The problem is that you are doing it in native space, and the native
space differs from one run to the next. If you do it in surface space or
mni305, then this problem will go away. You cannot use native space when
the native space differs from one run to the next
doug
On 03/09/2015 03:11 PM, Er
We use 'preproc-sess' before a single subject analysis. Here are the commands
we run:
>> preproc-sess -s SUBJECT_ID -fwhm 5 -per-run
>> mkanalysis-sess -analysis FT_TEST -TR 1.9 -paradigm FT.par -event-related
>> -runlistfile runlistFT -native -fwhm 5 -mcextreg -nconditions 10 -gammafit
>> 2.2
What is your mris_preproc command? And your mkanalysis-sess command?
On 3/9/15 2:41 PM, Eryilmaz, H. Hamdi wrote:
Hi Doug,
Yes, that's correct. Images in runs 015,016,017 have 37 slices, those
in run 018 have 35.
Hamdi
-
I think I would download a new version of mri_segstats (call it
something like mri_segstats-5.3)
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch
cd $SUBJECTS_DIR/subject
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.53.stats --pv
mri/norm.mgz --empty --brainmask mri/brain
Hi Doug,
Yes, that's correct. Images in runs 015,016,017 have 37 slices, those in run
018 have 35.
Hamdi
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday,
It looks like different runs have different number of slices. Is that right?
On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote:
Dear FS experts,
I got an error while running selxavg3-sess for a single subject. The
log (attached) says the following:
The first command sets the voxel-wise threshold to p<.0001, which is
pretty strict by itself. Is that what you wanted? Do voxels survive
uncorrected at that level? The 2nd sets the voxelwise threshold at about
.05. In both cases the clusterwise correction is .05 (ie, neither are
0.9), so I'm
Hi,
I was wondering how best to calculate total brain volume when using outputs
from free surfer 5.1. Could I use aseg SupraTentorial Volume measurements and
subtract aseg ventricle, csf, and choroid plexus measurements? Is there a way
to do calculate total brain volume using aparc outputs? I s
Dear FS experts,
I got an error while running selxavg3-sess for a single subject. The log
(attached) says the following:
*
** Input 018/tmp.mc-afni2.7515/invol.nii.gz and base
018/tmp.mc-afni2.7515/tempvol.nii.gz don't have same dimens
Hello Anastasia,
I’m using the nightly-built version for Mac OS Lion; I double checked it by the
command freesurfer -ver and got this response:
You are running this version of FreeSurfer:
freesurfer-Darwin-lion-dev-20150227
I’m using this version on Mac OS X Yosemite. I tried to re-download
Hi Amirhossein,
there are lots of reasons, why you see thickening, here are a few:
- scanner hardware or software update
- different hydration levels
- motion artifacts
- processing errors (e.g. skull strip failure etc)
- gradient non-linearities
- intensity inhomogeneities (most of these should
Hi Jennifer,
if you are interested in volumes from the stats file, you need to use
aseg_stats_to_table and aparc_stats… to stack those data across subjects and
time points into a single table that you then analyze with the LME tools.
mris_preproc is only for stacking surface maps.
The longitud
Dear all,
I’m trying to perform vertex-wise surface analysis on some PET data. After
performing the group contrast, significant differences (uncorrected) are
observed in a few clusters.These results apparently do not survive the Monte
Carlo method. In order to ensure that the MC-z is working fin
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