Dear list,
I want to limit my vertex-wise group analysis to a smaller spatial region,
then I ran my own Monte-Carlo simulation on fsaverage for the superior
temporal gyrus:
mri_mcsim --o lh/superiortemporal --base mc-z --surface /fsaverage lh
--nreps 1 --label superiortemporal
After 36 hours
So I have specified where the DTI file is. I am not sure why Tracula cannot
open it. Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz this is where the
the dti file is.
On Tue, Apr 12, 2016 at 11:45 AM, Alan Francis > wrote:
> Hi Jasmin -
>
> When replying please cc the FS group so that they may
It does not compute this. Often people use time-from-baseline for their analysis and control for age (@ baseline).
Best Martin
On Apr 12, 2016 6:23 PM, Mihaela Stefan wrote:Thanks Martin!
Related to the longitudinal analysis, should we use the demeaned age at baseline or the LME package automatic
On 04/11/2016 04:46 PM, Antonin Skoch wrote:
> Dear FreeSurfer experts,
>
> I am using mri_surfcluster to compare results from PALM and FreeSurfer
> cluster extent inference.
>
> I came across several issues in mri_surfcluster I cannot cope with.
>
> 1.
> I observed that --mask option in mri_sur
Thanks Martin!
Related to the longitudinal analysis, should we use the demeaned age at
baseline or the LME package automatically computes this?
Thanks again!
Mihaela
On Apr 12, 2016 5:39 PM, "Martin Reuter"
wrote:
> Hi Michael,
> the longitudinal image processing pipeline does not care which o
Can you tell me more about your design? Does each run have a separate
task? Do you want to test across tasks?
On 04/12/2016 11:53 AM, Shea, Conor wrote:
> Thanks so much. So, then, how does the Group Level Analysis work? How do I
> concatenate the runs together again, now that we've separated
In general, FreeSurfer does not care what orientation your images are in
as long as the geometry in the header file is correct. If you
re-oriented them for SPM and you are confident that the geometry info is
still correct (eg, no left-right flips) and you did not change the scale
of the images
On 04/12/2016 04:16 PM, Afzal, Afsana wrote:
> The source data is from a gambling task that has multiple levels of risk and
> reward. The offset refers to the risk level and the slope refers to the
> monetary reward for that particular risk level.
>
> We were doing some parametric modulation in
sorry, I could have sworn that I answered this one
On 04/12/2016 08:57 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> for the analysis in QDEC I created my own Monte Carlo correction.
> My questions relate to the threshold option.
>
> 1. Would I use neg if I have mostly blue clusters in the
Hi Michael,
the longitudinal image processing pipeline does not care which one is baseline and which are follow ups. It only cares what images belong to the same subject.
So, yes you can process this one with only two tone points instead of three.
Best Martin
On Apr 12, 2016 5:09 PM, Mihaela Stefa
Hello FreeSurfers,
We are conducting a longitudinal analysis and we have a subject who is
missing the structural at baseline (it has fMRI data though). That subject
returned for the 1st and the 2nd follow-up. Can we process the longitudinal
pipeline the usual way and account for the missing baseli
The source data is from a gambling task that has multiple levels of risk and
reward. The offset refers to the risk level and the slope refers to the
monetary reward for that particular risk level.
We were doing some parametric modulation in the first level analysis. For the
second levels, curr
Hi Jasmin -
When replying please cc the FS group so that they may weigh in on the
situation. Looking at the log, they key problem appears to be this:
niiRead(): error opening file
Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz
Tracula is not able to open your DTI.nii.gz
Please check this file
Thanks so much. So, then, how does the Group Level Analysis work? How do I
concatenate the runs together again, now that we've separated them into
different tasks?
Conor
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On
Hi Grant
That's pretty surprising. If you tar and gzip that whole subject's dir I will
take a look
Cheers
Bruce
> On Apr 12, 2016, at 11:03 AM, Grant O'Brien wrote:
>
> Hello,
> I’m an undergraduate at Duke University working on a study of pediatric
> structural imaging. We’ve recently come a
Hi Freesurfer users.
I performed the recomended reconstruction of 82 subjects with Freesurfer.
The images used for this reconstruction were previously reoriented to AC-PC
position, because they were previously used for SPM purposes.
Now I'm trying to perform the FSFAST workflow, and I had to unp
Hi Jasmin -
In your dmrirc file , the dcmlist refers to the dicom list. You have put
the BVEC/BVAL files there. That is not correct. You need to place the
actual pathway to your niftis in this position.
set subjlist = (40 39 36)
# Input diffusion DICOMs (file names relative to dcmroot)
# If orig
Dear FreeSurfer experts,
for the analysis in QDEC I created my own Monte Carlo correction.
My questions relate to the threshold option.
1. Would I use neg if I have mostly blue clusters in the QDEC display and pos
if I have mostly red clusters?
2. When do I use abs?
3. I compared the neg opti
Dear Freesurfer experts,
I need to extract the volume of the supplemental motor area (cortical structure)
I have used the aparch.stats2table and applied the both the ?h.aparc.stats and
the ?h.aparc.a2009s.annot.stats atlas; However, I am having trouble identifying
the supplemental motor area.
D
Hi Lee,
To be absolutely sure that i understand it correctly. By adding the -3T
flag, it used both the 3T atlas for Talairach alignment and the 3T-specific
NU intensity correction parameters. So, all i need to pass in the command
line (recon-all) is the -3T flag. I do not need to add additional fl
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