Thanks for your help. I've noticed, however, that 2 of the centres
contribute a smaller number of subjects and don't in fact have any
female controls. Should I remove these as classes (ie. take out
control_Female_centre1 and control_Female_centre2) and then change the
subsequent contrast file t
Hi,
I was wondering if you could explain the -make all flag. When you use it with
recon-all to rerun after edits, does it determine where to start the recon-all
process based on the stamps of the edited files? And if I use other flags (such
as -mprage) when I initially ran recon-all, do I need
On Mo, 2018-04-09 at 19:53 +0200, Kaushal, Mayank wrote:
> I am indeed considering LME model since I have multiple visits (4)
> for each subject and multiple groups (3).
>
> Based on your response, I am inclined to include the following.
>
> Intercept - random variable
> Slope (time_base_scan) - ra
I appreciate your providing the pros and cons associated with both options.
Lets say for now we want to pursue option 2.
My understating is that since you recommend not to include ‘visit’ and
'time_from_baseline’ in the same model, one of the steps in creating MLE model
for option 2 would be t
They are not in registration. Try running bbregister to create a
registration file (lta), then pass the lta to tkregisterfv instead of
--regheader
On 4/9/18 11:49 PM, Bruce Fischl wrote:
How did you generate the registration? And give us the details of what
you are trying to register
Cheers
It only looks at file time stamps. It knows the order in which files
should be created. If it sees the time staamps are out of order, then it
re-runs the processes needed to put them in order. You will have to
include any special flags like -mprage
On 4/10/18 9:42 AM, Boerwinkle, Anna wrote:
I would probably correct total GM, total WM, and total ventricular CSF
by head size. It is not surprising that they covary a lot (as you point
out). But what you want is what is left over after you remove the
effect. You can also divide by the eTIV rather than regressing it out,
but the results
Dear experts,
I would like to create an average surface template of fMRI activation for two
groups, and then determine areas of low cerebrovascular reactivity in my
disease group, create a ROI, and extract the cortical thickness in this region
and see how it compares to a control group by tran
I am getting the following output with error on this command:
trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23
INFO: SUBJECTS_DIR is
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/sub
Dear Pradeep,
this issue has appeared several times already here. See following thread:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52560.html
Antonin Skoch
Hello All, My $SUBJECTS_DIR is located on an external disk that was mounted and
recon-all exited with errors at ln -s lh.
Hi,
I was pleased to learn freesurfer runs with the standalone matlab runtime, and
installed this on CentOS7. It seems to be working well. I noticed that there's
also a version of spm12 that runs using this runtime, "with limitations." Two
questions:
1. Are there freesurfer limitations u
Thanks for getting back to me.
My hp is the same as for the volumetric analysis. I want to measure thickness
differences between patients and controls while controlling for major
confounders (head size included). However , since thickness doesn't scale with
eTIV as much as volume how can I cont
The fix that Anna needs was committed last Friday.
Andrew
From: on behalf of "Dicamillo, Robert"
Reply-To: FS Help
Date: Tuesday, April 10, 2018 at 12:27 AM
To: FS Help
Cc: "Dicamillo, Robert"
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at
110, cannot allocate
Hi Don - See:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Krieger, Donald N.
Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] newb
Great - thanks.
It's running.
I see several warnings which I presume can be ignored:
hostname: Name or service not known
Best - Don
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 4:24 PM
As far a I know, thickness does not vary with head size, so we don't
traditionally make a correction
On 04/10/2018 01:52 PM, Maria Gloria Rossetti wrote:
> Thanks for getting back to me.
> My hp is the same as for the volumetric analysis. I want to measure
> thickness differences between patien
Hi Don - If the output files described here show up in the end, all is well:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Krieger, Donald N.
Sent: Tuesday, April 10, 2018
When I run bbregister, it gives me an error. Attached is the
register.dat.log file for it.
Error:
reading source './tmp.bbregister.91068/template.nii'...
mri_robust_register.bin: only pass single frame MRI source
./tmp.bbregister.91068/template.nii.
No such file or directory
Any help is great
don't use --init-rr ( you don't need to spec an init in version 6)
On 4/10/18 9:48 PM, srishti goel wrote:
When I run bbregister, it gives me an error. Attached is the
register.dat.log file for it.
Error:
reading source './tmp.bbregister.91068/template.nii'...
mri_robust_register.bin: only p
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