Hi Tracy,
You can check out this page , on our FreeSurferWiki to find out more
information on longitudinal processing:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing
Also, our database of publications related to FreeSurfer in general is here:
https://www.zotero.org/freesurfer
B
Hi Tracy,
When you call recon-all -base simply pass only the single time point -tp.
Best Martin
Sent via my smartphone, please excuse brevity.
Original message From: Tracy Melzer
Date:10/22/2014 10:59 PM (GMT-05:00)
To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer]
Dear FreeSurfer Experts,
I am interested in how the longitudinal stream creates a base template with
only a single image. Could someone please explain how or point me to a
reference as to how this is accomplished?
Thank you,
Tracy Melzer
___
Freesurf
Hi Adam
it's impossible to say without seeing some examples. If you upload a
problematic subject (the entire subject directory from recon-all) we will
take a look
cheers
Bruce
On Wed, 22 Oct 2014, Adam Mezher wrote:
> Hi All,
> I'm running a number of subjects who have FTLD and their
> surfarce
Hi All,
I'm running a number of subjects who have FTLD and their
surfarce/parcellation outputs are quite poor (especially in the frontal
lobe obviously). Are there any expert commands that can be used to attempt
to fix this issue without having to do individual edits? Most of the
subjects have und
Hello FreeSurfer Experts,
Is it possible to estimate the sulcal CSF volume in Freesurfer processing?
If not directly are there any indirect means that can give me an estimate?
Thank you
Mohammed Goryawala, PhD
Department of Radiology
Miller School of Medicine, University of Miami
___
Why not just get it from the ?h.aparc.stats file?
On 10/22/2014 03:43 PM, Smith, Michael wrote:
> Hello Freesurfer’s
>
> I am trying to look at the cortical thickness for a specific ROI on
> the cortical surface (Primary Auditory Cortex: transverse temporal
> gyri). I found a specific tutorial
Dear all,
I used the the 3 steps of longitudinal analysis explained in freesurfer
longitudinal tutorial and need to compute the ratio Parenchyma/CSF for each
of time points. Is this equivalent to compute the (total gray matter
volume + total cortical matter volume)/CSF from aseg.stats file ?
Tha
Hello Freesurfer’s
I am trying to look at the cortical thickness for a specific ROI on the
cortical surface (Primary Auditory Cortex: transverse temporal gyri). I found
a specific tutorial
(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) however
the tutorial assumes I al
I would use mri_vol2vol to map the PET into the anatomical space, then
use mri_segstats to compute the statistics.
doug
On 10/22/2014 02:50 PM, Makaretz, Sara Johanna wrote:
> Hi,
> I have a PET volume that is registered to a recon, then projected to the
> surface via vol2surf. I would like to
Hi,
I have a PET volume that is registered to a recon, then projected to the
surface via vol2surf. I would like to pull stats for the PET using aparc
regions. Should I use mri_annotation2label, then pull stats for each label? Or
is there something similar to mri_segstats, ie. --annot lh.aparc.an
I'm not sure that anyone is maintaining this code any more. However, you
can try running
mri_convert --nskip 1 asl.nii asl.skip.nii
and then use asl.skip.nii as input. This just removes the 1st frame so
that the tag/control will be in the expected order
doug
On 10/22/2014 10:29 AM, Asif Jam
Hello,
I have pcASL data from a Siemens 3T scanner which I would like to process using
the provided rcbf-prep command. The process completes smoothly without error.
However when I inspect my roi.dat file, I observe that all the ROI values are
actually negative, and seem to be beyond physiologic
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