Re: [Freesurfer] MNI coordinates

[Douglas Greve]

We don't have those number available, but you can generate them with 
something like:


#1 Convert the annotation to a set of labels. This is for the Desikan 
atlas, but you can spec the destrieux instead

mri_annotation2label --subject fsaverage --hemi lh --outdir ~/tmp/aparc

# For each label, run mri_surfcluster to get the centroid
mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel 
lh.pericalcarine.label --sum sum.lh.pericalcarine --centroid --thmin 0 
--hemi lh --subject fsaverage


This will actually be weighted by the thickness, but that should not 
matter much


The centroid coordinates will be in MNI305 space

doug



On 7/23/13 11:57 AM, LAOUCHEDI MAKHLOUF wrote:

Hi
i am using corticals parcels (destrieux) as nodes in a 
connectivity study using the NBS (Network Based Statistics) tool; i 
want to assign MNI coordinates for these nodes. is there any MNI 
coordinates in freesurfer for each component of this parcellation (not 
for every vertex in those components) or any other strategy to assign 
coordinates for these components ?


otherwise, i intend to non-linearily register the freesurfer's labels 
for a healthy subject in MNI and for each label i will use coordinates 
of one of its points to represent that label


thanks for help


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Re: [Freesurfer] help needed with fsgd file and contrast matrix for correlation analysis

[Douglas Greve]

Hi Robert, both of those are correct. The 2nd will give you 
OldAgeSlope-YoungAgeSlope correcting for Gender and BEH

doug



On 7/23/13 10:40 AM, Robert Schulz wrote:

Dear all,
I have 2 short questions regarding a correlation analysis I'd like to 
perform with mri_glmfit (surface-based DTI data are correctly 
preprocessed and concatenated into mgh file, statistics are performed 
on fsaverage space).
1) I'd like to look for correlation between the surface-data and a 
behavioural measure BEH in one group, correcting for gender and age.

I set up the following fsgd:
GroupDescriptorFile 1
Class Male
Class Female
Variables BEH Age
Input subj1 Male 0.76 72
Input subj2 Male 0.44 67
Input subj3 Female 0.33 80

My contrast file is: 0 0 0.5 0.5 0 0 (referring to the FSGD examples 
Fsgd2G2V, GLM with 2*(2+1) columns).

Is this setup correct? If not, how would I have to set up fsgd and C?
2) In a next step, I'd like to answer the question (now including 
another group2): Where does group1 (OLD) show increased correlation 
with BEH compared to group2 (YOUNG), correcting for GENDER and AGE 
within each group. I wonder because AGE is the relevant difference 
between both groups.

GroupDescriptorFile 1
Class OldMale
Class OldFemale
Class YoungMale
Class YoungFemale
Variables BEH Age
Input subj1 OldMale 0.76 72
Input subj2 OldMale 0.44 67
Input subj3 OldFemale 0.33 80

Input subj11 YoungMale 0.80 20
Input subj12 YoungMale 0.55 21
Input subj13 YoungFemale 0.44 31

My contrast file would look like: 0 0 0 0 0.5 0.5 -0.5 -0.5 0 0 0 0 
(referring to GLM with 4*(2+1) columns).

Correct?
Thank you very much for your help! I am really not sure whether I did 
it correctly and whether I can trust my results.

Best wishes, Robert

Besuchen Sie uns auf: www.uke.de 



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Re: [Freesurfer] recon-all error

[Douglas Greve]

What is your command line? This is surely an initialization error. Try 
running tkregister2 with --regheader to see where it starts. If that is 
close, then use --init-header on bbregister


doug



On 7/23/13 4:13 PM, Smian wrote:
Thank you for your reponse. The registration has turned out quite 
strangely (please see attached). I checked the first value in the 
mincost file and it is quite high (~0.95). I'm assuming that means 
that the initialization was bad. I tried changing the initialization 
from fsl to spm and header, but that failed too. Would you know why 
this could be occurring and how I might be able to fix it?


Thank you!


On 2013-07-23 16:07, Bruce Fischl wrote:

you can use bbregister to register your T2* volumes to the surface, then
mri_vol2surf to sample and display it.

cheers
Bruce
On Tue, 23 Jul 2013, Smian wrote:


Hi everyone,

To put things into context, I am trying to follow the four step
methodology outlined in this paper (Cohen-Adad, 2013)
http://www.sciencedirect.com/science/article/pii/S1053811913000700

I have already performed recon-all on MPRAGE data. I have also carried
out the following steps:

1) Reconstruct cortical surface
2) Register T1 to the surface
3) Sample T1 at a given cortical depth
4) Register surface to fsaverage

I have now been told to use the T2* information from the fourth echo of
separately acquired T2* weighted data and to 'overlay' (I'm not sure if
this is the correct usage of this technical term) it on the surfaces
produced (as above) of the MPRAGE data. I realize that I can't perform
recon-all on this T2* weighted data. I am assuming that I need to carry
out steps similar to 1)-4) on this new data, but I'm not sure. Would 
you

have any guidance on how to go about this?

Any help would be appreciated!

Thank you!

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Re: [Freesurfer] issue with mri_label2vol

[Douglas Greve]

Hi Cesar, when you say that it is on the left hemi, do you mean the left 
side of the image or the right side of the image. tkmedit displays in 
radiological convention, so a right hemi label should show up on the 
left side.


doug




On 7/23/13 4:45 PM, Cesar Echavarria wrote:

Hello freesurfers

I want to convert a surface-defined label to an auxiliary volume file. 
I've created my label on the right hemisphere. I then enter the 
following command to convert this label into a volume


mri_label2vol --label 
/cluster/tootell/pitcairn/1/users/Cesar/good_subjects_anat/abir_anat/label/Retinotopy/RH_V1horizontal.label 
--temp 
/cluster/tootell/pitcairn/1/shahin/good_subjects_anat/abir_anat/mri/orig.mgz 
--regheader 
/cluster/tootell/pitcairn/1/shahin/good_subjects_anat/abir_anat/mri/orig.mgz 
--subject abir_anat --hemi rh --proj frac 0 1 .1 --o 
/cluster/tootell/pitcairn/1/users/Cesar/good_subjects_anat/abir_anat/mri/RH_V1horizontal.mgz


When I load the auxiliary volume file into tkmedit, I find that the 
volume is actually on the* left* hemisphere. I would appreciate any 
help pointing out where my commands/ my thinking went wrong. Let me 
know if images would be helpful


Thanks,

Cesar Echavarria


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Re: [Freesurfer] infant atlas segmentation

[Douglas Greve]

You can try using bbregister. Normally, you don't use bbregister on a 
segmentation, but the segmentation index numbers just happen to be 
"T1-weighted".

doug
ps. Please remember to copy the list when responding. thanks!


On 7/23/13 9:51 AM, Mark Plantz wrote:

Hi Doug,

   Sorry about that vague explanation. So I received a series of 
infant brain atlases from a UNC medical research group 
(http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlases). 
I have a series of infant MRI's that I would like to segment (using 
the infant atlases, instead of the default adult atlas in FreeSurfer).


   As a preliminary step, I was attempting to check the alignment of 
one of the atlas files ('avgseg.mgz') with one of the input brains 
('brain.mgz'). [I attached these two files, just in case].


So my command line would be:

tkmedit $Subject brain.mgz -segmentation avgseg.mgz 
$FREESURFER_HOME/FreeSurferColorLUT.txt


The result was the previously attached image. I was just wondering if 
there is any way to shift the two images manually so the alignment is 
better? Or maybe the two files are simply not compatible with one another?


Thanks for all the help!

Best,

Mark




On Mon, Jul 22, 2013 at 3:53 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:



Hi Mark, I have no idea what you are doing. Can you send a command
line?
Are either of the images generated by FS?
doug




On 07/22/2013 03:56 PM, Mark Plantz wrote:
> Hello FreeSurfers,
>
> I recently obtained a set of infant templates. Out of
curiousity,
> I decided to view one of the input brains with the provided
segmented
> volume file. It appears that there is some misalignment. I wouldn't
> expect the alignment to be perfect, since I am basically
overlaying an
> average of multiple brains onto one. However, it looks like this
> misalignment may be caused by either: 1.) the segmentation
volume file
> being shifted down or 2.) the slices not lining up properly
(i.e. one
> file starts before the other).
>
>Any ideas what could cause a problem like this? Could it be that
> the segmented files are simply not compatible with FreeSurfer?
>
> Thanks for the help,
>
> Mark
>
>
>
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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[Freesurfer] issue with mri_label2vol

[Cesar Echavarria]

Hello freesurfers

I want to convert a surface-defined label to an auxiliary volume file. I've
created my label on the right hemisphere. I then enter the following
command to convert this label into a volume

mri_label2vol --label
/cluster/tootell/pitcairn/1/users/Cesar/good_subjects_anat/abir_anat/label/Retinotopy/RH_V1horizontal.label
--temp
/cluster/tootell/pitcairn/1/shahin/good_subjects_anat/abir_anat/mri/orig.mgz
--regheader
/cluster/tootell/pitcairn/1/shahin/good_subjects_anat/abir_anat/mri/orig.mgz
--subject abir_anat --hemi rh --proj frac 0 1 .1 --o
/cluster/tootell/pitcairn/1/users/Cesar/good_subjects_anat/abir_anat/mri/RH_V1horizontal.mgz

When I load the auxiliary volume file into tkmedit, I find that the volume
is actually on the* left* hemisphere. I would appreciate any help pointing
out where my commands/ my thinking went wrong. Let me know if images would
be helpful

Thanks,

Cesar Echavarria
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Re: [Freesurfer] mri_ca_train bug

[Bruce Fischl]

Hi Mark

have you tried using  a transform? Usually with more than one subject we 
require that they be registered. I haven't looked at that code in a long 
time, so I am not positive that it would fix this problem, but it might. 
In any case if they aren't registered it won't generate a useful atlas, 
even if it does run to completion

Bruce

On Tue, 23 Jul 2013, Mark Plantz wrote:


Hello freesurfers,
    I recently ran into a problem with mri_ca_train, a function that creates
a .gca atlas from a manually segmented volume and input volume(s). 

  My command line is:

mri_ca_train -T1 T1.mgz CMH-11460 CMH-11461 ~/Desktop/atlas.gca

The results:

processing subject CMH-11461, 1 of 1...
   reading input 0:
/Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11461/mri/norm.mgz
filling holes in the GCA...
404261 classifiers: 1.5 per node, 7.59 in brain (0 holes filled)
computing covariances for subject CMH-11461, 1 of 1...
average std = 6.1   using min determinant for regularization = 3.7
298584 singular and 4268 ill-conditioned covariance matrices regularized
writing trained GCA to /Users/IngvalsonLab/Desktop/atlas1.gca...
classifier array training took 0 minutes and 27 seconds.
dhcp-165-124-23-230:LabMRIData IngvalsonLab$ 
dhcp-165-124-23-230:LabMRIData IngvalsonLab$ 
dhcp-165-124-23-230:LabMRIData IngvalsonLab$ mri_ca_train -T1 T1.mgz
CMH-11460 CMH-11461 ~/Desktop/atlas1.gca 
reading T1 data from subject's mri/T1.mgz directory
training on 2 subject and writing results to
/Users/IngvalsonLab/Desktop/atlas1.gca
***
processing subject CMH-11460, 1 of 2...
   reading input 0:
/Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11460/mri/T1.mgz
***
processing subject CMH-11461, 2 of 2...
   reading input 0:
/Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11461/mri/T1.mgz
filling holes in the GCA...
468392 classifiers: 1.8 per node, 10.41 in brain (0 holes filled)
computing covariances for subject CMH-11460, 1 of 2...
GCAupdateNodeCovariance(17, 35, 28, 4): could not find label
dhcp-165-124-23-230:LabMRIData IngvalsonLab$ 


   According to the fswiki, the same bug was eliminated in the 2009 version.
For some odd reason, this command works with one subject, but not with
multiple subjects.

Any ideas?

Thanks in advance,

MP

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Re: [Freesurfer] recon-all error

[Smian]

Thank you for your reponse. The registration has turned out quite 
strangely (please see attached). I checked the first value in the 
mincost file and it is quite high (~0.95). I'm assuming that means that 
the initialization was bad. I tried changing the initialization from fsl 
to spm and header, but that failed too. Would you know why this could be 
occurring and how I might be able to fix it?


Thank you!


On 2013-07-23 16:07, Bruce Fischl wrote:
you can use bbregister to register your T2* volumes to the surface, 
then

mri_vol2surf to sample and display it.

cheers
Bruce
On Tue, 23 Jul 2013, Smian wrote:


Hi everyone,

To put things into context, I am trying to follow the four step
methodology outlined in this paper (Cohen-Adad, 2013)
http://www.sciencedirect.com/science/article/pii/S1053811913000700

I have already performed recon-all on MPRAGE data. I have also carried
out the following steps:

1) Reconstruct cortical surface
2) Register T1 to the surface
3) Sample T1 at a given cortical depth
4) Register surface to fsaverage

I have now been told to use the T2* information from the fourth echo 
of
separately acquired T2* weighted data and to 'overlay' (I'm not sure 
if

this is the correct usage of this technical term) it on the surfaces
produced (as above) of the MPRAGE data. I realize that I can't perform
recon-all on this T2* weighted data. I am assuming that I need to 
carry
out steps similar to 1)-4) on this new data, but I'm not sure. Would 
you

have any guidance on how to go about this?

Any help would be appreciated!

Thank you!

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Re: [Freesurfer] inflate surface until sphere

[Bruce Fischl]

Hi Yi-Ping

try using the -i switch to mris_sphere.

cheers
Bruce
On Tue, 23 Jul 2013, Lo, Yiping 
wrote:

>
>
> Hi Freesurfer,
>
> I am tring to inflate pial surface until the sphere. I have tried 
> mris_inflate and set the number of iteration to be large. However, it seems 
> to inflate the brain to a limit and no further inflation. I have also tried 
> mris_sphere, but it seems not what I want. It more likely to map the pial 
> surface onto a sphere and inflate it along the sphere.  I should say in 
> advance, I only got .pial file. What should I do to get what I want?
>
> Best Wishes,
> Yi-Ping
>
>
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Re: [Freesurfer] recon-all error

[Bruce Fischl]

you can use bbregister to register your T2* volumes to the surface, then 
mri_vol2surf to sample and display it.

cheers
Bruce
On Tue, 23 Jul 2013, Smian wrote:

> Hi everyone,
>
> To put things into context, I am trying to follow the four step
> methodology outlined in this paper (Cohen-Adad, 2013)
> http://www.sciencedirect.com/science/article/pii/S1053811913000700
>
> I have already performed recon-all on MPRAGE data. I have also carried
> out the following steps:
>
> 1) Reconstruct cortical surface
> 2) Register T1 to the surface
> 3) Sample T1 at a given cortical depth
> 4) Register surface to fsaverage
>
> I have now been told to use the T2* information from the fourth echo of
> separately acquired T2* weighted data and to 'overlay' (I'm not sure if
> this is the correct usage of this technical term) it on the surfaces
> produced (as above) of the MPRAGE data. I realize that I can't perform
> recon-all on this T2* weighted data. I am assuming that I need to carry
> out steps similar to 1)-4) on this new data, but I'm not sure. Would you
> have any guidance on how to go about this?
>
> Any help would be appreciated!
>
> Thank you!
>
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>
>
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[Freesurfer] mri_ca_train bug

[Mark Plantz]

Hello freesurfers,

I recently ran into a problem with mri_ca_train, a function that
creates a .gca atlas from a manually segmented volume and input volume(s).

  My command line is:

mri_ca_train -T1 T1.mgz CMH-11460 CMH-11461 ~/Desktop/atlas.gca

The results:

processing subject CMH-11461, 1 of 1...
   reading input 0:
/Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11461/mri/norm.mgz
filling holes in the GCA...
404261 classifiers: 1.5 per node, 7.59 in brain (0 holes filled)
computing covariances for subject CMH-11461, 1 of 1...
average std = 6.1   using min determinant for regularization = 3.7
298584 singular and 4268 ill-conditioned covariance matrices regularized
writing trained GCA to /Users/IngvalsonLab/Desktop/atlas1.gca...
classifier array training took 0 minutes and 27 seconds.
dhcp-165-124-23-230:LabMRIData IngvalsonLab$
dhcp-165-124-23-230:LabMRIData IngvalsonLab$
dhcp-165-124-23-230:LabMRIData IngvalsonLab$ mri_ca_train -T1 T1.mgz
CMH-11460 CMH-11461 ~/Desktop/atlas1.gca
reading T1 data from subject's mri/T1.mgz directory
training on 2 subject and writing results to
/Users/IngvalsonLab/Desktop/atlas1.gca
***
processing subject CMH-11460, 1 of 2...
   reading input 0:
/Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11460/mri/T1.mgz
***
processing subject CMH-11461, 2 of 2...
   reading input 0:
/Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11461/mri/T1.mgz
filling holes in the GCA...
468392 classifiers: 1.8 per node, 10.41 in brain (0 holes filled)
computing covariances for subject CMH-11460, 1 of 2...
GCAupdateNodeCovariance(17, 35, 28, 4): could not find label
dhcp-165-124-23-230:LabMRIData IngvalsonLab$


   According to the fswiki, the same bug was eliminated in the 2009
version. For some odd reason, this command works with one subject, but not
with multiple subjects.

Any ideas?

Thanks in advance,

MP
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[Freesurfer] MNI coordinates

[LAOUCHEDI MAKHLOUF]

Hi
    i am using corticals parcels (destrieux) as nodes in a connectivity study 
using the NBS (Network Based Statistics) tool; i want to assign MNI coordinates 
for these nodes. is there any MNI coordinates in freesurfer for each component 
of this parcellation (not for every vertex in those components) or any other 
strategy to assign coordinates for these components ? 


otherwise, i intend to non-linearily register the freesurfer's labels for a 
healthy subject in MNI and for each label i will use coordinates of one of its 
points to represent that label

thanks for help
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[Freesurfer] Fwd: qdec -- confused by glm output for custom ROIs

[Maria Kharitonova]

Hi, I'm sorry for sending a duplicate request, but I am still really
confused about the discrepancy between group-level findings in qdec (ROIs
that are different across my 2 groups) and lack of a difference on the
extracted thickness measures for those same custom ROIs. More info is
below. Please let me know if you have any insight about this discrepancy.
Thanks in advance!

-- Forwarded message --
From: Maria Kharitonova 
Date: Thu, Jul 18, 2013 at 4:32 PM
Subject: qdec -- confused by glm output for custom ROIs
To: freesurfer , Douglas N Greve <
gr...@nmr.mgh.harvard.edu>


Hello,

I have a question regarding the interpretation qdec's output for the custom
ROI's thickness estimates. I ran an analysis comparing cortical thickness
in children with and without ADHD (categorical variable), controlling for
age and demeaned ICV, using 5.0. After controlling for multiple comparisons
with the monte-carlo simulation, there were 2 ROIs in the right hemisphere
that were significantly different across groups: a regions near
parstriangularis and near medial orbital cortex. I then created custom ROIs
for these regions, and extracted thickness estimates for each participant
for each of these ROIs.

I then decided to do a "sanity check" of the data -- run a linear
regression on these extracted thickness estimates to see if the mean
thickness in each region differed as a function of diagnosis (again
controlling for age and demeaned ICV). By logic, I should see differences
in thickness estimates for these 2 ROIs across the 2 groups, because that's
how these ROIs were defined, right? But in reality, there is no difference
at all between groups, with p-values around .9!

I tried saving the ROIs by both manually tracing and with the
mri_surfcluster command -- I get very similar estimates of thickness
(correlation coefficients of .9 across 32 subjects). So that's not the
cause of error. Both manual and automatic extraction fails to find
differences across subjects that I described above.

What am I missing? is the original GLM in QDEC that finds differences
between groups doings something other than looking for differences in each
voxel/region across groups?

Thanks in advance for the help!
Maria

***

Maria Kharitonova, Ph.D.
Postdoctoral Research Fellow
Laboratories of Cognitive Neuroscience
Boston Children's Hospital
Division of Developmental Medicine
Harvard Medical School
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[Freesurfer] recon-all error

[Smian]

Hi everyone,

To put things into context, I am trying to follow the four step 
methodology outlined in this paper (Cohen-Adad, 2013) 
http://www.sciencedirect.com/science/article/pii/S1053811913000700

I have already performed recon-all on MPRAGE data. I have also carried 
out the following steps:

1) Reconstruct cortical surface
2) Register T1 to the surface
3) Sample T1 at a given cortical depth
4) Register surface to fsaverage

I have now been told to use the T2* information from the fourth echo of 
separately acquired T2* weighted data and to 'overlay' (I'm not sure if 
this is the correct usage of this technical term) it on the surfaces 
produced (as above) of the MPRAGE data. I realize that I can't perform 
recon-all on this T2* weighted data. I am assuming that I need to carry 
out steps similar to 1)-4) on this new data, but I'm not sure. Would you 
have any guidance on how to go about this?

Any help would be appreciated!

Thank you!

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[Freesurfer] help needed with fsgd file and contrast matrix for correlation analysis

[Robert Schulz]

Dear all, 

I have 2 short questions regarding a correlation analysis I'd like to perform 
with mri_glmfit (surface-based DTI data are correctly preprocessed and 
concatenated into mgh file, statistics are performed on fsaverage space). 

1) I'd like to look for correlation between the surface-data and a behavioural 
measure BEH in one group, correcting for gender and age. 

I set up the following fsgd: 

GroupDescriptorFile 1
Class Male
Class Female
Variables BEH Age
Input subj1 Male 0.76 72
Input subj2 Male 0.44 67
Input subj3 Female 0.33 80


My contrast file is: 0 0 0.5 0.5 0 0 (referring to the FSGD examples Fsgd2G2V, 
GLM with 2*(2+1) columns).
Is this setup correct? If not, how would I have to set up fsgd and C?



2) In a next step, I'd like to answer the question (now including another 
group2): Where does group1 (OLD) show increased correlation with BEH compared 
to group2 (YOUNG), correcting for GENDER and AGE within each group. I wonder 
because AGE is the relevant difference between both groups. 

GroupDescriptorFile 1
Class OldMale
Class OldFemale
Class YoungMale
Class YoungFemale
Variables BEH Age
Input subj1 OldMale 0.76 72
Input subj2 OldMale 0.44 67
Input subj3 OldFemale 0.33 80

Input subj11 YoungMale 0.80 20
Input subj12 YoungMale 0.55 21
Input subj13 YoungFemale 0.44 31


My contrast file would look like: 0 0 0 0 0.5 0.5 -0.5 -0.5 0 0 0 0 (referring 
to GLM with 4*(2+1) columns).
Correct?

Thank you very much for your help! I am really not sure whether I did it 
correctly and whether I can trust my results. 

Best wishes, Robert
--

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Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe 
Koch-Gromus, Astrid Lurati (komm.), Joachim Prölß, Matthias Waldmann (komm.)
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[Freesurfer] help needed with fsgd file and contrast matrix for correlation analysis

[Robert Schulz]

Dear all, 

I have 2 short questions regarding a correlation analysis I'd like to perform 
with mri_glmfit (surface-based DTI data are correctly preprocessed and 
concatenated into mgh file, statistics are performed on fsaverage space). 

1) I'd like to look for correlation between the surface-data and a behavioural 
measure BEH in one group, correcting for gender and age. 

I set up the following fsgd: 

GroupDescriptorFile 1
Class Male
Class Female
Variables BEH Age
Input subj1 Male 0.76 72
Input subj2 Male 0.44 67
Input subj3 Female 0.33 80


My contrast file is: 0 0 0.5 0.5 0 0 (referring to the FSGD examples Fsgd2G2V, 
GLM with 2*(2+1) columns).
Is this setup correct? If not, how would I have to set up fsgd and C?



2) In a next step, I'd like to answer the question (now including another 
group2): Where does group1 (OLD) show increased correlation with BEH compared 
to group2 (YOUNG), correcting for GENDER and AGE within each group. I wonder 
because AGE is the relevant difference between both groups. 

GroupDescriptorFile 1
Class OldMale
Class OldFemale
Class YoungMale
Class YoungFemale
Variables BEH Age
Input subj1 OldMale 0.76 72
Input subj2 OldMale 0.44 67
Input subj3 OldFemale 0.33 80

Input subj11 YoungMale 0.80 20
Input subj12 YoungMale 0.55 21
Input subj13 YoungFemale 0.44 31


My contrast file would look like: 0 0 0 0 0.5 0.5 -0.5 -0.5 0 0 0 0 (referring 
to GLM with 4*(2+1) columns).
Correct?

Thank you very much for your help! I am really not sure whether I did it 
correctly and whether I can trust my results. 

--

Besuchen Sie uns auf: www.uke.de
_

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; 
Gerichtsstand: Hamburg
Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe 
Koch-Gromus, Astrid Lurati (komm.), Joachim Prölß, Matthias Waldmann (komm.)
_

SAVE PAPER - THINK BEFORE PRINTING
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[Freesurfer] inflate surface until sphere

[Lo, Yiping]

Hi Freesurfer,

I am tring to inflate pial surface until the sphere. I have tried mris_inflate 
and set the number of iteration to be large. However, it seems to inflate the 
brain to a limit and no further inflation. I have also tried mris_sphere, but 
it seems not what I want. It more likely to map the pial surface onto a sphere 
and inflate it along the sphere.  I should say in advance, I only got .pial 
file. What should I do to get what I want?

Best Wishes,
Yi-Ping


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Re: [Freesurfer] error with fast_selxavg3

[Leila Reddy]

Hi Doug,

Thanks for your reply. Yes, it does work with a longer -refeventdur. In 
fact, I had tried that yesterday before posting my original message but 
I'd forgotten to make the corresponding changes to the 3rd column of the 
paradigm file and so kept getting the error message.

The shortest I can bring -refeventdur down to is 0.05. Anything smaller 
causes the same error as before. In the end it's not a huge problem for 
us if we have to set an event duration of 50ms instead of 16.6 ms but 
I'd like to understand what is going on.

So, I wondered if the error had anything to do with the fact that when I 
run mkcontrast-sess the script automatically sets -TER to 0.05. I re-ran 
the analysis and set -TER and -refeventdur to 0.016 in mkanalysis-sess. 
The analysis runs with no error for selxavg-sess and visually (with 
tksurfer) the results look the same as with -TER and -refeventdur set to 
0.05.

Since the help for mkanalysis-sess -TER says " It is best to know what 
you are doing if you are going to change this.",  I'd like to know if it 
makes sense to change the TER like I have. What does the TER achieve (if 
that's not too complicated a question)?

Thanks again,
Leila
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