This is a question for the FS community in general,
I gather there is variability around this, but rather than an exact number
and time, I was hoping for an estimate on how many scans would I expect to
require manual edits(any of the check points recommended in the tutorials)
as well as an estimat
Hi,
RE the below post, we have longitudinal data from three time points, but a
number of participants have scans for only one or two time points. We've done
all of the cross-sectional analysis (including a lot of manual editing) and are
ready to run everything through the longitudinal stream. O
Using mri_label2vol will work a little better than mri_vol2vol.
doug
On 3/5/13 8:41 PM, Bruce Fischl wrote:
you'll have to look at the help. It's pretty extensive since Doug
wrote it :) Then you can use freeview to visualize the transformed
intensity and aseg volumes
cheers
Bruce
On Tue, 5 M
you'll have to look at the help. It's pretty extensive since Doug wrote
it :) Then you can use freeview to visualize the transformed intensity
and aseg volumes
cheers
Bruce
On Tue, 5 Mar 2013, Natalie Han wrote:
Thanks for the quick reply. Can you elaborate a little bit how to use
mri_vol2vol
Thanks for the quick reply. Can you elaborate a little bit how to use
mri_vol2vol to get what I want? what would be the final scipt for tkmedit
then?
On Tue, Mar 5, 2013 at 5:31 PM, Bruce Fischl wrote:
> Hi Natalie
>
> sorry, tkmedit won't do what you want. It's old and we are not developing
> i
Hi Natalie
sorry, tkmedit won't do what you want. It's old and we are not developing
it anymore. You can apply the transform using mri_vol2vol, just make sure
to use nearest nbr interp for the aseg.
cheers
Bruce
On Tue, 5 Mar 2013, Natalie Han
wrote:
Hi, all,
I have a tkmedit display iss
Hi, all,
I have a tkmedit display issue when I try to add transformation to the main
volume, but the segmentation volume won't conform to Talairach domain
accordingly. Here is the commandline
tkmedit subject norm.mgz -main-transform talairach.xfm -seg aseg.mgz
really appreciate any feedback on
Hi all,
I have installed FreeSurfer 5.2 to take advantage of improvements in TRACULA.
When I run trac-all -bedp I get an error:
.../freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected
Looking at the programming it is faulting on line 131 where it is checking the
FSL version.
DJ,
Agreed that the distribution has gotten bloated. In future releases I'd
like to change it to not include most of the data and to have recon-all
or other utilities print a 'wget' command to use to download the data
when needed.
I've updated the ReleaseNotes section with a list of some directo
A post-doctoral research fellow position is available in the Laboratory for
Computational Neuroimaging (with PI's Bruce Fischl and Mert Sabuncu) at the
Massachusetts General Hospital, Athinoula A. Martinos Center for Biomedical
Imaging and the Department of Radiology at Harvard Medical School.
Hi,
I'd like to use mris_flatten_cuda to accelerate the flattening process.
However, it seems that the code doesn't handle ripped vertices correctly.
mris_flatten by itself works correctly, but attempts to run
mris_flatten_cuda results in thousands of "PANIC: RIPFLAG IS NOT SUPPORTED
!" messages. T
Hi,
I was trying to install Freesurfer on a HPC cluster. It seems to be a
pretty large distribution, ~4.3 GB after unpacking. I wonder if all the
subfolders are needed for running freesurfer or is there any folders could
be skipped. Thanks in advance.
DJ
__
yes, my mistake
doug
On 03/05/2013 01:30 PM, Cesar Echavarria wrote:
> Also, did you mean ' fir 4 26' in your previous response? since the
> TimeWindow parameter should include the 'PreStimulus' time
> (I just want to double check since this is crucial to my question)
>
> Cesar
>
>
> On Tue, Mar
Hi Cesar, you cannot really do the analysis you want to do, it is
mathematically impossible. If you do not expect a response from one of
the conditions, then you could code it as 0. Alternatively, you can
consider both conditions as a single 20 sec event and get the FIR for
that event out to 2
Also, did you mean ' fir 4 26' in your previous response? since the
TimeWindow parameter should include the 'PreStimulus' time
(I just want to double check since this is crucial to my question)
Cesar
On Tue, Mar 5, 2013 at 1:00 PM, Douglas N Greve
wrote:
>
> If you presented the stimulus for 1
Does the post-stimulus period have to be as long as 12 seconds? With such a
long time window I get the following error when running selxavg3-sess:
XCond = 1.47995e+18 (normalized)
ERROR: design is ill-conditioned
To clarify: in our design we have 10 seconds of condition 1 followed
immediately aft
If you presented the stimulus for 10sec, then you should set the time
window to include about 12 sec after stimulus offset. If your stimulus
is 10 secand you want the time window to start 4 sec prior to onset and
go 12 sec after onset, then you will need a time window of
4+10+12=26sec, so it w
Hi Joost, I'm a little lost. Are you doing the initial mri_glmfit
analysis on thickness or CT?
doug
On 03/05/2013 03:31 AM, j janssen wrote:
> Hi Doug,
>
> using mri_glmfit with DODS and mri_glmfit-sim with a fsgd-file and
> contrast (attached) that looks like (2 discrete factors: 1 with 2
> l
On 03/05/2013 12:13 AM, Rongxiang Tang wrote:
> Dear All,
>
> I have some basic questions about groups analysis for cortical
> thickness, and I looked over the list and tutorial, but still have
> questions.
> I have two groups, experimental and control, and both were tested
> before and after t
Thanks Bruce. FYI, I got a couple of other emails off list. One of them
reminded me that the original ADNI protocol had this resolution.
Cheers,
Souheil
On Mar 5, 2013, at 9:50 AM, Bruce Fischl wrote:
> Hi Souheil
>
> our standard acquisition used to be 1.33x1x1 so I don't think there
> sho
That is correct (though you might not want to use Bonferroni as it is a
little harsh). QDEC will do the same thing. It provides a GUI but is
less flexible.
doug
On 03/05/2013 07:59 AM, std...@virgilio.it wrote:
> Hi list,
>
> I'm performing cortical thickness on three group of subject. I have
Hi Cesar, for your case, it would correspond to 4sec prior to stimulus
onset (the TR that goes from -4 to -3 sec). What seems to be wrong? The
last frame would be the TR that goes from +9sec to +10 sec. Not related
to your question, but Is 10 sec post stimulus long enough?
doug
On 03/05/2013 1
Hi Jon - I mean concatenating them:
mri_concat --i dwi1.nii.gz dwi2.nii.gz --o dwi.nii.gz
cat bvecs1.txt bvecs2.txt > bvecs.txt
cat bvals1.txt bvals2.txt > bvals.txt
Make sure though this doesn't leave any blank lines in between the two
sets of bvecs/bvals in the concatenated text files.
Hope
Hi Freesurfers,
I did an FIR analysis to get the BOLD response over time, the following way
mkanalysis-sess -analysis Afterimage_FIR2.rh -surface self rh -native
-fwhm 5 -paradigm ShapeAE_New.par -event-related -polyfit 1 -mcextreg -TR
1.000 -nconditions 8 -force -fsd bold -fir 4 14
I then ge
Hi Souheil
our standard acquisition used to be 1.33x1x1 so I don't think there
should be any problem (although it has been a long time since we used to
get those - 1.5T and single channel)
cheers
Bruce
On Tue, 5 Mar 2013, Inati, Souheil
(NIH/NIMH) [E] wrote:
> A colleague has some mprage scan
A colleague has some mprage scans collected on a 3T sagittally 1mmx1mm in
plane, 1.3mm thick. The SNR and CNR are pretty good. I figured I'd ping the
list to see if anyone have any experience running scans with the slightly
thickish voxels through the recon-all pipeline. Anything I ought to l
Hi Carolina
you can probabbly get reasonable asegs out of it, but I don't think
surfaces will work since your 5 or 6 mm is larger than the spacing between
many adjacent gyri.
cheers
Bruce
On Tue, 5 Mar 2013, carolina.mr wrote:
Hello,
Someone asked me if it is possible to process T1 images
Hello,
Someone asked me if it is possible to process T1 images with a 5mm slice / 1mm gap with FreeSurfer. Is it feasible to analyse? The person who asked used ITK tools to interpolate the images and reconstructed an isotropic voxel. I do not know if the post processed image with ITK can be validat
2013/3/5 Rotem Saar
> Hi
>
> Attached is some pictures that might help ? Is this what you meant ?
> Looking at this again - something is weird but I can't say what...
> I can ZIP the data of one subject and send it to you but I don't feel
> comfortable asking you to personally examine it...
> Hop
All,
I have completed base and long runs for qdec longitudinal analysis.Now I
am struggling to make qdec.table.dat.How can I do this.
Tx
chikku
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Hi list,
I'm performing cortical thickness on three group of subject. I have also three
covariates (age, gender and educational level).
I'm doing:
1-built a .fsgd file2-mris_preproc3-mri_surf2surf4-mri_glmfit5-Bonferroni
correction
Are those processes correct?
Alternatively should I use qdec op
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