Hi Colin,
actually there is no hard limit for the size of your input data, except for the
subcortical segmentation which behaves quite strange.
What I currently do is to run recon-all on the hires data normally conforming
the data. Then I use the upsampled brainmask as a mask to skullstrip my h
Dear Freesurfers,
Is it ok to rename a subject directory, then run tkmedit and recon-all
procedures and then rename the directory back again or will this cause
problems?
All the best,
Anders
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h
Dear FS team,
I processed two set of MRI data for a single patient,Thats BL scan and
TP1.I ran both scans on a Mcbook Pro and a PC with Virtual machine
installed.
Though I was expecting the same segstats,the results vary from Macpro to
VM.For eg , for BL in Mac SubCortGrayVol is 178038 but
Hi Doug and other FS-experts,
I succesfully applied the registration step of the Cortical Thickness of a
Volume-defined ROI wiki:
http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
However, I'm having troubles at the end.
3) Map the ROI-mask to the fsaverage surface, to create an
Hi,
I am considering using qdec, however due to our large dataset (and
different individuals having been in charge at different times) I just
realized that the folders fsaverage etc are "missing". As these are
necessary for the qdec use, is there anything else I can do? Eg a
command line t
On 01/19/2013 03:18 PM, Alex Kell wrote:
> Hi Freesurfers,
>
> I have two unrelated questions.
>
> 1. I want to pre-whiten some functional data without running a GLM on
> them (we're going to run the GLM in matlab). It looks like fsfast
> does autocorrelation correction as a part of the selxavg
Cite Donald Hagler's 2006 paper in NI.
doug
On 01/20/2013 01:06 PM, Shantanu Ghosh wrote:
> Hi Freesurfers,
>
> Can you point out the correct paper that I can cite for the clusterwise
> correction for multiple comparisons computed by mri_glmfit-sim in v5.0 ?
>
> Thanks,
> Shantanu
>
>
--
Dou
no, it should not cause problems.
doug
On 01/22/2013 07:47 AM, Anders Hougaard wrote:
> Dear Freesurfers,
>
>
> Is it ok to rename a subject directory, then run tkmedit and recon-all
> procedures and then rename the directory back again or will this cause
> problems?
>
> All the best,
>
> Anders
Hi Chikku, while we try to resolve these differences, you are not
guaranteed to get identical results when you use different platforms.
This is an issue with using different computes and applies to all
software, not just FS.It is caused by the use of different math
libraries and different binar
Hi Cedric, try it with --noreshape. If you're using mgh format, then
reshaping is not necessary.
doug
On 01/22/2013 09:16 AM, Koolschijn, Cédric wrote:
> Hi Doug and other FS-experts,
>
> I succesfully applied the registration step of the Cortical Thickness of a
> Volume-defined ROI wiki:
> http:/
Hi Catherine, fsaverage is part of the FS distribution. You can just:
cd $SUBJECTS_DIR
ln -s $FREESURFER_HOME/subjects/fsaverage .
This will create a symbolic link to fsaverage in your $SUBJECTS_DIR
doug
On 01/22/2013 09:17 AM, Catherine Bois wrote:
> Hi,
>
> I am considering using qdec, however d
That should not happen. Concentrating on the Mac for a moment, please
send the recon-all.log files for both runs.
doug
On 01/22/2013 10:36 AM, Varghese Chikku wrote:
> Many thanks Doug,
> I forgot to mention,I ran same patient,same time point,twice on
> Mac and VM and the results varied e
Dan: just to be clear this has nothing to do with nifti vs. dicom. It's
likely that your tech ran prescan normalize and the nifti is the series
that was normalized.
cheers
Bruce
On Tue, 22 Jan 2013, Dan LaFreniere wrote:
Hey Falk,
Much appreciated for your reply on this! Fortunately I was
That was exactly what he said as well; sorry that I wasn't more clear with
my email.
Cheers guys,
Dan
On Tue, Jan 22, 2013 at 9:04 AM, Bruce Fischl wrote:
> Dan: just to be clear this has nothing to do with nifti vs. dicom. It's
> likely that your tech ran prescan normalize and the nifti is the
Dear all,
I read the others posts about CSF but I didn't find the information that I
need. I would like to calculate total CSF and in the aseg.stats file there
are : Lateral-Ventricle, Inf-Lat-Vent, 3rd Ventricle, 4th Ventricle, 5th
Ventricle but what is CSF ? Because I read that freesurfer can
Hi Sophie
I think it's little bits of CSF sulcal and otherwise that for some reason
the CMA included in their labeling. I don't think it will contribute much,
but should be included.
cheers
Bruce
On Tue, 22 Jan 2013, Sophie Maingault
wrote:
Dear all,
I read the others posts about C
Hello Experts,
I am running bedpost x through fsl on
the dmri directory (as advised in a previous post). I receive the fsl
error message: “child process exited abnormally”. The command
line error states:
switching from
/8000_tracula/8000_tracula_out/8005_DTI/dmri to
/8000_tracula/8000_tracula_o
I was able to solve my problem in my earlier email included below. I downloaded
a new verison of mris_calc made it executable with chmod +x FILE and then
replaced it in the bin folder. I included this response in case anyone else
runs into the same problem and does a search.
ftp://surfer.nmr.mg
Hi Dough,
This might be a very basic question:
I would like to compare the results of an analysis with the perrun and
persession motion correction. Here is my analysis line:
*mkanalysis-sess \*
* -analysis Cat_all_new -fsd bold -runlistfile runlist_all.txt \*
* -native -mcextreg -stc siemens
Hi Maryam, when you say that they are practically identical, I assume
that there are at least some small differences indicating that something
was different? And what are you comparing exactly? Eg, single subject or
group? In principle, they should be pretty close to each other, it
depends enti
I am comparing the final beta.nii.gz by importing it to matlab and this is
on individual subjects. The subjects have not moved much (less than 3 mm).
But the number of voxels that have different values in betta.nii.gz are a
handful which does not seem right since the fmc.nii.gz and fmcpr.nii.gz are
also there is an issue in v5.1 where the second run of recon-all on a
given platform will produce different results from the first (but
subsequent runs should produce identical results). this issue has been
fixed in the upcoming v5.2 release.
nick
On Tue, 2013-01-22 at 10:18 -0500, Douglas N Gr
Oh, right, I remember now (at least mostly). I fixed that for version
5.2. Maryam, it may be that the code is not actually using the
persession data like it should.
doug
On 01/22/2013 03:19 PM, r...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> There at least used to be a bug in the way perrun/per
Hello list,
is there a quick way to decimate an overlay /while respecting surface
geomery)? I am looking to downsample by about a factor 100.
Alternatively, I know I can use mris_decimate to downsample a surface,
but I would have to project my highres overlays onto the downsampled
surface (w
Hello list,
is there a quick way to decimate an overlay /while respecting surface
geomery)? I am looking to downsample by about a factor 100.
Alternatively, I know I can use mris_decimate to downsample a surface,
but I would have to project my highres overlays onto the downsampled
surface (w
also I am have not done any smoothing so that means that I should expect
some differences between the beta values across the two analysis.
M
On Tue, Jan 22, 2013 at 3:00 PM, Maryam Vaziri Pashkam
wrote:
> I am comparing the final beta.nii.gz by importing it to matlab and this is
> on individual
Hi Cat - I hope this helps:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25987.html
a.y
On Tue, 22 Jan 2013, Cat Chong wrote:
Hello Experts,
I am running bedpost x through fsl on the dmri directory (as advised in a
previous post). I receive the fsl error message: “child proc
Dear FS experts
I run a longitudinal analysis, and all steps (cross, base, long) were run
without errors. I used QA tools in order to look at the results and all
recons are fine.
However, when running glmfit with the --osgm option there is no error
message, but there is also no results (sig=0, F=
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