I don't know. I mainly got annoyed that my desktop would freeze up when
doing fmri analysis.
On 05/28/2015 03:15 PM, Caspar M. Schwiedrzik wrote:
> thanks! in your experience, is there a big performance deficit when
> using "-singleCompThread"? caspar
>
> 2015-05-28 14:57 GMT-04:00 Douglas N
thanks! in your experience, is there a big performance deficit when using
"-singleCompThread"? caspar
2015-05-28 14:57 GMT-04:00 Douglas N Greve :
> This is actually a matlab problem. In the next version I have fixed this
> so that it only uses one cpu. You can't control the number in newer
> ver
This is actually a matlab problem. In the next version I have fixed this
so that it only uses one cpu. You can't control the number in newer
verisons of matlab, it is either all or one. You can try editing
selxavg3-sess to add "-singleCompThread" to the matlab command line.
On 05/28/2015 02:24
Hi Doug,
I noticed that selxavg3-sess uses about half of the currently available
CPUs on our system, depending on how many CPUs are available. I think this
is when it is calculating the contrasts. Is there a way to up- or
downregulate the number of CPUs that the script is using?
Thanks, Caspar
I was actually looking for total area.pial surface..? Sorry, I forget FS calls
it area.pial while area is wm. Is there a way to find this value?
Gabriella
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Doug
isn't that what you are looking for?
On 05/28/2015 02:05 PM, Hirsch, Gabriella wrote:
> Hmm, I tried looking and all I can find is total wm surface area and surface
> area of individual regions. I've attached an lh.aparc.stats file for one of
> the subjects. Am I missing something?
>
> Thanks so
Hmm, I tried looking and all I can find is total wm surface area and surface
area of individual regions. I've attached an lh.aparc.stats file for one of the
subjects. Am I missing something?
Thanks so much!
From: freesurfer-boun...@nmr.mgh.harvard.edu
Hi Devin
grab a beta version of V6 (Zeke can tell you how) and see if it improves
things. It is a lot better for very large ventricles
cheers
Bruce
On Thu, 28 May 2015, Bageac, Devin
(NIH/NINDS) [F] wrote:
>
> Hi Freesurfer experts,
>
> I am processing a patient with severe cortical atrophy
Perfect. Thank you!
> On May 28, 2015, at 1:49 PM, Douglas N Greve
> wrote:
>
> Your environment is set up to have a limit of one hour run time for all
> programs. If a program runs for more than one hour of cpu time, it is
> killed. Our programs run for more than 1 hour.
>
> You can see you
Hi Clara,
this sounds great. The short time distance between the scans should also
help, so I think there is a good change it will work like this.
good luck, Martin
On 05/28/2015 11:13 AM, Clara Kühn wrote:
> Hi Martin,
>
> thanks for your quick reply. I was indeed referring to the quality check
Your environment is set up to have a limit of one hour run time for all
programs. If a program runs for more than one hour of cpu time, it is
killed. Our programs run for more than 1 hour.
You can see your limits if you run the "limit" program. For you
cputime 1:00:00
filesize unlimite
It is actually in ?h.aparc.stats.
The "total" is the total for the hemi
On 05/28/2015 09:12 AM, Hirsch, Gabriella wrote:
> That's what I thought but it doesn't seem to be there; I only have the
> following:
>
> BrainSegVol
> BrainSegVolNotVent
> BrainSegVolNotVentSurf
> lhCortexVol
> rhCortexVol
Hi Doug,
I sincerely apologize for being unclear! I'm still relatively new to freesurfer
and learning the ropes.
I've attached the three aforementioned .stats files.
The lh.aparc.stats and DKTatlas40.stats were generated from running recon-all.
When comparing them it appears the grey matter v
hello developer~
reconstruction is well done, so i'm doing on 'qdec' step..
Actually, i don't know how to treat the Design menu exactly..
---
Discrete(fixed factors) : diagnosis
continuous (covariate) : age , Left-Lateral-Vent
Great! Thanks!
Mihaela
On Thu, May 28, 2015 at 12:36 PM, Martin Reuter wrote:
> Hi Mihaela,
>
> it should still work, but may require more edits than with adults (e.g. if
> head size changes, the skull strip may differ a lot across time points. We
> keep it fixed in the base by computing the u
Hi Amirhossein,
where exactly is your label. If it is in the first time point, then how
did it get there?
I think it is probably in fsaverage space (where the first time points
were mapped to perform your QDEC analysis). In that case use
mri_label2label from fsaverage to the individual base spa
Hi Mihaela,
it should still work, but may require more edits than with adults (e.g.
if head size changes, the skull strip may differ a lot across time
points. We keep it fixed in the base by computing the union, but that
may be too large for some earlier time points, so you may have to edit
I would think so - the changes are going to be smaller than say over 48
months in the ADNI study, which works fine.
cheers
Bruce
On Thu, 28 May 2015, Mihaela Stefan wrote:
Dear Martin,
I'm pitching in since this topic concerns me as well.
We are collecting structural data for a longitudinal
hello developer~
reconstruction is well done, so i'm doing on 'qdec' step..
Actually, i don't know how to treat the Design menu exactly..
---
Discrete(fixed factors) : diagnosis
continuous (covariate) : age , Left-Lateral-Vent
Dear Martin,
I'm pitching in since this topic concerns me as well.
We are collecting structural data for a longitudinal study with
adolescents. The youngest is 13 years old at baseline and the mean age is
around 16. We will collect 3 follow-ups with a gap of 1.5 - 2 years. The
adolescent brain is
SORRY THIS SHOULD HAVE GONE TO AFNI... SORRY!
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Jessica Lynn Hanson
Sent: Thursday, May 28, 2015 10:52 AM
To: Freesurfer support list
Subject: [Freesurfer] NO-DSET in final voxel resolution
Hi Freesurfe
Hi Freesurfer Experts,
I've just run my afni_proc.py script and began the review using
@ss_review_driver. I noticed that the "final stats dset" states "NO_STATS" and
the "final voxel resolution" states "NO-DSETNO-DSETNO-DSET". Do you
have any ideas why this could be?
I've attached:
Hello,
Thank you for the feedback. I have updated the system so that future dev
build will contain that library. That said, the mavericks build (the one
you used for this subject) probably won't be released as it doesn't seem
to provide and benefit over the lion build, which has been tested and
sh
Hi Martin,
thanks for your quick reply. I was indeed referring to the quality check. I
guess I interpreted that incorrectly. With the children data "inspecting"
almost always means "editing".
I also took a look at the cheat sheet again. I've been mulling it over and my
best idea so far is to
Thanks, Doug, the command seems to work. I guess it will take a while to
finish running.
On a different note, I have a large data set that doesn't seem to generate
corrected results. What's interesting is that the uncorrected results are
consistent with our previous findings and those from the rel
Hi Volker - The motion measures from our 2013 paper should not be affected
by B0 correction, because B0 correction will be the same for all volumes
in the diffusion scan, regardless of b-value or diffusion gradient
direction.
Of our 4 motion measures, the rotation and translation are compute
It is attached again.
I hope it was because kicked off the server,
Thanks a lot
Anvi
On Wed, May 27, 2015 at 3:24 PM, Douglas N Greve
wrote:
> don't know. Can you send the recon-all.log file?
> doug
>
> On 05/25/2015 07:13 PM, Anvi K Vora wrote:
> > Hi Doug,
> >
> > That file does not exist, b
Hi Clara,
how to edit depends a lot on the type of edit. The general rule is to
edit as early as possible. In some edits, there is shortcuts (e.g. start
with base, then check long and skip the cross). Take a look at the Cheat
Sheet on the first link. Also usually there is no need at all to edit
Dear Freesurfer Experts,
I'm working with the structural data of 4-year olds which we measured 3 times
to asses changes in cortical thickness.
During the preprocessing I've found some contradicting information on how to
best edit the longitudinal data. On this site
https://surfer.nmr.mgh.harvar
That's what I thought but it doesn't seem to be there; I only have the
following:
BrainSegVol
BrainSegVolNotVent
BrainSegVolNotVentSurf
lhCortexVol
rhCortexVol
CortexVol
lhCorticalWhiteMatterVol
rhCorticalWhiteMatterVol
CorticalWhiteMatterVol
SubCortGrayVol
TotalGrayVol
SupraTentorialVol
SupraTen
Dear experts,
First: We want to use B0 field map correction (unwarping) within the trac-all
-prep stream. However, as in
http://fsl.fmrib.ox.ac.uk/fsl/fsl-4.1.9/fugue/feat_fieldmap.html, we have one
magnitude and one real field map image, NOT one magnitude and one phase image.
Can Tracula handl
Thanks for pinpointing the problem, Elijah. We are working on a solution.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: "Elijah Mak"
To
Thanks Doug,
I am trying to extract mean thickness from the ROI but I get the following
error :
amir% aparcstats2table --hemi lh --subjects `cat list5.txt` --parc
transversetemporal --meas thickness --skip --tablefile lh.Cth.roi.txt
SUBJECTS_DIR : /Applications/freesurfer/subjects/longBO
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