Can you load another label, eg, lh.cortex.label? Also, I noticed that
there is a space between "label=" and "/data/..." in the command line
below. That space should not be there, so if it was there when you ran
the command try again without the space.
On 4/19/16 9:19 PM, Trisanna Sprung-Much w
Hi Trisanna
can you run:
head /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label
and send us the output?
cheers
Bruce
On Tue, 19
Apr 2016, Trisanna Sprung-Much wrote:
Hi Doug
I tried again in the terminal and got this:
trisanna@kaplan:~$ freeview -f
/data-01/trisanna/freesurfer
Hi Trisanna
your output is a .mgz file, which is *not* a label. Try loading it as an
overlay. The label format is different (ascii for one thing, and only part
of the surface for another).
cheers
Bruce
On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:
Hi Doug
I thought this was the case as
Hi Doug
I tried again in the terminal and got this:
*trisanna@kaplan:~$ freeview -f
/data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=
/data-01/trisanna/freesurfer/icbm-102/label/labeltest.label *
[0]PETSC ERROR:
[0]P
Hi Doug
I thought this was the case as well but when I try manually in Freeview and
select the correct label, Freeview crashes and gives this error in the
terminal:
trisanna@kaplan:~$ freeview
*** Error in `freeview.bin': double free or corruption (out):
0x29080920 ***
Abort (core dumped)
Hello
I intend to compute cortical thickness in retinotopic areas. However
retinotopic areas were delimited in BrainVoyager and the cortical thickness
maps with FreeSurfer.
There are any way to reconcile data from the two softawares?
--
Com os melhores cumprimentos,
Lília Jorge
__
I don't think that is the problem. The problem is that it cannot find
the file. Try giving it the whole path
On 04/19/2016 05:45 PM, Bruce Fischl wrote:
> Hi Trisanna
>
> if your output is .mgz it isn't a label file. Labels are stored in
> .label names and are text files. The .mgz is a scalar fi
Hi Trisanna
if your output is .mgz it isn't a label file. Labels are stored in .label
names and are text files. The .mgz is a scalar field over the surface (that
is, a vector with a single value at each surface location). In freeview you
can view it as:
freeview -f lh.inflated:overlay=surfac
Hi Doug
So I ran mri_vol2surf and generated my .mgz surface overlay using
--regheader as you suggested. I than ran mri_cor2label using that .mgz
file. This also completed successfully. *However, when I then try to open
the pial surface and the corresponding new label in freeview, it says it
cannot
Hi Bruce,
Thanks! I'll give it a whirl.
d
On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl
wrote:
> Hi Daniel
>
> the problems isn't that it it's ignoring the wm edits, it is that it starts
> the orig surface out there, but then retracts to the (same) visible
> gray/white boundary that it found in
Hi Daniel
the problems isn't that it it's ignoring the wm edits, it is that it starts
the orig surface out there, but then retracts to the (same) visible
gray/white boundary that it found in the first place. For this type of
lesion I think what you should do is also edit those voxels in the ase
can you send us the recon-all.log? I don't see an obvious reason why it
wouldn't have worked
On Tue, 19 Apr 2016, dgw wrote:
> Just to follow up, I have tried several different options with
> recon-all to get the white matter edits to stick on this participant,
> and it doesn't seem to be working
Just to follow up, I have tried several different options with
recon-all to get the white matter edits to stick on this participant,
and it doesn't seem to be working:
re-editing wm.mgz and running recon-all -autorecon2-wm
re-editing wm.mgz and running recon-all -make all
I can't seem to get any
many thanks - will give this a go!
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve
wrote:
> yes, but the surface overlay is in mgz (or nii.gz) format
>
> On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote:
> >
That means that there are no voxels in the final ROI in native
functional space. You should check your registration and also see how
big your original ROI is.
On 04/15/2016 11:32 PM, Julio Alberto González Torre wrote:
> I performed the preprocessing again with -per-run parameter.
> Everything
There is nothing obvious going wrong. If the exact same command
sometimes fails and sometimes works, then it may be a problem on your
system. In any event, without a reproducible error, I can't really debug it.
On 04/15/2016 08:31 PM, Elijah Mak wrote:
>
> On another note, I am running into a pu
On 04/15/2016 08:31 PM, Elijah Mak wrote:
> No, more like running the voxelwise comparisons only on voxels that
> have positive BP between 2 group. Is that possible?
I'm still not sure what you mean by "positive BP between 2 group". Do
you mean masking out voxels where either group is less tha
That was set assuming that the data have been slice-time corrected to
the middle of the TR.
On 04/19/2016 02:31 PM, Joseph Dien wrote:
> I’m taking a look at the effects of stimulus delay settings in one of
> my datasets so I was surprised to notice that the default setting
> of mkanalysis-sess
yes, but the surface overlay is in mgz (or nii.gz) format
On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote:
> Hi Doug
>
> below is the email I had written last Friday. I thought it got lost in
> the mix. I was told by Bruce to use identity.nofile as the
> transformation since my labels and T1s
sorry for the confusion. Some of our tools use identity.nofile, but these
use --regheader
cheers
Bruce
On Tue, 19 Apr 2016, Trisanna
Sprung-Much wrote:
Hi Doug
below is the email I had written last Friday. I thought it got lost in the
mix. I was told by Bruce to use identity.nofile as the
Hi Doug
below is the email I had written last Friday. I thought it got lost in the
mix. I was told by Bruce to use identity.nofile as the transformation since
my labels and T1s are already in the same space and I just want to resample
my labels to the surfaces.
*I will try, as you suggest, --regh
Yes!
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: "Patrick Sezen"
To: "Freesurfer support list"
Sent: Monday, April 18, 2016 7:20:46 PM
Subject: [Frees
I’m taking a look at the effects of stimulus delay settings in one of my
datasets so I was surprised to notice that the default setting of
mkanalysis-sess is a delay of -TR/2 seconds. What is the reasoning for this?
If, as I expect, it was just empirically found that it worked better than
wit
I'm not sure what identity.nofile is or what you are trying to do (no
previous info in the email). If whatever you are trying to map to the
surface is already in anatomical space (so no registration necessary),
then you can use --regheader with mri_vol2surf. mri_cor2label will take
a volume for
are you sure the label file is really a label file? Does the same thing
happen if you specify -l labelfile on the command line?
On 04/18/2016 05:08 PM, DeCross, Stephanie N. wrote:
> I can open the nii.gz output of the first step (vol2vol) just fine. But the
> .label output of the second step (c
Hi All!
Could someone please tell me how to run mri_vol2surf using identity.nofile
as the transformation? I cannot find any documentation on identity.nofile
Additionally, if my next step is to use the output of mri_vol2surf in
mri_cor2label, which takes surface overlays OR volumes, what format sh
Can you run
/mkbrainmask-sess//-debug -s FS_T1_501 //-fsd bold/ |& tee dng.log
and send me dng.log ?
doug
On 04/18/2016 04:51 PM, Mcnorgan, Christopher wrote:
> du -h /tmp/ shows 256GB available, so that doesn’t seem to be it. Is
> the “not found” error telling me that a binary is not found,
Hi Mihaela
adolescent girls probably have thicker cortex than older kids/adults. One
thing to watch our for is dura/tentorium. Particularly when the cortex is
thick it can be adjacent to cortical gray matter and difficult/impossible
to avoid including in the cortical ribbon unless you have som
Dear Freesurfers,
We noticed that some subjects in our study have the average cortical
thickness values in entorhinal and temporal pole above 4 mm. They are
adolescent girls so they're pretty young but we wonder if these values are
accurate. Visually, their segmentations seem good.
In an older em
OK. I will do it.
Xiaomin
Date: Tue, 19 Apr 2016 10:56:15 -0400
From: fis...@nmr.mgh.harvard.edu
To: yu...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu; macar...@libero.it
Subject: Re: [Freesurfer] temporal lobe pial surface problem
then you need to put some control points in the white matte
One of the tasks we use has three runs, and so each run has a specific B0 map.
We're wondering how we can concatenate the three runs back together again for
the Group analysis, since FSFAST is technically now considering each run to be
a separate "task."
-Original Message-
From: freesu
then you need to put some control points in the white matter. 70 is way
too low
On Tue, 19 Apr 2016, Xiaomin Yue wrote:
The white matter in the anterior temporal lobe is around 70, the gray matter
is about 30. The number is read from brain.finalsurfs.mgz.
Xiaomin
> Date: Tue, 19 Apr 2016 09:2
The white matter in the anterior temporal lobe is around 70, the gray matter is
about 30. The number is read from brain.finalsurfs.mgz.
Xiaomin
> Date: Tue, 19 Apr 2016 09:29:50 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> CC: macar...@libero.it; yu...@hotmail.
Hi Bruce,
the data was uploaded to the ftp site. The file name is xyueSubj.mgz.
thanks,Xiaomin
From: fis...@nmr.mgh.harvard.edu
Date: Mon, 18 Apr 2016 22:58:30 -0400
To: freesurfer@nmr.mgh.harvard.edu
CC: macar...@libero.it
Subject: Re: [Freesurfer] temporal lobe pial surface problem
It's tough
Dear FreeSurfer users,
I am a PhD student from Birkbeck University and I am trying to segment some
structural images of infants data.
After the classical segmentation done with the ‘-recon all’ function, I am
stuck with two issues:
1. How can I add the CSF, the skull and the scalp in my model?
yes, you can do that for both mris_make_surfaces and mri_segment, but
that will only help if you've removed the majority of the bias field. Is
anterior temporal white matter near 110? If so, what is the gray matter
at?
On Tue, 19 Apr 2016, Falk Lüsebrink wrote:
Hi Xiaomin,
currently I don't h
Hi Nasos
tkmedit has been deprecated for a few years. Can you try freeview?
cheers
Bruce
On Tue,
19 Apr 2016, Nasos Petridis wrote:
> Hello,
>
> Recently, I started using freesurfer on a Ubuntu system. I've noticed
> two issues, when using tkmedit, for example:
>
> tkmedit subj_name norm.mgz
Hello FS community,
I have made some custom labels based on retinotopy data and I wish to
export these as SPM ROIs so that I can use some specific tools.
I grouped the labels into an annotation file and I used mri_label2vol to
convert it into nifti, I then imported it into matlab and I get a volum
Hi Xiaomin,
currently I don't have access to my notes, however, if I remember correctly,
you can specify thresholds in mris_make_surfaces for consideration in the
surface placement. This obviously works well only if the contrast between
WM/GM/CSF is high enough.
If you are interested and nobod
Hello,
Recently, I started using freesurfer on a Ubuntu system. I've noticed
two issues, when using tkmedit, for example:
tkmedit subj_name norm.mgz -segmentation aparc.a2009s+aseg.mgz
(i) When I try to save TIFF (Tools > Save TIFF), a TIFF file is
created, and it can be opened in any image vi
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