[Freesurfer] segmentHA_T1.sh

[Erik Lindberg]

External Email - Use Caution

Hi,
I am trying to run the segmentHA_T1.sh with the suffix CA but I seem not be
able to write the call correctly

How should I call this?

best
Olof
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[Freesurfer] Volume-defined roi

[Erik Lindberg]

External Email - Use Caution

Hi I am reading your tutorial about how to extract  Cortical Thickness of a
volume-defined ROI

Wonder if there is a script that would run these steps in a bach

particularly the steps that needs to be done on each individual subjects:

map subject thickness data to the fsaverage

and run mri_segstats to extract mean thickness

Best
Olof
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[Freesurfer] Post-doc position in fMRI research available at karolinska institute

[Erik Lindberg]

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Hi we are looking for a new post-doc in neuroimaging at Karolinska
Institutet at the Department of NVS. The Department of Neurobiology, Care
Sciences and Society (NVS) conducts world leading research in aging,
dementia, epidemiology and care sciences.

For this position we are looking for someone that has experience in
analyzing functional magnetic resonance images. Working with resting-state
and experimental fMRI will be the applicants main duty in this project.

The applicant may also work with different imaging modalities such as
structural, diffusion tensor- and functional magnetic resonance imaging
(fMRI) and its applications to Alzheimer’s disease and frontotemporal
dementia. In particular, the person is expected to take an active role in
applying advanced imaging methods. There are also possibilities to initiate
individual research projects, based on the person´s interests and in
collaboration with the University of Gothenburg. The successful candidate
should show a high level of independency, be able to work in a team and be
willing to supervise students.

Further information can be found at:
https://ki.varbi.com/se/what:job/jobID:295452/type:job/where:4/apply:1
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[Freesurfer] (no subject)

[Erik Lindberg]

External Email - Use Caution

Post-doc position for MRI-research on dementia and normal aging available
at Karolinska institute.

We are looking for a Post-doc researcher for a 1-year scholarship (with a
possibility for an extension to 2-year) at our section at the
NVS-department at Karolinska institute.

For further information see:

https://ki.mynetworkglobal.com/se/what:job/jobID:273493/type:job/where:4/apply:1
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[Freesurfer] Post-doc position for MRI-research on frontotemporal dementia available at Karolinska institute.

[Erik Lindberg]

External Email - Use Caution

Post-doc position for MRI-research on frontotemporal dementia available at
Karolinska institute.

We are looking for a Post-doc researcher for a 1-year scholarship (with a
possibility for an extension to 2-year) at our section at the
NVS-department at Karolinska institute.

For further information see:

https://ki.mynetworkglobal.com/se/what:job/jobID:273493/type:job/where:4/apply:1
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[Freesurfer] Postdoctoral position in multimodal neuroimaging on frontotemporal dementia

[Erik Lindberg]

External Email - Use Caution

Dear all,

We are  looking for a post-doc student for our lab at Karolinska institute
in Stockholm. We are doing structural and functional MRI research on
dementia. In current project we are acquiring multimodal MRI on
frontotemporal dementia patients. We are also running an experimental fMRI
paradigm on these patients.

We are looking for a person that is well familiar with doing analysis of
multimodal MRIs, to relate findings to other variables such as CSF-data,
neuropsychology etc.

See further: https://ki.mynetworkglobal.com/what:job/jobID:254449/
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[Freesurfer] Running multiple variables in mri_glmfit

[Erik Lindberg]

External Email - Use Caution

Dear Freesurfer experts,

I am in the processing of running correlation with cortical thickness for
almost 500 CSF variables. Thus I would like to use some sort of script. I
previously used the common steps (mri_preproc,  mri_glmfit and
mri_glmfit-sim) but this procedure does not allow a .fsgd file with all the
500 CSF variables in it  … correct?

When running qdec many csf variables can be in the file … but then I cannot
run it by script … right?



So I wonder if there is a way to use one large file with the CSF data and
then to make a script so that each variable is run iteratively until all is
finished. Best case scenario I would also like to include snapshots from
each correlation analysis.

Is this possible to do?

Thanks

Olof Lindberg
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[Freesurfer] Hippocampal sufields

[Erik Lindberg]

Dear Freesurfer experts,

I am currently running your new pipeline for hippocampal subfield
segmentation. However the resolution on my MRI images is  too bad for
identifying specific cellular layers such as stratum moleculare.

My preferred option would be not to divide the different subfields into
different cellular layers and only have one volume for the presubiculum for
instance.

Is there any way I can know how much volume of the molecular layer that
should be included into each separate subfield? So forinstance I can add
the volume of subiculum with the volume of the molecular layer in the
subicula

Best

Erik
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[Freesurfer] Contrast matrix regressing out effect of diagnosis and age

[Erik Lindberg]

Dear Freesurfer experts,

I am running a GLM-model in which I have 6 classes (diagnosis) and two
covariates age and variable X).

I want to look at mean correlation of variable X.

My contrast matrix is as follows: 0 0 0 0 0 0 0 0 0 0 0 0 0.17 0.17 0.17
0.17 0.17 0.17

0.17 (approx. 1/6)

Did I get this right?

Thanks
Eric
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[Freesurfer] Creating an illustration on what Freesurfer has considered to be intracranial volume

[Erik Lindberg]

Dear Freesurfer experts,

I would like to create an image on tissue that Freesurfer has been included
into the intracranial volume calculation.
Is there anyway to summarize segmentations masks so I get one mask
containing all tissue that has been included into the intracranial volume?

best
Erik
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[Freesurfer] Optimal combination of MRI-sequences

[Erik Lindberg]

Dear Freesufer experts,



We are in the process of starting a large MRI project on normal aging and
dementia.



There has been a lot of discussions about what sequences to use.



We are now thinking about combining several sequences. Is there an optimal
combination of MRI sequences for Freesufer?
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[Freesurfer] dividing Freesufer subfields into one anterior, middle and posterior region

[Erik Lindberg]

Dear FS experts. I want to divid the FS subfield segementation into a
anterior part, one middle part and posterior segment - or potentially
divide the rang into 10% of the whole rang - and then move backword until I
extracted 10 subparts.

Is there some way I can do that?

Thanks
Erik
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[Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh

[Erik Lindberg]

Dear Bruce and Freesurfer,

Yes, that is what I am saying! This what appears in the commandprompt when
running the command:

input  cache.th13.abs.sig.cluster.mgh
frame  0
nErode3d   0
nErode2d   0
output thresholded.mgh
Binarizing based on threshold
min1.3
max+infinity
binval1
binvalnot 0
Found 12485 values in range
Counting number of voxels
Found 12485 voxels in final mask
mri_binarize done

Yet nothing is visible when I open the thresholded surface in tksurfer.


previous:

what was the command line and screen output of the binarization? And are
you saying that pre-binarization you have locations that are above
threshold, but they are set to 0 anyway?
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[Freesurfer] Re mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05 {Disarmed}

[Erik Lindberg]

Dear Bruce and Freesufers,


I get the following message:


surfer: Interpreting overlay volume
/media/EHD/ALLA_FREESUFER_PROCESSING_TIDIS_NOMAS_AD/qdec/lh.kvot_gender.glmdir/Gend/thresholded.mgh
as encoded scalar volume.


the two volumes I tried to convert:

1)

Volume information for sig.mgh
  type: MGH
dimensions: 163842 x 1 x 1
   voxel sizes: 1., 1., 1.
  type: FLOAT (3)
   fov: 163842.000
   dof: 0
xstart: -81921.0, xend: 81921.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.5
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
0.
  : x_a =   0., y_a =   0., z_a =   1., c_a =
0.
  : x_s =   0., y_s =  -1., z_s =   0., c_s =
0.

talairach xfm :
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0. 81921.
0.   0.   1.-0.5000
0.  -1.   0. 0.5000
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.   0.   0. 81921.
   -0.  -0.  -1. 0.5000
   -0.   1.  -0. 0.5000
0.   0.   0. 1.


2)


Volume information for cache.th13.abs.sig.cluster.mgh
  type: MGH
dimensions: 163842 x 1 x 1
   voxel sizes: 1., 1., 1.
  type: FLOAT (3)
   fov: 163842.000
   dof: 0
xstart: -81921.0, xend: 81921.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.5
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
0.
  : x_a =   0., y_a =   0., z_a =   1., c_a =
0.
  : x_s =   0., y_s =  -1., z_s =   0., c_s =
0.

talairach xfm :
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0. 81921.
0.   0.   1.-0.5000
0.  -1.   0. 0.5000
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.   0.   0. 81921.
   -0.  -0.  -1. 0.5000
   -0.   1.  -0. 0.5000
0.   0.   0. 1.


Although both these overlays have significant areas - nothing appears on
the binarized version after the conversion


Best wishes,

Olof Lindberg

Olof Lindberg PhD
Novum plan 5
NVS department section clinical geriatrics
14186 Stockholm
+46722255711
http://www.oloflindberg.se

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[Freesurfer] Re mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

[Erik Lindberg]

Dear Bruce and Freesufers,



I tried to run the command  and then to load it as an overlay - however I
get nothing on the surface of the fsaverage brain. The program is telling
me that it is including x-number of voxels into the mask but when I check I
see nothing on the surface. What is going wrong here?



Further the approach you proposed doing fMRI on the surface sounds
interesting – but I have never used this approach. Could you give me a hint
on the steps I need to take in order to do this?



Thanks in advance!

Eric


yes, but do you want to do the fMRI analysis on the surface or in the
volume? There are lots of advantages to doing it on the surface. If your
sig.cluster.mgh was a surface overlay then the threholded.mgh might be
exactly what you want. Load it on an inflated surface and take a look

cheers
Bruce
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Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

[Erik Lindberg]

Dear Bruce and Freesurfers,


I probably then go about this in the wrong way. My aim is to create a
binary mask for regions that I found differences in - in a
group-comparison. I then want to export the mask so I can use it as
seed area in an fMRI analysis.


Can this be done


Thanks
Eric



Hi Erik


what is the dimensionality of sig.cluster.mgh? You can tell this with mri_info.
It is problaby a surface overlay (so nvertices in one dimension), and can't
be viewed in the volume but only on the surface.

cheers
Bruce
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Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

[Erik Lindberg]

Dear Douglas and Freesufers,



You suggested:

mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 =
-log10(.05)



I tried this and was expecting that I would get a three-dimensional mask in
which the statistical significant part would be white and the rest black.

This seems not to be the case. While the program is telling me that it is
creating a mask in which x-number of voxels are included I cannot see
anything when I open the thresholded.mgh (in Freeview) Further when I look
at the dimensions of the generated image it seems to have 27307 “slices” in
one direction but only one and 6 slices in the other directions.





Is this the wrong approach for creating a 3-dimensional mask for the region
with the significant clusters?



Best

Eric
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[Freesurfer] (no subject)

[Erik Lindberg]

I just want to run plane correlation with the csf-variable

best
Eric
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[Freesurfer] (no subject)

[Erik Lindberg]

I just want to investigate significant correlation with the csf variable
correcting for apoe-status, gender, diagnosis and age

below previous correspondence


your classes are right. What are you trying to test with your contrast
matrix?

On 01/20/2016 05:33 AM, Erik Lindberg wrote:
> Dear Freesurfers,
>
> I am running a design in which I want to correct for a number of
> categorical variables: diagnosis, gender and apoe status and one
> continuous variable (age) in a correlation analysis
>
> Did I get this right? (below)
>
> Thanks, Eric
>
> GroupDescriptorFile 1
>
> Title MyTitle
>
> Class AMCI_F_APOE-
>
> Class AMCI_F_APOE+
>
> Class AMCI_MALE_APOE-
>
> Class AMCI_MALE_APOE+
>
> Class CTL_FEMALE_APOE-
>
> Class CTL_FEMALE_APOE+
>
> Class CTL_MALE_APOE-
>
> Class CTL_MALE_APOE+
>
> Class NON_A_MCI_FEMALE_APOE-
>
> Class NON_A_MCI_FEMALE_APOE+
>
> Class NON_A_MCI_MALE_APOE-
>
> Class NON_A_MCI_MALE_APOE+
>
> Class SCI_FEMALE_APOE-
>
> Class SCI_FEMALE_APOE+
>
> Class SCI_MALE_APOE-
>
> Class SCI_MALE_APOE+
>
> Variables AGE_DEMEAN CSF_Ab40_ADx
>
>
> With the contrast matrix: corr.mtx:
>
> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1
> 1 1 1 1 1 1 1 1 1 1 1 1 1
>
>
>
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[Freesurfer] converting cache.th13.abs.sig.cluster.mgh into a binary mask

[Erik Lindberg]

Dear Freesurfers,

I like to convert a cache.th13.abs.sig.cluster.mgh into a binary mask - so
that everything that is below 0.05 will be included in the mask - how can I
do this?

Eric
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[Freesurfer] Regressing out various categorical variables

[Erik Lindberg]

Dear Freesurfers,

I am running a design in which I want to correct for a number of
categorical variables: diagnosis, gender and apoe status and one continuous
variable (age) in a correlation analysis

Did I get this right? (below)

Thanks, Eric

GroupDescriptorFile 1

Title MyTitle

Class AMCI_F_APOE-

Class AMCI_F_APOE+

Class AMCI_MALE_APOE-

Class AMCI_MALE_APOE+

Class CTL_FEMALE_APOE-

Class CTL_FEMALE_APOE+

Class CTL_MALE_APOE-

Class CTL_MALE_APOE+

Class NON_A_MCI_FEMALE_APOE-

Class NON_A_MCI_FEMALE_APOE+

Class NON_A_MCI_MALE_APOE-

Class NON_A_MCI_MALE_APOE+

Class SCI_FEMALE_APOE-

Class SCI_FEMALE_APOE+

Class SCI_MALE_APOE-

Class SCI_MALE_APOE+

Variables AGE_DEMEAN CSF_Ab40_ADx


With the contrast matrix: corr.mtx:

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1
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[Freesurfer] MatrixReadTxT: could not scan value [1][1], ERROR: loading C AAA.mtx

[Erik Lindberg]

Dear Freesufer experts,

I have trouble loading a contrast matrix - however I am not sure if
something is going wrong earlier ... and this is causing this problem.

Below is the error messages that I get plus the contrast matrix and the
.fsgd file I am trying to run.

I checked this previous mesages on this topic -  and excluded the
possitility that it would be related to windows formating or something like
that.


Can you see what is wrong? Would the most grateful for any advice on this



Thanks!




Error message:



Saving mask to rh.Abeta_Gender_Apoe_age.glmdir/mask.mgh

Reshaping mriglm->mask...

search space = 74490.928733

MatrixReadTxT: could not scan value [1][1], ERROR: loading C AAA.mtx



Abeta_Gender_Apoe_age.fsgd:



GroupDescriptorFile 1

Title  Abeta_Apoe_Gender

Class
AbetaNegativeApoeNegativeMen

Class AbetaNegativeApoeNegativeWomen

Class
AbetaNegativeApoePositiveMen

Class
AbetaNegativeApoePositiveWomen

Class
AbetaPositiveApoeNegativeMen

Class
AbetaPositiveApoeNegativeWomen

Class
AbetaPositiveApoePositiveMen

Class
AbetaPositiveApoePositiveWomen

Variables   Age

Input 0d93d314-d7fe-4615-9b00-ea8011255a81
AbetaPositiveApoeNegativeWomen   9.61

Input 36643d8d-caf1-47be-9025-e5662092a0c1
AbetaPositiveApoeNegativeWomen   5.61

Input 12ee5f59-b7de-431c-9c93-fc737465cf24
AbetaPositiveApoePositiveWomen6.61



AAA.mtx:   {1 1 1 1 -1 -1 -1 -1}/4 0





mris_preproc --fsgd Abeta_Gender_Apoe_age.fsgd \

  --cache-in thickness.fwhm10.fsaverage \

  --target fsaverage --hemi lh \

  --out lh.Abeta_Gender_Apoe_age.10.mgh



mris_preproc --fsgd Abeta_Gender_Apoe_age.fsgd \

  --cache-in thickness.fwhm10.fsaverage \

  --target fsaverage --hemi rh \

  --out rh.Abeta_Gender_Apoe_age.10.mgh



mri_glmfit \

  --y lh.Abeta_Gender_Apoe_age.10.mgh \

  --fsgd Abeta_Gender_Apoe_age.fsgd doss \

  --C AAA.mtx \

  --surf fsaverage lh \

  --cortex \

  --glmdir lh.Abeta_Gender_Apoe_ager.glmdir







mri_glmfit \

  --y rh.Abeta_Gender_Apoe_age.10.mgh \

  --fsgd Abeta_Gender_Apoe_age.fsgd doss\

  --C AAA.mtx \

  --surf fsaverage rh \

  --cortex \
  --glmdir rh.Abeta_Gender_Apoe_age
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[Freesurfer] interaction in glm

[Erik Lindberg]

Dear Freesurfer experts,

I know this has been an ongoing topic in the mailing list – however I would
like to raise the issue one more time. In the choice between doss and dods
– I usually check if there is a significant interaction and if so my choice
is dods.

As I understand it you do not recommend to use doss if an interaction is
present. Is the reason for this that I would “over-correct” for the
variable in one group while “under-correcting” for the same variable in the
other group?

It is some time tempting to present result both from a dods and a doss – to
tell where the interaction is present, and where difference are present
while controlling for the variable

But if I understand Doug´s previous comments on this – this would not be a
correct approach?



Thanks

Erik
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[Freesurfer] Did not find any volume geometry information in the surface

[Erik Lindberg]

Hi,
I am running mri_glmfit followed by mri_glmfit-sim

running the left hemisphere everything works perfect all the way to the
visualization in freeview  - then I just chift the command to rh instead -
running exactly the same command and when I am opening my results in
freeview everything gets yellow and I get the following error message: Did
not find any volume geometry information in the surface.

could you please inform me how this can happen?

THANKS
ERIC
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[Freesurfer] Doss/Dods

[Erik Lindberg]

Dear Freesufers,
I am currently running mri_glmfit using a relatively simple design: Two
groups and one covariate. Design is: 1 -1 0 0  .. to control for the
co-variate (age).

It is the example with two groups and one covariate in your web-page
http://freesurfer.net/fswiki/Fsgdf2G1V

I was under the impression that I was comparing two groups controlling for
effect of age .but it seems more like the results I get is displaying
regions that is more strongly correlated with age in one of the groups
 (thus an interaction test).

Is this correct - and if so - is the way to go 1 -1 0 (and change to doss)?

thanks
Eric
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[Freesurfer] smoothing

[Erik Lindberg]

Dear freesufers,

I quick question about smoothing of data in cortical thickness analysis. I
have a comparison that is rather borderline significant. When using
smoothing of 10 mm I get a limited region in the frontal lobe that is
differs between groups. Changing to 15 mm I get larger regions - and also
some parts of the temporal lobe differs in the comparison.

The 15 mm smoothing provides results that are more consistent with the
hypothesis - however I do not know if this amount of smoothing overestimate
the difference between groups?

Eric
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[Freesurfer] Regression coefficient qdec

[Erik Lindberg]

Dear Freesurfers,

I am trying to display the regional regresssion coefficent for age in qdec.
However the colorbar still gives me the traditional 0, 1.3 etc

is there anyway to change the colorbar. I would like to be able to display
only regions that have more than say 0.3 correlation with age - so it would
be god if I can get the colorbar to display the r-values. Is that possible?

best
Eric
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[Freesurfer] Other things to consider when setting -min_border_white -min_gray_at_white_border?

[Erik Lindberg]

Dear Bruce and Freesufers,

Adding to our previous discussion. You managed to fix a very bad
segmentation by setting some expert options (mri_normalize -gentle and setting
a fixed level for -min_border_white  -min_gray_at_white_border).

It was a very nice recovery of, what I thought to be, a hopeless image.  As
I in my project have around 800 images I was also testing these options on
10 more images that you used to recover the bad image.

The test on the 10 other images (that also worked well without expert
options) was quite good. The segmentation looked ok.

What I am wondering now is if there is other aspects to consider when
setting fixed levels in mris_make_sufaces? As I told you I looked into the
recon-all log file and found that when FS is running normally in creates
different levels of -min_border_white  -min_gray_at_white_border for each
image.

As this is the Normal way for FS to run I suppose that this is the optimal
way to run. So what is the disadvantages of setting fixed levels for
-min_border_white  -min_gray_at_white_border?


Thanks!


Erik
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[Freesurfer] Can -min_border_white and -min_gray_at_white_border be edited for single subject in a large group of subjects?

[Erik Lindberg]

Dear Freesufers,

I am trying to understand what happens if I go in and edit the numbers for
-min_border_white  -min_gray_at_white_border  in a single subjects in a
large group.

Generally we aim to set everything identical when running a group of
subjects in FS.  I went in and had a look at the recon-all log file and I
can see that the numbers for -min_border_white
 -min_gray_at_white_border  different for different subjects.

Thus - what will happened if I go and edit the -min_border_white
 -min_gray_at_white_border numbers for  a single subjects in a large bach
 will I still be able compare cortical thickness with subjects that I
did not edit?

Or is it necessary to keep the number identical for all subjects when
editing the min_border_white  -min_gray_at_white_border
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[Freesurfer] Combining FS commands

[Erik Lindberg]

Dear Freesufers,

I want to run: mri_normalize gentle,


And


mris_make_surfaces min_border_white 85 -min_gray_at_white_border 80



In as few steps as possible as I will run around 800 images. So far I only
managed to this by braking up the process several subparts (like doing
autorecon1 before mri_normalize, and autorecon2 before mris_make_sufaces



If this could be combined somehow it would of course be a lot easier than
running step by step 800 times.



Thanks in advance

Erik
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[Freesurfer] combining FS commands

[Erik Lindberg]

Dear Freesurfers,



I want to run: mri_normalize gentle,



And



mris_make_surfaces min_border_white 85 -min_gray_at_white_border 80





in  MY recon-all script. I understand that I have to put the flag -expert
to do this - but I seem to make errors in my command



It would be greatly appreciated if you can tell me how the command should
be written



Thanks in advance!



Erik
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[Freesurfer] How to combine attached commands into one run

[Erik Lindberg]

Dear Freesufers,


I want to use the following commands in my recon-all to try to improve my
output some difficult images:

-gentle to mri_normalize

and

 -min_border_white 85 -min_gray_at_white_border 80

So far I only managed to do this by making one step at a time. I was
wondering if there is a way to combine these commands so I do not have to
run it step by step.
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[Freesurfer] Segmentation/cortical thickness

[Erik Lindberg]

Dear FS expersts!

I have two questions: 1) I am looking at the output from a FS run. When
looking at the red and yellow lines it appears as the cortical thickness
has bin estimated too thin.  But when I take away the two lines and just
look at the segmentation it looks quite god (and much thicker than the
estimation of cortical thickness). How should I interpret this: Can it be
that the cortical thickness measure is not completely correct while the
cortical volumes from the segmentation is OK?

I have run this dataset in both 5.3 and 5.1 FS versions. To me it looks
like the 5.3 is making the cortex even thinner than the 5.1.
In the 5.3 version I am using -mprage and -3T flags - while no flags was
used in the 5.1 run. Is there any logical explanation for this?

Is there any trick to make affect the program so that the yellow line
(white matter border) is more consistent with what I see in the
segmentation.

Thanks in advance!

Erik
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[Freesurfer] Freesurfer versions

[Erik Lindberg]

Dear Freesurfer experts,



I am attaching a document showing the segmentation of a brain in version
5.1 and 5.3 with and without a 3-T flag. Image is from a 3-T camera.



What I am wondering about is that it seems that the cortex is too thin in
the later version of Freesurfer (both when using 3T flag and when not using
this flag).



Is there some other flag that could be used to deal with this?



Thanks

Olof Erik


._Freesurfer_versions.docx
Description: application/vnd.openxmlformats-officedocument.wordprocessingml.document
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[Freesurfer] Demean covariate

[Erik Lindberg]

Dear Doug and Freesurfers,
I noticed that the DOSS option no longer exists in qdec and that Doug said
there was a bug related to it.
If i want to assess the differences in cortical thickness between groups
while covariating for age and gender, since i don't expect any
interactions, can i just demean the covariates and make my analysis in qdec
with dods?
Thanks!
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[Freesurfer] Demean Covariates Qdec

[Erik Lindberg]

Dear Doug and Freesurfers,
I noticed that the DOSS option no longer exists in qdec and that Doug said
there was a bug related to it.
If i want to assess the differences in cortical thickness between groups
while covariating for age and gender, since i don't expect any
interactions, can i just demean the covariates and make my analysis in qdec
with dods?
Thanks!
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[Freesurfer] z-scores versus raw_age for correction in GLM_FIT or qdec

[Erik Lindberg]

Dear Douglas,
attached you´ll find the two y.fsgd file from the analysis run in GLM_FIT.
the results are completely different (the z-score converted age produces a
believable result, while the result correcting with raw age scores seems
completely wrong.

best regards

Olof


y.fsgd_raw_age
Description: Binary data


y.fsgd_zscores
Description: Binary data
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