Hello Freesurfer World,
I am trying to decide how to threshold my probabilistic tractography data.
Does anyone have recommendation on best define a threshold?
Thank you,
Kate Damme
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Hi Alexander - These measures (both averages and along-the-tract values)
are extracted in each subject's native space, so inter-subject
registration is not an issue in the difference that you found. I suspect
it is because the along-the-tract measures are sampled at a certain number
of cross-
Anastasia, thank you for the prompt response. It is helpful.
I’ve already examined pathstats.byvoxel.txt files combining them with
“-stat” command. First, I compared every voxel along the particular tract.
Then I split this tract by 3 equal parts and tried to calculate
between-group difference at
That is the "cost" of the registration. You can look in Greve & Fischl
2009 to see how it is computed.
doug
On 2/9/15 3:45 PM, sabin khadka wrote:
Hi Doug- Works fine. I appreciate your help.
Related but different question: Would you help me understand how the
QA value(0-1)while checking reg
Hi Alexander - When you average over a larger region, you are potentially
reducing noise but you may also potentially wash out an effect that is
very localized by including more voxels where the effect is not present.
That's the difference between the two measures, so they are at different
po
Great, thanks!
Am 09.02.2015 um 13:10 schrieb Anastasia Yendiki :
>
> Hi Janosch - Yes, it's possible. In your config file use:
> set doregmni = 0
> set doregcvs = 1
>
> You do not need to rerun any of the preprocessing steps before the
> inter-subject registration, so skip those w
Hi Janosch - Yes, it's possible. In your config file use:
set doregmni = 0
set doregcvs = 1
You do not need to rerun any of the preprocessing steps before the
inter-subject registration, so skip those when you run "trac-all -prep" to
save time.
Hope this helps,
a.y
On Mon, 9
Hey Anastasia (and list),
I decided to go with affine registration to MNI when I processed my
longitudinal dataset with Tracula, because I didn't realize that one has the
option to do both MNI and CVS registration in parallel.
Is there a way to rerun Tracula with the CVS option without having t
Hi Doug- Works fine. I appreciate your help.
Related but different question: Would you help me understand how the QA
value(0-1)while checking registration using following command is calculated.
tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum
Cheers,
Sabin Khadka
Dear FreeSurfer Expert,
I've run qdec to do group analysis and got display of result. However,
while I tried to change the threshold, I found I can't change or input
anything...Then, I also found that I cannot change the Common-Space
Subject...Is there approach to address this issue?
Best,
Zhichao
On 2/9/15 3:16 PM, sabin khadka wrote:
Thanks Doug. I am now able to get average time series from cortical
ROIs. I used
mri_segstats --annot fsaverage lh aparc --i
sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --avgwf test1.txt
That's right, but I would use the unsmoothed data since smoothin
Thanks Doug. I am now able to get average time series from cortical ROIs. I
usedmri_segstats --annot fsaverage lh aparc --i
sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --avgwf test1.txtHow would I
get time series of the sub-cortical ROIs (fmcpr.up.sm5.mni305.2mm.nii.gz)?I
tried doingmri_se
Dear Anastasia and Freesurfer team,
I used TRACULA to get FA values for two groups: patients and controls.
After that, I ran between group comparison and got circa >0.05 p-values for
FA _Avg_Weight values BUT circa 0.001-0.005 p-values for FA_Avg_Center for
the same tract.
Then I ran correlation
Hi all,
We're having some trouble using interhemispheric registration. It works fine
for files that are automatically registered eg thickness, volume etc. but not
for mgh files, like ?h.w-g.pct.mgh.
Is there a way of adding files to xhemi/surf/ so that other surfaces files can
be compared betwe
Yes, mri_segstats. Run it with --help. See esp example 6
On 2/9/15 12:31 PM, sabin khadka wrote:
Hi FS Users,
I've preprocessed resting state fmri data using preproc-sess as shown
in FSFAST functional connectivity walk through manual. I know I can
extract mean time series of a seed region usi
Dear FreeSurfer experts,
when I run e.g.:
mri_nu_correct.mni --i orig.mgz --mask brainmask.mgz --o nu.mgz --n 1
--proto-iters 1000 --uchar transforms/talairach.xfm —cm
where orig.mgz and brainmask.mgz have 577 x 577 x 577 voxels, there is an error:
$Id: mri_segstats.c,v 1.109 2014/10/17 19:31
Hi FS Users,
I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST
functional connectivity walk through manual. I know I can extract mean time
series of a seed region using fcseed-sess. I am trying to find a command to
extract mean time series from all Desikan (or Dest
On 2/8/15 1:48 PM, maaike rive wrote:
But how can i run the appropriate preprocessing and smoothing? The --X
flag s not recognised using mris_preproc.
mri_preproc only uses the fsgd file to get the list of subjects to
assure that they are ordered in the same way as when mri_glmfit builds
the X
Good morning, Bruce.
Sounds good. Thank you very much.
Regards,
Sourav
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, February 09, 2015 8:00 AM
Hi Noam
it looks like the talairach alignment failed. You can usually find answers
on our wiki for what to do in this type of case. For example:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_tktools
cheers
Bruce
On Mon, 9 Feb 2015, Ben Eliezer, Noam wrote:
Hi Freesurfer su
Hi Sourav
that won't work - particularly if you are trying to crop in the a/s
dimension. Many brains might squeeze into 160 l/r but probably not all, and
certainly not with skull. And there won't be any consistent starting coord
as it will depend on where the head is in the FOV. The only way f
Hi Freesurfer support,
I am receiving an error from recon-all and would be happy to get your opinion.
This dataset, I am processing, is generated by a 3D MPR (Sagittal orientation)
protocol.
It’s only one of many datasets I have and this is the only one giving me
problems…
The run seems to gen
Hi Lilla,
I would be interested in any tips on processing neonate scans as well.
Currently we are wanting to process subjects of 1 month up until 2 years of age
through Freesurfer. Help is very much appreciated.
Kind regards,
Fraukje Coopmans
PhD Student | Department Psychiatry | Brain Divi
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