Hi FreeSurfer team,
I was wondering if it is possible to use a measure of annualised percentage
change instead of raw thickness within the FreeSurfer toolbox for Matlab
(i.e. when running linear mixed models)?
Thanks for your help,
Nandi
___
Freesurfer
For the intercept, you are testing for a difference in the mean CBF
between the groups regressing out the effects of gender and age.
For the slope, you are testing for an interaction between group and age
regressing out the effects of gender.
doug
On 3/12/15 1:30 PM, Matthieu Vanhoutte wrote
Yes, that probably is the reason.
doug
On 3/12/15 4:31 PM, Wolthusen, Rick Peter Fritz wrote:
> To be honest, I checked the between subject alignment and it looked pretty
> good. None of my subjects was way out of alignment. However, since we cannot
> fit the whole brain in the slice during scan
Sorry, I believe I have fixed this by using --surface fsaverage lh.
Thanks,
Kate
On Fri, Mar 13, 2015 at 9:59 AM, Kate Riggall
wrote:
> Bruce and Martin,
>
> Thanks, I now have it running of an external hard drive and it is working
> well. As a follow-up question:
>
> When I run the paired ana
Bruce and Martin,
Thanks, I now have it running of an external hard drive and it is working
well. As a follow-up question:
When I run the paired analysis, the final command (mri_glmfit --glmdir
lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd
paired-diff.fsgd --C mean.mtx --C age.mtx)
Hi,
I am trying to eTIV correct the volumetric stats output from recon-all
(ie aseg stats and aparc stats). I read the "eTIV-estimated Total
Instranial Volume, aka ICV" wiki information, but I still have some
questions.
1. Do all structures need to be eTIV corrected?
2. To use mri_label_volum
To be honest, I checked the between subject alignment and it looked pretty
good. None of my subjects was way out of alignment. However, since we cannot
fit the whole brain in the slice during scanning, we are always cutting of the
top of the brain, sometimes more, sometimes less, depending on th
sorry, I don't know what you've done or what you are trying to do or
what the mri_info command is related to. Can you fill in the details?
On 03/12/2015 04:20 PM, Krieger, Donald N. wrote:
> Do the results in the attached images make sense?
> Does it make sense that the transformation was obtaine
Do the results in the attached images make sense?
Does it make sense that the transformation was obtained: mri_info --vox2ras-fls
?
Regards,
Don
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.ha
what do you want us to check?
On 03/12/2015 03:27 PM, Krieger, Donald N. wrote:
>
> Dear List,
>
> I’ve done a couple of spot checks which appear to work but want to
> double check with you.
>
> Attached are 5 axial cuts from fsaverage’s orig.mgz 5 mm apart.
>
> The “white” surface vectors are sh
I forget to include that the transform I used was obtained: mri_info aseg.mgz
-vox2ras-fsl
Regards,
Don
[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] O
I meant which ones are causing the problems when you run mri_glmfit.
When you run fslview you will see something that looks like a brain. As
you scroll thru the different time points, you'll see the CBF maps for
different subjects. They should be more-or-less in alignment. Look for
ones that a
Well, I checked the proper match of ASL and anatomical scans again and one of
the subjects I reported before was indeed wrongly matched. Thanks!
What do you mean with "So the next thing I would do is to find which subjects
are the
ones that are off."? You mean off when I check for registration?
Hello,
I have run GLM group analyses with Freesurfer tools according DODS model,
with six classes ((Male,Female) ; (Control,Left,Right)) and one age
variable :
*Class MaleControlClass MaleLeftClass MaleRightClass FemaleControlClass
FemaleLeftClass FemaleRightVariables Age *
I wanted to tes
If the registration looks ok, then that is all that counts. However, I'm
a bit sceptical that the reg looks ok but the mincost is that much
different than the others. You should double check that the ASL is
properly matched with the corresponding anatomical (ie, it is not two
different subject
Hi Doug et al.,
I indeed found 3 subjects, whose registration looked ok when I eyeballed them
with the tkregister 2 command, with values of .9 and higher (all the other
subjects had values between .44 and .61). Do you recommend to redo the analysis
without them or to run the first level analysi
Dear Anastasia,
I was wondering if there is a way to automatically (in command line) derive the
FA/V1 vector image.
fslview FA.nii.gz V1.nii.gz allows to load the FA and V1 image, but then
manual section of the (lines) is needed.
freeview -dti V1 FA does it too (with different xy
The psdwin controls the window over which HRF overlap correction needs
to be done. This is usually something like 0-22 sec, enough time for the
HRF to return to baseline. If you want to set the minimum/maximum ITI,
then use --tnullmin and --tnullmax
doug
On 03/11/2015 08:08 PM, Michael T Comp
Thanks for getting back so quickly and for the clear answers.
I was able to get the axial slices out by using mri_convert --split to create a
.nii file.
ImageJ could read that in and reslice it.
Thanks again.
Don
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
On 03/12/2015 09:54 AM, Krieger, Donald N. wrote:
>
> Dear List,
>
> I have sets of vectors in RAS coordinates from many volunteers.
>
> I want to transform them into coordinates for a standard volume.
>
> (1) I presume the standard volume that makes sense to use is orig.mgz
> in $FREESURFER_HOME
Dear List,
I have sets of vectors in RAS coordinates from many volunteers.
I want to transform them into coordinates for a standard volume.
(1) I presume the standard volume that makes sense to use is orig.mgz in
$FREESURFER_HOME/subjects/fsaverage/mri. Please confirm.
(2)I presume tha
Hi Martin,
Thank you for your help and clarifications. I did run the *_to_table
commands and now my LME analyses are running smoothly.
Best,
Jennifer Legault
On Mon, Mar 9, 2015 at 11:35 AM, Martin Reuter
wrote:
> Hi Jennifer,
>
> if you are interested in volumes from the stats file, you need
From Rahul Desikan:
-- Forwarded message --
From: Rahul Desikan
To: paulo.ba...@usp.br, freesurfer@nmr.mgh.harvard.edu
Cc:
Date: Wed, 11 Mar 2015 08:42:31 -0700
Subject: Re: [Freesurfer] aparc superior occipital lobe labeled as
superior
parietal (fwd)
Hi Paulo,
This is a
Hi FS Community,
I emailed with Doug a week ago with regards to limiting the results of a PASL
Regression analysis to subcortical areas only in the tal output file (see
below). I redid the analysis from scratch adding the flag --mask
$SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after perfor
Sorry, I don't have time to deconstruct that script. Can you simplify it
for me?
On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote:
> This is the script I am using to create cbf.talaraich.mgz (attached).
>
> Thanks,
> Rick
>
> From: freesurfer-bou
Dear FreeSurfer developers and users,
I’m wondering if any of you worked on further segmentation of the thalamus into
thalamic nuclei or e.g. dorsal vs. medial thalamus.
Thanks,
Bengi
Bengi Baran, Ph.D.
Post-Doctoral Fellow
Martinos Center for Biomedical Imaging
Harvard Medical School
Massac
can you upload your glmdir to our filedrop (see end of email)
doug
On 03/10/2015 02:13 PM, Wolthusen, Rick Peter Fritz wrote:
> Hi FS Community,
>
> I emailed with Doug a week ago with regards to limiting the results of a PASL
> Regression analysis to subcortical areas only in the tal output file
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