Dear Freesurfer experts,
I am using MNE (with MEG data) to define my ROIs for a connectivity analysis. I
am going through the following steps to get the MNI coordinates of the regions:
1. Morph the subject's brain to fslaverage;
2. Load the inflated surface of fslaverage to MNE analyze;
3. Lo
ni305 space. Is that what you want?
On 07/06/2016 04:17 PM, Li, Baojuan wrote:
> Dear Freesurfer experts,
>
>
> I am using MNE (with MEG data) to define my ROIs for a connectivity
> analysis. I am going through the following steps to get the MNI
> coordinates of the regions:
>
>
: [Freesurfer] fslaverage/MNI coordinates
I've just added your use case to this page. See Case 8.
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 07/06/2016 05:09 PM, Li, Baojuan wrote:
> Hi Doug,
>
> Thank you so much! Because I will do the analysis using SPM, I need the
&g
Hi Freesurfer experts,
I am trying to use the clusters to run BedpostX on a Connectome
dataset.
Although the job is running now, it is running slowly. It has only got
though 18 slices over the last 10 hours:
pbsubmit -n 8 -m bl744 -c "bedpostx
/space/iggy/5/users/baojuan/mgh_1007/diff/preproc/m
Hi all,
I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner)
but running into an error.
I have two questions and hope someone can kindly help me with them:
1. Why can not I successully unpack images for run10?
2. I got the DTI.nii image, the bvecs and bvals for run4
, November 09, 2015 11:04 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] unpacksdcmdir
On 11/9/15 7:41 PM, Li, Baojuan wrote:
Hi all,
I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner)
but running into an error.
I have two questions and hope someone can
the
current version in $FREESURFER_HOME/bin (just make backup of it before
you do). After that, all programs will use the new version
On 11/10/2015 01:51 PM, Li, Baojuan wrote:
> Dear Douglas,
>
> Thank you so much for your help. I have tried the new version of
> mri_convert and it wor
environment (but only for unpacking)
source /usr/local/freesurfer/nmr-dev-env
On 11/10/2015 02:31 PM, Li, Baojuan wrote:
> Dear Douglas,
>
> Thank you!
>
> I am using a desktop of the Martinos Center. Seems I am not allowed to
> replace the mri_convert file under the $FREESURFER_HOME
that is causing the problem? It
could be that unpacksdcmdir does not work. I've noticed that many data
sets are coming off the scanner with each run in a separate folder,
which breaks unpacksdcmdir. However, dcmunpack should work.
On 11/10/2015 04:26 PM, Li, Baojuan wrote:
> Dear Douglas,
: [Freesurfer] unpacksdcmdir
yes
On 11/10/2015 04:35 PM, Li, Baojuan wrote:
> Yes, seems dcmunpack does not work with our new dataset.
> So can I still use the images obtained from running mri_convert directly?
> Actually, I got the filenames for run13 by running dcmunpack and then used
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