Dear Anastasia,
As we are analyzing DTI data acquired in patients with epilepsy we are
especially interested in the fornix.
I've come across the mri_cc -f option for fornix segmentation (native
space) but I've also read that manual tracing/labeling of the tracts
would be needed in the 33 contr
*Post-Doc*
*Neuroscientist with focus on multimodal brain imaging*
The *medical faculty of the University of Mainz*, Germany, invites
applications for a
Post Doc Position
for a functional translational neuroscience (FTN) scholarship two years
position to work on multi-modal imagi
Dear Freesurfer community,
I would like to apply ACPC alignment to Freesurfer output.
Data was previously segmented with recon -all and a lot of manual editing using
ITK. Unfortunately, the data was not aligned to ACPC and this causes errors in
my pipeline (I am using the labels and white matt
Hi Freesurfer Developers,
I would like to ask for your expertise in the following problem I encountered:
I want to create subject specific labels based on a label I created in
fsaverage. The transformation needs to be based on Talairach intermediate
registration, since my label was drawn based
Dear FreeSurfer Experts,
I'm following the LME tutorial to analyze my data. The example that is given in
the tutorial is for a left hemispheric cortical thickness analysis. I would
also like to look at surface area. Would I follow the same steps? At the point
in the tutorial that uses the lme_m
Dear Freesurfers,
I've got data pertaining to patients with left and right-sided temporal
lobe epilepsy (TLE).
My aim is to group those tracts according to side of epilepsy for
waypoint comparisons.
Basically for patients with right TLE I'd like to look at right tracts
and at the same time for
What is the exact name of the file that you are trying to include as a
taskreg?
On 7/25/16 12:26 AM, Erik Jahner wrote:
Dear Free Surfer experts
I am attempting to run a functional connectivity analysis on some
resting state data. However, I keep getting stuck in this final step
of the onli
If you have a registration matrix that maps to the desired orientation,
then you can apply it to a segmentation with mri_label2vol. But why not
just register the anatomical to the DTI (bbregister) and then run
mri_label2vol with that registration to map the WM mask directly into
the native DTI
When you use --regmethod volume, it assumes that the label coordinates
are in native anatomical space and then applies the mni305 registration
(talairach.xfm). In this case, your source subject is fsaverage so the
native space is assumed to be mni305 space (and talairach.xfm is the
identity). S
Can you send your new fsgd file and new design matrix?
On 7/24/16 6:06 PM, miracle ozzoude wrote:
Hello Doug or Bruce,
I demeaned and normalize like you suggested but I'm still getting the
same results. I created a new fsgd file using the demeaned and
normalized variables (n = (x-mean)/std(x)
It looks like one of two things:
1. The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM,
AFNI) can read the file
2. You have run out of disk space
On 7/24/16 10:52 AM, Fred Sampedro wrote:
Dear FS experts,
I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 an
No, that flag does not exist, but it is a good idea! You'll have to
normalize them by hand.
On 7/24/16 1:33 PM, miracle ozzoude wrote:
Hello freesurfer experts,
I am trying to normalize my continuous variables in my fsgd file. Is
this the correct term to add to my fsgd file in order for mri_g
Hi Dr. Fischl,
Thank you for clarifying that about norm.mgz for checking segmentations.
Good to know that brain and brainmask wash out low contrast borders.
Cheers,
Reema
--
*Reema Jayakar, M.A.*
Doctoral Candidate - Clinical Neuropsychology
Health Resources and Services Administration (HRSA)
Hi Douglas,
Thank you very much for answering. Unfortunately, I can read all the files
without any problem in FSL/SPM, and I still have more than 40GB of free
space. In fact, running the exact same instruction in freesurfer 5.3 works
fine.
:(
On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve
wro
Hi Dorsa
you need to give us more details. What was your reslicing command line?
And the screen output?
Bruce
On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:
Hi,
I re-sliced my left thalamus so that the size and number of slices correspond
with the original MRI, but when I open it in free
Hi Kari
what do you mean when you say "when I look at them in freeviewer the voxels
are definitely not in the correct spot". Do you mean the spectroscopy
voxels?
cheers
Bruce
On Fri, 22 Jul 2016, Kari Parsons wrote:
> Hi Bruce,
>
> Yes, I agree it doesn't seem right. They're LAG and AC
Hi Dorsa
did you create the aseg.mgz from 1mm data (using the standard "conform"
process), or higher res? The file you sent is higher:
mri_info resliceduncoregtahalmus.nii.gz
Volume information for resliceduncoregtahalmus.nii.gz
type: nii
dimensions: 512 x 512 x 288
voxel size
Hi there
Do we have a potential date for the Freesurfer 6.0 release? I was told I
would want to re-run all my subjects to create better surfaces using
Freesurfer 6.0 and I am wondering if it really will improve surface
extraction that much.
Many thanks!
Trisanna
--
Ph.D. Candidate
McGill Unive
Hi Doug,
thank you - using this new version changed everything back to "normal"
(small clusters, few results), so it may indeed have been a problem with
that particular version.
Thanks again,
Nicola
On 7/22/2016 8:22 PM, Douglas N Greve wrote:
>
> That version may have had a bug. Try this on
Actually, I checked the code and found that I had already put a flag in
there to do this (I'm so clever). Add
ReScaleFlag 1
in addition to
DeMeanFlag 1
On 7/25/16 11:22 AM, Douglas Greve wrote:
No, that flag does not exist, but it is a good idea! You'll have to
normalize them by hand.
Sorry, I have no idea and I'm not going to try to dig in to 5.1 to see.
You can just copy mri_convert from 5.3 into 5.1 (make a backup first)
On 7/25/16 12:31 PM, Fred Sampedro wrote:
Hi Douglas,
Thank you very much for answering. Unfortunately, I can read all the
files without any problem i
Hello,
I have been trying to run several versions of the same GLM analysis, trying
out different parameters to see if they affect the results. For instance, I
am running the GLM with different levels of smoothing, per-session versus
per-run motion correction, etc. To speed this up, I am trying to
Try this: on line 160 of preproc-sess, change
if(-w .) then
to
if(-w . && $nolog != 1)
I think that should do it.
On 7/25/16 7:53 PM, Taylor, Johnmark wrote:
Hello,
I have been trying to run several versions of the same GLM analysis,
trying out different parameters to see if they aff
We are working pretty hard to get it out but we are still reluctant to
set a hard date. I think we'll have a beta version in two weeks, but
that's just a guess.
doug
On 7/25/16 4:01 PM, Trisanna Sprung-Much wrote:
Hi there
Do we have a potential date for the Freesurfer 6.0 release? I was
Wow, longitudinal segmentation is absolutely awesome! It reduced our
measurement error by more than 30%. I can't wait when the hippocampal
longitudinal segmentation is ready.
By the way, I want to run (cross-sectional) hippocampal subfields on
longitudinal data using additional T2 with lower resol
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