[Freesurfer] cespct in FS 5.3

[S.V.Shepherd [work]]

Hi all,

I ran an analysis on data after dividing each voxel mean across the run,
and then multiplying by 100. (My intuition was that the percent signal
change should be more consistent across varying SNR that the non-normalized
betas).

I had naively expected ces.nii and cespct.nii to be equivalent in this
case, but in fact, cespct.nii is steeply larger and only imperfectly
correlated with ces.nii. What am I missing?

stephen


*stephen v. shepherd   phd*
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
// 212.327.7699
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[Freesurfer] converting Tracula outputs to Wavefront OBJ files

[David Allan Ziegler]

Dear Freesurfer/Tracula team,

I would like to convert some of the outputs from Tracula into wavefront
objects in order to render them in Unity.  Does anyone have any advice
on how to do so?

Based on previous threads and looking into Brainder.org's aseg2surf, I
assume I need to use a combination of mri_pretess and mri_tess to
generate tesselated surfaces that can then be converted into ascii files
and then into .obj files using Brainder's surf2obj.  My problem is in
figuring out how to generate the surface meshes from the Tracula
outputs. If anyone can point me to documentation on how to do this or
provide any advice, I'd appreciate it.

Cheers,
David


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[Freesurfer] CORRECTING DEFECT

[maryam koochaki]

Hi Bruce,I am wondering if you saw my last email, about uploading my subject in 
your ftp server.I uploaded the subject  "test_emc_039.tar.gz".I appreciate any 
help.
Thank you, Maryam







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Re: [Freesurfer] CORRECTING DEFECT

[maryam koochaki]

Hi Bruce,Did you get my email regarding to the subject I upload in fft server?
Best,Maryam

 





Regards,Maryam Kouchakidivkolaei 

On Friday, June 3, 2016 10:16 PM, maryam koochaki 
 wrote:
 

 Hi Bruce,I already uploaded it.File name:  test_emc_039.tar.gz
Thanks,Maryam
 





Regards,Maryam Kouchakidivkolaei 

On Friday, June 3, 2016 9:35 PM, Bruce Fischl  
wrote:
 

 Hmmm, that sounds like a bug. If you upload the subject we will take a 
lookCheersBruce
On Jun 3, 2016, at 6:54 PM, maryam koochaki  wrote:


Dear freesurfer experts,I have a subject ending up with this error after 
recon-all.I tried to edit the aseg and run it, but it stuck at topological step.
CORRECTING DEFECT 79 (vertices=54196, convex hull=8490)
error in the retessellation 
normal vector of length zero at vertex 97187 with 0 faces
vertex 97187 has 0 face
No such file or directory
Linux cs-cbl-03 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s test_emc_039 exited with ERRORS .
Could you guide me how I can correct it.Thank you,Maryam 





Regards,Maryam Kouchakidivkolaei

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Re: [Freesurfer] Longitudinal Studies Question

[Martin Reuter]

Hi Carolyn,

not sure what you are asking. You want to do statistics on N=1 subject ?

Anyway, in order to use QDEC, you'd have to reduce the longitudinal data 
(thickness, measured at different time points) to a single number: the 
slope of a linear fit. This is called the 2-stage-approach.


Or you skip Qdec and do a Linear Mixed Effects model directly.

Either approach only makes sense if you have a bunch of subjects (per 
group).


Best, Martin

Ps info on longituidnal statistics:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics

On 06/06/2016 09:45 AM, Carolyn Drobak wrote:

Hello,

I have six scans for a single subject. I have performed "group 
analysis," but wish to use longitudinal data analysis. In particular, 
I was able to get a base for the subjects, so can view in freeview and 
all of that. My issue arises when I try to use QDEC. Because QDEC 
can't use my long.qdec.table.dat file, nor does it like my 
cross.qdec.table.dat file. The problem seems to be that I only have 
one base, i.e. one subject. Is there some way to run analysis on this 
so I can still get all the statistics I want (mostly interested in 
cortical thickness) using just my one subject?


I'm still fairly new to FS, but have done the large majority of the 
tutorials, so am pretty sure I'm not just messing up my files here.


Thanks,
CMD

On Mon, Jun 6, 2016 at 9:40 AM, Carolyn Drobak 
mailto:carolyn.droba...@gmail.com>> wrote:


Hello,

I have six scans for a single subject. I have performed "group
analysis," but wish to use longitudinal data analysis. In
particular, I was able to get a base for the subjects, so can view
in freeview and all of that. My issue arises when I try to use
QDEC. Because QDEC can't use my long.qdec.table.dat file, nor does
it like my cross.qdec.table.dat file. The problem seems to be that
I only have one base, i.e. one subject. Is there some way to run
analysis on this so I can still get all the statistics I want
(mostly interested in cortical thickness) using just my one subject?

I'm still fairly new to FS, but have done the large majority of
the tutorials, so am pretty sure I'm not just messing up my files
here.

Thanks,
CD




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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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Re: [Freesurfer] volumetric difference between 1.5 T and 3.0 T...

[Jovicich, Jorge]

Hi Gonzalo,

indeed, here are the references Bruce is refering to:
http://www.ncbi.nlm.nih.gov/pubmed/19233293
http://www.ncbi.nlm.nih.gov/pubmed/16651008

Image contrast to noise ratio per unit time of acquisition is different 
because of different T1s and lower SNR. Different scan durations will 
also give different head motion biases. Then differences can also 
increase depending on protocol and scanner model/vendor differences. It 
is in general cleaner to not mix data from multiple fields. If you have 
large numbers and well balanced cohorts you can test for differences in 
healthy controls.


Jorge

On 06/06/2016 17:40, Bruce Fischl wrote:

Hi Gonzalo

we seek to minimize these explicitly, but given the difference in T1s 
at different field strength it's pretty hard to get rid of them 
completely. Xiao Han wrote a paper on this, and I think Jorge Jovicich 
did as well


cheers
Bruce


 On Mon, 6 Jun 2016, Gonzalo Rojas Costa wrote:


Hi:

 There exist any difference between the volumetric values obtained
using 1.5T and 3.0T images ? Any paper about it ?

 Sincerely,

Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl

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--
Jorge Jovicich, Ph.D.

MR Lab Head
Center for Mind Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/

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Re: [Freesurfer] Build fsaverage

[Douglas N Greve]

fsaverage is distributed with freesurfer. Do you have freesurfer 
installed on your new computer? If so, then just create a symbolic link with
cd $SUBJECTS_DIR
ln -s $FREESURFER_HOME/subjects/fsaverage



On 06/04/2016 04:44 PM, shi yao wang wrote:
> Hello, Thank you very much for the reply!
>
> 1. I copied  calculated data into a new computer and I cannot find 
> "fsaverage".
> 2. Bruce, thank you! I used make_average_subject command. However, it 
> shows that error message: "lack of memory".
>
> I am wondering how can I do that.
>
> Thank you for helps again!
> Lawrence
>
>
>
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-- 
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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
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Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

[Douglas N Greve]

looks like you put your command on two different lines

On 06/06/2016 05:16 AM, Hao wen wrote:
> Sorry, if you received my email, cuz I really stucked here, and i 
> didnt find the related topics in the freesurfer support archive!
> Thank you in advance
> 
> *De :* Hao wen
> *Envoyé :* mercredi 1 juin 2016 19:32:24
> *À :* freesurfer@nmr.mgh.harvard.edu
> *Objet :* RE: [Freesurfer] CM_Group_analysis_Create tha contrast and 
> design matrix by myself
> Ok, sorry:
>
> wen@HP1973:/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version$
>  
> mri_glmfit \
> >   --glmdir lh.AD_CN_COVARIAETS_AGE_GENDER.glmdir
> ERROR: must specify an input X file or fsgd file or --osgm
> wen@HP1973:/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version$
>  
>   --y lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mgh \
> >   --C contrast.mtx \
> >   --X X.mat
> --y: command not found
> wen@HP1973:/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version$
>  
>   --surf fsaverage lh \
> >   --cortex \
>
> Thanks
>
>
> 
> *De :* freesurfer-boun...@nmr.mgh.harvard.edu 
>  de la part de Douglas N Greve 
> 
> *Envoyé :* mercredi 1 juin 2016 18:47:19
> *À :* freesurfer@nmr.mgh.harvard.edu
> *Objet :* Re: [Freesurfer] CM_Group_analysis_Create tha contrast and 
> design matrix by myself
> Can you send me just the terminal output from mri_glmfit?
>
> On 06/01/2016 12:45 PM, Hao wen wrote:
> > Hi, thanks for your reply, here is the output of the terminal in txt
> > file, hope to hear from you soon
> > Merci
> > Hao
> > 
> > *De :* freesurfer-boun...@nmr.mgh.harvard.edu
> >  de la part de Douglas Greve
> > 
> > *Envoyé :* mercredi 1 juin 2016 17:06:19
> > *À :* freesurfer@nmr.mgh.harvard.edu
> > *Objet :* Re: [Freesurfer] CM_Group_analysis_Create tha contrast and
> > design matrix by myself
> > please send the terminal output that includes the error
> >
> > On 6/1/16 8:10 AM, Hao wen wrote:
> >>
> >> Hello, freesurfers:
> >>
> >> I am doing group analysis, with two diff groups, so I want to know
> >> that how to create my own Contrast and Design matrix, because that I
> >> know in QDEC and CMline, in the freesurfer wiki, You just give the
> >> example for the DODS & DOSS, but it is not so flexible!
> >>
> >>
> >> I know that we should define --X in the command mris_glmfit, but I
> >> got some problems, here is my work flow:
> >>
> >>
> >> *#set the SUBJECTS_DIR*
> >> *export
> >> 
> SUBJECTS_DIR=/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/*
> >> *cd
> >> 
> $SUBJECTS_DIR/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version*
> >> *
> >> *
> >> *
> >> *
> >> *mris_preproc --fsgd AD_CN_COVARIATES_AGE_GENDER.fsgd \*
> >> *  --cache-in thickness.fwhm15.fsaverage \*
> >> *  --target fsaverage \*
> >> *  --hemi lh \*
> >> *  --out lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mgh*
> >> *
> >> *
> >> *
> >> mri_glmfit \
> >>   --glmdir lh.AD_CN_COVARIAETS_AGE_GENDER.glmdir
> >>   --y lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mgh \
> >>   --C AD_CN_COVARIATS_AGE_GENDER.mtx \
> >>   or --C contrast.mat
> >>   --X X.mat
> >>   --surf fsaverage lh \
> >>   --cortex \
> >>
> >>
> >> *
> >> so, after I run the mri_glmfit, i got the errors, like, *you should
> >> define the --X or without --C, or cant find command --surf, --cortex,
> >> *i dont really understand what is the problem, and I create the
> >> design matrix and contrast matrix in Matlab
> >>
> >> Actually, I run the DODS, it works well, and the workflow, I dont
> >> change for the command mris_preproc, I just change the flags in
> >> mri_glmfit, someone could help me for this?
> >>
> >> Thanks in advance!
> >>
> >> Hao
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://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
>
> -- 
> 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 
> 
> Outg

Re: [Freesurfer] volumetric difference between 1.5 T and 3.0 T...

[Bruce Fischl]

Hi Gonzalo

we seek to minimize these explicitly, but given the difference in T1s at 
different field strength it's pretty hard to get rid of them completely. 
Xiao Han wrote a paper on this, and I think Jorge Jovicich did as well


cheers
Bruce


 On Mon, 6 Jun 2016, Gonzalo Rojas Costa 
wrote:



Hi:

 There exist any difference between the volumetric values obtained
using 1.5T and 3.0T images ? Any paper about it ?

 Sincerely,

Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl

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[Freesurfer] volumetric difference between 1.5 T and 3.0 T...

[Gonzalo Rojas Costa]

Hi:

  There exist any difference between the volumetric values obtained
using 1.5T and 3.0T images ? Any paper about it ?

  Sincerely,

Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl

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Re: [Freesurfer] Longitudinal Studies Question

[Carolyn Drobak]

Hello,

I have six scans for a single subject. I have performed "group analysis,"
but wish to use longitudinal data analysis. In particular, I was able to
get a base for the subjects, so can view in freeview and all of that. My
issue arises when I try to use QDEC. Because QDEC can't use my
long.qdec.table.dat file, nor does it like my cross.qdec.table.dat file.
The problem seems to be that I only have one base, i.e. one subject. Is
there some way to run analysis on this so I can still get all the
statistics I want (mostly interested in cortical thickness) using just my
one subject?

I'm still fairly new to FS, but have done the large majority of the
tutorials, so am pretty sure I'm not just messing up my files here.

Thanks,
CMD

On Mon, Jun 6, 2016 at 9:40 AM, Carolyn Drobak 
wrote:

> Hello,
>
> I have six scans for a single subject. I have performed "group analysis,"
> but wish to use longitudinal data analysis. In particular, I was able to
> get a base for the subjects, so can view in freeview and all of that. My
> issue arises when I try to use QDEC. Because QDEC can't use my
> long.qdec.table.dat file, nor does it like my cross.qdec.table.dat file.
> The problem seems to be that I only have one base, i.e. one subject. Is
> there some way to run analysis on this so I can still get all the
> statistics I want (mostly interested in cortical thickness) using just my
> one subject?
>
> I'm still fairly new to FS, but have done the large majority of the
> tutorials, so am pretty sure I'm not just messing up my files here.
>
> Thanks,
> CD
>
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Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

[Hao wen]

Sorry, if you received my email, cuz I really stucked here, and i didnt find 
the related topics in the freesurfer support archive!
Thank you in advance

De : Hao wen
Envoyé : mercredi 1 juin 2016 19:32:24
À : freesurfer@nmr.mgh.harvard.edu
Objet : RE: [Freesurfer] CM_Group_analysis_Create tha contrast and design 
matrix by myself

Ok, sorry:

wen@HP1973:/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version$
 mri_glmfit \
>   --glmdir lh.AD_CN_COVARIAETS_AGE_GENDER.glmdir
ERROR: must specify an input X file or fsgd file or --osgm
wen@HP1973:/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version$
   --y lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mgh \
>   --C contrast.mtx \
>   --X X.mat
--y: command not found
wen@HP1973:/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version$
   --surf fsaverage lh \
>   --cortex \

Thanks



De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Douglas N Greve 

Envoyé : mercredi 1 juin 2016 18:47:19
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design 
matrix by myself

Can you send me just the terminal output from mri_glmfit?

On 06/01/2016 12:45 PM, Hao wen wrote:
> Hi, thanks for your reply, here is the output of the terminal in txt
> file, hope to hear from you soon
> Merci
> Hao
> 
> *De :* freesurfer-boun...@nmr.mgh.harvard.edu
>  de la part de Douglas Greve
> 
> *Envoyé :* mercredi 1 juin 2016 17:06:19
> *À :* freesurfer@nmr.mgh.harvard.edu
> *Objet :* Re: [Freesurfer] CM_Group_analysis_Create tha contrast and
> design matrix by myself
> please send the terminal output that includes the error
>
> On 6/1/16 8:10 AM, Hao wen wrote:
>>
>> Hello, freesurfers:
>>
>> I am doing group analysis, with two diff groups, so I want to know
>> that how to create my own Contrast and Design matrix, because that I
>> know in QDEC and CMline, in the freesurfer wiki, You just give the
>> example for the DODS & DOSS, but it is not so flexible!
>>
>>
>> I know that we should define --X in the command mris_glmfit, but I
>> got some problems, here is my work flow:
>>
>>
>> *#set the SUBJECTS_DIR*
>> *export
>> SUBJECTS_DIR=/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/*
>> *cd
>> $SUBJECTS_DIR/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version*
>> *
>> *
>> *
>> *
>> *mris_preproc --fsgd AD_CN_COVARIATES_AGE_GENDER.fsgd \*
>> *  --cache-in thickness.fwhm15.fsaverage \*
>> *  --target fsaverage \*
>> *  --hemi lh \*
>> *  --out lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mgh*
>> *
>> *
>> *
>> mri_glmfit \
>>   --glmdir lh.AD_CN_COVARIAETS_AGE_GENDER.glmdir
>>   --y lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mgh \
>>   --C AD_CN_COVARIATS_AGE_GENDER.mtx \
>>   or --C contrast.mat
>>   --X X.mat
>>   --surf fsaverage lh \
>>   --cortex \
>>
>>
>> *
>> so, after I run the mri_glmfit, i got the errors, like, *you should
>> define the --X or without --C, or cant find command --surf, --cortex,
>> *i dont really understand what is the problem, and I create the
>> design matrix and contrast matrix in Matlab
>>
>> Actually, I run the DODS, it works well, and the workflow, I dont
>> change for the command mris_preproc, I just change the flags in
>> mri_glmfit, someone could help me for this?
>>
>> Thanks in advance!
>>
>> Hao
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
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--
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
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