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Thank you Matthew for your reply.
I just ran recon-all to get cortical thickness, area and volume values for
specific ROIs using the steps here:
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
and correlated the morphometric
you have to use the output of mri_label2vol in the freeview command
On 5/13/2019 5:02 PM, Sam W. wrote:
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Hi,
After bbregister, I ran mri_label2vol to convert a segmentation file to native
functional space
mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat
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There are different kinds of geometric distortion that affect your data to
differing extents. What kind of MRI data was in your study?
Matt.
From: on behalf of Martin Juneja
Reply-To: Freesurfer support list
Date: Monday, May 13, 2019 at 6:53
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Hi experts,
I have following question from one of the reviewers regarding recon-all
pipeline:
*"Was geometric distortion corrected? If not, this should be discussed or
mentioned in the study limitation."*
I was wondering if the reviewer is referring
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Hi,
After bbregister, I ran mri_label2vol to convert a segmentation file to
native functional space
mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat --subject s01 --o
aseg-in-func.nii --temp example_func.nii
Now I would like to check how well the
The Laboratory for Visual Neuroplasticity at the Massachusetts Eye and Ear
Infirmary (Harvard Medical School), located in Boston, MA is seeking a
full-time research assistant to start between July and September 2019.
Candidates who would be able to commit to the position for a minimum of two
I would use the high res stream I made for the HCP
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/
On 5/13/19 4:23 PM, Fuller-Deets, Josh (NIH/NEI) [C] wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer users,
>
>
> we have a new Terra 7T scanner and I'm
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Hi Freesurfer users,
we have a new Terra 7T scanner and I'm having issues collecting a clean MP2RAGE
scan and subsequently reconstructing it. Does anyone with experience with this
scanner have any suggestions about modifications to the standard
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Dear Freesurfer experts.
Now I am using preproc-sess to preprocess functional MRI data. I would like
to smooth the data first and then resample them into the standard space.
Hence I run 'preproc-sess -s sub001 -fsd func -stc odd -fwhm 0 -per-run'
Great!
Thanks
> On May 13, 2019, at 9:56 AM, Bruce Fischl wrote:
>
> Hi Mona
>
> sure. As I said it is a bit more complicated than it seems. Ruopeng will post
> a note when something usable is in the dev version
>
> Bruce
>
>
> On Mon, 13 May 2019, Nasiriavanaki, Zahra wrote:
>
>> Yes
Hi Mona
sure. As I said it is a bit more complicated than it seems. Ruopeng will
post a note when something usable is in the dev version
Bruce
On Mon, 13 May
2019, Nasiriavanaki, Zahra wrote:
Yes Bruce.
It doesn't work.
I appreciate if you could let me know when you had any updates
Yes Bruce.
It doesn't work.
I appreciate if you could let me know when you had any updates on it.
Thanks
Mona
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
Sent: Friday, May 10, 2019 6:15:05 PM
To: Freesurfer support list
Subject:
Hi Alberto
yes, you should be able to. Do you have the individual datasets or some
type of average?
cheers
Bruce
On Mon, 13 May 2019, albertotricker wrote:
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>
> Hello FreeSurfer technical staff
>
> I hava a data set provided by ADNI initiative, which is
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Sorry, I realized I used the pathstats.byvoxel.txt instead of
pathstats.overall.txt.
Attached is the correct .txt file and the new error I get from the python
script called by tractstats2table
pathstats.overall.txt
Parsing the .stats files
Building
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Hello,
I just ran trac-all on my data and am trying to use tractstats2table to run
some tract-based group level analysis.
I have created a text file with the full paths to each conditions stats
file (attached below and tried to run the following
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Hi Martin,
thanks for your quick reply and the clarification regarding the output.
I have processed the 1 and 0.8 mm separately, so one base for each subject and
resolution - no mixing has been conducted! :)
Actually, I want to look into changes
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Dear Freesurfer Experts!
The idea is to transform freesurfer output in to the MNI 1mm space using
following command:
mni152reg --s subject_id --1
But mni152reg crashes with following error:
flirt.newdefault.20080811.sch
terminate called after
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Hi There,
I’m currently trying to run mri_vol2surf on some animal data and surfaces I’ve
been working with.
I’m having a bit of a problem with the command mri_vol2surf.
I seem to be able to project my functional volume to my surface, however I’m
Hi Falk,
yes, the output of long_mris_slopes and long_stats_slopes is in percent
(100 * rate / value_of_fit_at_mid_time).
Also running 1mm data is different (as you know :-) from .8 so maybe
you would analyze both separately, e.g. creating one base on 1mm time
points and another on the .8mm ?
Hi William,
you can use freesurfer's pctsurfcon to compute the gray/white contrast
on the longitudinal directories. This will produce a surface overlay
at: tp.long.base/surf/?h.w-g.pct.mgh
I don't think the long_mris_slopes script can deal with those files
directly, so you have two options:
-
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Hello FreeSurfer technical staff
I hava a data set provided by ADNI initiative, which is formed by a set
of pre-processed T1-weighted MRI using FreeSurfer. The feature space
consists of cortical thickness and subcortical volumes.
Well, I want to
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Hi expert,
I selected hippocampus and amygdala as ROIs to estimated the reliability of a
well-controlled multi-site study. The travelling volunteers were scanned in
each site with the same type scanners and scan protocol. But, amygdala volume
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