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Hello Z K,
Were you able to fix the bug?
Best,
Paul
On Fri, Mar 3, 2017 at 12:14 PM, Z K wrote:
> Im looking into this now, but I think their might be a bug when using
> the -parallel flag on Mac platforms. I should have a fix shortly. I will
> let you know.
>
> On 03/03/2017 12:10 PM, miracle o
Hello Paul,
I've been trying to replicate it the issue on my Mac without any success. But I
do have what might be a potential solution ide like you to try. Could you please
source freesurfer, then run the following command.
$> sudo -E fs_update
(This will update a freesurfer file on your machi
Hello Z K,
Thank you. I will do it later and update you.
Best,
Paul
On Mon, Mar 6, 2017 at 9:07 AM, Z K wrote:
> Hello Paul,
>
> I've been trying to replicate it the issue on my Mac without any success.
> But I do have what might be a potential solution ide like you to try. Could
> you please
>
Hi, just following up on this question to see if there were any suggestions
for how to best complete seed to seed RS analysis in FreeSurfer.
Thanks!
Corinna
On Thu, Mar 2, 2017 at 12:09 PM, Corinna Bauer wrote:
> Hi all,
>
> I was just wondering if it was possible to do seed to seed resting st
yes, I have the /Applications/freesurfer/lib/gcc directory.(actually, ‘had’ as
I reinstalled 5.3) I installed 6.0 on top of 5.3 without uninstalling 5.3
first, so it was not a clean install. I will try a clean re-install with the
tar file with the steps you suggest. Thanks.
Date: Sun, 5 Mar
Try fcseedcor. Run with -help to get docs
On 03/06/2017 09:52 AM, Corinna Bauer wrote:
> Hi, just following up on this question to see if there were any
> suggestions for how to best complete seed to seed RS analysis in
> FreeSurfer.
>
> Thanks!
>
> Corinna
>
> On Thu, Mar 2, 2017 at 12:09 PM,
Hello everyone,
I am trying to extract clusters showing significant correlation between LGI
and a behavioral measure. I am able to extract PCC and sig.mgh but at the
last step when I try to run simulation command to view corrected results
and I run:
mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cac
Hi all,
i am having problem with recon-all function. Whenever i call that function
from a terminal with my high resolution Nifti file ("MPRAGE.nii") it aborts
with an error: "nifti1Read(): unsupported slice Timing pattern in ..."path
to file".
Can some one please help? I need to generate Labels
Hello,
We have a PET dataset where we expect to see pathogenic changes in the
meninges. We'd like to extract the meningeal signal in subject space, and were
hoping to come up with an automated strategy to create meningeal ROIs,
containing no brain or scalp.
So my question is: can you suggest an
HI Dhaval
can you send us the full command line, screen output and recon-all.log?
Also: what does mri_info tell you when run on that file?
cheers
Bruce
On Mon, 6 Mar 2017,
Dhaval Shah wrote:
Hi all,
i am having problem with recon-all function. Whenever i call that function from
a termina
I cannot replicate the missing last label. Can you upload the relevant
data so I can take a look? Using the --l instead should work too. For
your other problem, I would probably run mri_label2label with the
--outstat option to create an overlay of the statistic, then create a
segmentation base
yes, that looks right to me
On 03/03/2017 11:12 AM, Gabor Perlaki wrote:
> Dear all,
>
> We've segmented some brain regions on orig.mgz using another program
> (this custom segmentation is called our_segmentation.mgz). Is it
> possible to transform this segmentation into the original native
>
When you run isxconcat-sess, specify all subjects, then just follow the
examples here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
for two groups
On 03/03/2017 01:29 PM, Bailin, Emma wrote:
>
> Hello,
>
> I’m currently doing a resting state functional connectivity analysis.
> I have
what is your command line? Also, please send the entire terminal output
On 03/03/2017 01:52 PM, Peled, Noam wrote:
> Hey all,
> I'm running preproc-sess, and getting the following error:
> ...
> Reading in mov rest/tmp.bbregister.28405/template.nii
> Reading in ref .../mri/brainmask.mgz
> Reading
What is that input file? It looks like a mask of some part of the brain
On 03/03/2017 06:14 PM, Redwan Maatoug wrote:
> Hi Douglas,
>
> Thank you for your help,
>
> So I still can't convert my volumetric file to a surface file and I
> don't know what I am doing wrong.
>
> My nifti volumetric fil
I think that is a good method (better than the method I just sent).
On 03/03/2017 07:12 PM, Antonin Skoch wrote:
> Dear experts,
>
> concerning my question regarding thresholding method of entorhinal and
> perirhinal labels, I looked at
>
> Augustinack JC et al, Predicting the location of human
This is a problem with using LGI in that it is already extremely smooth
that the smoothness exceeds the limit of the look up table that we
supply. I recommend that you not use a gaussian-based correction for
LGI. Instead, use permutation (see mri_glmfit-sim --help).
On 03/06/2017 01:36 PM, M
I think you might be doing something wrong during preprocessing. Can you
send your command lines?
On 03/06/2017 12:11 PM, Martin Juneja wrote:
> Hello experts,
>
> I am trying to correlate cortical surface area measure with behavioral
> measures using instructions from here:
> https://surfer.n
You could remove the brain (as found in aseg.mgz) from the
brainmask.mgz. This will leave some dura. It is not an elegant or
accurate solution
On 03/06/2017 02:24 PM, Albrecht, Daniel S. wrote:
> Hello,
>
> We have a PET dataset where we expect to see pathogenic changes in the
> meninges. We'd
Hi Bruce,
Thank you for your prompt e-mail. I have attached here the recon-all.log.
The mri_info command gives me the same error message as i mentioned before.
Thank you for your help.
On Mon, Mar 6, 2017 at 2:54 PM, Bruce Fischl
wrote:
> HI Dhaval
>
> can you send us the full command line, sc
I think this problem is fixed in version 6. You can download version 6
and use the v6 mri_convert to convert the file. The converted file
should be readable by v5 (I think).
On 03/06/2017 04:14 PM, Dhaval Shah wrote:
> Hi Bruce,
>
> Thank you for your prompt e-mail. I have attached here the rec
Hi Dr. Greve,
I am using following commands:
recon-all -all -subject S01 -i T1w_S01.nii -qcache
mris_preproc --fsgd MEQ.fsgd --target fsaverage --hemi lh --meas area --out
lh.MEQ_area.mgh
mri_surf2surf --hemi lh --s fsaverage --sval lh.MEQ_area.mgh --fwhm 10
--cortex --tval lh.MEQ_area.10.mgh
mri
Hmm, something is going wrong because medial wall areas should have been
masked out. Take a look at the medial wall area in lh.MEQ_area.10.mgh
file with something like
tksurferfv fsaverage lh inflated -aparc -ov lh.MEQ_area.10.mgh -fminmax
.001 .1
scroll through the subjects to see if you see
Dear Daniel,
For the "outer" boundary of your ROI, I would try the betsurf from FSL for the
inner skull surface estimation. This should be more precise than using
brainmask.mgz.
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET/UserGuide
Antonin
You could remove the brain (as found in aseg.mgz) from
This has to do with the labeling around the medial wall, which is
asymmetric in bert (and probably other subjects). In bert's left side,
the medial OFC wraps around the lateral OFC to meet the insula. On the
right side, the insula wraps around to reach up to the the MOFC. The
wmparc is generate
Hi Dr. Greve,
I tried to run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3
permcsd --sim-sign abs --cwpvalthresh .05
It gives error that ERROR: design matrix is not orthogonal, cannot be used
with permutation.
But when I run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 100
If you don't have an orthogonal design, then you can't use
mri_glmfit-sim. I think you can use PALM:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM
I have not tried it yet.
Anderson, can you use PALM with surfaces?
On 03/06/2017 05:23 PM, Martin Juneja wrote:
> Hi Dr. Greve,
>
> I tried to r
That red dot is fine. I bigger question is why you are using a
development version from July 2016? The development versions are often
unstable.
On 03/06/2017 05:27 PM, Martin Juneja wrote:
> Hi Dr. Greve,
>
> I looked at the medial wall area in lh.MEQ_area.10.mgh and noticed a
> small cluster
Dear Doug,
I am sorry, the problem with missing perirhinal label in .annot was due to typo
in my .ctab file (also seen in my previous mail). Now it works OK.
I have already solved my problem by creating annotation just of entorhinal and
perirhinal labels (like I wrote in my post here:
http://w
Dear Martin,
I think yes, you can use PALM with FreeSurfer surfaces, see my conversation
with Anderson on FSL list:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1604&L=FSL&D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=239088
but beware not to forget to include average the vertex ar
Could i get a solution for the earlier version than 6.0? I can't use the
new one unfortunately.
On Mon, Mar 6, 2017 at 4:19 PM, Douglas N Greve
wrote:
> I think this problem is fixed in version 6. You can download version 6
> and use the v6 mri_convert to convert the file. The converted file
> s
Hi Martin,
Thank you for your response, that is much clearer.
I am also a little confused about how to specify the exact contrasts we wish to
test and was hoping to get some advice. My design matrix X includes the
following columns:
1. Intercept
2. Years from baseline
3. Age at baseline
4. Gro
why not? YOu don't need all of 6 - just mri_convert. You can rename it
mri_convert.v6 if you want so you don't overwrite the older one
On Mon, 6
Mar 2017, Dhaval Shah wrote:
Could i get a solution for the earlier version than 6.0? I can't use the new
one unfortunately.
On Mon, Mar 6, 2017 at
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