freeview and see if it is correct
>>
>> cheers
>> Bruce
>> On Wed, 2 May 2018, Lucia Billeci wrote:
>>
>>> External Email - Use Caution
>>> Dear Brouce,
>>> thanks again.
>>> I would like exactly how to set mri_vol2label for subcortical 
>>> regions as the way I used
>>> give me all the values of the first column equal to -1. This is a 
>>> problem when I want
>>> to obtain obtain the centroid of the ROI using mri_surfcluster as I 
>>> get an empty file.
>>> Hope Doug can help me.
>>> Thanks
>>> Lucia
>>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>>> Dr. Lucia Billeci, PhD
>>> Institute of Clinical Physiology (IFC) National Research Council (CNR)
>>> via Moruzzi 1, 56124, Pisa, Italy
>>> e-mail: lucia.bill...@ifc.cnr.it 
>>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>>>
>>>  On 2 May 2018, at 16:01, Bruce Fischl 
>>>  wrote:
>>> Hi Lucia
>>> can you cc the list so others can answer? You can't get a 
>>> surface-based label for
>>> a subcortical region as they aren't on (or close) to the surrface. I 
>>> think
>>> mri_vol2label is the right binary to create a volumetric ROI for 
>>> each one, but
>>> Doug will know
>>> cheers
>>> Bruce
>>> On Wed, 2 May 2018, Lucia Billeci wrote:
>>>
>>>  External Email - Use Caution
>>>  Dear Bruce,
>>>  thanks for your answer.
>>>  I would like to obtain .label file for each subcortical  region. I
>>>  have tried the commands I
>>>  reported in the previous messages but probably they are not 
>>> correct.
>>>  Could you please indicate me
>>>  the correct way to have the .label file for subcortical 
>>> regions? I am
>>>  not sure if
>>>  using mri_vol2label is the right way or maybe there is another
>>>  strategy.
>>>  Thanks
>>>  regards
>>>  Lucia
>>>  _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>>>  Dr. Lucia Billeci, PhD
>>>  Institute of Clinical Physiology (IFC) National Research Council
>>>  (CNR)
>>>  via Moruzzi 1, 56124, Pisa, Italy
>>>  e-mail: luci

Re: [Freesurfer] Differences in aseg.stats automatic results

[Douglas N. Greve]

You are using two different versions of mri_segstats (probably two 
different versions of FS) and  getting different results. Why not just 
use one version?


On 05/02/2018 01:24 PM, Fernanda Hansen P. de Moraes wrote:
>
>
> Good afternoon,
>
> I've got two types of aseg.stats results from the file automatically 
> created from the regular script (recon-all -all). I am especially 
> interested in the SupraTentorialVolNotVent.
>
> Here goes two examples:
>
> /Title Segmentation Statistics
> #
> # generating_program mri_segstats
> # cvs_version $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks 
> Exp $
> # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
> mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent 
> --subcortgray --in mri/norm.mgz --in-intensity-name norm 
> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol 
> --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 
> SUBJ123
> # sysname Linux
> # hostname rachael.localdomain
> # machine x86_64
> # user fernanda.hansen
> # anatomy_type volume
> #
> # SUBJECTS_DIR 
> /dados1/PROJETOS/PRJ1513_GIRIFICACAO_CONTROLES/03_PROCS/PREPROC_DATA/3DT1_ALZ_FOLLOWS/DICOM_PARA_RECONVERSAO2NII/SEG
> # subjectname SUBJ123
> # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter 
> volume, 211672.093308, mm^3
> # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter 
> volume, 216185.270458, mm^3
> # Measure Cortex, CortexVol, Total cortical gray matter volume, 
> 427857.363767, mm^3
> # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left 
> hemisphere cortical white matter volume, 227845.296875, mm^3
> # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right 
> hemisphere cortical white matter volume, 227386.531250, mm^3
> # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical 
> white matter volume, 455231.828125, mm^3
> # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 
> 171469.00, mm^3
> # Measure TotalGray, TotalGrayVol, Total gray matter volume, 
> 599326.363767, mm^3
> # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 
> 1050908.034545, mm^3
> # Measure IntraCranialVol, ICV, Intracranial Volume, 1734351.873615, mm^3
> # SegVolFile mri/aseg.mgz Title Segmentation Statistics
> #
> # generating_program mri_segstats
> # cvs_version $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks 
> Exp $
> # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
> mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent 
> --subcortgray --in mri/norm.mgz --in-intensity-name norm 
> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol 
> --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 
> SUBJ123
> # sysname Linux
> # hostname rachael.localdomain
> # machine x86_64
> # user fernanda.hansen
> # anatomy_type volume
> #
> # SUBJECTS_DIR 
> /dados1/PROJETOS/PRJ1513_GIRIFICACAO_CONTROLES/03_PROCS/PREPROC_DATA/3DT1_ALZ_FOLLOWS/DICOM_PARA_RECONVERSAO2NII/SEG
> # subjectname SUBJ123
> # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter 
> volume, 211672.093308, mm^3
> # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter 
> volume, 216185.270458, mm^3
> # Measure Cortex, CortexVol, Total cortical gray matter volume, 
> 427857.363767, mm^3
> # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left 
> hemisphere cortical white matter volume, 227845.296875, mm^3
> # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right 
> hemisphere cortical white matter volume, 227386.531250, mm^3
> # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical 
> white matter volume, 455231.828125, mm^3
> # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 
> 171469.00, mm^3
> # Measure TotalGray, TotalGrayVol, Total gray matter volume, 
> 599326.363767, mm^3
> # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 
> 1050908.034545, mm^3
> # Measure IntraCranialVol, ICV, Intracranial Volume, 1734351.873615, mm^3
> # SegVolFile mri/aseg.mgz/
>
>
> and
>
> /Title Segmentation Statistics
> #
> # generating_program mri_segstats
> # cvs_version $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve 
> Exp $
> # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
> mri/norm.mgz --empty --brainmask mri/brainmask.mgz 
> --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent 
> --subcortgray --in mri/norm.mgz --in-intensity-name norm 
> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol 
> --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt 
> --subject PRI018
> # sysname Linux
> # hostname deckard.localdomain
> # machine x86_64
> # user fernanda.hansen
> # anatomy_type volume
> #
> # SUBJECTS_DIR 
> /dados1/PROJETOS/PRJ1513_GIRIFICACAO_CONTROLES/03_PROCS/PREPROC_DATA/3DT1_ALZ_FOLLOWS
> # subjectname PRI018
> # Measure BrainSeg, BrainSegVol, Brain Segmentati

Re: [Freesurfer] mri_vol2surf warning

[Douglas N. Greve]

When you ran bbregister, what was the voxel resolution of the mov volume?


On 05/02/2018 01:28 PM, Rachel Bencic wrote:
>
>
> Hello FreeSurfer Developers,
>
> I'm attempting to resample beta weights generated from AFNI’s 
> 3dDeconvolve command to individual subjects’ cortical surfaces. Prior 
> to running 3dDeconvolve, I ran bbregister to coregister subjects’ 
> (unwarped) functional data to their T1 anatomical scans and to 
> generate a registration file to be used in the mri_vol2surf command.
>
> However, I get the following warning when I run the mri_vol2surf command:
>
> WARNING: the voxel resolution in the source volume (3.75, 3.75, 3.75) 
> differs from that listed in the registration file (3.75, 3.75, 5)
>
> I've searched the list and came across a potentially similar case from 
> Apr. 26, 2011 (SUBJECT: (no subject), AUTHOR: Kevin Bickart), which 
> included the following advice:
>
> Hi Kevin, you can ignore that warning. The values in the registration
>
> file are not correct.
>
> doug
>
> I thought I would reach out to inquire as to whether this is still the 
> case (i.e., that this warning can be ignored) or if it might be a more 
> serious issue? I will add that mri_vol2surf did appear to run 
> successfully (i.e., it did not error out) and provided a .mgh file as 
> output.
>
> In case it is helpful, as a next step I plan to convert the .mgh file 
> to an ASCII file to extract the time series. Ultimately, I plan to run 
> graph analyses on the time series data.
>
> Any feedback you have would be greatly appreciated.
>
> Rachel
>
> 1) FreeSurfer version: freesurfer_6.0_x86_64
>
> 2) Platform: OSX High Sierra
>
> Here is my command:
>
> mri_vol2surf --mov ../betaEPI/Betas_EPIpreproc.nii--srcreg 
> ../bbregistration.dat --hemi lh --projfrac 0.5 --o ./lh.1.mgh
>
> mris_convert -c ./lh.1.mgh $parc_dir/${1}/surf/lh.white 
> ../lh_ascii/lh.1.asc
>
> And the full output:
>
> srcvol = ../betaEPI/Betas_EPIpreproc.nii
>
> srcreg = ../bbregistration.dat
>
> srcregold = 0
>
> srcwarp unspecified
>
> surf = white
>
> hemi = lh
>
> ProjFrac = 0.5
>
> thickness = thickness
>
> reshape = 0
>
> interp = nearest
>
> float2int = round
>
> GetProjMax = 0
>
> INFO: float2int code = 0
>
> Done loading volume
>
> INFO: This REGISTER_DAT transform is valid only for volumes betweenCOR 
> types with c_(r,a,s) = 0.
>
> Input reg is register.dat
>
> WARNING: the voxel resolution in the source volume (3.75,3.75,3.75) 
> differs
>
> from that listed in the registration file (3.75,3.75,5)
>
>  original matrix ---
>
> 0.99988-0.009970.01155-0.43638;
>
> -0.01472-0.430230.9026022.14351;
>
> 0.004030.902660.4303334.58801;
>
> 0.00.00.01.0;
>
>  original matrix ---
>
> Reading surface 
> /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.white
>
> Done reading source surface
>
> Reading thickness 
> /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.thickness
>
> Done
>
> Mapping Source Volume onto Source Subject Surface
>
> 1 0.5 0.5 0.5
>
> using old
>
> Done mapping volume to surface
>
> Number of source voxels hit = 8657
>
> Writing to ./lh.1.mgh
>
> Dim: 146930 1 1
>
> srcvol = ../betaEPI/Betas_EPIpreproc.nii
>
> srcreg = ../bbregistration.dat
>
> srcregold = 0
>
> srcwarp unspecified
>
> surf = white
>
> hemi = rh
>
> ProjFrac = 0.5
>
> thickness = thickness
>
> reshape = 0
>
> interp = nearest
>
> float2int = round
>
> GetProjMax = 0
>
> INFO: float2int code = 0
>
> Done loading volume
>
> INFO: This REGISTER_DAT transform is valid only for volumes betweenCOR 
> types with c_(r,a,s) = 0.
>
> Input reg is register.dat
>
> WARNING: the voxel resolution in the source volume (3.75,3.75,3.75) 
> differs
>
> from that listed in the registration file (3.75,3.75,5)
>
>  original matrix ---
>
> 0.99988-0.009970.01155-0.43638;
>
> -0.01472-0.430230.9026022.14351;
>
> 0.004030.902660.4303334.58801;
>
> 0.00.00.01.0;
>
>  original matrix ---
>
> Reading surface 
> /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.white
>
> Done reading source surface
>
> Reading thickness 
> /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.thickness
>
> Done
>
> Mapping Source Volume onto Source Subject Surface
>
> 1 0.5 0.5 0.5
>
> using old
>
> Done mapping volume to surface
>
> Number of source voxels hit = 8681
>
> Writing to ./rh.1.mgh
>
> Dim: 148618 1 1
>
>
>
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Re: [Freesurfer] Differences in aseg.stats automatic results

[Fernanda Hansen P. de Moraes]

External Email - Use Caution

Thank you very much. I´ll check that!.

On Wed, May 2, 2018 at 3:16 PM Douglas N. Greve 
wrote:

> You are using two different versions of mri_segstats (probably two
> different versions of FS) and  getting different results. Why not just
> use one version?
>
>
> On 05/02/2018 01:24 PM, Fernanda Hansen P. de Moraes wrote:
> >
> >
> > Good afternoon,
> >
> > I've got two types of aseg.stats results from the file automatically
> > created from the regular script (recon-all -all). I am especially
> > interested in the SupraTentorialVolNotVent.
> >
> > Here goes two examples:
> >
> > /Title Segmentation Statistics
> > #
> > # generating_program mri_segstats
> > # cvs_version $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks
> > Exp $
> > # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
> > mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent
> > --subcortgray --in mri/norm.mgz --in-intensity-name norm
> > --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol
> > --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject
> > SUBJ123
> > # sysname Linux
> > # hostname rachael.localdomain
> > # machine x86_64
> > # user fernanda.hansen
> > # anatomy_type volume
> > #
> > # SUBJECTS_DIR
> >
> /dados1/PROJETOS/PRJ1513_GIRIFICACAO_CONTROLES/03_PROCS/PREPROC_DATA/3DT1_ALZ_FOLLOWS/DICOM_PARA_RECONVERSAO2NII/SEG
> > # subjectname SUBJ123
> > # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter
> > volume, 211672.093308, mm^3
> > # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter
> > volume, 216185.270458, mm^3
> > # Measure Cortex, CortexVol, Total cortical gray matter volume,
> > 427857.363767, mm^3
> > # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left
> > hemisphere cortical white matter volume, 227845.296875, mm^3
> > # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right
> > hemisphere cortical white matter volume, 227386.531250, mm^3
> > # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical
> > white matter volume, 455231.828125, mm^3
> > # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume,
> > 171469.00, mm^3
> > # Measure TotalGray, TotalGrayVol, Total gray matter volume,
> > 599326.363767, mm^3
> > # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume,
> > 1050908.034545, mm^3
> > # Measure IntraCranialVol, ICV, Intracranial Volume, 1734351.873615, mm^3
> > # SegVolFile mri/aseg.mgz Title Segmentation Statistics
> > #
> > # generating_program mri_segstats
> > # cvs_version $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks
> > Exp $
> > # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
> > mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent
> > --subcortgray --in mri/norm.mgz --in-intensity-name norm
> > --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol
> > --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject
> > SUBJ123
> > # sysname Linux
> > # hostname rachael.localdomain
> > # machine x86_64
> > # user fernanda.hansen
> > # anatomy_type volume
> > #
> > # SUBJECTS_DIR
> >
> /dados1/PROJETOS/PRJ1513_GIRIFICACAO_CONTROLES/03_PROCS/PREPROC_DATA/3DT1_ALZ_FOLLOWS/DICOM_PARA_RECONVERSAO2NII/SEG
> > # subjectname SUBJ123
> > # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter
> > volume, 211672.093308, mm^3
> > # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter
> > volume, 216185.270458, mm^3
> > # Measure Cortex, CortexVol, Total cortical gray matter volume,
> > 427857.363767, mm^3
> > # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left
> > hemisphere cortical white matter volume, 227845.296875, mm^3
> > # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right
> > hemisphere cortical white matter volume, 227386.531250, mm^3
> > # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical
> > white matter volume, 455231.828125, mm^3
> > # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume,
> > 171469.00, mm^3
> > # Measure TotalGray, TotalGrayVol, Total gray matter volume,
> > 599326.363767, mm^3
> > # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume,
> > 1050908.034545, mm^3
> > # Measure IntraCranialVol, ICV, Intracranial Volume, 1734351.873615, mm^3
> > # SegVolFile mri/aseg.mgz/
> >
> >
> > and
> >
> > /Title Segmentation Statistics
> > #
> > # generating_program mri_segstats
> > # cvs_version $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve
> > Exp $
> > # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
> > mri/norm.mgz --empty --brainmask mri/brainmask.mgz
> > --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent
> > --subcortgray --in mri/norm.mgz --in-intensity-name norm
> > --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol
> > --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt

Re: [Freesurfer] Starting with Neuroimaging

[Douglas N. Greve]

there are also videos of the class lectures on the wiki


On 05/02/2018 12:14 PM, Bruce Fischl wrote:
> Hi Lan
>
> we have tutorials on our wiki with associated data that you could try 
> going through
>
> cheers
> Bruce
> On Wed, 2 May 2018, Lan Naoyuki wrote:
>
>>
>> External Email - Use Caution
>>
>> Hello Freesurfer experts,
>> I am a junior in Computer Science, and am planning to join a 
>> neuroimaging lab in the summer. As far as I know, one of the
>> projects that the lab is interested in is structural MRI analyses of 
>> bovine brains, and they would like to modify the pipeline
>> of Freesurfer to achieve this.
>>
>> I have little to no experience with neuroimaging, and would like to 
>> prepare myself better before joining. My question is: is
>> there any good resources (online courses, videos, reading, etc...) 
>> that can give me a high level picture of the analysis
>> process? Or how to start getting into neuroimaging from a Computer 
>> Science perspective in general?
>>
>> Thank you for taking time to consider my questions. I apologize if 
>> they are too trivial.
>>
>> Best,
>>
>> Lan
>>
>>
>
>
> ___
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[Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions

[Alexopoulos, Dimitrios]

External Email - Use Caution

We have acquired data on a few kids and have generated nice surfaces, however, 
the diffusion data we acquired (102 directions and AP/PA distortion maps) were 
suspect due to motion and results from Tracula were not ideal.

We have since brought these kids back for a repeat scan, but only acquired the 
diffusion sequences, and no structural T1.
Can we use the original surfaces/output as input to tracula with the DTI data 
from the repeat MR session?

Jim

"The materials in this email are private and may contain Protected Health 
Information. If you are not the intended recipient, be advised that any 
unauthorized use, disclosure, copying, distribution or the taking of any action 
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have received this email in error, please immediately notify the sender via 
telephone or return email."



The materials in this message are private and may contain Protected Healthcare 
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Re: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions

[Yendiki, Anastasia]

Yes, you can. The only thing that TRACULA uses from the structural is the 
aparc+aseg, and specifically the relative positions (left, right, anterior, 
etc.) of each tract with respect to the segmentation labels in the aparc+aseg. 
It's safe to assume that those positions will not have changed between 
sessions. If the sessions are not too far apart, the registration between the 
diffusion and structural within-subject across sessions will probably be OK, 
but that's something to check.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alexopoulos, Dimitrios 

Sent: Wednesday, May 2, 2018 3:02:16 PM
To: Freesurfer support list
Subject: [Freesurfer] using diffusion for tracula, but with surfaces from a 
different MR sessions


External Email - Use Caution

We have acquired data on a few kids and have generated nice surfaces, however, 
the diffusion data we acquired (102 directions and AP/PA distortion maps) were 
suspect due to motion and results from Tracula were not ideal.



We have since brought these kids back for a repeat scan, but only acquired the 
diffusion sequences, and no structural T1.

Can we use the original surfaces/output as input to tracula with the DTI data 
from the repeat MR session?



Jim



“The materials in this email are private and may contain Protected Health 
Information. If you are not the intended recipient, be advised that any 
unauthorized use, disclosure, copying, distribution or the taking of any action 
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have received this email in error, please immediately notify the sender via 
telephone or return email.”







The materials in this message are private and may contain Protected Healthcare 
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[Freesurfer] visualizing seeds on surface

[Eryilmaz, H. Hamdi]

Dear freeview experts,

Is it possible to display multiple seeds (i.e., as a small circle) on freeview 
surface view by specifying their coordinates? If there is no such feature, 
could you suggest an alternative way to visualize seeds?

Thanks in advance!

Best,
Hamdi


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Re: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions

[Alexopoulos, Dimitrios]

External Email - Use Caution

The MR sessions were a few weeks apart on 9-10 year olds.

How would I go about confirming the registration between the diffusion and 
structural data across sessions?

Jim

"The materials in this email are private and may contain Protected Health 
Information. If you are not the intended recipient, be advised that any 
unauthorized use, disclosure, copying, distribution or the taking of any action 
in reliance on the contents of this information is strictly prohibited. If you 
have received this email in error, please immediately notify the sender via 
telephone or return email."

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, May 02, 2018 2:10 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] using diffusion for tracula, but with surfaces from a 
different MR sessions


Yes, you can. The only thing that TRACULA uses from the structural is the 
aparc+aseg, and specifically the relative positions (left, right, anterior, 
etc.) of each tract with respect to the segmentation labels in the aparc+aseg. 
It's safe to assume that those positions will not have changed between 
sessions. If the sessions are not too far apart, the registration between the 
diffusion and structural within-subject across sessions will probably be OK, 
but that's something to check.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Alexopoulos, Dimitrios 
mailto:dimitriosalexopou...@wustl.edu>>
Sent: Wednesday, May 2, 2018 3:02:16 PM
To: Freesurfer support list
Subject: [Freesurfer] using diffusion for tracula, but with surfaces from a 
different MR sessions


External Email - Use Caution

We have acquired data on a few kids and have generated nice surfaces, however, 
the diffusion data we acquired (102 directions and AP/PA distortion maps) were 
suspect due to motion and results from Tracula were not ideal.



We have since brought these kids back for a repeat scan, but only acquired the 
diffusion sequences, and no structural T1.

Can we use the original surfaces/output as input to tracula with the DTI data 
from the repeat MR session?



Jim



"The materials in this email are private and may contain Protected Health 
Information. If you are not the intended recipient, be advised that any 
unauthorized use, disclosure, copying, distribution or the taking of any action 
in reliance on the contents of this information is strictly prohibited. If you 
have received this email in error, please immediately notify the sender via 
telephone or return email."







The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions

[Yendiki, Anastasia]

You should be OK. After running the preprocessing, you can look at the 
structural segmentation that's been mapped to diffusion space 
(dlabel/diff/aparc+aseg.bbr.nii.gz) on the FA map (dmri/dtifit_FA.nii.gz).


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alexopoulos, Dimitrios 

Sent: Wednesday, May 2, 2018 3:15:38 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] using diffusion for tracula, but with surfaces from a 
different MR sessions


External Email - Use Caution

The MR sessions were a few weeks apart on 9-10 year olds.



How would I go about confirming the registration between the diffusion and 
structural data across sessions?



Jim



“The materials in this email are private and may contain Protected Health 
Information. If you are not the intended recipient, be advised that any 
unauthorized use, disclosure, copying, distribution or the taking of any action 
in reliance on the contents of this information is strictly prohibited. If you 
have received this email in error, please immediately notify the sender via 
telephone or return email.”



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, May 02, 2018 2:10 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] using diffusion for tracula, but with surfaces from a 
different MR sessions



Yes, you can. The only thing that TRACULA uses from the structural is the 
aparc+aseg, and specifically the relative positions (left, right, anterior, 
etc.) of each tract with respect to the segmentation labels in the aparc+aseg. 
It's safe to assume that those positions will not have changed between 
sessions. If the sessions are not too far apart, the registration between the 
diffusion and structural within-subject across sessions will probably be OK, 
but that's something to check.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Alexopoulos, Dimitrios 
mailto:dimitriosalexopou...@wustl.edu>>
Sent: Wednesday, May 2, 2018 3:02:16 PM
To: Freesurfer support list
Subject: [Freesurfer] using diffusion for tracula, but with surfaces from a 
different MR sessions



External Email - Use Caution

We have acquired data on a few kids and have generated nice surfaces, however, 
the diffusion data we acquired (102 directions and AP/PA distortion maps) were 
suspect due to motion and results from Tracula were not ideal.



We have since brought these kids back for a repeat scan, but only acquired the 
diffusion sequences, and no structural T1.

Can we use the original surfaces/output as input to tracula with the DTI data 
from the repeat MR session?



Jim



“The materials in this email are private and may contain Protected Health 
Information. If you are not the intended recipient, be advised that any 
unauthorized use, disclosure, copying, distribution or the taking of any action 
in reliance on the contents of this information is strictly prohibited. If you 
have received this email in error, please immediately notify the sender via 
telephone or return email.”







The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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[Freesurfer] Difference between freesurfer home folders

[Hurtado, Aura Maria]

Hi all,

I’m digging into data that was reconned a while ago. I see in the 
recon-all.done files and some say:

CMDPATH /usr/local/freesurfer/stable6/bin/recon-all

and others say:

CMDPATH /usr/local/freesurfer/stable6_0_0/bin/recon-all

Is there a difference between the recon-all commands in the stable 6 and the 
stable6_0_0 freesurfer folders?

Thanks,

Aura M.






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Re: [Freesurfer] mri_vol2surf warning

[Douglas N. Greve]

And what is the voxel resolution of the input to mri_vol2surf?


On 05/02/2018 03:35 PM, Rachel Bencic wrote:
>
>
> Hello,
>
> The voxel resolution of the unwarped mov volume used in bbregister was:
>
> voxel sizes: 3.75, 3.75, 5.00
>
> So the reported values in the warning appear correct.
>
> Rachel
>
>
>
> On 05/02/2018, Douglas Greve wrote:
>
> When you ran bbregister, what was the voxel resolution of the mov volume?
> On 05/02/2018 01:28 PM, Rachel Bencic wrote:
> >
> >
> > Hello FreeSurfer Developers,
> >
> > I'm attempting to resample beta weights generated from AFNI’s 
> > 3dDeconvolve command to individual subjects’ cortical surfaces. Prior 
> > to running 3dDeconvolve, I ran bbregister to coregister subjects’ 
> > (unwarped) functional data to their T1 anatomical scans and to 
> > generate a registration file to be used in the mri_vol2surf command.
> >
> > However, I get the following warning when I run the mri_vol2surf command:
> >
> > WARNING: the voxel resolution in the source volume (3.75, 3.75, 3.75) 
> > differs from that listed in the registration file (3.75, 3.75, 5)
> >
> > I've searched the list and came across a potentially similar case from 
> > Apr. 26, 2011 (SUBJECT: (no subject), AUTHOR: Kevin Bickart), which 
> > included the following advice:
> >
> > Hi Kevin, you can ignore that warning. The values in the registration
> >
> > file are not correct.
> >
> > doug
> >
> > I thought I would reach out to inquire as to whether this is still the 
> > case (i.e., that this warning can be ignored) or if it might be a more 
> > serious issue? I will add that mri_vol2surf did appear to run 
> > successfully (i.e., it did not error out) and provided a .mgh file as 
> > output.
> >
> > In case it is helpful, as a next step I plan to convert the .mgh file 
> > to an ASCII file to extract the time series. Ultimately, I plan to run 
> > graph analyses on the time series data.
> >
> > Any feedback you have would be greatly appreciated.
> >
> > Rachel
> >
> > 1) FreeSurfer version: freesurfer_6.0_x86_64
> >
> > 2) Platform: OSX High Sierra
> >
> > Here is my command:
> >
> > mri_vol2surf --mov ../betaEPI/Betas_EPIpreproc.nii--srcreg 
> > ../bbregistration.dat --hemi lh --projfrac 0.5 --o ./lh.1.mgh
> >
> > mris_convert -c ./lh.1.mgh $parc_dir/${1}/surf/lh.white 
> > ../lh_ascii/lh.1.asc
> >
> > And the full output:
> >
> > srcvol = ../betaEPI/Betas_EPIpreproc.nii
> >
> > srcreg = ../bbregistration.dat
> >
> > srcregold = 0
> >
> > srcwarp unspecified
> >
> > surf = white
> >
> > hemi = lh
> >
> > ProjFrac = 0.5
> >
> > thickness = thickness
> >
> > reshape = 0
> >
> > interp = nearest
> >
> > float2int = round
> >
> > GetProjMax = 0
> >
> > INFO: float2int code = 0
> >
> > Done loading volume
> >
> > INFO: This REGISTER_DAT transform is valid only for volumes betweenCOR 
> > types with c_(r,a,s) = 0.
> >
> > Input reg is register.dat
> >
> > WARNING: the voxel resolution in the source volume (3.75,3.75,3.75) 
> > differs
> >
> > from that listed in the registration file (3.75,3.75,5)
> >
> >  original matrix ---
> >
> > 0.99988-0.009970.01155-0.43638;
> >
> > -0.01472-0.430230.9026022.14351;
> >
> > 0.004030.902660.4303334.58801;
> >
> > 0.00.00.01.0;
> >
> >  original matrix ---
> >
> > Reading surface 
> > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.white
> >
> > Done reading source surface
> >
> > Reading thickness 
> > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.thickness
> >
> > Done
> >
> > Mapping Source Volume onto Source Subject Surface
> >
> > 1 0.5 0.5 0.5
> >
> > using old
> >
> > Done mapping volume to surface
> >
> > Number of source voxels hit = 8657
> >
> > Writing to ./lh.1.mgh
> >
> > Dim: 146930 1 1
> >
> > srcvol = ../betaEPI/Betas_EPIpreproc.nii
> >
> > srcreg = ../bbregistration.dat
> >
> > srcregold = 0
> >
> > srcwarp unspecified
> >
> > surf = white
> >
> > hemi = rh
> >
> > ProjFrac = 0.5
> >
> > thickness = thickness
> >
> > reshape = 0
> >
> > interp = nearest
> >
> > float2int = round
> >
> > GetProjMax = 0
> >
> > INFO: float2int code = 0
> >
> > Done loading volume
> >
> > INFO: This REGISTER_DAT transform is valid only for volumes betweenCOR 
> > types with c_(r,a,s) = 0.
> >
> > Input reg is register.dat
> >
> > WARNING: the voxel resolution in the source volume (3.75,3.75,3.75) 
> > differs
> >
> > from that listed in the registration file (3.75,3.75,5)
> >
> >  original matrix ---
> >
> > 0.99988-0.009970.01155-0.43638;
> >
> > -0.01472-0.430230.9026022.14351;
> >
> > 0.004030.902660.4303334.58801;
> >
> > 0.00.00.01.0;
> >
> >  original matrix ---
> >
> > Reading surface 
> > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.white
> >
> > Done reading source surface
> >
> > Reading thickness 
> > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.thickness
> >
> > Done
> >
> > Mapping Source Volume onto Source Subject Surface
> >

Re: [Freesurfer] Difference between freesurfer home folders

[Douglas N. Greve]

I don't know. It looks like FS was installed twice into two separate 
directories. I assume from the names that they are both verrion 6, but I 
can't say for sure.


On 05/02/2018 03:39 PM, Hurtado, Aura Maria wrote:
> Hi all,
>
> I’m digging into data that was reconned a while ago. I see in the 
> recon-all.done files and some say:
>
> CMDPATH /usr/local/freesurfer/stable6/bin/recon-all
>
> and others say:
>
> CMDPATH /usr/local/freesurfer/stable6_0_0/bin/recon-all
>
> Is there a difference between the recon-all commands in the stable 6 
> and the stable6_0_0 freesurfer folders?
>
> Thanks,
>
> Aura M.
>
>
>
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions

[Alexopoulos, Dimitrios]

External Email - Use Caution

Anastasia, Thank you for the input.

Jim

"The materials in this email are private and may contain Protected Health 
Information. If you are not the intended recipient, be advised that any 
unauthorized use, disclosure, copying, distribution or the taking of any action 
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have received this email in error, please immediately notify the sender via 
telephone or return email."

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, May 02, 2018 2:22 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] using diffusion for tracula, but with surfaces from a 
different MR sessions


You should be OK. After running the preprocessing, you can look at the 
structural segmentation that's been mapped to diffusion space 
(dlabel/diff/aparc+aseg.bbr.nii.gz) on the FA map (dmri/dtifit_FA.nii.gz).


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Alexopoulos, Dimitrios 
mailto:dimitriosalexopou...@wustl.edu>>
Sent: Wednesday, May 2, 2018 3:15:38 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] using diffusion for tracula, but with surfaces from a 
different MR sessions


External Email - Use Caution

The MR sessions were a few weeks apart on 9-10 year olds.



How would I go about confirming the registration between the diffusion and 
structural data across sessions?



Jim



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From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, May 02, 2018 2:10 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] using diffusion for tracula, but with surfaces from a 
different MR sessions



Yes, you can. The only thing that TRACULA uses from the structural is the 
aparc+aseg, and specifically the relative positions (left, right, anterior, 
etc.) of each tract with respect to the segmentation labels in the aparc+aseg. 
It's safe to assume that those positions will not have changed between 
sessions. If the sessions are not too far apart, the registration between the 
diffusion and structural within-subject across sessions will probably be OK, 
but that's something to check.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Alexopoulos, Dimitrios 
mailto:dimitriosalexopou...@wustl.edu>>
Sent: Wednesday, May 2, 2018 3:02:16 PM
To: Freesurfer support list
Subject: [Freesurfer] using diffusion for tracula, but with surfaces from a 
different MR sessions



External Email - Use Caution

We have acquired data on a few kids and have generated nice surfaces, however, 
the diffusion data we acquired (102 directions and AP/PA distortion maps) were 
suspect due to motion and results from Tracula were not ideal.



We have since brought these kids back for a repeat scan, but only acquired the 
diffusion sequences, and no structural T1.

Can we use the original surfaces/output as input to tracula with the DTI data 
from the repeat MR session?



Jim



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[Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

[Mark Wagshul]

External Email - Use Caution

Hi.  I am just getting my feet wet with running my subjects through the 
Freesurfer processing stream, so the following question night be a bit trivial 
(I hope):

I have run qvlSegmentHippocampal subfields on one of my subjects, and it 
completed just fine with what seem to be the appropriate outputs in the 
subject's mri folder.  I have another 100 subjects to run, but want to make 
sure I can accomplish what I would like to on this subject first.  The images 
which I see are sub-images, i.e. these have fewer voxels compared to the 
original image, but in the native T1 space resolution (= 1 mm3).  I would now 
like to register the subfields in the native space (my DTI/NODDI maps are 
already registered into this space), to obtain mean values within each 
subfield.  How can I transform these sub-field images back into the native T1 
space, or is there a method within Freesurfer to perform the math (e.g. similar 
to fslmaths)?

Thanks,

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einstein.yu.edu

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Re: [Freesurfer] Trouble getting git-annex files

[Ricardo Valle]

External Email - Use Caution

Hello,

I need help recompiling dmri_train for Mac. It seems like the instructions in 
the Mac Developer’s don’t work.

When I cd to the trc subdirectory and run make, I am told there is nothing to 
do. I tried editing the Makefile, adding bin_PROGRAMS = dmri_train, at which 
point I got a different error. I then uncommented some other lines in the 
Makefile and managed to start compiling dmri_train, but I’ve been getting a 
never-ending sequence of errors, essentially telling me that the compiler can’t 
find various dependencies (boost/program_options.h, itk*.h, etc.). I’ve tried 
running ./configure with various flags that disable or enable various build 
options, copying over .h files from other locations, adding -I  
directives for the compiler in the Makefile, etc. etc. to no avail.

Thank you,
Ruy
> On Apr 30, 2018, at 5:19 PM, Ricardo Valle  wrote:
> 
> Dear Freesurfer community,
> 
> I am trying to recompile Freesurfer in order to get a binary of the latest 
> version of dmri_train. I have been following the instructions in the 
> Freesurfer Mac Developer’s page 
>  
> and am stuck at the following:
> git annex get --metadata fstags=makeinstall .
> 
> I am attaching the output (stdout and stderr) from this command to this 
> email. Please note that I called the git-annex repository mgh rather than 
> datasrc. The purpose of running this is so I can run make install.
> 
> Is there a way of recompiling only dmri_train or only the dmri_* programs? If 
> not, do you know why git-annex might be giving me problems and how to solve 
> this?
> 
> Thank you,
> Ruy
> 

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Re: [Freesurfer] visualizing seeds on surface

[Douglas N. Greve]

What coordinate system are the seed coordinates in? Do you know the 
vertex number on the surface?


On 05/02/2018 03:13 PM, Eryilmaz, H. Hamdi wrote:
>
> Dear freeview experts,
>
> Is it possible to display multiple seeds (i.e., as a small circle) on 
> freeview surface view by specifying their coordinates? If there is no 
> such feature, could you suggest an alternative way to visualize seeds?
>
> Thanks in advance!
>
> Best,
> Hamdi
>
>
>
>
> ___
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Re: [Freesurfer] fMRI timecourse plot

[Douglas N. Greve]

No, that is just the raw time course. Are you trying to do an FIR model?


On 05/02/2018 03:54 PM, Sarah Cole wrote:
>
>
> Hi Doug,
>
> In the FSFAST tutorials, I keep seeing the attached slide.
> I can tell this is a simple block design experiment. However, I am not 
> sure how the bottom left graph is being generated Is it FIR analysis?
>
> I am using simple SPM hrf model to analyze my data and I am not 
> getting anything close to this plot.
>
> Sorry for the naiive question.
>
> Thanks,
> S
>
>
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Re: [Freesurfer] freesurfer selxavg3-sess error

[Douglas N. Greve]

oops, sorry. Looks like it is having a problem loading your paradigm 
file. Check that. If the error does not pop out to you then send it to me.


On 05/02/2018 10:06 AM, Francesca Strappini wrote:
> Hi, sorry, maybe my last email got lost. Is there anything I can try 
> to fix this problem with selxavg3-sess?
>
> Thanks!
> Best
> Francesca
>
> 2018-04-24 20:35 GMT+03:00 Francesca Strappini 
> mailto:francescastrapp...@gmail.com>>:
>
> Thank you for the reply!
> I deleted the contrasts and run this command line:
>
> selxavg3-sess -a FF-MonkeyCassis.sm03.rh -s MonkeyCassis-FF -no-con-ok
>
>
> --- matlab output 
> MATLAB is selecting SOFTWARE OPENGL rendering.
>
>     < M A T L A B (R) >
>   Copyright 1984-2016 The MathWorks, Inc.
>    R2016b (9.1.0.441655) 64-bit (glnxa64)
>  September 7, 2016
>
>
> To get started, type one of these: helpwin, helpdesk, or demo.
> For product information, visit www.mathworks.com
> .
>
> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> >> /usr/local/freesurfer/matlab/MRIread.m
> >> >> >> starting fast_selxavg3b
>
>
> #@# MonkeyCassis-FF ###
> /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
> -
> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
> -
> outtop = /usr/local/freesurfer/fsfast/Monkeys
> Extension format = nii.gz
> INFO: key nSliceGroups unrecognized, line 11, skipping
> Subscripted assignment dimension mismatch.
>
> Error in fast_ldpar4 (line 97)
>   par4(nthrow,1) = tonset;
>
> Error in flac_customize (line 121)
>     [par partype] = fast_ldpar4(parpath);
>
> Error in fast_selxavg3b (line 129)
> flac0 = flac_customize(flac0);
>
> >> --
> ERROR: fast_selxavg3() failed\n
>
>
> 2018-04-24 20:27 GMT+03:00 Douglas Greve  >:
>
> Try deleting the contrasts (.mat files) and rerunning
>
>
> On 4/24/18 5:48 AM, Francesca Strappini wrote:
>>
>>
>> Dear FreeSurfer experts,
>>
>> I'm trying to analyze some monkey functional data. I got this
>> error message with selxavg3-sess.
>>
>> I run the following commands:
>>
>> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast
>> ON-vs-OFF -a 1 -c 0
>> mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast
>> ON-vs-OFF -a 1 -c 0
>> preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s
>> MonkeyCassis-FF -fsd bold -per-session
>> selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF
>>
>>
>> --- matlab output 
>> MATLAB is selecting SOFTWARE OPENGL rendering.
>>
>>     < M A T L A B (R) >
>>   Copyright 1984-2016 The MathWorks, Inc.
>>    R2016b (9.1.0.441655) 64-bit (glnxa64)
>> September 7, 2016
>>
>>
>> To get started, type one of these: helpwin, helpdesk, or demo.
>> For product information, visit www.mathworks.com
>> .
>>
>> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
>> >> /usr/local/freesurfer/matlab/MRIread.m
>> >> >> >> starting fast_selxavg3b
>>
>>
>> #@# MonkeyCassis-FF ###
>> /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
>> -
>> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
>> -
>> outtop = /usr/local/freesurfer/fsfast/Monkeys
>> Extension format = nii.gz
>> INFO: key nSliceGroups unrecognized, line 11, skipping
>>  1 ON-vs-OFF.mat
>> Subscripted assignment dimension mismatch.
>>
>> Error in fast_ldpar4 (line 97)
>>   par4(nthrow,1) = tonset;
>>
>> Error in flac_customize (line 121)
>>     [par partype] = fast_ldpar4(parpath);
>>
>> Error in fast_selxavg3b (line 129)
>> flac0 = flac_customize(flac0);
>>
>> >> --
>> ERROR: fast_selxavg3() failed\n
>>
>> Thank you!
>> Best
>>
>> Francesca
>>
>> -- 
>> Francesca Strappini, Ph.D.
>> Neurobiology Department
>> Weizmann Institute of Science
>> 234 Herzl Street, Rehovot 7610001 Israel
>> Tel.: +972 58 444 2584
>> E-mail: francesca.strapp...@weizmann.ac.il
>> 
>>
>>
>>   

Re: [Freesurfer] visualizing seeds on surface

[Eryilmaz, H. Hamdi]

Hi Doug,

They are in MNI but I can find out their vertex numbers if that would be easier.

Thanks!
Hamdi



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

Sent: Wednesday, May 2, 2018 5:42:20 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] visualizing seeds on surface

What coordinate system are the seed coordinates in? Do you know the
vertex number on the surface?


On 05/02/2018 03:13 PM, Eryilmaz, H. Hamdi wrote:
>
> Dear freeview experts,
>
> Is it possible to display multiple seeds (i.e., as a small circle) on
> freeview surface view by specifying their coordinates? If there is no
> such feature, could you suggest an alternative way to visualize seeds?
>
> Thanks in advance!
>
> Best,
> Hamdi
>
>
>
>
> ___
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Re: [Freesurfer] Fw: Query regarding creation of atlas directly from probabilistic information

[Douglas N. Greve]

For vol2surf, you should make sure that the registration is correct by 
running

tkregisterfv --mov ID076_LL_PHGa_l_HvOx_prob.mgz --reg 
$FREESURFER_HOME/average/mni152.register.dat --surfs

You ROI should be in the right spot and the surface should cut through 
it (or near enough given your projection).

If those are probabilities, then you will need to binarize it 
(mri_binarize) before running mri_cor2label


Not sure about your other question. Do you want to get the probabilities 
for the DK atlas?



On 05/02/2018 10:26 AM, Mageshwar Selvakumar wrote:
>
> Dear Everyone,
>
> A kind reminder. I'm unable to look beyond this step and am really 
> looking for some help. I would like to know if we can use the 
> probabilistic information directly on mri_train
>
> Thank you,
>
> Kind regards
>
> Mageshwar Selvakumar, M.Sc
>
> Department of Pharmakologische Bildgebung und Bildanalyse
>
> Friedrich Alexander Universität Erlangen Nürnberg
>
>
> Office:Fahrstr. 17, 91054 Erlangen
>
> Phone:+ 49-9131-8522898
>
>
>
> 
> *From:* Mageshwar Selvakumar 
> *Sent:* Monday, April 23, 2018 10:36 AM
> *To:* freesurfer@nmr.mgh.harvard.edu; Bruce Fischl
> *Subject:* Query regarding creation of atlas directly from 
> probabilistic information
> Dear All and Bruce,
>
> This mail is on top of the query I had a couple of weeks back where I 
> misinterpreted that I had binary mask of each structure 
> as individual nifti volume files but on closer look, the nifti files 
> had the probability that the structure is present at that certain 
> location. On looking into the freesurfer website, I came across this 
> documentation of creation of Atlas, 
> https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceLabelAtlas
> SurfaceLabelAtlas - Free Surfer Wiki 
> 
> Overview. This document provides an overview of two related topics: 
> How the FreeSurfer pipeline automatically labels a subject's regions 
> (producing an annotation file) by comparing the subject's curvature 
> data to an "atlas" ("gcs") file.
> surfer.nmr.mgh.harvard.edu
>
>  In this documentation the process is done by looping through N 
> subjects to get the probability information, and these subjects are 
> registered to the registration template derived from average of 
> reference templates. I would like to know if I could use these 
> probability information directly and since the atlas information is 
> already in the MNI152 space, can I use the registration template which 
> is already available with freesurfer, and if yes, can someone guide me 
> on which registration files I must use.
>
> Secondly, I tried using mri_vol2surf and tried to convert the volume 
> data to a surface data before creating labels, but on doing so I had 
> errors when creating labels from the surface files.
> To convert into volume I ran the below code:
>
>
> *mri_vol2surf --mov ID076_LL_PHGa_l_HvOx_prob.mgz  --ref 
> ID076_LL_PHGa_l_HvOx_prob.mgz  --out 
> ID076_LL_PHGa_l_HvOx_prob_surf.mgz  --hemi lh --mni152reg 
> --projdist-max -2 0 .1 --reshape --interp nearest*
>
>
> Then I to convert this surface file into label I ran
>
> *mri_cor2label --i ID080_CPuP_l_HvOx_prob_surf.mgz --l area1.label 
> --id 076*
>
>
> And I got the error
>
> *Found 0 label voxels
>
> ERROR: found no voxels matching id 76*
>
>
> But the process runs fine if I run the mri_cor2label on the volume 
> file. It would be nice if someone can help me out on where I'm going 
> wrong here.
>
> Thank you,
>
> Kind regards
>
> Mageshwar Selvakumar, M.Sc
>
> Department of Pharmakologische Bildgebung und Bildanalyse
>
> Friedrich Alexander Universität Erlangen Nürnberg
>
>
> Office:Fahrstr. 17, 91054 Erlangen
>
> Phone:+ 49-9131-8522898
>
>
>
>
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Re: [Freesurfer] visualizing seeds on surface

[Douglas N. Greve]

If you know the vertex number, then you can do something like

mri_volsynth --template $SUBJECTS_DIR/subject/surf/lh.thickness --pdf 
delta --delta-crsf vertexno 0 0 0 --o delta.mgz

mris_fwhm --smooth-only --fwhm 5 --i delta.mgz --subject subject --hemi 
lh --o delta.sm05.mgz

mri_binarize --i delta.sm05.mgz --min .1 --o delta.sm05.bin.mgz

tksurferfv subject lh inflated -fminmax .5 1 -ov delta.sm05.bin.mgz

This is a fairly convoluted method that basically creates a surface 
overlay with  a 1.0 in your vertex and 0 everywhere else (delta.mgz), 
then smooths that to distribute non-zero values around the vertex, then 
binarizes it.




On 05/02/2018 05:52 PM, Eryilmaz, H. Hamdi wrote:
> Hi Doug,
>
> They are in MNI but I can find out their vertex numbers if that would 
> be easier.
>
> Thanks!
> Hamdi
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N. Greve 
> 
> *Sent:* Wednesday, May 2, 2018 5:42:20 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] visualizing seeds on surface
> What coordinate system are the seed coordinates in? Do you know the
> vertex number on the surface?
>
>
> On 05/02/2018 03:13 PM, Eryilmaz, H. Hamdi wrote:
> >
> > Dear freeview experts,
> >
> > Is it possible to display multiple seeds (i.e., as a small circle) on
> > freeview surface view by specifying their coordinates? If there is no
> > such feature, could you suggest an alternative way to visualize seeds?
> >
> > Thanks in advance!
> >
> > Best,
> > Hamdi
> >
> >
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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>
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Re: [Freesurfer] combinesurfs problem: shifts and rotates

[Douglas N. Greve]

Does it work if you don't save it as an stl file?


On 05/02/2018 06:39 AM, Klink-3, N.E.C. van wrote:
>
>
> Dear all,
>
> I am struggling with coverting and combining pial surfaces back to 
> native space. My result is 90 degrees rotated, and shifted from the 
> original MRI.
>
> The initial lh.pial and rh.pial look good, and when I translate them 
> to native space they still look good. However when I combined them, 
> they suddenly shift and rotate. Does anyone know what happens, how I 
> can prevent it, or reliably can shift and rotate back?
>
> Also, if I do not save directly to STL, the surfaces get messed up in 
> –combinesurfs, with a lot of vertices shifted to the center of the 
> surface (see picture below). But this is not my biggest problem, as I 
> want STL in the end.
>
> My code:
>
> /tkregister2 --mov rawavg.mgz --targ orig.mgz --reg 
> register.native.dat --noedit –regheader/
>
> //
>
> /mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz 
> --tval lh.pial.native --tval-xyz --hemi lh --s {SUBJECT}/
>
> /mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz 
> --tval rh.pial.native --tval-xyz --hemi rh --s {SUBJECT}/
>
> //
>
> /mris_convert --combinesurfs 
> $SUBJECTS_DIR/${subject}/surf/lh.pial.native 
> $SUBJECTS_DIR/${subject}/surf/rh.pial.native $SUBJECTS_DIR/bh_native.stl/
>
> Thanks in advance,
>
> Nicole
>
> 
>
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Re: [Freesurfer] Trouble getting git-annex files

[Dicamillo, Robert]

Hello Ruy,

Do you mean the mri_train binary that gets built under ./freesurfer/mri_train ?
(I see a ./freesurfer/dmri_poistats, ./freesurfer/dmri_tensroreig but not a 
./freesurfer/dmri_train).

Things are not necessarily setup so you can cd to ./freesurfer/ and 
just build
what is there in isolation from the rest of the tree.

But for ./freesiurfer/mri_train, you could try the following, which worked for 
me on a Mac, e.g.,
after changing mri_train.c,

$ cd ./freesurfer/mri_train
$ rm -f mri_train mri_train.o
$ make -r mri_train

- rob




On May 2, 2018, at 5:37 PM, Ricardo Valle 
mailto:ruyval...@gmail.com>> wrote:


External Email - Use Caution

Hello,

I need help recompiling dmri_train for Mac. It seems like the instructions in 
the Mac Developer’s don’t work.

When I cd to the trc subdirectory and run make, I am told there is nothing to 
do. I tried editing the Makefile, adding bin_PROGRAMS = dmri_train, at which 
point I got a different error. I then uncommented some other lines in the 
Makefile and managed to start compiling dmri_train, but I’ve been getting a 
never-ending sequence of errors, essentially telling me that the compiler can’t 
find various dependencies (boost/program_options.h, itk*.h, etc.). I’ve tried 
running ./configure with various flags that disable or enable various build 
options, copying over .h files from other locations, adding -I  
directives for the compiler in the Makefile, etc. etc. to no avail.

Thank you,
Ruy
On Apr 30, 2018, at 5:19 PM, Ricardo Valle 
mailto:ruyval...@gmail.com>> wrote:

Dear Freesurfer community,

I am trying to recompile Freesurfer in order to get a binary of the latest 
version of dmri_train. I have been following the instructions in the Freesurfer 
Mac Developer’s 
page 
and am stuck at the following:
git annex get --metadata fstags=makeinstall .

I am attaching the output (stdout and stderr) from this command to this email. 
Please note that I called the git-annex repository mgh rather than datasrc. The 
purpose of running this is so I can run make install.

Is there a way of recompiling only dmri_train or only the dmri_* programs? If 
not, do you know why git-annex might be giving me problems and how to solve 
this?

Thank you,
Ruy


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[Freesurfer] freesurfer masks for fsl processed data

[Rongxiang Tang]

External Email - Use Caution

Dear All,
I ran fsl feat on my functional data and have all my data transformed into 
standard MNI space. However, I would like to use freesurfer generated white 
matter parcellation (wmparc.mgz) to extract white matter signals from my MNI 
space functional data.I noticed that both are in completely different space, so 
I was wondering what steps do I need to do to transform wmparc.mgz into the 
same space as my processed functional data. 
Thanks!Catherine___
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Re: [Freesurfer] Trouble getting git-annex files

[Ricardo Valle]

External Email - Use Caution

Hello Rob,

No, I mean the dmri_train binary that is part of Tracula. The main source file 
is ./freesurfer/trc/dmri_train.cxx. I don’t mind building the whole tree if 
necessary, but I haven’t been able to do so either. Do you know what the -r 
flag to make does?

Thank you,
Ruy
> On May 2, 2018, at 6:51 PM, Dicamillo, Robert  
> wrote:
> 
> Hello Ruy,
> 
> Do you mean the mri_train binary that gets built under ./freesurfer/mri_train 
> ?
> (I see a ./freesurfer/dmri_poistats, ./freesurfer/dmri_tensroreig but not a 
> ./freesurfer/dmri_train).
> 
> Things are not necessarily setup so you can cd to ./freesurfer/ and 
> just build
> what is there in isolation from the rest of the tree.
> 
> But for ./freesiurfer/mri_train, you could try the following, which worked 
> for me on a Mac, e.g.,
> after changing mri_train.c,
> 
> $ cd ./freesurfer/mri_train
> $ rm -f mri_train mri_train.o
> $ make -r mri_train
> 
> - rob
> 
> 
> 
> 
>> On May 2, 2018, at 5:37 PM, Ricardo Valle > > wrote:
>> 
>> External Email - Use Caution
>> 
>> 
>> Hello,
>> 
>> I need help recompiling dmri_train for Mac. It seems like the instructions 
>> in the Mac Developer’s don’t work.
>> 
>> When I cd to the trc subdirectory and run make, I am told there is nothing 
>> to do. I tried editing the Makefile, adding bin_PROGRAMS = dmri_train, at 
>> which point I got a different error. I then uncommented some other lines in 
>> the Makefile and managed to start compiling dmri_train, but I’ve been 
>> getting a never-ending sequence of errors, essentially telling me that the 
>> compiler can’t find various dependencies (boost/program_options.h, itk*.h, 
>> etc.). I’ve tried running ./configure with various flags that disable or 
>> enable various build options, copying over .h files from other locations, 
>> adding -I  directives for the compiler in the Makefile, etc. etc. to 
>> no avail.
>> 
>> Thank you,
>> Ruy
>>> On Apr 30, 2018, at 5:19 PM, Ricardo Valle >> > wrote:
>>> 
>>> Dear Freesurfer community,
>>> 
>>> I am trying to recompile Freesurfer in order to get a binary of the latest 
>>> version of dmri_train. I have been following the instructions in the 
>>> Freesurfer Mac Developer’s page 
>>>  
>>> and am stuck at the following:
>>> git annex get --metadata fstags=makeinstall .
>>> 
>>> I am attaching the output (stdout and stderr) from this command to this 
>>> email. Please note that I called the git-annex repository mgh rather than 
>>> datasrc. The purpose of running this is so I can run make install.
>>> 
>>> Is there a way of recompiling only dmri_train or only the dmri_* programs? 
>>> If not, do you know why git-annex might be giving me problems and how to 
>>> solve this?
>>> 
>>> Thank you,
>>> Ruy
>>> 
>> 
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> 
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Re: [Freesurfer] Fw: Yeo Atlas Network 3 segmentation FEF

[Thomas Yeo]

External Email - Use Caution

Hi Catherine,

We have extracted the 7 and 17 networks into 51 and 114 regions
respectively. See figures in
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering

Unfortunately, we have only provided the parcellation in fsaverage5 (
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels),
so you should add one more mri_surf2surf step to upsample the parcellation
from fsaverage5 to fsaverage. Check that it is good and then proceed with
your previous steps.

I am emailing the freesurfer list, so that my reply might hopefully be
useful for other folks.

Regards,
Thomas

On Thu, May 3, 2018 at 8:46 AM, Catherine Joe 
wrote:

> Hello Dr Yeo,
>
>
> Yes, I want to be able to split network 3 into different component regions
> so that I can have a nii file for FEF. This will then allow me to get the
> signal intensity and hopefully, the volume of the FEF region for each
> participant in my Honour's project.
>
>
> Thank you.
>
>
> Kind regards,
>
> Catherine
> --
> *From:* Thomas Yeo 
> *Sent:* Thursday, 3 May 2018 9:36:52 AM
>
> *To:* Catherine Joe
> *Cc:* 李婧玮
> *Subject:* Re: Fw: Yeo Atlas Network 3 segmentation FEF
>
> Hi Catherine,
>
> Can I verify what you need is network 3 split into different component
> regions like FEF, etc?
>
> Regards,
> Thomas
>
> On Wed, May 2, 2018 at 11:08 AM Catherine Joe 
> wrote:
>
> Hi Dr Yeo and Jingwei,
>
>
> Yes, I did use that link to subscribe to the mailing list about 2.5 weeks
> ago and they still haven't gotten back to me. I simply thought I didn't get
> a confirmation email and tried again, which was the message I forwarded to
> you today. Just now, I tried subscribing again.
>
>
> So the commands I've used so far is as follows:
>
> mri_surf2surf --srcsubject fsaverage --trgsubject subject11GS --hemi lh
> --sval-annot $subjectdir/Yeo_Neurophysiol11_Freesurfer/
> fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --tval lh.7Networks.annot
>
> (same was done for the rh before doing mri_aparc2aseg)
>
>
> mri_aparc2aseg --s subject11GS --o $subjectdir/subject11GS/test/test.mgz
> --annot 7Networks --annot-table path_to/Yeo2011_7Networks_colorlux.txt
>
>
> mri_annotation2label --subject subject11GS --outdir
> $subjectdir/subject11GS/test --hemi lh --annotation
> $subjectdir/subject11GS/label/lh.7Networks.annot
>
>
> mri_label2vol --label $subjectdir/subjet11GS/test/lh.7Networks_3.label
> --temp $subjectdir/subject11GS/mri/rawavg.mgz --subject subject11GS
> --hemi lh 00o $subjectdir/subject11GS/test/lh7Networks.nii.gz --proj frac
> 0 1 0.01 --reg $subjectdir/subject11GS/corticalroi/subject11GS_
> register.dat
>
>
> And after doing that, all I got was the volume for network 3 but not
> actually having any separation with the FEF and the other areas.
>
>
> Thank you for your help.
>
>
> Kind regards,
>
> Catherine
>
> --
> *From:* yeoye...@gmail.com  on behalf of Thomas Yeo <
> ytho...@csail.mit.edu>
> *Sent:* Wednesday, 2 May 2018 10:33:18 AM
> *To:* Catherine Joe
> *Cc:* 李婧玮
> *Subject:* Re: Fw: Yeo Atlas Network 3 segmentation FEF
>
> Hi Catherine,
>
> Have you tried subscribing to the mailing here (
> http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)?
>
> Can you please let me know the exact commands you have tried so far?
>
> I am cc-ing my grad student (Jingwei), who might be able to answer more
> rapidly. Please reply all to keep her in the loop.
>
> Thanks,
> Thomas
>
> On Wed, May 2, 2018 at 8:14 AM, Catherine Joe 
> wrote:
>
> Hi Dr Yeo,
>
>
> Thank you for your help before with actually aligning and extracting your
> atlas. I know that you mentioned before that I should try and email into
> the FreeSurfer mailing list for any further queries.
>
> However, as you can see, I am apparently not subscribed to the list even
> though I sent in a request before. I've been trying to send in a question
> for the past week.
>
> I was wondering if you'd be able to help me with this problem I've had
> after extracting the Network 3 ROI. The message I tried sending to the
> FreeSurfer Mailing list is as below:
>
>
> Hello,
>
>
> I'm having trouble getting the segmentation for the FEF using the Yeo
> Atlas 2011 Network 3. Although I've been able to get Network 3 as a volume
> file, it doesn't show me two individual labels for the network (primarily
> the three areas of the dorsal attention network). In Freesurfer, it simply
> has all three areas labelled as the same colour called the 'left cerebral
> exterior'. I even did mri_aparc2aseg using the following code:
>
>
> mri_aparc2aseg --s subject11GS --o /data/cai-wks2/data
> _local_temp/Cathy/freesurfersubjects/subject11GS/test/test.mgz --annot
> 7Networks --annot-table path_to/Yeo2011_7Networks_colorLUT.txt
>
>
> I am still unable to find the labels that qualify as

[Freesurfer] Hippocampal subfield analysis did not run or produce right hemisphere outpus

[Zola Mannie]

External Email - Use Caution

Dear all



I ran the hippocampal subfield analysis with this script: recon-all -s HP_0015 
-hippocampal-subfields-T1, and this completed without errors. However, looking 
at outputs inside the mri directory, there is only the left hemisphere (3 of 
them) but no right hemisphere outputs.

Why did this occur and how can I correct it?

Any help would be most appreciated
Best wishes
Zola

Dr Zola Mannie BSc(Hons), MSc, PhD
Senior Research Officer; CADE Clinic
Department of Academic Psychiatry
Royal North Shore Hospital
St Leonards
Sydney.
NSW; 2065; Australia
Tel: +61294629908
E: zola.man...@sydney.edu.au

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Re: [Freesurfer] Hippocampal subfield analysis did not run or produce right hemisphere outpus

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Zola,
What version of FreeSurfer was this?
Can you please send us the log?
Cheers
Eugenio

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zola Mannie 

Sent: Thursday, May 3, 2018 4:52:24 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampal subfield analysis did not run or produce 
right hemisphere outpus


External Email - Use Caution

Dear all



I ran the hippocampal subfield analysis with this script: recon-all -s HP_0015 
-hippocampal-subfields-T1, and this completed without errors. However, looking 
at outputs inside the mri directory, there is only the left hemisphere (3 of 
them) but no right hemisphere outputs.

Why did this occur and how can I correct it?

Any help would be most appreciated
Best wishes
Zola

Dr Zola Mannie BSc(Hons), MSc, PhD
Senior Research Officer; CADE Clinic
Department of Academic Psychiatry
Royal North Shore Hospital
St Leonards
Sydney.
NSW; 2065; Australia
Tel: +61294629908
E: zola.man...@sydney.edu.au

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