[Freesurfer] TRACULA

[Jasmin Alves]

Hello Freesurfer Team,

I attended the conference last week in Boston and really enjoyed all I
learned! But while trying to run through the Tracula tutorial with my own
data, I am having an error with my configuration file:

ERROR: must specify as many DWI dicoms as subjects.

My files are in nifti format, could this possibly be the cause of this
error? I have attached my configuration file for reference.

FREESURFER_HOME: /Applications/freesurfer

Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

Kernel info: Darwin 14.5.0 x86_64

Thanks so much!

Jasmin

Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR $SUBJECTS_DIR

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = $SUBJECTS_DIR

# Subject IDs
#
set subjlist = (40 39 36)
   
# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then bvecfile and bvalfile must be specified
#
set dcmroot = Users/jasminalves/Desktop/data/DTI
set dcmlist = (40/DTI.nii.gz DTI.bvec DTI.bval 39/DTI.nii.gz DTI.bvec DTI.bval 
36/DTI.nii.gz DTI.bvec DTI.bval)

set bveclist = (Users/jasminalves/Desktop/data/DTI/40/DTI.bvec 
Users/jasminalves/Desktop/data/DTI/39/DTI.bvec 
Users/jasminalves/Desktop/data/DTI/36/DTI.bvec)

set bvecfile = (Users/jasminalves/Desktop/data/DTI/40/DTI.bvec 
Users/jasminalves/Desktop/data/DTI/39/DTI.bvec 
Users/jasminalves/Desktop/data/DTI/36/DTI.bvec)

set bvalfile = (Users/jasminalves/Desktop/data/DTI/40/DTI.bval 
Users/jasminalves/Desktop/data/DTI/39/DTI.bval 
Users/jasminalves/Desktop/data/DTI/36/DTI.bval)

set dob0 = 0

set doeddy = 1

set dorotbvecs = 1

set thrbet = 0.5

set doregflt = 0

set doregbbr = 1

set doregmni = 1

set mnitemp = 
/Applications/Utilities/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz

set doregcvs = 0

set usemaskanat = 1

set pathlist = ( lh.cst_AS rh.cst_AS \
 lh.unc_AS rh.unc_AS \
 lh.ilf_AS rh.ilf_AS \
 fmajor_PP fminor_PP \
 lh.atr_PP rh.atr_PP \
 lh.ccg_PP rh.ccg_PP \
 lh.cab_PP rh.cab_PP \
 lh.slfp_PP rh.slfp_PP \
 lh.slft_PP rh.slft_PP )

set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)

set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt

set nstick = 2

set nburnin = 200

set nsample = 7500

set nkeep = 5

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[Freesurfer] mri_surfcluster issues

[Antonin Skoch]

Dear FreeSurfer experts,

I am using mri_surfcluster to compare results from PALM and FreeSurfer cluster 
extent inference. 

I came across several issues in mri_surfcluster I cannot cope with.

1.
I observed that --mask option in mri_surfcluster does not prevent cluster to 
growing outside the mask. 

When I run 

mri_surfcluster --in lh.thickness.fsaverage_masked.mgh --sum summary.txt 
--subject fsaverage --surf white --hemi lh --thmin 0 --ocn cluster_summary.mgz 
--mask ./mask.mgh 

the cluster is growing outside mask and covers all surface including 
non-cortical (masked) regions.

Is this intended behavior? This behavior (allowing clusters leak outside mask) 
seems strange to me since it could possibly influence results of cluster-extent 
inference in case of mask-constrained analysis.

2.
How behaves mri_glmfit-sim in permutation-based building cluster-extent null 
distribution with mask? Is in this case also allowed to clusters to leak 
outside mask?

3.
Another issue is concerning reported cluster area. I tested mri_surfcluster on 
data where overlay values (lh.thickness.fsaverage.mgh) were set to 0 outside 
cortex mask (they were non-zero also in some portion of non-cortical vertices). 
When I set thmin to non-zero value in mri_surfcluster

mri_surfcluster --in lh.thickness.fsaverage_masked.mgh --sum summary.txt  
--subject fsaverage --surf white --hemi lh --thmin 0.1 --ocn  
cluster_summary.mgz --mask ./mask.mgh 

 I get cluster comprising (almost) all cortex, not leaking to non-cortical 
areas. But what is strange, the reported cluster size is far larger than area 
of the whole cortical surface.

number of voxels in search space = 149953
Done loading source values (nvtxs = 163842)
overall max = 5 at vertex 817
overall min = 0 at vertex 8
surface nvertices 163842
surface area 65417.097656
surface area 65416.648438
NOT Adjusting threshold for 1-tailed test
Searching for Clusters ...
thmin=0.000100 (0.000100), thmax=-1.00 (-1), thsignid=0, minarea=0.00
Found 2 clusters
Max cluster size 76431.562500
Saving cluster numbers to pok.mgz


Here is output of mri_surfcluster:
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ    NVtxs
   1    5.000 817  76431.56    -25.8    4.6  -37.5  149874
   2    2.670  144205  0.53    -15.8  -40.4   -3.8 1

How it is possible?

4.
Does the fsaverage/surf/lh.area correspond to area of particular vertices on 
fsaverage/surf/lh.white? I expect yes.

5.
How it is possible to calculate area of specified vertex of surface? I tried to 
do that by creating .label file with particular vertex number and running

mri_surfcluster --in lh.thickness.fsaverage_masked.mgh --sum summary.txt  
--subject fsaverage --surf white --hemi lh --thmin 0.1 --clabel 
myVertex.label

I indeed got report of 1 cluster with 1 vertex, with VtxMax value identical to 
vertex index in myVertex.label
but the area value in summary.txt is different that value in 
fsaverage/surf/lh.area.

Thank you very much in advance for clarification,

Antonin Skoch
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[Freesurfer] August FreeSurfer course in Copenhagen, Denmark

[Allison Stevens]

There are still some spots available in the Copenhagen FreeSurfer Course 
which will be held from August 10th to 12th, 2016. The course will be 
organized by the Neurobiology Research Unit, Copenhagen University 
Hospital in cooperation with the Laboratory for Computational Neuroimaging 
of the Athinoula A. Martinos Center for Biomedical Imaging.

The course will be a three-day course for beginners and experienced users 
of FreeSurfer and the lectures will be held by FreeSurfer developers from 
the Laboratory for Computational Neuroimaging.

For further information and to register for this course, please visit:
http://fscph2016.nru.dk/

Please feel free to contact my friends at NRU (cc'd) with any questions.

Allison Stevens
Lab Manager/Course Organizer
Laboratory for Computational Neuroimaging
FreeSurfer Development Team

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Re: [Freesurfer] LME for functional data, 3 factors

[jorge luis]

Hi Laura
 In the 
wikihttps://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModelswe 
recommended to order the columns of the design matrix in thefollowing way: 
Column 1: theintercept term (which is a column of ones)
Colum 2: the timecovariate if it varies across subjects (eg. time from baseline)
Column 3-q: anytime-varying covariates (eg. training: 0 before training, 1 
aftertraining)
Column q+1-r: thegroup covariates of interest (eg. a binary variable 
indicatingwhether or not the subject is a patient), for n groups you will 
haven-1 binary covariates
Column r+1-s:interactions between group covariates with the 
time-varyingcovariates (only the interesting interactions)
Column s+1-p: anyother nuisance time-invariant covariates (eg. age-at-baseline, 
gender,etc...)

LME is a type oflinear regression model that integrates both a model for the 
mean anda model for the covariance into a single statistical model. So ifyou 
want to compare different models for the mean (with differentcovariates) then 
you need to start with a “maximal model for themean” that includes all the 
possible covariates of interest. Then you selectthe random effects for that 
"maximal model" using the model selectionprocedure with lme_mass_LR. Random 
effects can only be time-varyingcovariates (i.e a subset of the columns from 1 
to q above, thosecomprise the Zcols parameter in lme_mass_fit_vw)
After you choosewhich time-varying covariates are going to be considered as 
randomeffects then you can test if any single fixed effects covariate in your 
designmatrix has a significant contribution to the model in the same wayyou 
would for a traditional GLM. You will use F-tests for that.Covariates that do 
not significantly contribute to the model can beruled out of the model and a 
new model with less covariates but the same random effects can thenbe fitted. 
Keep in mind thatfitting lme models is computationally expensive and the 
computationoverhead quickly increases with the number of random effects and 
fixedeffects in your model.  Also considering one or two random effects 
including the intercept term (or atmost three) is usually enough but this 
really depends on the natureof the data. 

Best-Jorge


 
  De: Laura Rueda Delgado 
 Para: Freesurfer support list  
 Enviado: Lunes 11 de abril de 2016 13:05
 Asunto: Re: [Freesurfer] LME for functional data, 3 factors
   
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div.yiv9346679664WordSection1 {}#yiv9346679664 Dear Martin,    Thank you for 
your quick response.    My research question is focused on the group and day 
effect, so I could simplify the model. From your response, I thought of 
including in the design matrix the binary code for Condition 2, and for 
Condition 3 in two columns, like you suggested; however, adding only the 
interaction effect of group and day. This way, the model takes into account the 
repeated measures of Condition while remaining relatively simple.    Now, to 
add more complexity and be more specific, I'm interested on neural correlates 
of learning, which is (un)fortunately tangled with performance. Therefore, I 
was thinking to add the learning gains (e.g. [performance_day_2 - 
performance_day_1]/performance_day_1) as a fixed effect. Checking the example 
datasets that come with the LME toolbox, I see that other measures (e.g. age, 
gender) are repeated for all the measures at different days of the same 
subject. And, when the age of participants at the first measurement is used as 
a fixed effect, "baseline age", the value is repeated for the baseline day and 
the other days. I was wondering if this could be applied for the Learning Gain 
as well (which is a measure of change of performance over the training days). I 
have my doubts because I would understand that this type of coding 

[Freesurfer] From Talairach to Vertex Index

[Ilaria Mazzonetto]

Hi FS users,
I need to check if a specific point in Talairach coordinates is inside a
label that I created from a significative cluster of a previous group
analysis (the template is fsaverage). How can I do this quickly?
Thanks a lot.
Best regards.

Ilaria
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Re: [Freesurfer] LME for functional data, 3 factors

[Laura Rueda Delgado]

Dear Martin,

Thank you for your quick response.

My research question is focused on the group and day effect, so I could 
simplify the model. From your response, I thought of including in the design 
matrix the binary code for Condition 2, and for Condition 3 in two columns, 
like you suggested; however, adding only the interaction effect of group and 
day. This way, the model takes into account the repeated measures of Condition 
while remaining relatively simple.

Now, to add more complexity and be more specific, I'm interested on neural 
correlates of learning, which is (un)fortunately tangled with performance. 
Therefore, I was thinking to add the learning gains (e.g. [performance_day_2 - 
performance_day_1]/performance_day_1) as a fixed effect. Checking the example 
datasets that come with the LME toolbox, I see that other measures (e.g. age, 
gender) are repeated for all the measures at different days of the same 
subject. And, when the age of participants at the first measurement is used as 
a fixed effect, "baseline age", the value is repeated for the baseline day and 
the other days. I was wondering if this could be applied for the Learning Gain 
as well (which is a measure of change of performance over the training days). I 
have my doubts because I would understand that this type of coding would 
describe two mixed aspects: a "prediction" of Gain from the brain data at Day 
1, along with the appropriate relationship of Gain with brain data at Day 2. I 
would think that adding 0s for Day 1 in the variable Gain would be more 
appropriate, and this way the fixed effect of Day would be coded in the 
variable Gain. But of course, I recur to the experts to settle this issue.

Additionally, I see that I could compare two models with different number of 
random effects with lme_mass_LR. However, I would like to compare models with 
different covariates (other covariates of no interest, like gender and years of 
education). Is this possible within this toolbox?


Best regards,

Laura Rueda

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter
Sent: donderdag 7 april 2016 18:20
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] LME for functional data, 3 factors

Hi Laura,

1)
you would need to model the 3 level variable differently, as 1,2,3 will be 
understood as continuous and that is not what you want. Instead you have two 
columns: one column for group 2, where all instances are binary (1 if group is 
2, else 0), and one for group 3. Then the intercept and slope will be for group 
1 and these columns contain the offsets for group 2 and 3 respectively.
About interactions, make sure you really want to model all interactions. Some 
may be not very meaningful and keeping the model simple is usually a good idea. 
But if you want them all, add them all.

2) Zcols: Vector with the indices of the colums of X that will be considered  
as random effects. Usually the intercept is a random effect and maybe other 
variables (e.g. the time, if you want to allow slopes to be different across 
subjects). For just the intercept column use [ 1]
ni should be correct

3) yes, but with the design above, since you model a global intercept and then 
the offset of each group (or whatever that three condition variable is) you 
need to make sure you interpret things correctly. E.g. a 1 in such a column for 
group 2 or three indicates that there is a difference from the first group. 
This is not the group 2 effect.

4) Sorry, I don't know. Maybe someone else has a suggest.

Since you have all interactions, you should be able to specify contrast 
according to your test in this model and don't need to create a new one. Your 
setup is a little complicated, so it would be wise to involve a local 
statistician to make sure you are interpreting things correctly.

Best, Martin


On 04/07/2016 10:57 AM, Laura Rueda Delgado wrote:
Dear FreeSurfers and LME experts,

I've just started using the LME toolbox by Bernal-Rusiel et al (2012, 2013) in 
Matlab, apart from FreeSurfer. My experimental design includes one 
between-subjects factor (group with two levels, 24 vs 22 subjects), and two 
within-subjects (WS) factors (day with two levels, and condition with three 
levels). As far as I understand, the LME toolbox can be used for longitudinal 
data and for investigating modulations of neural activity with behavioral 
measures. However, it's been difficult for me to set up both the design matrix 
and the input of the LME functions given three fixed factors in my design (I 
haven't included behavior yet). So I have a few questions that I hope you can 
help me answer. I follow these steps:

1) Following the wiki, I've created a pre-design matrix, M, with:
First column: Day factor coded as 0 (first day) and 7 (7 days later, as during 
acquisition).
Second column: Group factor binary coded.
Third column: Condition factor coded with dummy variables 1 to 3 (three 

Re: [Freesurfer] $FREESURFER_HOME/sources.csh

[Douglas N Greve]

That is something we had to put in to be able to run under newer mac 
OSs. You can remove that line in your version.

On 04/11/2016 11:52 AM, Marco Loggia wrote:
> Good morning Doug and all,
>
> I am running epidewarp.fsl (using the dev version since I need it to 
> be compatible with the recent versions of FSL; 
> /usr/local/freesurfer/dev/bin/epidewarp.fsl).
>
> However, for the first time I see that it complains that it can no 
> longer find /usr/local/freesurfer/stable5_3_0/sources.csh.
>
> How can this be fixed??
>
> Thanks!
>
> Marco
> ___
>
> *Marco L. Loggia, PhD
> *Assistant Professor of Radiology, Harvard Medical School
> Associate Director, Center for Integrative Pain NeuroImaging (CiPNI)
>
> A. A. Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 Thirteenth Street, Room 2301
> Charlestown, MA 02129
> Phone: (617) 643-7267
> Fax: (617) 726-7422
> Email: ma...@nmr.mgh.harvard.edu 
> Web: http://scholar.harvard.edu/loggia
>
>
>
>
>
> ___
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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
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/

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Re: [Freesurfer] Accuracy of D-K atlas for different age ranges

[Bruce Fischl]

Hi Kirstie

I can't imagine that there is any serious variability in that age range. 
The folds are set long before then

cheers
Bruce


On 
Mon, 11 Apr 2016, Kirstie Whitaker wrote:

> Hi Freesurfer community,
> 
> A reviewer has asked how accurate the application of freesurfer regional
> labels are to different age ranges (specifically our study is between 14 and
> 24 years old).
> 
> I'm sure this question has been answered elsewhere so please do forgive me
> for being lazy and simply asking you to recommend good references rather
> than searching for them in PubMed!
> 
> Thank you!
> 
> Kirstie x
> 
> --
> Kirstie Whitaker, PhD
> Research Associate
> 
> Department of Psychiatry
> University of Cambridge
> 
> Mailing Address
> Brain Mapping Unit
> Department of Psychiatry
> Sir William Hardy Building
> Downing Street
> Cambridge CB2 3EB
> 
> Phone: +44 7583 535 307
> Website: www.kirstiewhitaker.com
> 
>
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[Freesurfer] $FREESURFER_HOME/sources.csh

[Marco Loggia]

Good morning Doug and all,

I am running epidewarp.fsl (using the dev version since I need it to be 
compatible with the recent versions of FSL; 
/usr/local/freesurfer/dev/bin/epidewarp.fsl).

However, for the first time I see that it complains that it can no longer find 
/usr/local/freesurfer/stable5_3_0/sources.csh.

How can this be fixed??

Thanks!

Marco
___

Marco L. Loggia, PhD
Assistant Professor of Radiology, Harvard Medical School 
Associate Director, Center for Integrative Pain NeuroImaging (CiPNI)

A. A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 Thirteenth Street, Room 2301
Charlestown, MA 02129
Phone: (617) 643-7267
Fax: (617) 726-7422 
Email: ma...@nmr.mgh.harvard.edu
Web: http://scholar.harvard.edu/loggia



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[Freesurfer] TRACULA dev version: Error message

[Elijah Mak]

Hi Freesurfer Community,

I am running TRACULA on a single subject in the dev version
(freesurfer-Darwin-OSX-stable-v6-beta-20151015)

#-

/Applications/freesurfer6beta/bin/trac-preproc

#-

#@# Image corrections Mon Apr 11 16:15:19 BST 2016

mri_convert /Users/MacPro/Documents/NIMROD_DTI/16084.nii.gz
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz

mri_convert /Users/MacPro/Documents/NIMROD_DTI/16084.nii.gz
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz

$Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $

reading from /Users/MacPro/Documents/NIMROD_DTI/16084.nii.gz...

TR=11700.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0.998406, -0.0447105, -0.0344521)

j_ras = (-0.0435914, 0.998518, -0.0325768)

k_ras = (-0.0358576, 0.0310231, 0.998875)

writing to
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz...

cp 16084.bvec
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvecs

cp 16084.bval
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvals

mv -f
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvecs.tmp
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvecs

mv -f
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvals.tmp
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvals

flip4fsl
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.nii.gz

INFO: input image orientation is LAS

INFO: input image determinant is -8

fslswapdim
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz
x y z
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.nii.gz

fslorient -forceradiological
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.nii.gz

mv -f
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.mghdti.bvecs
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvecs

mv: rename
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.mghdti.bvecs
to */Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvecs:
No such file or directory*


*trac-preproc exited with ERRORS at Mon Apr 11 16:16:26 BST 2016*
---

What has gone wrong here?

Thanks!
Elijah
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Re: [Freesurfer] Viewing eroded structure after -seg-erode 1

[Elijah Mak]

Thanks Doug.

Do you mean loading the structure (i.e. LeftHippocampus2diff.mgz) on the
orig.mgz as an overlay? I am able to do that but I can't seem to find an
option for thresholding. Sorry if I misunderstood your original email.

Best Wishes,
Elijah
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Re: [Freesurfer] Group level analysis: Specifying contrasts

[Douglas N Greve]

What is your source data? It looks like you have two time points per 
subject, but the names of "offset" and "slope" suggest some preprocessing?

Input hc001-lRsk_offset hc001100
Input hc001-lRsk_slope  hc001000
Input hc001-mRsk_offset hc001010
Input hc001-mRsk_slope  hc001000
Input hc001-hRsk_offset hc001001
Input hc001-hRsk_slope  hc001000



On 04/11/2016 10:09 AM, Afzal, Afsana wrote:
> Hi Doug,
>
> I've attached the fsgd file and the contrast matrix file. Thanks for your 
> help!
>
> - Afsana
>
> __
> Afsana Afzal
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, April 08, 2016 12:07 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts
>
> I don't know what you mean, can you just send the header of the fsgd
> file and the contrast matrix?
>
> On 04/04/2016 11:20 AM, Afzal, Afsana wrote:
>> Hi,
>>
>> I want to perform a linear regression for a task with 3 different risk
>> conditions (low, medium, high) with the following linear trend: low =
>> 1, medium = 2, high = 3.
>>
>> Right now I'm specifying the above weighted under each risk condition
>> in my contrast matrix. Is this the correct approach? I want to make
>> sure I am calculating a regression and not a weighted average.
>>
>> Thank you for your help,
>>
>> Afsana
>>
>>
>> __
>> *Afsana Afzal*
>> Clinical Research Coordinator
>> Massachusetts General Hospital
>> Division of Neurotherapeutics
>> Department of Psychiatry: Neurosciences
>> 149 13th St, Room 2612
>> Charlestown, MA 02129
>> Phone: 617-643-5129
>> Fax: 617-726-4078
>>
>>
>> ___
>> 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/
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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> 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/

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Re: [Freesurfer] Viewing eroded structure after -seg-erode 1

[Douglas N Greve]

You can load it as an overlay in freeview make sure to specify the 
registration file as that compted for the DTI. Also make sure to set the 
threshold to something like 0.5

On 04/11/2016 09:41 AM, Elijah Mak wrote:
> Hi Freesurfer Community,
>
> I have performed -seg-erode 1 during mri_segstats on resampled 
> subcortical strutures (T1 to FA/MD). Can I view the eroded masks in T1 
> anatomical space to visually inspect whether PVE has been adequately 
> accounted for?
>
> Thank you.
>
> Best Wishes,
> Elijah
>
>
>
>
> ___
> 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/

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Re: [Freesurfer] Group level analysis: Specifying contrasts

[Afzal, Afsana]

Hi Doug, 

I've attached the fsgd file and the contrast matrix file. Thanks for your help! 

- Afsana

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, April 08, 2016 12:07 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts

I don't know what you mean, can you just send the header of the fsgd
file and the contrast matrix?

On 04/04/2016 11:20 AM, Afzal, Afsana wrote:
> Hi,
>
> I want to perform a linear regression for a task with 3 different risk
> conditions (low, medium, high) with the following linear trend: low =
> 1, medium = 2, high = 3.
>
> Right now I'm specifying the above weighted under each risk condition
> in my contrast matrix. Is this the correct approach? I want to make
> sure I am calculating a regression and not a weighted average.
>
> Thank you for your help,
>
> Afsana
>
>
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
> ___
> 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/

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avg.risk.mod.fsgd
Description: avg.risk.mod.fsgd


weight_avg.mtx
Description: weight_avg.mtx
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[Freesurfer] Accuracy of D-K atlas for different age ranges

[Kirstie Whitaker]

Hi Freesurfer community,

A reviewer has asked how accurate the application of freesurfer regional
labels are to different age ranges (specifically our study is between 14
and 24 years old).

I'm sure this question has been answered elsewhere so please do forgive me
for being lazy and simply asking you to recommend good references rather
than searching for them in PubMed!

Thank you!

Kirstie x

-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
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[Freesurfer] Viewing eroded structure after -seg-erode 1

[Elijah Mak]

Hi Freesurfer Community,

I have performed -seg-erode 1 during mri_segstats on resampled subcortical
strutures (T1 to FA/MD). Can I view the eroded masks in T1 anatomical space
to visually inspect whether PVE has been adequately accounted for?

Thank you.

Best Wishes,
Elijah
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