master.ms...@gmail.com
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We have already skull stripped and white matter segmented volume ( used lesion
explorer) . Hence, I want to replace freesurfer 's generated outputs for this
steps ( brainmask.mgz for skull strip and wm.seg.mgz (not wm.mgz ) for white
matter) with ours. I know recon-all -all performs all 31 ste
Hi Paul
can we take a step back. What are you trying to achieve by avoiding these
steps?
cheers
Bruce
On Fri, 4 Nov 2016, miracoo...@gmail.com wrote:
Thanks Bruce. Another question, since " -no segmentation " flag skips the
white matter segmentation step of recon-all. Can I also use the s
Thanks Bruce. Another question, since " -no segmentation " flag skips the white
matter segmentation step of recon-all. Can I also use the same logic as the
"-noskullstrip" flag to replace the wm.seg.mgz file? That's, run " recon-all
-autorecon1 -autorecon2 -nosegmentation -s subjid ". Then copy/
Thank you! I uploaded the subject which is labeled as
SAIS_138_midline_deviation.tar.gz.
On Nov 3, 2016, at 4:46 PM, Bruce Fischl
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Jackie
that's surprising. If you upload the subject we can take a look. You could also
try relabeling the aseg (i.e.
Thank you very much Doug!
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Friday, November 4, 2016 12:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc
projfra
projfrac = -2 appears to be pointing at the ventricle. It should be
2*thickness away from the white surface into the white matter
On 11/04/2016 12:11 PM, Alshikho, Mohamad J. wrote:
> Hi Doug,
> I am sorry for sending multiple emails. I wanted to be sure that I understand
> it properly. Kindly:
Do you have a question about the image?
On 11/04/2016 11:09 AM, Alshikho, Mohamad J. wrote:
> Thank you Doug!
> Kindly in the attached figure are the "projfrac" values for #4 and #5 correct
> for at which level the analysis will be carried out.
>
> -Original Message-
> From: freesurfer-b
On 11/04/2016 07:30 AM, anonymous anonymous wrote:
> Hi all,
>
> I'm new to freesurfer and I'm having some issues.
>
> 1) First of all I tried recon-all in one subject but I got an error on
> nu_correct. This is what the log says:
>
> Can't use 'defined(@array)' (Maybe you should just omit the de
Hi Doug,
I am sorry for sending multiple emails. I wanted to be sure that I understand
it properly. Kindly:
My question is regarding "projfrac = -1" and "projfrc=-2" are the pointers in
the figure located correctly where the analysis will be carried out?
Thanks again
-Original Message---
Hello Freesurfer Developers,
I have gotten ahold of the dev version of mri_label2label.
Currently I have a .w file that I need to “fill in the holes” on. Could
you please specify the steps I will need to take to make my .w file an
acceptable input for mri_label2label, and any recommendations you
Hi Paul
we required the T1.mgz, brainmask.auto.mgz and brainmask.mgz volumes so
must create them somehow. I think if you copy/convert your already-stripped
and name it brainmask.mgz we should treat that as if you had edited our
skull stripping and you should be able to run from their forward
You should be able to apply the mris_preproc command on the xhemi page
https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
substituting your average subject for fsaverage_sym
On 11/04/2016 10:41 AM, Daya P wrote:
> I went to the shell script and changed the input for aparc+aseg and
> aseg. and ma
I went to the shell script and changed the input for aparc+aseg and aseg. and
managed to make it work.
My other question is that now that I have it running, after it is done I would
like to run a vertex wise analysis.
Is there a tutorial/help or command that I should apply to do asymmetry
anal
Please can someone answer this. Thanks " Hello Freesurfer, I have couple of ques
Try adding --zilles --reg
It is a hack, but it might just work
On 11/04/2016 07:34 AM, daianapu...@gmail.com wrote:
>
> Hi,
>
> Thank you for your reply, when I run xhemireg I get an error for
> cannot find aseg. is there any way to avoid that? in the way there is
> a noaseg flag for other co
On 11/04/2016 07:25 AM, Alshikho, Mohamad J. wrote:
>
> Dear FS experts,
>
> I ran surface based analysis using PET maps, and the pipeline
> reported, in FS list, by multiple colleagues as the following:
>
> ·spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
>
> ·mris_preproc
oops, sorry,
download these files
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_volcluster
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surfcluster
Copy them into $FREESURFER_HOME/bin (after making a backup of the
Hi,
Thank you for your reply, when I run xhemireg I get an error for cannot find
aseg. is there any way to avoid that? in the way there is a noaseg flag for
other commmands. I built a cortical Atlas and dont have subcortical labels
Thank you ,
Daiana
Daiana Pur
On Wed, Nov 2, 2016 at
Hi all,
I'm new to freesurfer and I'm having some issues.
1) First of all I tried recon-all in one subject but I got an error on
nu_correct. This is what the log says:
Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em l
Dear FS experts,
I ran surface based analysis using PET maps, and the pipeline reported, in FS
list, by multiple colleagues as the following:
* spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
* mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.
Hi Doug,
I want to use GRF. Will you be willing to share the new versions of the programs? Your help is highly appreciated.
Thanks!
Jon
on: Friday, October 28, 2016 at 11:53 AM
From: "Douglas Greve"
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Re: surface bas
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