Hi Doug
I copied the new script into $FREESURFER_HOME/bin and made it executable, but
unfortunately it throws the following error to the Terminal:
axm676% mri_mergelabels
'nknown option: `-
Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
Best
Agoston
-Original Message-
From: freesur
Hi Doug,
I've done a surface-based analysis using qdec and want to mask my significance
maps before performing an FDR correction.
So I think I've figured out that I don't need to turn my mask label into a mgh
file - I think I can use my label to restrict the search space for the FDR
correction
Thank you Doug!
but i tried it in many cases but I've always received the same error
message...
Is there something else I can try?
Francesco
2014-08-07 0:46 GMT+02:00 Douglas N Greve :
> Try it with -notal-check
> doug
>
> On 08/06/2014 04:39 PM, Francesco Deleo wrote:
> > I all!
> >
> > I am a
Dear list-members,
I submitted a paper regarding cortical thickness in relation to body
fat distribution. The analysis was based on the mri_glmfit procedure
implemented in freesurfer 5.1. Version. Gender was defined as a
categorical or group factor and age, Body Mass Index, total surface
a
Hi guys!
Is there an easy way to get Brodmann Area stats to table like there is for aseg
and aparc stats?
Thanks!
Silas
PS. I looked the question up and it was answered in 2011 - I was just wondering
if you guys made an easy way around the problem since then :)
Dear Experts,
I have calculated distances with mris_pmake on the individual brain of a
subject. I would like to compute the distance between the corresponding points
on the mni brain (fsaverage). Is there a simple way to transform the distances?
Best pfannmoe
___
Hi Franesco
can you post an image of the scan you are trying to run through
recon-all? And give us some idea of what it is (resolution,
etc...)? Something is badly wrong if they are all failing. You can also
upload the orig.mgz of one of them and we will take a look if you want.
cheers
Bruce
Hi pfannmoe
I guess you could make a label of each of the endpoints, transform them
to fsaverage using mri_label2label and run mri_pmake on the transformed
points. A bit cumbersome, but it should work
cheers
Bruce
On Thu, 7 Aug 2014,
pfannmo...@uni-greifswald.de wrote:
> Dear Experts,
>
> I h
Try running
tcsh mri_mergelabels
On 08/07/2014 05:21 AM, Agoston Mihalik wrote:
> Hi Doug
>
> I copied the new script into $FREESURFER_HOME/bin and made it executable, but
> unfortunately it throws the following error to the Terminal:
> axm676% mri_mergelabels
> 'nknown option: `-
> Usage:
Yes, that can happen when there are very few active voxels.
On 08/07/2014 06:22 AM, Sarah Whittle wrote:
> Hi Doug,
>
> I've done a surface-based analysis using qdec and want to mask my
> significance maps before performing an FDR correction.
>
> So I think I've figured out that I don't need to
wow, I don't know if something from 2007 even applies now. What are you
trying to do exactly?
On 08/07/2014 05:08 AM, Katharina Zech wrote:
> Hi Doug,
>
> I am looking at freesurfer tutorial 2007-08-20, pages 152 - 155. I
> attached the certain pages to this email. Here the command within the
Have you looked in transforms/talairach_avi.log?
On 08/07/2014 07:57 AM, Francesco Deleo wrote:
> Thank you Doug!
> but i tried it in many cases but I've always received the same error
> message...
> Is there something else I can try?
>
> Francesco
>
>
> 2014-08-07 0:46 GMT+02:00 Douglas N Greve
I start tcsh automatically when opening the terminal window.
Anyway, typing 'tcsh mri_mergelabels' throws this error to the terminal:
mri_mergelabels: No such file or directory.
In addition, I also tried out the previous mri_mergelabels, it does not throw
the error:
'nknown option: `-
Usage: tcs
You have to be in the folder where mri_mergelabels is located to run the
tcsh command. Can you look at the first line in that file and see if it
matches the first line in the old one? Something might have gotten added
by the mail program
On 08/07/2014 11:25 AM, Agoston Mihalik wrote:
> I start
Hi all,
I could really use some help with this
I am trying to convert a group cluster to GIFTI (.gii) format. I just need
some help running mris_convert.
The example for a label to GIFTI is
mris_convert --label lh.V1.label V1 lh.white lh.V1.label.gii
I'm trying to figure out what is required h
Hi All,
In Tksurfer it is possible to view a scatter plot of a relationship
analyzed by mri_glmfit, by File -> Load Group Descriptor File
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization).
Is this also possible in Freeview? I tried Tools -> Plot FSGD Data, but
that does not
Hi Matt,
Overall, I've made the following changes that have led to some improvements:
- Remove excess dura from the brainmask that hasn't been stripped away
- Erasing voxels from wm in areas where white matter should be, even if the
voxels don't show up as what on the wm mask. (If you view the wm
No, I don't think so.
On 08/07/2014 12:07 PM, Righart, Ruthger wrote:
> Hi All,
>
> In Tksurfer it is possible to view a scatter plot of a relationship
> analyzed by mri_glmfit, by File -> Load Group Descriptor File
> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization).
>
> Is thi
There should already be ?h.BA.stats and ?h.BA.thresh.stats. Do those work?
On 08/07/2014 09:45 AM, Silas wrote:
> Hi guys!
>
> Is there an easy way to get Brodmann Area stats to table like there is
> for aseg and aparc stats?
>
> Thanks!
> Silas
>
> PS. I looked the question up and it was answer
Yes, it must have been something added by the mail program. I did not see any
differences manually (perhaps a new line?), but worked fine when I overwrote
the old file with the changes you made in the new one.
Thanks a lot.
Agoston
-Original Message-
From: freesurfer-boun...@nmr.mgh.ha
Does this not work for you?
cd $SUBJECTS_DIR/subject/label
mris_convert --label lh.V1.label V1 ../surf/lh.white lh.V1.label.gii
On 08/07/2014 12:05 PM, Tara Miskovich wrote:
> Hi all,
>
> I could really use some help with this
>
> I am trying to convert a group cluster to GIFTI (.gii) format.
Hi Doug thank you for the response. I just wasn't sure what was required
here. Specifically why we need to call on the white matter surface. And
what the second V1 would be for.
Thank you,
Tara
On Thu, Aug 7, 2014 at 11:05 AM, Tara Miskovich wrote:
> Hi all,
>
> I could really use some help wi
Hi Tara
the second "V1" is for looking up the name of the label in
FreeSurferColorLUT.txt. If you were converting to an annotation for example
we would embed the proper colors into it.
cheers
Bruce
On Thu, 7 Aug 2014, Tara Miskovich wrote:
Hi Doug thank you for the response. I just wasn't s
p.s. oh, and lh.white is so that we have a surface. The label is just a
(small) set of points on the surface, and doesn't contain other
information needed to generate a surface (like connectivity)
On Thu, 7 Aug
2014, Tara Miskovich wrote:
Hi Doug thank you for the response. I just wasn't sure
Hello,
I was just looking for some suggestions for the best way to manually edit
an image such as the one attached. As you can see, there is both white and
gray matter excluded from the pial surface on the medial aspect of the
right hemisphere. Is this best corrected by adding voxels to the
brainm
Dear Freesurfer Experts
We decided to reprocess our T1 and DTI data with the latest stream v.5.3 – we
would like to give TRACULA longitudinal stream a try. Before we go ahead and
reprocess our recons and DTI data with FS v 5.3 we were wondering if you plan
to release a new version of the TRACULA
Thank you for the help Bruce. I really appreciate it! So if we have a
custom made label to we need to somehow add it to the
FreeSurferColorLUT.txt.
mris_convert --label lh.cluster1.label lh.white lh.cluster1.label.gii
The above is not working for me. I keep getting no errors or anything, just
the
you are missing one argument (the name of the label). It should be:
mris_convert --label lh.cluster1.label NAME lh.white lh.cluster1.label.gii
On Thu, 7 Aug 2014,
Tara Miskovich wrote:
Thank you for the help Bruce. I really appreciate it! So if we have a custom
made label to we need to some
It worked! Thank you so much Bruce!
Tara
On Thu, Aug 7, 2014 at 1:59 PM, Bruce Fischl
wrote:
> you are missing one argument (the name of the label). It should be:
>
> mris_convert --label lh.cluster1.label NAME lh.white lh.cluster1.label.gii
>
>
>
> On Thu, 7 Aug 2014, Tara Miskovich wrote:
>
Thanks for your help. It is most appreciated.
I thought I would mention that these subjects are quite young (3-4 years
old). I've read a few posts that free surfer is not ideal for analyzing
young subjects, so I am wondering if this might be causing some errors.
Maybe there is a way to register t
Hi Matt
the young age is probably why you are having to do extra work -
incomplete myelination.
cheers
Bruce
On Thu, 7 Aug 2014, Walton, Matt wrote:
Thanks for your help. It is most appreciated.
I thought I would mention that these subjects are quite young (3-4 years
old). I've read a few p
Hi Christine
why don't you upload an example subject and we will see what we can do
cheers
Bruce
On
Thu, 7 Aug 2014, Christine Smith wrote:
Hello,
I am working with some scans that have poor signal, particularly at the
lateral aspects of the cortex (i.e., lateral temporal lobes). The measur
Hi Mike
I'm not sure - I think the insula was an additional label that Ron Killiany
added. I'll cc Ron to see if he has any insight. It certainly looks too
medial to me.
I would also check on the white surface just to make sure that it's not a
quirk of the inflation. If the aseg looks right
I asked a neuroanatomist and insula expert on my campus about this a while
back and this was his response:
"This is the region of the "limen insulae" that you will remember Dr.
Heimer referring to often in the brain dissection course. The insula is
defined as cortex which is covered by a lid of ot
Yeah, the insula label is present medially when viewed on the white
surface as well, so its not just a quirk of the inflation.
Not sure if I follow what you mean by the "aseg looking right". The
aparc+aseg.mgz is actually where the RA first noticed the issue, since she
noticed that some of the v
so that region really is cortex? It's not filled in ventricle or
anything?
On Thu, 7 Aug 2014, Harms, Michael wrote:
>
> Yeah, the insula label is present medially when viewed on the white
> surface as well, so its not just a quirk of the inflation.
>
> Not sure if I follow what you mean by the "
wow, I like that answer much more than "it's a bug"! Can we go with
Paul's explanation?
Bruce
On Thu, 7 Aug 2014, Paul Beach wrote:
I asked a neuroanatomist and insula expert on my campus about this a while
back and this was his response:
"This is the region of the "limen insulae" that you w
Yeah, it is labelled as "Cerebral-cortex" in the aseg.mgz, and is just
medial to the "Accumbens" label.
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of
I see. So maybe it is correct then?
On Thu, 7 Aug 2014, Harms, Michael
wrote:
>
> Yeah, it is labelled as "Cerebral-cortex" in the aseg.mgz, and is just
> medial to the "Accumbens" label.
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center
I'm not itching to re-process this data so I like that explanation as
well. I think my main concern is that that bit of insula label seems
somewhat arbitrary and inconsistent, in that some subjects have this bit
of medial tissue labelled as insula, whereas others don't. (Even within
the same sub
With a staff of 4700, Forschungszentrum Jülich – a member of the Helmholtz
Association – is one of the largest interdisciplinary research centres in
Europe.
Work with us on the grand challenges in the fields of health, energy &
environment, and information technology, as well as on the many and
With a staff of 4700, Forschungszentrum Jülich – a member of the Helmholtz
Association – is one of the largest interdisciplinary research centres in
Europe.
Work with us on the grand challenges in the fields of health, energy &
environment, and information technology, as well as on the many and
Hi Michael
the limen insula explanation sounds ok, even if it's extension on the medial
surface seem really large. would you have a snapshot to look on the volume to
which structure this label anatomically corresponds to ?
Also did you had a look to the results of the insula aparc with the 2009a
we have freesurfer set up on our big condor cluster, i asked that the
-hippo-subfields be added. they have it set up to run in 3 stages
autorecon1 autorecon2 autorecon3
they added the flag to all 3, i think it would only be needed on autorecon3,
but don't think it would
cause harm, just be ign
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Hi Doug et al,
After solving one issue with QDEC we have run into another. I previously
posted an error related to QDEC being unable to find subjects in the subjects
directory. That problem was solved by updating the /bin/sh location for ubuntu
(will post the solution that worked for us to th
Solution to the issue with QDEC being unable to find subjects in the subjects
directory with the following fix:
sudo mv /bin/sh /bin/sh.orig
sudo ln -s /bin/bash /bin/sh
Thanks,
Kate
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mg
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