Hi,
I would like to to obtain FA data from the white matter ROIs in
WMParcStatsLUT.txt. or FreeSurferColorLUT.txt. So would it work to coregister a
DWI file, either produced by dt_recon (or perhaps better - from Tracula) and
an anatomy file in atlas space and then use WMParcStatsLUT.txt or
F
Dear Juan and FreeSurfer team,
We are trying to test out the longitudinal hippocampus subfield segmentation
pipeline, but can't seem to run/find the script (longHippoSubfieldsT1.sh). We
have done the standard processing in v5.3 and have the following dev version:
freesurfer-Linux-centos6_x86_
Hi Christian,
I believe you were unlucky enough to download the dev version during the days
that this module was broken.
I would strongly suggest that you either download the beta version of 6.0 or
wait until the official release of this version, which should be happening soon.
Cheers,
/Eugenio
Hi Knut Jørgen - The aparc+aseg doesn't contain the wm-* labels, only the
cortical labels from the aparc (in the 1000's and 2000's) and subcortical
labels from the aseg. The wm labels (in the 3000's and 4000's) are in the
wmparc only.
a.y
From: freesurfe
We will get the beta for now then.
Thanks Eugenio!
regards,
Christian
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Iglesias Gonzalez,
Eugenio
Sent: 30 November 2016 15:46
To: Freesurfer support list
Subject: Re: [Freesurfer] longHippoSub
Hi,
I was wondering if there is any way in FreeSurfer/FSL/MATLAB to determine
whether the DTI data (in DICOM format) I have is multi-band sequence?
I used dicominfo in MATLAB but couldn't find any information related to
multi-band in the dicom header.
Any help would be really appreciated.
__
Hi Martin,
I’ve addressed this in your query to the FSL list. Please see my response
there.
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry
I can't remember the tag numbers, but I believe the time of slice
acquisition is in the dicom. You should be able to just pull that
field on one volume and compare the field for all slices and see if
any of them have the same time.
hth
d
On Wed, Nov 30, 2016 at 12:10 PM, Martin Juneja wrote:
> H
That would be yet another way.
For those that are curious, the field is “MosaicRefAcqTimes”.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department o
Actually, it is the lack of a dot (".") in the file name. This is a
short-coming of recon-all. I'm really surprised that it took this long
to manifest itself. The short-term fix is to convert the files to mgz,
then pass the mgz files to recon-all.
On 11/30/2016 11:41 AM, Douglas Merkitch wrote
Doug, can you do me a favor and check to see if this modified version of
recon-all works on your data?
https://gate.nmr.mgh.harvard.edu/safelinks/greve/recon-all
On 11/30/2016 11:41 AM, Douglas Merkitch wrote:
> Hmmm it is a dicom file. Could it be that the lack of file extension
> gives it p
Hello Freesurfer experts,
I am trying to run longitudinal TRACULA but I am getting an error early
on in the process that seems to originate from mri_convert:
#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
#
Hi Vincent - Looks like an mri_convert error, so not specific to TRACULA but
probably something about the format of your input nifti volume. How did you
create that volume? Can you open it in freeview and view it normally?
a.y
From: freesurfer-boun...@n
Dear Anastasia,
I have checked the image and it looks good. I don't think the image is
the problem, especially considering that my issue is also popping up
with standard data. See for example the following code:
$ echo $FREESURFER_HOME
/home/mriuser/privatemodules/freesurfer
$ cksum $(which m
Hello Jean-Simon,
If indeed you are running the same subject on the same machine, then the
reason its failing has to be because of an update to perl. It's possible
your Linux update also updated the version of perl, even if only a minor
verion update, and this is what created the issue. You hav
Dear experts,
given sub-optimal results of my surfaces I referred to in my previous post, I
have tested several different settings and input data preparation to obtain
optimal pial surfaces in my modified HCP pipeline. I tested all variants in 5
representative subjects.
My modified HCP pipelin
Hi Anastasia
If I want to use Tracula DTI files instead, which file do I choose: Is it
FA_ditifit.nii?
Best
Knut Jørgen
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The i
Hi Antonin,
In our experience with FreeSurfer 5.3 we were getting very consistent
results. We are going to try some of this locally and work with the
FreeSurfer folks to get the T2w stream working robustly in FreeSurfer v6.0+.
Thanks for testing this,
Matt.
From: on behalf of Antonin Skoch
Dear Anastasia,
I emailed with Dr. Knut Jørgen Bjuland because he had a similar issue
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39745.html).
He mentioned that obtaining a new license could solve the issue. It did,
so my problem is resolved.
Best,
Vincent
__
Hey Doug,
Sorry for keep bothering, today I was trying to do what you told me yesterday,
but some doubts arose. I ran QDEC using DODS to see if there were any
interactions (significant regions) between age (age variable was not demeaned)
and group. I didn’t found anything, no significant region
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