[Freesurfer] cortical and subcortical masks

[Nayyereh Ghazi]

DearExperts,Iwant to create some cortical and subcortical masks to use as seed 
regions infsl’s Probtrackx and have faced some questions that ask you help me 
with them. Toextract subcortical regions I have used the below commands (e.g. 
for thalamus_r): {mri_label2vol \    --seg  
$SUBJECT_DIR/${subject}/mri/aparc+aseg.mgz \    --fillthresh  0 > /dev/null \   
 --identity \    --temp  $SUBJECT_DIR/${subject}/mri/orig.mgz \    --o  
${datadir}/aparc+aseg.nii.gz \ mri_binarize --i 
${datadir}/aparc+aseg.nii.gz--match 49 --o ${datadir}/thalamus_r.nii.gz}
I noticed that the number of voxels of the created masks inthis way are 
different from which is written in aseg.stats file. Could youplease explain the 
reason and the way to make these numbers as close as possible.
For cortical regions I used both the above and below commands(e.g. for 
rh.superiortemporal):{mri_annotation2label --subject ${subject} \    --hemi rh 
\    --annotation$SUBJECTS_DIR/${subject}/label/rh.aparc.annot \    --outdir 
$SUBJECTS_DIR/${subject}/label\    --surface white mri_label2vol \    --label 
$SUBJECTS_DIR/${subject}/label/rh.superiortemporal.label\    --temp  
$SUBJECT_DIR/${subject}/mri/orig.mgz \    --identity \    --o 
${datadir}/rh.superiortemporal.nii.gz\    --fillthresh 0> /dev/null}Again I 
have noticed differences in number of voxels of theresults from two methods for 
cortical regions and also a difference fromaparc.stats’s numbers. My final goal 
in to use the masks in probtrackx to findthe connections between subcortical 
structures and corticalregions in temporal lobe and I wonder which method is 
more accurate to create cortical masks. Also I want to know using which atlas 
is better for my purpose, aparc+aseg or aparc.a2009s+aseg.
Your help is greatly appreciated.
Wishes,Nayyereh
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Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

[Julio Alberto González Torre]

I have the same problem.

I observed that this error appears when you select a factor with 3 or more
levels. Factors of 2 levels works fine.

2016-01-18 9:32 GMT+01:00 BAUTISTA-PERPINYA Maximilià <
maximila.bautista-perpi...@etu.unistra.fr>:

> Thank you for the reply Douglas,
>
> Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi
> editor, one line for each level. Same as factor 2.
>
> Max
>
>
>
> On dijous 14 gener 2016 22:20 CET, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
> > how many levels does factor 1 have? How did you make the factor file?
> >
> > On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote:
> > > Hi there experts,
> > >
> > > I'm runing qdec to analyze my subject data. I am able to import the
> qdec.table.dat, but the problem comes in the Design step. I select
> 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and
> 'LeftAmygdala' as the continuous variable. I don't select any nuisance
> factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but
> gives me the following error:
> > >
> > >
> ---
> > >
> > > ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
> > > ninputs = 137
> > > Checking inputs
> > > nframestot = 137
> > > Allocing output
> > > Done allocing
> > > nframes = 137
> > > Writing to
> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh
> > > gdfReadHeader: reading
> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd
> > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> > > Continuous Variable Means (all subjects)
> > > 0 LeftAmygdala 1502.65 189.974
> > > Class Means of each Continuous Variable
> > > 1 diagnosisBPD 1497.7548
> > > 2 diagnosisCCP 1540.8923
> > > 3 diagnosisNPC 1488.5490
> > > INFO: gd2mtx_method is dods
> > > Reading source surface
> /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white
> > > ERROR: no contrasts specified.
> > > Error in Analyze: command failed: mri_glmfit --y
> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd
> /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods
> --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis
> --surf fsaverage lh
> > >
> > >
> ---
> > >
> > > Any recommendations? Any help is much appreciated :)
> > >
> > >
> > > Best,
> > >
> > > Max
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> >
> > -- Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > 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.
>
> --
> Maximilià Bautista-Perpinyà, BSc
> Master student at Joint Master in Neuroscience (JMN)
> Université de Strasbourg (in partnership with Universität Freiburg and
> Universität Basel)
> &
> Master Intern at Biological and Personality Psychology Laboratory
> Department of Psychology, Universität Freiburg
>
> (+49) 015759302368
> maximila.bautista-perpi...@etu.unistra.fr
> maxbau...@gmail.com
>
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>
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Re: [Freesurfer] New User - Gyrification Index question

[Arindam Chatterjee]

Great! Thank you for the prompt response and the pointers. I am going
through the tutorials now to learn how to use freesurfer and will try out
what you suggested.

Thanks!
Ankita

On Mon, Jan 18, 2016 at 2:26 PM Bruce Fischl 
wrote:

> Hi Ankita
>
> dicom is perfect. Just give recon-all a single file from the correct dicom
> series and it will figure out the rest of them
> Bruce
> On Mon, 18 Jan 2016, Arindam Chatterjee wrote:
>
> >
> > Hi Bruce,
> > Thank you for your prompt response! Sorry for my novice questions - does
> > T1-weighted scan with voxels have to be in a specific format like jpg,
> dicom
> > or mesh format?
> > Ankita
> >
> > On Mon, Jan 18, 2016 at 1:59 PM Bruce Fischl  >
> > wrote:
> >   Hi Ankita
> >
> >   sure, we compute GI. You need to get a good T1-weighted scan
> >   with voxels
> >   that are about 1mm isotropic, then run it through our recon-all
> >   script
> >
> >   cheers
> >   Bruce
> >   On
> >   Mon, 18 Jan 2016, Arindam Chatterjee wrote:
> >
> >   > Hello,I am a new user of the freesurfer platform. I am a high
> >   school junior
> >   > conducting research on brain MRI scans and came across this
> >   wonderful
> >   > platform. However I am not very sure how to proceed with my
> >   research - I am
> >   > trying to find the whole brain Gyrification Index, which I did
> >   manually on a
> >   > different software called ImageJ using multiple image scans of
> >   brain slices.
> >   > Will freesurfer be able to analyze brain scan images and
> >   provide a whole
> >   > brain GI or does it only analyse and provide local GI which is
> >   what I found
> >   > through some forums? If so, are there any tutorials to learn
> >   how to do that?
> >   > Do I need any other software like MatLab to find out the
> >   Gyrification Index?
> >   >
> >   > Thank you in advance!
> >   > Ankita
> >   >
> >   >
> >   ___
> >   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.
> >
> >
> >
> ___
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>
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Re: [Freesurfer] New User - Gyrification Index question

[Bruce Fischl]

Hi Ankita

dicom is perfect. Just give recon-all a single file from the correct dicom 
series and it will figure out the rest of them
Bruce
On Mon, 18 Jan 2016, Arindam Chatterjee wrote:

> 
> Hi Bruce,
> Thank you for your prompt response! Sorry for my novice questions - does
> T1-weighted scan with voxels have to be in a specific format like jpg, dicom
> or mesh format?
> Ankita
> 
> On Mon, Jan 18, 2016 at 1:59 PM Bruce Fischl 
> wrote:
>   Hi Ankita
>
>   sure, we compute GI. You need to get a good T1-weighted scan
>   with voxels
>   that are about 1mm isotropic, then run it through our recon-all
>   script
>
>   cheers
>   Bruce
>   On
>   Mon, 18 Jan 2016, Arindam Chatterjee wrote:
>
>   > Hello,I am a new user of the freesurfer platform. I am a high
>   school junior
>   > conducting research on brain MRI scans and came across this
>   wonderful
>   > platform. However I am not very sure how to proceed with my
>   research - I am
>   > trying to find the whole brain Gyrification Index, which I did
>   manually on a
>   > different software called ImageJ using multiple image scans of
>   brain slices.
>   > Will freesurfer be able to analyze brain scan images and
>   provide a whole
>   > brain GI or does it only analyse and provide local GI which is
>   what I found
>   > through some forums? If so, are there any tutorials to learn
>   how to do that?
>   > Do I need any other software like MatLab to find out the
>   Gyrification Index?
>   >
>   > Thank you in advance!
>   > Ankita
>   >
>   >
>   ___
>   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.
> 
> 
>
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Re: [Freesurfer] New User - Gyrification Index question

[Arindam Chatterjee]

Hi Bruce,
Thank you for your prompt response! Sorry for my novice questions - does
T1-weighted scan with voxels have to be in a specific format like jpg,
dicom or mesh format?

Ankita

On Mon, Jan 18, 2016 at 1:59 PM Bruce Fischl 
wrote:

> Hi Ankita
>
> sure, we compute GI. You need to get a good T1-weighted scan with voxels
> that are about 1mm isotropic, then run it through our recon-all script
>
> cheers
> Bruce
> On
> Mon, 18 Jan 2016, Arindam Chatterjee wrote:
>
> > Hello,I am a new user of the freesurfer platform. I am a high school
> junior
> > conducting research on brain MRI scans and came across this wonderful
> > platform. However I am not very sure how to proceed with my research - I
> am
> > trying to find the whole brain Gyrification Index, which I did manually
> on a
> > different software called ImageJ using multiple image scans of brain
> slices.
> > Will freesurfer be able to analyze brain scan images and provide a whole
> > brain GI or does it only analyse and provide local GI which is what I
> found
> > through some forums? If so, are there any tutorials to learn how to do
> that?
> > Do I need any other software like MatLab to find out the Gyrification
> Index?
> >
> > Thank you in advance!
> > Ankita
> >
> >
> ___
> 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.
>
>
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[Freesurfer] Longitudinal analysis with single timepoint scans

[Bronwyn Overs]

Hi Freesurfer Mailing List,

We are running a longitudinal analysis (in R) using 2 time points with 
scans that have been through the Freesurfer longitudinal pipeline. We 
were also hoping to incorporate individuals with only a single scan into 
our analysis. Does it make sense to use long images (2 timepoints) with 
cross images (1 timepoint) in the same analysis, or can they not be used 
together because the cross sectional images have not undergone the same 
processing steps?

--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to the 
NeuRA Magazine 


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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] New User - Gyrification Index question

[Bruce Fischl]

Hi Ankita

sure, we compute GI. You need to get a good T1-weighted scan with voxels 
that are about 1mm isotropic, then run it through our recon-all script

cheers
Bruce
On 
Mon, 18 Jan 2016, Arindam Chatterjee wrote:

> Hello,I am a new user of the freesurfer platform. I am a high school junior
> conducting research on brain MRI scans and came across this wonderful
> platform. However I am not very sure how to proceed with my research - I am
> trying to find the whole brain Gyrification Index, which I did manually on a
> different software called ImageJ using multiple image scans of brain slices.
> Will freesurfer be able to analyze brain scan images and provide a whole
> brain GI or does it only analyse and provide local GI which is what I found
> through some forums? If so, are there any tutorials to learn how to do that?
> Do I need any other software like MatLab to find out the Gyrification Index?
> 
> Thank you in advance!
> Ankita
> 
>
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] New User - Gyrification Index question

[Arindam Chatterjee]

Hello,
I am a new user of the freesurfer platform. I am a high school junior
conducting research on brain MRI scans and came across this wonderful
platform. However I am not very sure how to proceed with my research - I am
trying to find the whole brain Gyrification Index, which I did manually on
a different software called ImageJ using multiple image scans of brain
slices. Will freesurfer be able to analyze brain scan images and provide a
whole brain GI or does it only analyse and provide local GI which is what I
found through some forums? If so, are there any tutorials to learn how to
do that? Do I need any other software like MatLab to find out the
Gyrification Index?

Thank you in advance!
Ankita
___
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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
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but does not contain patient information, please contact the sender and properly
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[Freesurfer] glmfit flag --frame-mask

[Victor Montal Blancafort]

Dear FS Experts,

I have seen few posts about this mri_glmfit flag, and I would like to know
how it works.
In an older post, (
https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32412.html),
Doug suggested to use this flag when only some subjects should be exclude
for each vertex (i, e. differnet number of subjects to exclude per vertex).
Could anyone give me an insight on how this works?

My intention is to perform a  GLM analysis of some DTI metric volumes
projected into the surface. However, some of the DWI volumes are cutted, so
I would like exclude those vertexs where there is no signal (i,e value 0).
Will --frame-mask work for this? Any other suggestion?

Any help will be very appreciated!
Thank you in advance,

Victor Montal
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Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

[BAUTISTA-PERPINYA Maximilià]

Thank you for the reply Douglas,

Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi 
editor, one line for each level. Same as factor 2.

Max

 
 
On dijous 14 gener 2016 22:20 CET, Douglas N Greve  
wrote: 
 
> how many levels does factor 1 have? How did you make the factor file?
> 
> On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote:
> > Hi there experts,
> >
> > I'm runing qdec to analyze my subject data. I am able to import the 
> > qdec.table.dat, but the problem comes in the Design step. I select 
> > 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 
> > 'LeftAmygdala' as the continuous variable. I don't select any nuisance 
> > factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but 
> > gives me the following error:
> >
> > ---
> >
> > ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
> > ninputs = 137
> > Checking inputs
> > nframestot = 137
> > Allocing output
> > Done allocing
> > nframes = 137
> > Writing to 
> > /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh
> > gdfReadHeader: reading 
> > /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd
> > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> > Continuous Variable Means (all subjects)
> > 0 LeftAmygdala 1502.65 189.974
> > Class Means of each Continuous Variable
> > 1 diagnosisBPD 1497.7548
> > 2 diagnosisCCP 1540.8923
> > 3 diagnosisNPC 1488.5490
> > INFO: gd2mtx_method is dods
> > Reading source surface 
> > /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white
> > ERROR: no contrasts specified.
> > Error in Analyze: command failed: mri_glmfit --y 
> > /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd 
> > /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods 
> > --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis 
> > --surf fsaverage lh
> >
> > ---
> >
> > Any recommendations? Any help is much appreciated :)
> >
> >
> > Best,
> >
> > Max
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> 
> -- Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> 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.
 
-- 
Maximilià Bautista-Perpinyà, BSc
Master student at Joint Master in Neuroscience (JMN)
Université de Strasbourg (in partnership with Universität Freiburg and 
Universität Basel)
&
Master Intern at Biological and Personality Psychology Laboratory
Department of Psychology, Universität Freiburg

(+49) 015759302368
maximila.bautista-perpi...@etu.unistra.fr
maxbau...@gmail.com 

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