Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

[Jörg Stadler]

External Email - Use Caution

Hi Bruce,
this did not change anything. But I tried the process of mris_ca_train,
mris_ca_label with lh.oasis.chubs.annot and this worked fine.

A closer look to my source annot file from mris_seg2annot showed that
the label 'unknown' is missing.

How can I add the unknown to all unlabeled vertices?

cheers,
Joerg



> Hi Joerg
>
> I'm not positive that I understand, but have you tried giving
> mris_ca_label the switch:
>
> mris_ca_label -l $SUBJECTS_DIR/$subject/label/$hemi.cortex.label ...
>
>
> that should remove non-cortical regions from your output annot
>
> cheers
> Bruce
>
> On Tue, 5 Mar 2019, Jörg Stadler wrote:
>
>>    External Email - Use Caution
>> Hi,
>>
>> I transfered the SPM Anatomy Toolbox
>> (http://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/SPMAnatomyToolbox/SPMAnatomyToolbox_node.html)
>>
>> from Collin space to fsaverage using
>>
>> Wu J, Ngo GH, Greve DN, Li J, He T, Fischl B, Eickhoff SB, Yeo BTT.
>> *Accurate nonlinear mapping between MNI volumetric and FreeSurfer
>> surface coordinate systems*
>> ,
>>
>> /Human Brain Mapping/ 39:3793–3808, 2018.
>>
>>
>> mris_seg2annot --seg rh_Anatomy_v22c.nii.gz --ctab-auto Anatomy_v22c --s
>> fsaverage --hemi rh --o rh.anat_v22c
>>
>> mris_seg2annot --seg lh_Anatomy_v22c.nii.gz --ctab-auto Anatomy_v22c --s
>> fsaverage --hemi lh --o lh.anat_v22c
>>
>>
>> This gave me the annot files for fsaverage (annotation.png) and a
>> template for the color lookup table.
>>
>>
>> Training of the classifier:
>>
>> mris_ca_train -t Anatomy_v22c_LUT.txt lh lh.sphere.reg anat_v22c.annot
>> fsaverage lh.Anatomy_v22c.gcs
>>
>> mris_ca_train -t Anatomy_v22c_LUT.txt rh rh.sphere.reg anat_v22c.annot
>> fsaverage rh.Anatomy_v22c.gcs
>>
>>
>> Transfer to individual subject fsaverage:
>>
>> mris_ca_label fs_average lh sphere.reg lh.Anatomy_v22c.gcs
>> Anatomy_v22c.annot
>> mris_ca_label fs_average rh sphere.reg rh.Anatomy_v22c.gcs
>> Anatomy_v22c.annot
>>
>>
>> Now the miracle occurred and the whole surface got labeled.
>> (mris_ca_label.png)
>>
>> How can a keep unassigned regions unlabeled?
>>
>>
>> Joerg
>
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-- 
Dr. rer. nat. Joerg Stadler
Leibniz Institute for Neurobiology (LIN)
Special Lab Non-Invasive Brain Imaging
Brenneckestr. 6, D - 39118 Magdeburg
Tel.: +49-391-6263-92171 Fax: +49-391-6263-92589
Gnupg-Key:http://keyserver.ubuntu.com search for E-Mail Adress
Key fingerprint:B005 A785 8191 BED1 1B75  9B06 120C F20F 3E08 D20F 


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Re: [Freesurfer] 回复： How to extract cortical features of a ROI

[Bruce Fischl]

Oh, the vertex indices of the label are stored in the label file. You can use 
the. To index into the thickness vector
Cheers
Bruce

> On Mar 5, 2019, at 10:09 PM, 310913949 <310913...@qq.com> wrote:
> 
> External Email - Use Caution
> 
> Hi Bruce，
>The  ‘mris_anatomical_stats‘’ and  'mri_segstats’ command line just output 
> mean thickness of ROI, but I want to know cortical thickness for each vertex 
> in the ROI. So I think the  key is to find the coordination of each vertex in 
> the ROI,but I dont know how. I found that  the RAS coordinates in the 
> lh.cortex.label do not correspond to the coordinates in the lh.thickness.
> 
> -- 原始邮件 --
> 发件人: "Bruce Fischl";
> 发送时间: 2019年3月5日(星期二) 晚上11:35
> 收件人: "Freesurfer support list";
> 主题: Re: [Freesurfer] How to extract cortical features of a ROI
> 
> Hi Kan
> 
> you can give the surface-based label to mris_anatomical_stats and it will 
> constrain it's calculations to the label (where it makes sense):
> 
> mris_anatomical_stats -l  ...
> 
> you can probably do it with mri_segstats too - Doug will know
> 
> cheers
> Bruce
> 
> 
> On Tue, 5 
> Mar 2019, 310913949 wrote:
> 
> > 
> > External Email - Use Caution
> > 
> > Hi bruce??
> >I still have some questions about extracting cortical features of a ROI. 
> > I used the
> > mri_label2label to sample the volumetric label to the surface of the 
> > subject. But I dont know how to
> > do next, as i found that the RAS coordinates do  not correspond to the 
> > coordinates in the
> > lh.thickness, and why?
> > Besides, I found the  web of how to extract cortical thickness values 
> > for a region-of-interest
> > (ROI) defined in volume
> > space(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness).But
> >  it doesn't report
> > the coordinates information. How can I get the ROI's coordinates 
> > information if i use this method?
> > Thanks for your help!
> > Kan Deng
> >  
> > 
> > 
> > -- Original --
> > From:  "Bruce Fischl";
> > Date:  Fri, Jan 25, 2019 10:58 PM
> > To:  "Freesurfer support list";
> > Subject:  Re: [Freesurfer] How to extract cortical features of a ROI
> > 
> > Hi Kan
> > 
> > if you draw a volumetric label you first need to sample it to the surface
> > of that subject (mri_label2label --sample). If all you want are stats from
> > the subject there is no need to map it to fsaverage - that is only
> > necessary if you want to use a group coordinate system.
> > 
> > cheers
> > Bruce
> > 
> > 
> > 
> > On Fri, 25 Jan 2019,
> > 310913949 wrote:
> > 
> > >
> > >  External Email - Use Caution
> > >
> > >
> > > Dear Freesurfer Experts,
> > >I want to extract cortical features of a ROI that I drawn manually 
> > > on  the rawavg.mgz in
> > Freesurfer, but i
> > > don't know how to do that. I think maybe first the  lesion mask should be 
> > > registered to the
> >  standard templates
> > > fsaverage, but I don't know what the command line is , could  you tell 
> > > me?  And secondly, I should
> > use
> > > mri_label2label to map the label to individual subject  and extract the 
> > > cortical features of the
> > ROI, am I right?
> > >   I am looking forward to your reply!Thanks.
> > >
> > >   Best wishes!
> > >   Kan Deng
> > >
> > >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> >
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[Freesurfer] ?????? How to extract cortical features of a ROI

[310913949]

External Email - Use Caution

Hi Bruce??
   The  ??mris_anatomical_stats and  'mri_segstats?? command line just 
output mean thickness of ROI, but I want to know cortical thickness for each 
vertex in the ROI. So I think the  key is to find the coordination of each 
vertex in the ROI,but I dont know how. I found that  the RAS coordinates in the 
lh.cortex.label do not correspond to the coordinates in the lh.thickness.


--  --
??: "Bruce Fischl";
: 2019??3??5??(??) 11:35
??: "Freesurfer support list";

: Re: [Freesurfer] How to extract cortical features of a ROI



Hi Kan

you can give the surface-based label to mris_anatomical_stats and it will 
constrain it's calculations to the label (where it makes sense):

mris_anatomical_stats -l  ...

you can probably do it with mri_segstats too - Doug will know

cheers
Bruce


On Tue, 5 
Mar 2019, 310913949 wrote:

> 
> External Email - Use Caution
> 
> Hi bruce??
>I still have some questions about extracting cortical features of a ROI. I 
> used the
> mri_label2label to sample the volumetric label to the surface of the subject. 
> But I dont know how to
> do next, as i found that the RAS coordinates do  not correspond to the 
> coordinates in the
> lh.thickness, and why?
> Besides, I found the  web of how to extract cortical thickness values for 
> a region-of-interest
> (ROI) defined in volume
> space(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness).But
>  it doesn't report
> the coordinates information. How can I get the ROI's coordinates information 
> if i use this method?
> Thanks for your help!
> Kan Deng
>  
> 
> 
> -- Original --
> From:  "Bruce Fischl";
> Date:  Fri, Jan 25, 2019 10:58 PM
> To:  "Freesurfer support list";
> Subject:  Re: [Freesurfer] How to extract cortical features of a ROI
> 
> Hi Kan
> 
> if you draw a volumetric label you first need to sample it to the surface
> of that subject (mri_label2label --sample). If all you want are stats from
> the subject there is no need to map it to fsaverage - that is only
> necessary if you want to use a group coordinate system.
> 
> cheers
> Bruce
> 
> 
> 
> On Fri, 25 Jan 2019,
> 310913949 wrote:
> 
> >
> >  External Email - Use Caution
> >
> >
> > Dear Freesurfer Experts,
> >I want to extract cortical features of a ROI that I drawn manually 
> > on  the rawavg.mgz in
> Freesurfer, but i
> > don't know how to do that. I think maybe first the  lesion mask should be 
> > registered to the
>  standard templates
> > fsaverage, but I don't know what the command line is , could  you tell me?  
> > And secondly, I should
> use
> > mri_label2label to map the label to individual subject  and extract the 
> > cortical features of the
> ROI, am I right?
> >   I am looking forward to your reply!Thanks.
> >
> >   Best wishes!
> >   Kan Deng
> >
> >
> ___
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> 
>
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[Freesurfer] Postdoc positions at Washington University

[Aristeidis Sotiras]

External Email - Use Caution

** Apologies for cross-postings **

The research group of Dr. Sotiras (www.asotiras.com), a part of the
Electronic Radiology Lab at Washington University in St. Louis (
https://wustl.edu), is currently seeking a highly motivated postdoctoral
research associate with a strong research record in computational
neuroscience, computational image analysis, computer vision, or machine
learning, who is interested in solving important clinical problems. The lab
is a diverse and interdisciplinary team whose research focuses on advancing
imaging informatics technology and developing advanced computational
techniques for quantitative image analysis.

The successful candidate will lead or participate in projects developing,
implementing and applying machine learning algorithms for the analysis and
interpretation of medical images and related clinical data. More
specifically, the successful candidate will develop and apply computational
and analytical techniques to quantify morphology and function from
multi-modal imaging data, analyze the relationship between brain imaging
markers and cognition or clinical status, and integrate this information
into predictive tools for patient-specific diagnosis and prognosis with the
goal of improving our understanding of brain structure in health and
disease. Applications of interest include multi-modal neuroimaging studies
in neurology and psychiatry. The successful candidate will have a unique
opportunity to work closely with clinical investigators and will have ample
opportunities to present research methods and scientific findings at
national and international conferences, and to publish results in academic
journals.

The Mallinckrodt Institute of Radiology (https://www.mir.wustl.edu/)
encompasses a multi-disciplinary research center, home to more than 200
research faculty, postdocs, and graduate students, with a vibrant culture
of collegiality (e.g., journal groups, weekly seminars, etc). Researchers
study the human brain using a number of biomedical imaging modalities, such
as MRI, PET, optical imaging and microscopy and collaborate with academic
institutions and industry across the world. MIR is considered a premier
biomedical imaging center in the world and is a great place to grow as a
scientist, and build a highly visible career at the intersection of
neuroscience, medicine, and engineering.

For more information, please follow the link
https://tinyurl.com/SotirasPostDocAd, or contact Dr. Sotiras (
aristeidis.soti...@wustl.edu).

Interested applicants should send
  1.  a one-page cover letter summarizing their interests, how they can
contribute to the lab, as well as the earliest date that they can start the
appointment,
  2.  curriculum vitae, and
  3.  contact information for two references
to Dr. Aristeidis Sotiras, aristeidis.soti...@wustl.edu. Only applicants
considered for employment will be contacted. Applications are reviewed on a
rolling basis.
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[Freesurfer] HCP Course 2019: Get ready for more data, and a new way of getting it

[Jennifer Elam]

External Email - Use Caution

*More HCP data are comingand will be released in a new way.will you
be ready? *

This spring, the first data from the Lifespan Human Connectome Projects -
(HCP) Development (healthy subjects ages 5-21) and HCP Aging (ages 36-100+)
will be publicly released. Yay!

Also, for the first time, we will be releasing these data on the cloud, via
the NIMH Data Archive (NDA). This will enable computing on the cloud to
analyze HCP and Lifespan data.

Come to the 2019HCP Course: "Exploring the Human Connectome"


, July 8 – 12, 2019 in Portland, Oregon, USA to learn all about the new
data, how to access it on NDA, and using HCP methods, tools, and pipelines
on your own neuroimaging data.
This 5-day intensive course will provide training in acquisition,
processing, analysis and visualization of whole brain imaging and
behavioral data of humans and non-human primates using methods and tools
developed by the WU-Minn-Oxford HCP consortium. Both new and current users
of HCP data, methods, and tools are welcome and the course will cover both
basic and advanced topics.

For more info and to register visit the HCPCourse 2019 website

. If you have any questions, please contact us at:
hcpcou...@humanconnectome.org
We look forward to seeing you in Portland!

Best,
2019 HCP Course Organizers
-- 
Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org
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Re: [Freesurfer] extracting cortical parcellation

[Bruce Fischl]

Hi Atena

yes, mri_annotation2label should work, although it really depends on what 
you want to do next


cheers
Bruce
On Wed, 6 Mar 2019, Atena Rezaei wrote:



External Email - Use Caution

Hello,

I am trying to extract the cortical parcellation(atlas) file from freesurfer 
with all the labels. I found
the lh.aparc.annot file in label folder. Should I use mri_annotation2label to 
create labels? or how can I
extract the whole file?
Thanks for ur help!

BR,
Atena


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[Freesurfer] PETSurfer and thickness data

[Boris Rauchmann]

External Email - Use Caution

Dear FS community,

I would like to assess how PET tracer uptake is related to thickness changes in 
AD patients. Is it possible to generate difference maps for both methods and 
run a GLM? Or would you suggest another approach?

Thanks,
Boris

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[Freesurfer] extracting cortical parcellation

[Atena Rezaei]

External Email - Use Caution

Hello,

I am trying to extract the cortical parcellation(atlas) file from
freesurfer with all the labels. I found the lh.aparc.annot file in
label folder. Should I use mri_annotation2label to create labels? or how
can I extract the whole file?
Thanks for ur help!

BR,
Atena
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Re: [Freesurfer] Computing LGI using Octave instead of Matlab

[Tim Schäfer]

External Email - Use Caution

Maybe you already know this, but just in case: mris_compute_lgi is a shell 
script, so you can open it in an editor and check what it does.cat 

The output of the following command gives a good first impression:

   cat `which mris_compute_lgi` | grep -B 8 MATLAB

It seems to prepare the arguments for a number of matlab functions, write the 
full command including args to temporary files and then pipes the contents into 
'${MATLAB} -display iconic -nojvm -nosplash', where ${MATLAB} is set at the 
beginning of the script to be the output of `getmatlab`.

I'm not sure whether that helps, but I think one could try to create an Octave 
version of the script from that.




> On March 5, 2019 at 8:35 PM Natasha Sharma  wrote:
> 
> 
> External Email - Use Caution
> 
> Hello all,
> 
> Is there a way to run LGI commands listed below using Octave instead of
> Matlab? I've read somewhere on the forums of being able to get Freesurfer
> to use Octave instead of Matlab in FSFAST but I'm not sure if it will work
> with the commands below. Could I please get instructions on how to do this?
> 
> mris_compute_lgi --i lh.pial
> mris_compute_lgi --i rh.pial
> 
> Any help is appreciated!
> Thank you.
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-- 
Tim

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Re: [Freesurfer] Processing MEMPRAGE

[Rusche, Johann]

Great - thanks for clarifying!


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Andre van der Kouwe 

Sent: Tuesday, March 5, 2019 2:57:13 PM
To: Bruce Fischl
Cc: Freesurfer support list; Sevinc, Gunes; Lazar, Sara
Subject: Re: [Freesurfer] Processing MEMPRAGE

Yes, that's correct, it's the smaller RMS file. FreeSurfer will complain
if it's supplied with a multi-frame (4 echo) volume i.e. you should get a
warning if you use the wrong file.

On Tue, 5 Mar 2019, Bruce Fischl wrote:

> Hi Johann
>
> I believe that is the case, but Andre (ccd) can confirm
>
> cheers
> Bruce
>
> On Tue, 5 Mar 2019, Rusche, Johann wrote:
>
>>
>>  Dear Freesurfers,
>>
>>
>>  Reading through the mailing list I understood how to
>>  process our nmr MEPRAGEs and I would like to
>>  double-check we are using unpacksdcmdir correctly.
>>
>>
>>  Unpacking with unpacksdcmdir gives me two nifti files, a 4-echo nifti file
>>  (92MB) and a 1-echo nifti file
>>  (23MB). Am I correct to understand that the smaller 1-echo nifti file is
>>  the RMS created automatically? Can
>>  you confirm that this is the file that I want to send to recon-all
>>  vis-a-vis VBM processing?
>>
>>
>>  From the unpacklog:
>>
>>7 MEMPRAGE_tfl_mgh_multiecho_1mm_iso  ok  256 256 176   4
>>  MR.1.3.12.2.1107.5.2.19.45407.2014103021271096561867095
>>8 MEMPRAGE_tfl_mgh_multiecho_1mm_iso  ok  256 256 176   1
>>  MR.1.3.12.2.1107.5.2.19.45407.2014103021271165037167199
>>
>>  Thanks for your time!
>>
>>  Johann
>>
>>
>>
>>
>>  __
>>  Johann Rusche
>>
>>  Graduate Research Student, Lazar Lab
>>  Department of Psychiatry – Neurosciences
>>  Massachusetts General Hospital
>>
>>
>
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Re: [Freesurfer] Processing MEMPRAGE

[Andre van der Kouwe]

Yes, that's correct, it's the smaller RMS file. FreeSurfer will complain 
if it's supplied with a multi-frame (4 echo) volume i.e. you should get a 
warning if you use the wrong file.


On Tue, 5 Mar 2019, Bruce Fischl wrote:


Hi Johann

I believe that is the case, but Andre (ccd) can confirm

cheers
Bruce

On Tue, 5 Mar 2019, Rusche, Johann wrote:



 Dear Freesurfers,


 Reading through the mailing list I understood how to
 process our nmr MEPRAGEs and I would like to
 double-check we are using unpacksdcmdir correctly.


 Unpacking with unpacksdcmdir gives me two nifti files, a 4-echo nifti file
 (92MB) and a 1-echo nifti file
 (23MB). Am I correct to understand that the smaller 1-echo nifti file is
 the RMS created automatically? Can
 you confirm that this is the file that I want to send to recon-all
 vis-a-vis VBM processing? 


 From the unpacklog:

   7 MEMPRAGE_tfl_mgh_multiecho_1mm_iso  ok  256 256 176   4
 MR.1.3.12.2.1107.5.2.19.45407.2014103021271096561867095
   8 MEMPRAGE_tfl_mgh_multiecho_1mm_iso  ok  256 256 176   1
 MR.1.3.12.2.1107.5.2.19.45407.2014103021271165037167199

 Thanks for your time!

 Johann




 __
 Johann Rusche

 Graduate Research Student, Lazar Lab
 Department of Psychiatry – Neurosciences
 Massachusetts General Hospital


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[Freesurfer] Computing LGI using Octave instead of Matlab

[Natasha Sharma]

External Email - Use Caution

Hello all,

Is there a way to run LGI commands listed below using Octave instead of
Matlab? I've read somewhere on the forums of being able to get Freesurfer
to use Octave instead of Matlab in FSFAST but I'm not sure if it will work
with the commands below. Could I please get instructions on how to do this?

mris_compute_lgi --i lh.pial
mris_compute_lgi --i rh.pial

Any help is appreciated!
Thank you.
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Re: [Freesurfer] Processing MEMPRAGE

[Bruce Fischl]

Hi Johann

I believe that is the case, but Andre (ccd) can confirm

cheers
Bruce

On Tue, 5 Mar 2019, Rusche, Johann wrote:



Dear Freesurfers,


Reading through the mailing list I understood how to process our nmr MEPRAGEs 
and I would like to
double-check we are using unpacksdcmdir correctly.


Unpacking with unpacksdcmdir gives me two nifti files, a 4-echo nifti file 
(92MB) and a 1-echo nifti file
(23MB). Am I correct to understand that the smaller 1-echo nifti file is the 
RMS created automatically? Can
you confirm that this is the file that I want to send to recon-all vis-a-vis 
VBM processing? 


From the unpacklog:

  7 MEMPRAGE_tfl_mgh_multiecho_1mm_iso  ok  256 256 176   4
MR.1.3.12.2.1107.5.2.19.45407.2014103021271096561867095
  8 MEMPRAGE_tfl_mgh_multiecho_1mm_iso  ok  256 256 176   1
MR.1.3.12.2.1107.5.2.19.45407.2014103021271165037167199

Thanks for your time!

Johann




__
Johann Rusche

Graduate Research Student, Lazar Lab
Department of Psychiatry – Neurosciences
Massachusetts General Hospital

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[Freesurfer] Processing MEMPRAGE

[Rusche, Johann]

Dear Freesurfers,


Reading through the mailing list I understood how to process our nmr MEPRAGEs 
and I would like to double-check we are using unpacksdcmdir correctly.


Unpacking with unpacksdcmdir gives me two nifti files, a 4-echo nifti file 
(92MB) and a 1-echo nifti file (23MB). Am I correct to understand that the 
smaller 1-echo nifti file is the RMS created automatically? Can you confirm 
that this is the file that I want to send to recon-all vis-a-vis VBM processing?


>From the unpacklog:

  7 MEMPRAGE_tfl_mgh_multiecho_1mm_iso  ok  256 256 176   4 
MR.1.3.12.2.1107.5.2.19.45407.2014103021271096561867095
  8 MEMPRAGE_tfl_mgh_multiecho_1mm_iso  ok  256 256 176   1 
MR.1.3.12.2.1107.5.2.19.45407.2014103021271165037167199


Thanks for your time!

Johann




__
Johann Rusche

Graduate Research Student, Lazar Lab
Department of Psychiatry – Neurosciences
Massachusetts General Hospital
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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

[Arsenije Subotic]

External Email - Use Caution

Hi,

I am still struggling to examine differences in thickness using the command 
line stream for my two groups after controlling for age and sex. I get the 
following error when running the command line:


ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y CAA_CTRL_RH.thickness.10.mgh --fsgd
CAA_CTRL_RH_Age_Sex.fsgd --C Contrasts/CAA-CTRL_Age_Sex.mtx --surf fsaverage rh
--cortex --glmdir CAA_CTRL_RH_Age_Sex_Unix.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.00 (col 5), Max=611.699463 (col 4)
 The scale is much different between columns 5 and 4, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.
Column 5,  all values are 0
Column 6,  all values are 0
Columns 5 and 6 are the same




My design matrix is:
1 -1 0 0 0 0 (Examining difference in thickness after controlling for effects
of age and sex)

I’ve also attached the FSGD file that I’ve been using. Please let me know 
if there is something wrong with the file (although I have used a similar file 
without the covariates and did not have any issues).

Thanks!
Arsenije
---
Arsenije Subotic | MSc Student
Department of Clinical Neurosciences
Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada
Tel: (403) 918-6970
arsenije.subot...@ucalgary.ca



CAA_CTRL_RH_Age_Sex.fsgd
Description: CAA_CTRL_RH_Age_Sex.fsgd
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[Freesurfer] Masks in mri_segstats

[Zhi Li]

External Email - Use Caution

Hello Freesurfer experts,

I would like to use mri_segstats with two different masks and thresholds,
such as:

mri_segstats --mask mask1 --maskthresh thresh1 --mask mask2 --maskthresh
thresh2

This command can run smoothly with our any error. However, I am not clear
if the results are correct. I mean if mri_segstats uses the overlap between
two masks or only uses the last input mask and threshold? Any suggestions?

Thank you and best regards,

Lizhi
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Re: [Freesurfer] Should I edit or reject?

[Bruce Fischl]

Hi Ryan

I'm not sure we have much useful advice to give you as it depends a lot 
on your subject population. Basically we make the decision of whether or 
not a given dataset is good enough quality to extract biologically 
meaningful results from. If you are only interested in a bit of the brain 
then maybe you don't care about artifacts in other regions. Alternatively 
if you have tons of subject maybe you don't mind getting rid of low quality 
data. You do have to be careful that you aren't biasing your sampling 
though.


cheers
Bruce


On Tue, 5 Mar 2019, Ryan Wales wrote:



External Email - Use Caution

Hi,
Although there are many ways to correct for pial, WM, and segmentation defects, 
it seems common in
the literature to forego any edits and simply either accept or reject a 
subject's FreeSurfer output
in order to avoid subjectivity and potential over-editing. Another group 
rejected subjects if their
defects spanned 6 or more slices, for example.
Are there any guide lines on how much editing is too much editing? Should it 
just be edited enough
so it looks tolerable by eye? Maybe by a few different raters?

The defects vary in their severity, so it's difficult to know if a subject 
should be considered
passable or requiring edits based on a minor defect.

My current plan is to conduct my analysis once with excluding subjects with 
poor segmentation and
then again, including  those subjects' edited outputs. Do you agree with this 
logic?

Thanks for your advice,
Ryan

--
Ryan Wales
Graduate Student
Cognition and Motor Control Neuroscience Laboratory
Integrative Neuroscience
Psychology Department
Stony Brook University
E-mail: ryan.wa...@stonybrook.edu

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[Freesurfer] Should I edit or reject?

[Ryan Wales]

External Email - Use Caution

Hi,

Although there are many ways to correct for pial, WM, and segmentation
defects, it seems common in the literature to forego any edits and simply
either accept or reject a subject's FreeSurfer output in order to avoid
subjectivity and potential over-editing. Another group rejected subjects if
their defects spanned 6 or more slices, for example.
Are there any guide lines on how much editing is too much editing? Should
it just be edited enough so it looks tolerable by eye? Maybe by a few
different raters?

The defects vary in their severity, so it's difficult to know if a subject
should be considered passable or requiring edits based on a minor defect.

My current plan is to conduct my analysis once with excluding subjects with
poor segmentation and then again, including  those subjects' edited
outputs. Do you agree with this logic?

Thanks for your advice,
Ryan

-- 
Ryan Wales
Graduate Student
Cognition and Motor Control Neuroscience Laboratory
Integrative Neuroscience
Psychology Department
Stony Brook University
E-mail: ryan.wa...@stonybrook.edu 
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Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

[Bruce Fischl]

Hi Joerg

I'm not positive that I understand, but have you tried giving 
mris_ca_label the switch:


mris_ca_label -l $SUBJECTS_DIR/$subject/label/$hemi.cortex.label ...


that should remove non-cortical regions from your output annot

cheers
Bruce

On Tue, 
5 Mar 2019, Jörg Stadler wrote:


   External Email - Use Caution 


Hi,

I transfered the SPM Anatomy Toolbox
(http://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/SPMAnatomyToolbox/SPMAnatomyToolbox_node.html)
from Collin space to fsaverage using

Wu J, Ngo GH, Greve DN, Li J, He T, Fischl B, Eickhoff SB, Yeo BTT.
*Accurate nonlinear mapping between MNI volumetric and FreeSurfer
surface coordinate systems*
,
/Human Brain Mapping/ 39:3793–3808, 2018.


mris_seg2annot --seg rh_Anatomy_v22c.nii.gz --ctab-auto Anatomy_v22c --s
fsaverage --hemi rh --o rh.anat_v22c

mris_seg2annot --seg lh_Anatomy_v22c.nii.gz --ctab-auto Anatomy_v22c --s
fsaverage --hemi lh --o lh.anat_v22c


This gave me the annot files for fsaverage (annotation.png) and a
template for the color lookup table.


Training of the classifier:

mris_ca_train -t Anatomy_v22c_LUT.txt lh lh.sphere.reg anat_v22c.annot
fsaverage lh.Anatomy_v22c.gcs

mris_ca_train -t Anatomy_v22c_LUT.txt rh rh.sphere.reg anat_v22c.annot
fsaverage rh.Anatomy_v22c.gcs


Transfer to individual subject fsaverage:

mris_ca_label fs_average lh sphere.reg lh.Anatomy_v22c.gcs
Anatomy_v22c.annot
mris_ca_label fs_average rh sphere.reg rh.Anatomy_v22c.gcs
Anatomy_v22c.annot


Now the miracle occurred and the whole surface got labeled.
(mris_ca_label.png)

How can a keep unassigned regions unlabeled?


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Re: [Freesurfer] Surface Misplacement

[Bruce Fischl]

Hi Banu

can you send us an image to show us what you mean?
cheers
Bruce
On Tue, 5 Mar 2019, Banu 
Femir wrote:




External Email - Use Caution

Hi,
I've a problem about surface placement. For my PhD thesis, I've been analyzing 
T1 images of 103  AD,
MCI and SCI subjects. I'm using FS 6.0 stable version on Linux.

Some of my data, especially AD data have a surface problem. White matter 
includes both white and
gray matter, and CSF is included as a gray matter. So, it looks like the 
surfaces has shifted. (The
MR images do not have any lesion).

Until now, I tried to clean dura for one subject, but nothing changed.
I also run reconall again for another subject, got the same result. All done in 
FreeView.

I do not know what to do in this case. It looks like troubleshooting does not 
solve my problem,
since mine is very complicated.

I would be so happy if anyone has an idea of what can I try to do?

Many thanks in advance,

Banu.


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Re: [Freesurfer] How to extract cortical features of a ROI

[Bruce Fischl]

Hi Kan

you can give the surface-based label to mris_anatomical_stats and it will 
constrain it's calculations to the label (where it makes sense):


mris_anatomical_stats -l  ...

you can probably do it with mri_segstats too - Doug will know

cheers
Bruce


On Tue, 5 
Mar 2019, 310913949 wrote:




External Email - Use Caution

Hi bruce??
   I still have some questions about extracting cortical features of a ROI. I 
used the
mri_label2label to sample the volumetric label to the surface of the subject. 
But I dont know how to
do next, as i found that the RAS coordinates do  not correspond to the 
coordinates in the
lh.thickness, and why?
    Besides, I found the  web of how to extract cortical thickness values for a 
region-of-interest
(ROI) defined in volume
space(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness).But 
it doesn't report
the coordinates information. How can I get the ROI's coordinates information if 
i use this method?
    Thanks for your help!
    Kan Deng
 


-- Original --
From:  "Bruce Fischl";
Date:  Fri, Jan 25, 2019 10:58 PM
To:  "Freesurfer support list";
Subject:  Re: [Freesurfer] How to extract cortical features of a ROI

Hi Kan

if you draw a volumetric label you first need to sample it to the surface
of that subject (mri_label2label --sample). If all you want are stats from
the subject there is no need to map it to fsaverage - that is only
necessary if you want to use a group coordinate system.

cheers
Bruce



On Fri, 25 Jan 2019,
310913949 wrote:

>
>  External Email - Use Caution
>
>
> Dear Freesurfer Experts,
>        I want to extract cortical features of a ROI that I drawn manually on  
the rawavg.mgz in
Freesurfer, but i
> don't know how to do that. I think maybe first the  lesion mask should be 
registered to the
 standard templates
> fsaverage, but I don't know what the command line is , could  you tell me?  
And secondly, I should
use
> mri_label2label to map the label to individual subject  and extract the 
cortical features of the
ROI, am I right?
>       I am looking forward to your reply!Thanks.
>
>                                                   Best wishes!
>                                                       Kan Deng
>
>
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Re: [Freesurfer] mri_vol2surf sample inside and outside of pial

[Bruce Fischl]

yes, although note that neither one is guaranteed to be "inside" or 
"outside" at that distance (it might reenter the surface in the outwards 
normal direction, or leave the surface in the inwards direction)


cheers
Bruce
On Tue, 5 
Mar 2019, Michael Jordan wrote:




External Email - Use Caution

Hi,

I have a short question concerning the mri_vol2surf command.
Do the following parameters of the command return the maximum volume value (for 
each vertex) which
occurs between 10 mm outside and 10 mm inside the pial surface (along normal 
vector)?

 --projdist-max -10 10 0.25 --interp nearest --surf pial

Thank you very much!!

Regards Michael





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[Freesurfer] Surface Misplacement

[Banu Femir]

External Email - Use Caution

Hi,

I've a problem about surface placement. For my PhD thesis, I've been
analyzing T1 images of 103  AD, MCI and SCI subjects. I'm using FS 6.0
stable version on Linux.

Some of my data, especially AD data have a surface problem. White matter
includes both white and gray matter, and CSF is included as a gray matter.
So, it looks like the surfaces has shifted. (The MR images do not have any
lesion).

Until now, I tried to clean dura for one subject, but nothing changed.
I also run reconall again for another subject, got the same result. All
done in FreeView.

I do not know what to do in this case. It looks like troubleshooting does
not solve my problem, since mine is very complicated.

I would be so happy if anyone has an idea of what can I try to do?

Many thanks in advance,

Banu.
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Re: [Freesurfer] How to extract cortical features of a ROI

[310913949]

External Email - Use Caution

Hi bruce??
   I still have some questions about extracting cortical features of a ROI. I 
used the mri_label2label to sample the volumetric label to the surface of the 
subject. But I dont know how to do next, as i found that the RAS coordinates do 
 not correspond to the coordinates in the lh.thickness, and why?
Besides, I found the  web of how to extract cortical thickness values for a 
region-of-interest (ROI) defined in volume 
space(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness).But 
it doesn't report the coordinates information. How can I get the ROI's 
coordinates information if i use this method?
Thanks for your help!
Kan Deng

 




-- Original --
From:  "Bruce Fischl";
Date:  Fri, Jan 25, 2019 10:58 PM
To:  "Freesurfer support list";

Subject:  Re: [Freesurfer] How to extract cortical features of a ROI



Hi Kan

if you draw a volumetric label you first need to sample it to the surface 
of that subject (mri_label2label --sample). If all you want are stats from 
the subject there is no need to map it to fsaverage - that is only 
necessary if you want to use a group coordinate system.

cheers
Bruce



On Fri, 25 Jan 2019, 
310913949 wrote:

> 
> External Email - Use Caution
> 
> 
> Dear Freesurfer Experts,
>I want to extract cortical features of a ROI that I drawn manually on  
> the rawavg.mgz in Freesurfer, but i
> don't know how to do that. I think maybe first the  lesion mask should be 
> registered to the  standard templates
> fsaverage, but I don't know what the command line is , could  you tell me?  
> And secondly, I should use
> mri_label2label to map the label to individual subject  and extract the 
> cortical features of the ROI, am I right?
>   I am looking forward to your reply!Thanks.
> 
>   Best wishes!
>   Kan Deng
> 
>
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[Freesurfer] mri_vol2surf sample inside and outside of pial

[Michael Jordan]

External Email - Use Caution

Hi,

I have a short question concerning the mri_vol2surf command.
Do the following parameters of the command return the maximum volume value
(for each vertex) which occurs between 10 mm outside and 10 mm inside the
pial surface (along normal vector)?

 --projdist-max -10 10 0.25 --interp nearest --surf pial

Thank you very much!!

Regards Michael
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