Dear FreeSurfers,
I didn't notice a resolution to this thread. I'm experiencing the same
'problem';
When I run Qdec and perform a Monte Carlo correction of 1.3, the terminal
window output gives me the following clusters and values (during the MC
correction I used the 'abs' option):
# ClusterN
Hello FreeSurfer experts,
I am wondering if it is possible to run trac-all -bedp without
generating the email notification at the end of the post-processing
stage?
After submitting a long list of -bedp jobs to the local cluster, I
received a message from our IT center reporting being spammed by th
Dear Freesurfer experts,
I have a problem with Tksurfer. Whereas this worked previously fine it suddenly
crashes every time I try to start it. This happens with every subject or
fsaverage.
A similar problem was reported before with similar terminal output but
unfortunately I could not find a s
Hi Ruthger
we need a lot more info. What version are you running? On what hardware
and software platform? Does it crash with different datasets? With bert?
How much RAM do you have?
cheers
Bruce
On Tue, 20 Nov 2012, Righart, Ruthger Dr. wrote:
> Dear Freesurfer experts,
>
> I have a problem w
Dear doug
Thank you for your reply!
+AOM -BOM -APM -BPM00000
+AOM -BOM00 -AQM +BQM000
+AOM0 -APM000 -COM +CPM0
+AOM000 -AQ
Hi Joy-Loi,
You can edit the bedpostx script (make sure you figure out which version
of that script trac-all is calling). Find this line and delete the
"@fmrib.ox.ac.uk" part:
mailto=`whoami`@fmrib.ox.ac.uk
Hope this helps,
a.y
On Tue, 20 Nov 2012, Loi wrote:
> Hello FreeSurfer exper
Hi Surfers,
I was wondering if FreeSurfer v5.1.0 (CentOS 4 x86 (64b)) or V5.X will work
on Red Hat Enterprise Linux 6?
The reason I ask is that the supercomputer at Brigham Young University is
going through a major overhaul: changing the OS, adding more nodes, and
adding more storage.
I am just
I've had no problems with it.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Brain Apprentice
[bapprent...@gmail.com]
Sent: Tuesday, November 20, 2012 11:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject:
Dear Freesurfer experts,
I have a general question regarding data
analysis. Our group has collected data from patients with OA, some of them
received treatment on their left leg, some of them on their right leg. We would
like to flip the brain for the people t
Hi Helen, I would follow these steps
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
this describes the interhemispheric analysis assuming that you want to
study asymmetry. This is not quite your application, but I think it will
work well for it. In general, you don't want to simply left-right
re
Bo,
Doug asked me to chime in on your issue. Here are some points that you
(and others) will hopefully find useful.
(1) Inferences are two-step process. First, you create and estimate
the design matrix. Every column in the design matrix accounts can
account for some of the variance in the data. S
Yes, that -BPM should be +BPM, sorry about that. It will not change the
p-values if you multiply by 0.5 or not. It will change the size of the
contrast. Most people don't report this number, especially for an
F-test, so I would not worry about it.
doug
On 11/20/2012 09:17 AM, xiangbo_2010 wrote
Thanks Donald. Is this the standard way to do this? I had used 8 rows
instead of 4 with the difference being that 8 rows gives you an
opportunity to look for an effect in males OR females. If there is an
effect in both males and females but the effects go in opposite
directions, then the 4 row
On 11/19/2012 12:28 PM, angela.fav...@unipd.it wrote:
> Dear list,
> I am quite new in the use of freesurfer and I have two doubts.
>
> 1. I am studying the visual areas of the brain, but I do not know how to
> perform a vertex analysis within a ROI. I already know how to obtain
> thickness data
Hi all,
Back in January and October Bruce mentioned that he had under development some
scripts designed to utilize T2-SPACE images for better pial surface
reconstruction in the presence of dura -- I was just wondering if any of that
is ready for trial?
Thanks!
Warren
--
Warren Winter
Researc
It sounds like you need a conjunction to show that P4 > P1 AND P1 > C
Does that make sense? If so, then run the analysis as Donald suggests,
creating contrast matrices for the above contrasts. Then run mri_concat
--conjunct p1gtc/sig.mgh p4gtp1/sig.mgh --o conjunction.mgh
doug
On 11/19/2012 01:
Hi Wei, do you have both polar and eccentricity? It looks like you only
have polar.
doug
On 11/19/2012 01:39 PM, Zhou, Wei wrote:
> Please find the Xtmp.mat in the attachment.Thank you, Doug.
> Best
> Wei
>
> Can you send me the Xtmp.mat file?
> dloug
>
> On 11/16/2012 01:01 PM, Zhou, Wei wr
Hi Warren
yes, it will be part of the upcoming 5.2 release, hopefully in Dec. It
will use either a FLAIR or T2 (ideally T2-SPACE for either one)
cheers
Bruce
On Tue, 20
Nov 2012, Winter, Warren wrote:
> Hi all,
>
> Back in January and October Bruce mentioned that he had under development
> so
On Mon, Nov 19, 2012 at 12:36 PM, Mahinda Yogarajah wrote:
> Hi Donald and Doug,
>
> Thanks for advice. Can I be a little bit clearer as I suspect I need a little
> more guidance.
>
> When comparing controls (gp c) and whole patient group (gp p) I see
> interesting differences in area (DOSS mode
On Tue, Nov 20, 2012 at 12:56 PM, Douglas N Greve
wrote:
> Thanks Donald. Is this the standard way to do this? I had used 8 rows
> instead of 4 with the difference being that 8 rows gives you an opportunity
> to look for an effect in males OR females.
Yes. Having 8 rows would tell you if you have
The difference is that the columns are different. The "Max" in the first
table refers to the maximum statistic found in the ROI. The "Max" in the
2nd table is not actually a maximum. It is just the -log10(p) of the
cluster. This corresponds to the CWP value in the first table (eg,
cluster 4 has
Hi Longchuan, mris_fill create a volume with a different geometry than
orig.mgz (though it is in the same space). What do you want to do
exactly? Map the output of mris_fill into the DTI space? The transform
from the output of mris_fill to orig.mgz is easy to obtain:
tkregister2 --noedit --mo
Doug,
I received this question from a colleague, "Exactly which segmentation
file from "recon -all" is being used in the "bbregister" command?"
Thanks,
Donald
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/m
Hi Donald,
It does not use any of the segmentations. In fact, it does not use any
of the anatomical volumes. It only uses the surfaces.
doug
On 11/20/2012 03:19 PM, MCLAREN, Donald wrote:
> Doug,
>
> I received this question from a colleague, "Exactly which segmentation
> file from "recon -all"
Which surfaces does it use?
On Tue, Nov 20, 2012 at 2:21 PM, Douglas N Greve
wrote:
> Hi Donald,
> It does not use any of the segmentations. In fact, it does not use any
> of the anatomical volumes. It only uses the surfaces.
> doug
>
>
> On 11/20/2012 03:19 PM, MCLAREN, Donald wrote:
>> Doug,
>>
It uses the white, and it also uses the thickness measures.
On 11/20/2012 03:23 PM, MCLAREN, Donald wrote:
> Which surfaces does it use?
>
> On Tue, Nov 20, 2012 at 2:21 PM, Douglas N Greve
> wrote:
>> Hi Donald,
>> It does not use any of the segmentations. In fact, it does not use any
>> of the
Hello all,
I'm doing a training comparison (training type A vs. type B), and I
created thickness difference files (the rate files from the
long_mris_slopes command) for each subject. How can I conduct an FSGD
analysis with these thickness difference files?
I tried replacing all of the lh.thic
p.s. and may use the pial in the future
On Tue, 20 Nov 2012, Douglas N Greve
wrote:
> It uses the white, and it also uses the thickness measures.
>
> On 11/20/2012 03:23 PM, MCLAREN, Donald wrote:
>> Which surfaces does it use?
>>
>> On Tue, Nov 20, 2012 at 2:21 PM, Douglas N Greve
>> wrote:
>>
I don't think it should be as long as you are consistent. It might be
worth trying to track down this problem just so that you don't have to
mix versions.
doug
On 11/20/2012 03:37 PM, Berg, S.F. van den wrote:
> Hi Doug,
>
> Thanks for respons. We also install the dev version of freesurfer. We
Hi Bruce,
So would you recommend acquiring a T2 in addition to an (ME)MPRAGE/SPGR? i.e.
is it worth squeezing another acquisition into a protocol?
Chris
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bru
Yes, definitely. The t2-space flair is a big help
On Nov 20, 2012, at 5:40 PM, "Watson, Christopher"
wrote:
> Hi Bruce,
> So would you recommend acquiring a T2 in addition to an (ME)MPRAGE/SPGR? i.e.
> is it worth squeezing another acquisition into a protocol?
>
> Chris
> __
Hi, Doug
Thank you very much for the information. What I want to do is to use the white
and pial surfaces in the FreeSurfer space as the seeds for surface-based
tractography implemented in FSL. In order to do that, I need a transformation
between the white matter surface and diffusion MR data.
If you get an MPRAGE and T2-SPACE you can make myelin maps too.
FreeSurfer's final surface placement benefits a lot from high resolution
images (less than 1mm) and you can still get good SNR with when you use
32-channel coils.
Peace,
Matt.
On 11/20/12 4:41 PM, "Bruce Fischl" wrote:
>Yes, def
hi
matt: could you generate the myelin maps say from two flash scans at
different flip angles?
bruce: if one had a choice between an mprage + t2 flair and 2 flash scans
at 5/20 flip angles, what would be your recommendation?
cheers,
satra
On Tue, Nov 20, 2012 at 6:35 PM, Matt Glasser wrote:
If you make a T1 map you can use that to look at differences in myelin
content, but I don't know all of the ways to calculate T1 or if you could
get that from only two flip angles. Two images with roughly the same
contrast won't work for the ratio method. You need to have opposite
contrast.
Also
Hi Satra
the T1 maps accomplish much of what the ratio does - it gets rid of
receive bias effects. I'm not really sure which is better. They are about
the same amount of scan time.
The advantage of including the flair inversion pulse in the T2 space is
that it nulls fluid and lets intensitie
Hi Bruce,
Can you get good FLAIRs at 0.7mm isotropic?
The fluid thing makes sense for surface reconstruction, but I think it
would mess up myelin maps if someone also wanted to do that using the
ratio method. If the CSF is now dark and you divide the dark CSF in the
T1w with dark CSF in the T2w,
yes, that's probably true. The FLAIR we use is just a T2-SPACE scan with
an inversion pulse to put CSF at the null point, so if you can get T2-space
at .7 you should be able to get FLAIR (although you do burn some SNR with
the inversion)
On Tue, 20 Nov 2012, Matt Glasser wrote:
> Hi Bruce,
>
>
thanks matt and bruce. this is very helpful.
cheers,
satra
On Tue, Nov 20, 2012 at 7:53 PM, Bruce Fischl wrote:
> yes, that's probably true. The FLAIR we use is just a T2-SPACE scan with
> an inversion pulse to put CSF at the null point, so if you can get T2-space
> at .7 you should be able to
sure. Note that whichever you do it's absolutely critical to bandwidth
and readout match them so there is no differential distortion between the
contrast types
Bruce
On Tue, 20 Nov 2012, Satrajit Ghosh wrote:
thanks matt and bruce. this is very helpful.
cheers,
satra
On Tue, Nov 20, 2012 at
You can correct the readout distortion with a field map. The main
residual is just signal loss in the gradient echo image.
Peace,
Matt.
On 11/20/12 7:22 PM, "Bruce Fischl" wrote:
>sure. Note that whichever you do it's absolutely critical to bandwidth
>and readout match them so there is no dif
Hi Matt
I doubt you could accurately correct the 0.25mm distortions that would be
widespread, not to mention the extra interpolation. Much better to distortion
match the acquisitions
Bruce
On Nov 20, 2012, at 8:45 PM, Matt Glasser wrote:
> You can correct the readout distortion with a field
Hi Bruce,
How are you matching the BW for T2-SPACE vs. MPRAGE -- the former
typically has a BW around 700+ Hz/Px, while the latter is typically around
200 Hz/Px.
thanks,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of
We use Andre's multiecho mprage
On Nov 20, 2012, at 10:31 PM, Michael Harms wrote:
>
> Hi Bruce,
> How are you matching the BW for T2-SPACE vs. MPRAGE -- the former
> typically has a BW around 700+ Hz/Px, while the latter is typically around
> 200 Hz/Px.
>
> thanks,
> -MH
>
> --
> Michael
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