Dear all,
I am currently using freesurfer 6.0 (development version) to run hippocampal
subfields segmentation and encountered a 'mkdir' error, which is attached
below. Our troubleshooting found that some scripts in the
...freesurfer/dev/sys/bin directory with things like:
if(-e /scratch) se
Hi Amy
looks like you processed them on different machines that use different
version of freesurfer. One is centos4 with FS 5.0 and one is centos 6 with
5.3. You definitely don't want to mix these.
Bruce
On Thu, 3 Dec 2015, Amy L wrote:
> Hi all,
>
> I'm sorry if this is a silly question, b
Dear All,
I was wondering whether there is a simple way to pass T1 segmentations I
have from another software to Freesurfer, in order to do the remaining
recon-all steps?
Thank you in advance,
James
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thanks Fengji
sounds like something we should fix.
cheers
Bruce
On Thu, 3 Dec 2015, Fengji Geng wrote:
Dear all,
I am currently using freesurfer 6.0 (development version) to run hippocampal
subfields segmentation
and encountered a 'mkdir' error, which is attached below. Our troubleshooting
Hi James
what kind of segmentation? If gray/white you could replace the wm.mgz and
go from there, otherwise you would replace the aseg.mgz. In either case,
make sure you use our conventions (the FreeSurferColorLUT.txt for the
aseg, or set every wm voxel to the brain.mgz intensity if it is in t
Thank you!
I run the recon-all on the MNI brain and now the first step, label2label,
produced a label which is perfectly mapped on the surface of the MNI
template.
I tried to run the second step, mapping the new label to the volume, but I
still got the shift downward.
mri_label2vol --label lh.V1d
Hi Ajay
I have found the problem that messed up the surfaces and fixed it. We can
get you an updated mris_fix_topology that will not generate corrupted
surfaces. However, the underlying problem is huge topological defects
caused by low gray/white contrast in this data. For example in the left
Use --regheader /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz
instead of --identity
On 12/3/15 8:46 AM, Francesca Strappini wrote:
Thank you!
I run the recon-all on the MNI brain and now the first step,
label2label, produced a label which is perfectly mapped on the surface
of the MNI te
Thanks!
I run this command:
mri_label2vol --label lh.V1dorsalLG_MNI.label --temp
/usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --regheader
/usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
lh.V1dorsalLG_MNI.nii.gz
but unfortunately, it gave me the same big downward shift (I checked it
wi
Hi Bruce,
If it isn't too much trouble could you send the program update? I have
another set of images (2009c template) which I can contrast enhance for
GM/WM regions so I can try this set of images to process along with the
images I sent you.
Thanks,
Ajay
On Thursday, December 3, 2015, Bruce
Hi Francesca
your output is a volume not an ROI, so you need to load it as a volume in
freeview to check it
cheers
Bruce
On Thu, 3 Dec 2015, Francesca Strappini wrote:
Thanks!
I run this command:
mri_label2vol --label lh.V1dorsalLG_MNI.label --temp
/usr/share/fsl/data/standard/MNI152_T1_2m
sure Zeke can get it to you if you tell himn your hardware/software env,
but as I said if you have defects that are that big they are unlikelly to
be corrected to produce geometrically accurate surfaces.
cheers
Bruce
On Thu, 3 Dec 2015,
Ajay Kurani wrote:
Hi Bruce, If it isn't too much tr
oops, gave you the wrong option, it should be
--regheader $SUBJECTS_DIR/mni152-recon/mri/orig.mgz
On 12/03/2015 10:22 AM, Francesca Strappini wrote:
> Thanks!
>
> I run this command:
>
> mri_label2vol --label lh.V1dorsalLG_MNI.label --temp
> /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --
Dear FreeSurfer experts,
My question is in the title. I'm working on Alzheimer case where most of
the cases have large ventricles. Is it better in general use to apply
-bigventricles option on all subjects (for homogeneous calculus or
something like that...) or to distinct subtle cases of patients
Dear all,
I'd be very grateful for a bit of help with the following problem.
I'm running FreeSurfer 6.0 (I read a suggestion that there had been some
compatibility issues running the current stable FS release with newer versions
of openSUSE) on a cluster. However, nu_correct seems to be hitting
Hi Matthie
do you find that it doesn't work well without bigventricles? You just
want to be sure that you process your data in the same way so there is no
bias in the results. We have found that most early AD cases work fine
without needing special flags. It's more for late stage AD or hydrocep
Dear FreeSurfer Experts,
I'm trying to follow the steps described in the univeriate LME for longitudinal
data (https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels).
Could you explain how you did this step:
"The qdec.table.dat file was then used to collect volumetric data for all
Dear FreeSurfer Support team and Community
I am wondering if someone can give me an explanation of the difference between
g-w.pct and g:w ratio (as calculated by; fscalc lh.gm.mgh div lh.wm.mgh -o
lh.ratio.mgh)
Will both these measures essentially measure the relationship between grey and
whit
Hello,
I want to calculate the Grey matter, white matter and CSF volumes.
The total gray matter volume is already in the ASEG file.
Then
I add up following volumes for ventricular CSF: Left Lateral Ventricle +
Left Inferior Lateral Ventricle + Right lateral Ventricle + Right Inf
Lateral Ventr
g-w.pct is computed as
pct = 100*(w-g)/((w+g)/2)
in the pctsurfcon script
On 12/03/2015 12:18 PM, Andrews, Derek wrote:
> Dear FreeSurfer Support team and Community
>
> I am wondering if someone can give me an explanation of the difference
> between g-w.pct and g:w ratio (as calculated by; fsc
looks mostly right. For CSF there is a "CSF" label that should be
included. For WM, you may or may not want to include brainstem.
On 12/03/2015 12:20 PM, Jinsong Tang wrote:
> Hello,
>
> I want to calculate the Grey matter, white matter and CSF volumes.
>
> The total gray matter volume is alrea
Thank you Doug and Bruce now everything works and the region is
perfectly aligned!
Best
Francesca
2015-12-03 18:03 GMT+02:00 Douglas N Greve :
> oops, gave you the wrong option, it should be
>
> --regheader $SUBJECTS_DIR/mni152-recon/mri/orig.mgz
>
>
>
> On 12/03/2015 10:22 AM, Francesca Strappi
glad it worked out
Bruce
On Thu, 3 Dec 2015, Francesca Strappini wrote:
Thank you Doug and Bruce now everything works and the region is perfectly
aligned!
Best
Francesca
2015-12-03 18:03 GMT+02:00 Douglas N Greve :
oops, gave you the wrong option, it should be
--regheader $SUBJEC
Hello Doug,
Thank you so much for your help.
Best,
Jinsong
On Fri, Dec 4, 2015 at 1:28 AM, Douglas N Greve
wrote:
> looks mostly right. For CSF there is a "CSF" label that should be
> included. For WM, you may or may not want to include brainstem.
>
> On 12/03/2015 12:20 PM, Jinsong Tang wrot
Dear Experts,
I tried to run the following to get the segmentation volumes but encountered
the errors below... How can I get the volumes of the insula and thalamus and
also the inferior prefrontal cortex please?
[spjwker@nanlnx2 FSL]1% asegstats2table --subjects PAC01... PAC70 --segno 9 48
19
Hello Everyone,
I've run the Freesurfer 6.0 and created the sub-brainstem structures (e.g.,
pons, midbrain, etc.). I would like to convert the
brainstemSsLabels.v10.mgz results to a .nii file. However, unlike when I
use mri_convert for aseg.mgz, I only get an image of the brainstem itself
as a sin
Hi there,
Would it be possible to use pctsurfcon to calculate the ratio of white matter
signal intensity between left and right hemispheres?
Thank you
Sabrina
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see if this tool is what you need. It allows you to map to the homolgous
vertex on the contralateral hemisphere
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 12/03/2015 05:25 PM, Sabrina Yu wrote:
>
> Hi there,
>
>
> Would it be possible to use pctsurfcon to calculate the ratio of white
> m
Hi Doug,
Thanks for the quick reply. Is Xhemi only for measuring volumes for both
hemispheres?
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html
You mentioned editing pctsurfcon to set white matter and gray matter in this
email thread here. Can this be used to measure
I guess I'm not sure what you are trying to do. Can you elaborate?
On 12/3/15 6:24 PM, Sabrina Yu wrote:
> Hi Doug,
>
> Thanks for the quick reply. Is Xhemi only for measuring volumes for both
> hemispheres?
>
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html
> You menti
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