Hi-
I've come across a peculiar behavior with recon_checker, and am hoping someone
can shed some light on this.
I have used it 100's of times in the past, but not for about 2 months. I
recently processed a large set of cases I wanted to QC. When I ran it, some,
but not all, of the snaps were c
Dear Freesurfer experts,
I have encountered the following error while running the tracula
pre-processing command and was hoping you could help me understand how
to correct this.
Selection from log:
mri_convert /Users/Desktop/Tracula/diffusion_DTI/
/Users/Desktop/Tracula/diffusion_DTI/Subje
Hi Allison - The mri_convert command at the top of your log file is trying
to convert the directory /Users/Desktop/Tracula/diffusion_DTI to a nifti
file. From the name of that nifti file, it looks like it's expecting to
find a field map and not finding it.
Hope this helps,
a.y
On Tue, 8 Jan 2
Hi list,
I have done an analysis using QDEC and now I would like to do set up similar
statistical analysis in SPSS on some parcellated structures.
I have the following setup in QDEC:
2 cohorts (patients, healthy control subjects)
Continuous variable : demeaned Age
Nuisance Factor: demeaned intr
run
mri_glmfit-sim --glmdir lh.lgi.glmdir --cache 2 pos
get
cmdline mri_glmfit --y lh.lgi.10.mgh --fsgd lgi.fsgd dods --C CC.mtx --surf
subset_average lh --cortex --glmdir lh.lgi.glmdir
SURFACE: subset_average lh
log file is lh.lgi.glmdir/cache.mri_glmfit-sim.log
cd /study5/aa-scratch/UTAH/
The 10mm is what you applied, but data will have an intrinsic
smoothness, and the final smoothness is a combo of the two. LGI data
tends to start out extremely smooth. I would re-run it without smoothing
and see what fwhm you get
doug
On 01/08/2013 03:24 PM, Gregory Kirk wrote:
>
>
>
> run
>
Hi,
I would like to try running recon-all for some subjects using two source
images in combination. The first image is a FLAIR with dimensions
288x288x30, while the second is a T1 with dimensions 256x256x165.
Furthermore, the each FLAIR voxel has dimensions of 0.79x0.79x4.5 mm, while
each T1 voxel
Hi Dierdre
not sure a FLAIR with that thick slices will be very useful, but the
typical workflow is to run recon-all with the T1, then when it's done you
can run recon-all with a special switch to register and use the FLAIR.
Note that this is only in 5.2, which isn't quite out yet (although you
Dear doug
I used the command: mri_segstats --i y.mgh --slabel fsaverage lh
yourlabel.label > --avgwf avg.dat --id 1, and the terminal is following:
cmdline mri_segstats --i /media/freesurfer1/CT/qdec/Untitled/y.mgh --slabel
fsaverage rh control_AA_GG_ba.label --avgwf avg.dat --id 1
sysname Linu
Hi Efrat,
To look for aseg outliers you'll need to generate a aseg lookup table
based on all the subjects in your dataset (-gen-asegLUT). Additionally,
in the current version some of the labels the script uses are old and no
longer appear in the aseg generated by recon-all, so they will be 0 +
Hi Irwin,
It sounds like the snapshots from tksurfer are fine, but the ones from
tkmedit are not being generated properly. It may be this peculiar bug
where ImageMagick has trouble reading rgb files. Try converting an rgb
file to a jpg 'convert file.rgb file.jpg'. You may get the error
'Impr
Are those 3 numbers the values in the avg.dat file? Why do you think
they are volume? In any event, they have the same interpretation as the
values in y.mgh
On 1/8/13 8:43 PM, xiangbo_2010 wrote:
Dear doug
I used the command: mri_segstats --i y.mgh --slabel fsaverage lh
yourlabel.label > --
Dear doug
In the avg.dat file, where have 61 values which were equal with number of my
subjects, however, I used these values in SPSS, there still no signifiant
difference, thanks!
Bo Xiang
At 2013-01-09 11:53:15,"Douglas Greve" wrote:
Are those 3 numbers the values in the avg.dat file?
are you positive that the SPSS model is exactly the same as the model in
QDEC? You can get the design matrix from Xg.dat
On 1/8/13 11:15 PM, xiangbo_2010 wrote:
Dear doug
In the avg.dat file, where have 61 values which were equal with number
of my subjects, however, I used these values in S
Hi Nasim, I don't use SPSS, so I'm not sure I can help, but I think what
you have is right but you'll need another factor which is ICV*group. The
Xg.dat file contains the design matrix for QDEC, so you might be able to
compare it to what you get for SPSS
doug
On 1/8/13 3:05 PM, Maleki, Nasim
Hi,
The link
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux
from
the release notes for freesurfer 5.1 (
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) appears broken. I
also checked the anonymous ftp site and found only the directories
bbr-papers and growt
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