Hi Anastasia,
you´re right, the values are reasonable! The problem is that I cannot read out all the decimal places that I can see in FreeView as described! When I save the values of distinct ROIs to a .stats file, I can only see e.g. 0.0007 but I need 0.000770333 for further processing. Do you h
FreeSurfer will preserve your previous edits (e.g., brainmask.mgz edit, or wm.mgz edits, among others) when you run a newer version on top of an older version. However, that is no guarantee that there won't be any issues following the re-processing with
the newer version, so it is best to a
Hi Doug,
I am still trying to resolve the different results for GLMs completed in
Freesurfer and SPSS. Interestingly, I get the same p-values for each
method when I remove my continuous covariate (age) from the model
(leaving gender, group, and genderXgroup effects). This suggests that
the tw
btw, to check, you can run this on the thicknesses and compare to what
you get with mris_preproc
On 2/11/15 6:01 PM, Douglas Greve wrote:
> Probably easier to use mris_apply_reg, something like
>
> mris_apply_reg --src lh.w-g.pct.mgh --trg xhemi.lh.w-g.pct.mgh \
> --streg $SUBJECTS_DIR/$subje
Probably easier to use mris_apply_reg, something like
mris_apply_reg --src lh.w-g.pct.mgh --trg xhemi.lh.w-g.pct.mgh \
--streg $SUBJECTS_DIR/$subject/surf/lh.fsaverage_sym.sphere.reg \
$SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg
mris_apply_reg --src rh.w-g.pct.mgh --trg xhemi
Just give it one of the dicoms (ie, don't use the "*" wild card, just
give it the actual file name of one of the files in the series, it will
find the rest)
doug
On 2/11/15 4:28 PM, Sampada Sinha wrote:
Dear freesurfer experts,
Sorry for posting such a long message but I am trying to run dt
Dear freesurfer experts,Sorry for posting such a long message but I am trying to run dt_recon command on DTI images acquired in dicom format using 3T_Toshiba (Toshiba_MEC_MR3). Image parameters are: Scanning sequence =Spin Echo; TR=9 ; TE=082.0 ; Flip angle = 90; Slice thickness= 3.; acquisitio
Hi Konrad
you should be able to do this with mri_surf2surf, although the syntax
might be tricky.
cheers
Bruce
On Mon, 9 Feb 2015, Konrad Wagstyl wrote:
> Hi all,
>
> We're having some trouble using interhemispheric registration. It works fine
> for files that are automatically registered eg th
Hello,
I have a large set of images previously run in FreeSurfer 5.0. I'm also
preparing to run a new batch of images and debating whether to use 5.3 or stick
with 5.0. If I updated all the old datasets to 5.3, would I need to visually QC
them a second time, or are the versions similar enough t
Hi Tom - These are reasonable values for mean diffusivity (a.k.a. ADC).
Only FA is normalized to take values in the 0-1 range.
a.y
On Wed, 11 Feb 2015, Thomas Potrusil wrote:
Dear FreeSurfers!
A question concerning DTI analysis came up:
I already run dt_recon on my dataset which works ver
Hi Amanda - It doesn't look like the new registration was applied to the
aparc+aseg. Can you tell us the exact sequence of steps that you followed,
including your bbregister command line and the trac-all command lines that
you ran after running bbregister?
Thanks,
a.y
On Wed, 11 Feb 2015, Wor
Thanks again, Bruce.
The time problem precludes running with a single cpu.
But you jogged my memory and I was fooling around with freeview while recon-all
was running.
I might have overrun the memory with it as I was loading 10's of 1000's of
points to plot which really pushes it.
I'll try with 5
Hi Don
does it repeatably die in the same place when you run it with openmp 5? Are
you sure nothing else was running at the time? Try running it with openmp 1
and make sure nothing else is running and see if it finishes
sorry, not sure what else to suggest. If it dies in the same spot, upload
Thanks for responding so quickly, Bruce.
Yes I was running a single job on the 6-core machine and have used it and this
version of recon-all successfully before.
The freesurfer instance was downloaded a few weeks ago - it is the Centos6 one.
I don't know how to tell which version of the entire pac
Dear FreeSurfers!
A question concerning DTI analysis came up:
I already run dt_recon on my dataset which works very well. I also used the output to extract FA-values of distinct ROIs - no Problem. Now I want to do the same for ADC but I only get values in my .stats files like 0.0007 or 0.0008
Hi Don
are you running a single job on the 8G machine? What FS version? We haven't
seen any core dumps in mri_ca_register recently. If you run it without
openmp does it work? Kind of worrisome that it dies in a different place on
a different machine
Bruce
On Wed, 11 Feb 2015, Krieger, Donal
Dear list:
We are under a significant deadline on which this freesurfer run depends.
I'm reposting from last night along with a bit of additional information.
A 2nd run on a different box yielded:
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=256)
Also, the box
Hi Andre
sorry, there is no way to run only part of the steps as there is lots of
interdependancy. You need to run -all. That said, the new version that
should be coming out in a couple of months is significantly faster and has
a lot more openmp support.
cheers
Bruce
On Wed, 11 Feb 2015, An
Dear free surfer experts,
I intend to do a parcellation on my mprage images. The purpose of that is to
use them further as seeds for tractography analysis. So far I used recon-all as
follows:
recon-all -subject xy -i xy.nii.gz -all
But this is quite time-consuming and I want to ask for the com
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