I can't replicate this under linux. Zeke, do we have a virtual box that
we can run this on?
On 11/18/15 2:40 PM, Lawrence Ryner wrote:
Hi,
I'm a new FS user just trying to run through the tutorials. In the
Group Analysis tutorial, doing the multiple comparisons correction,
when I run mri_flm
Can you try mri_coreg instead of fsl?
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
On 11/19/15 5:25 PM, Caspar M. Schwiedrzik wrote:
Hi!
I am trying to align a mean EPI volume and a Bruker magnitude map from
a fieldmap measurement using tkregister2, fsl_rigid_regist
Hi!
I am trying to align a mean EPI volume and a Bruker magnitude map from a
fieldmap measurement using tkregister2, fsl_rigid_register and mri_vol2vol.
Unfortunately, it seems that somewhere, most likely during
fsl_rigid_register, the image orientation get scrambled, and the output has
the wrong o
Try copying the following linux binaries to your $FREESURFER_HOME/bin
folder (make a back up of mri_convert first)
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/dcmdjpeg.fs
ftp://surfer.nmr.mgh.harvard.ed
I'm not sure what you mean. do you have a behavioral value (eg, reaction
time) for each stimulus presentation? If so, you'll want to do a
parametric modulation
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation
On 11/19/15 5:13 PM, Joseph Andreano wrote:
> Hi Freesurfer expert
Hi Freesurfer experts,
I'd like to generate a correlation map showing the strength of correlation
between a behavioral value and the value of a functional contrast between
two conditions.
>From previous cortical thickness analysis, I know that if I use the
-notask tag on mkanalysis, I can use a f
Hey Freesurfer experts,
I had a quick question. Is there any way to modify QDEC in such a way to have
other options other than 0, 5, 10, 15, 20 etc, for smoothing? I know I would
also have to -qcache the data for the desired smoothing too but I was wondering
if anyone had done this before?
Any
Hi FreeSurfer list,
Lately, we have noticed that a bunch of DICOMs obtained on our 3T Tim Trio (at
McLean Hospital) are getting labeled with TransferSyntax IDs that are causing
DICOM unpacking scripts (like mri_convert) to fail.
In particular, the offending TransferSyntaxIDs appear to be
"1.
Hi Guido
someone else will have to point you at the QA tools as I haven't used them
myself
cheers
Bruce
On Thu, 19 Nov 2015,
Guido Orlando Pascariello wrote:
Bruce
I understand your point. I think I could try to do some test in order to
know if the results are affected too much. I'm goi
Bruce
I understand your point. I think I could try to do some test in order to
know if the results are affected too much. I'm going to tell you my
conclusion once I get it.
Can you tell me what are these tools you mentioned?
Guido
2015-11-19 15:56 GMT-03:00 Bruce Fischl :
> Hi Guido
>
> all au
Hi Guido
all automated algorithms have failure modes, so you are always advised to
look at the results to make sure that they aren't artifactual. We have
some QA tools that makes this process less onerous if you want. You can
certainly run in an automated fashion, but then you won't know for s
The problem is that the registration is bad. You can get a measure of
the quality of the registration with
tkregister-sess -s hc016 -per-run -bbr-sum bbrcost.dat -fsd msit -b0dc
The cost for this subject was 0.9859, which is pretty bad. The values
for the other subjects are below. You can see
Bruce, thanks for your reply
My goal about cortical morphometry is measure the mean thickness of some
areas.
Do you know if these pieces can mess up the pial surface enough to affect
the mean thickness?
I ask you about it because I am trying to avoid operator control on the
process, I want to make
Can you tar up the glmdir and send it to me on our file drop?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 11/18/15 2:40 PM, Lawrence Ryner wrote:
Hi,
I'm a new FS user just trying to run through the tutorials. In the
Group Analysis tutorial, doing the multiple comparisons correction,
when
yes, that is correct.
On 11/19/15 11:07 AM, Pradeep wrote:
Thank you for the response Doug!
The PET images I have are static images. Six * 5 min frames which I
have summed together after realigning.
mri_gtmpvc --i summed.nii --psf 4 --auto-mask PSF+2 0.01 --seg
gtmseg.mgz --reg output.lta
On 11/19/15 9:53 AM, Danielle Miller wrote:
> Hi Doug,
>
> Thanks for your response. So you are saying to rename a correctly
> identified condition as the empty condition? That is if I have a
> correct trial, rename it to an incorrect trial? Won't this pull onset
> times from the wrong cond
Thank you for the response Doug!
The PET images I have are static images. Six * 5 min frames which I have
summed together after realigning.
mri_gtmpvc --i summed.nii --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz
--reg output.lta --default-seg-merge --mgx 0.01 --o gtmpvc.output
This command ha
yes, that's pretty much it. Alternatively we could just give you all the
current BA labels and the command lines need to run to map them from
fsaverage to your subjects
On Thu, 19 Nov 2015,
BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote:
Dear Bruce,
Thank you, I will try to do that, but I am
Dear Bruce,
Thank you, I will try to do that, but I am not so clear about it. I should
install the 6.0beta version of FS, but keep the one I have currently (v
1.379.2.73)? Then I should run with the 6.0beta version recon-all -balabels -i
/path/to/file -s subjid; and then the complete recon-al
that means the FS version you have didn't have those labels. We can get
you the entire set of BA labels, but you will need a new version of
recon-all. Maybe your best bet is to insteall 6.0 beta and just run the
-balabels target from it?
On Thu, 19 Nov 2015, BAUTISTA-PERPINYA
Maximilia (ETU V
Dear Bruce,
# ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label
ls: Kein Treffer.
(meaning: no match)
# ls /usr/local/freesurfer/subjects/fsaverage
ls: Zugriff auf /usr/local/freesurfer/subjects/fsaverage nicht möglich: Zu
viele Ebenen aus symbolischen Links
(meaning: access to /us
Can you run:
ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label
and report the results?
cheers
Bruce
On Thu, 19
Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE)
wrote:
Dear all,
I get the same error when running any subject. I think it may be related to the
step concerning: fs
Hi Guido
bits of dura or skull that are left by the skull stripping don't matter
*unless* they mess up the surfaces in the vicinity (e.g. by being included
in the pial surface or creating topological defects that are incorrectly
fixed).
cheers
Bruce
On Thu, 19 Nov 2015, Guido Orlando Pasca
Dear FreeSurfer Users,
I was trying to segment hippocampal subfields using FreeSurfer 6 with data that
have already undergone the FreeSurfer 5 pipeline recon-all -all.
According to the usage described on the webpage of HippocampalSubfields
(http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSub
Hi Experts
I'm using Freesurfer to quantify some subcortical volumes and cortical
areas.
I have been preprocessing my data using 'recon-all autorecon1'
I have a question About Skullstripping. It is leaving a little bit of dura
behind the head. I found '-gcut' which is useful to solve it but it ha
Dear freesurfer users,
I run the command *'recon-all -lgi' *for my participants and for two of
them I get the following error message:
... remeasuring lGI value for vertex iV = 39301. It may take a few minutes.
WARNING -- Problem for vertex iV = 39301, lGI value is aberrantly high
(lGI=44.297
Dear Tracula users,
I reconstructed uncinate fasciculus using the latest version of Freesurfer
and Tracula. However, there seems to be a problem with produced stats files
in dpath folder
. I have -nan values for the center_avg variables in the file
"pathstats.overall.txt"
and there is no ent
Dear All,
I have completed recon-all on my dataset of controls and patients. My patients
have hippocampal/MTL atrophy and I would like to conduct multiple comparisons
on the data to ensure that the atrophy is indeed focal in each patient and if
not, identify where else atrophy is occurring in t
Hi,
I'm unable to initiate tksurfer. Can anyone tell me why this happens?
[10:57 lmr@dmed4870 lmr] > tksurfer fsaverage lh inflated
subject is fsaverage
hemiis lh
surface is inflated
surfer: current subjects dir: /home/lmr/subjects
surfer: not in "scripts" dir ==> using cwd for session root
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