Hi - See my answer to Knut Jørgen about the isosurfaces. I forgot to answer the
second part of your question: the outliers of the -stat step are tracts that
have a very different shape from the rest, so you can check those and see if
they failed, but hopefully any QA/reinitialization would have
Hi Marisa - Is there by any chance the same file saved with 2 different
extensions, like .nii and .nii.gz? I'd have to look at the entire trac-all.log
to get a better idea when this happens.
Thanks,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-b
Hi - It's not a requirement, but if the # of control points is specified for
each tract, so if you've changed pathlist to a subset of the tracts, you have
to do the same to the # of control points.
The fewer control points the smoother the curve. More control points are more
degrees of freedom.
Hi Lauren - The transforms are all under dmri/xfms/... and the one you're
looking for is the output of bbregister, which is called anatorig2diff.bbr.dat
or .mat.
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on
Hi Kris - The tracts have to be labeled manually in a set of subjects, that
TRACULA uses as its training data. It takes the manually labeled tracts and the
anatomical segmentation of each of the training subject and it computes the
probability that a tract will go through or next to each segment
Hi Doug - Yes, there used to be a bug in how freeview used to interpret
orientation info from the header of volumes loaded with the -dti option.
Hopefully it's fixed now!
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu]
Hi Alex - Have you run the freesurfer setup script?
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configuration
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Alexander Zent
[az...@p
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
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
If you want to use the FA map, it's dmri/dtifit_FA.nii.gz
From: Knut J Bjuland [knutjor...@outlook.com]
Sent: Wednesday, November 30, 2016 4:40 PM
To: Yendiki, Anastasia
Cc: Freesurfer support list
Subject: Re: [Freesurfer] obtain fa FA data from the white m
Hi Katherine - The error occurs when processing this file:
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
Can you send this file? Thanks!
a.y
From: Katherine Damme [katherine.da...@gmail.com]
Sent: Saturday, December 03, 2016 3:42 PM
To: Freesur
Hi Vivek - I suspect that you are specifying the DWI dicom of one of the
subjects, and trac-all uses the default 60-direction Siemens gradient table.
It's hard to know without seeing your configuration file.
How are you merging the DWIs of the two subjects? You only mention how you
co-register
...@gmail.com]
Sent: Wednesday, December 07, 2016 12:41 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Set: No Match
On Mon, Dec 5, 2016 at 12:00 PM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Katherine - The error occurs when processing this file:
/media/Data/
linux Temple_Tracula]$ xfmrot
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs
set: No match.
On Wed, Dec 7, 2016 at 2:41 PM, Yendiki, Anastasia
mailto:
128/dmri/dwi.ecclog
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs
set: No match.
On Wed, Dec 7, 2016 at 2:41 PM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Thanks. This looks fine. When you run that xfmro
nux katelinux.psych.northwestern.edu<http://katelinux.psych.northwestern.edu>
2.6.32-642.6.2.el6.x86_64 #1 SMP Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64
x86_64 GNU/Linux
I check all of these images and I can open them.
On Tue, Dec 13, 2016 at 7:59 PM, Yendiki, Anastasia
mailto:ayend...@m
Hi Hao - It looks like it didn't find the freesurfer recons of the subjects'
structural data. They should be under whatever you have defined as SUBJECTS_DIR.
On a separate note, it looks like you're using an old version of TRACULA. There
is an update that you can download from the TRACULA wiki p
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la part de Yendiki, Anastasia
Envoyé : samedi 17 décembre 2016 17:26
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA trac-all preprocessing errors
Hi Hao - It looks like it didn't find the freesurfer recons of the subjects'
Hi Hao - This is also coming in the next version :)
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hao wen
[hao.freesur...@hotmail.com]
Sent: Monday, December 19, 2016 5:43 AM
To: freesurfer@nmr.mgh.harvard.
Thanks
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la part de Yendiki, Anastasia
Envoyé : dimanche 18 décembre 2016 14:51
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA trac-all preprocessing errors
Hi Hao - That is strange, thank you for
good job!
Good day
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la part de Yendiki, Anastasia
Envoyé : lundi 19 décembre 2016 15:10
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA to define multiple bvals
Hi Hao - This is also coming in the ne
by an earlier step in the trac-all -prep right?
On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
It doesn't recognize the format of your field map. It assumes that the field
map has either 2 frames (2 phase maps) or 1 frame (a phas
, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
No, it's a separate scan that you provide.
From: Katherine Damme
[katherine.da...@gmail.com<mailto:katherine.da...@gmail.com>]
Sent: Monday, December 19, 2016 1:43 PM
To: Freesurfer suppor
Hi Hao - This will also be fixed in the new version. For now, if you do not
have them as dicoms, please do your testing without a field map.
Thanks,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hao wen
[
, 2016 at 10:09 PM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
No - there is no relation between B0 field inhomogeneities (measured by a field
map) and b=0 volumes. The capital B refers to the magnetic field in the
scanner, the small b is the b-value (diffusi
Hi Michal - Are you running the freesurfer setup script?
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configuration
Also, in your config file:
- You're missing a "\" at the end of the line with the first nifti file
- bvalfile is for defining a single b-value table,
Hi Mahtab - If your dicom file is anonymized, can you upload it here for us to
take a look?
https://gate.nmr.mgh.harvard.edu/filedrop2/
Please address the upload to ayendiki and greve.
Thanks,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun..
Hi Hao - Every single image in your DWI series should have a corresponding
column (or row) in the b-value and gradient table. So if the first image in
your DWI series is a b=0 image, and it doesn't have a corresponding column (or
row), you should add 0 to the b-value table and "0 0 0" to the gra
: Re: [Freesurfer] Tracula Set: No Match
Is it possible to run tracula with out a phase mapping MRI scan? All I have in
this data is a MPRAGE and DWI images weighted at either 0 or 1000.
Thank you.
On Tue, Jan 3, 2017 at 1:07 PM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wro
Hi Hao - The simplest way to get around this is to create under $SUBJECTS_DIR/
symbolic links to the subjects' recon-all directories, wherever those may be in
your own hierarchy.
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh
Hi Derek - Thanks for testing the 6.0 release candidate. Does it keep running
after this message? Since this is a warning and not an error, it may not be
critical. If you run mri_info on your dwi.nii.gz, does the TE show up as zero?
Best,
a.y
From: freesurfer-bo
of: 0
xstart: -115.0, xend: 115.0
ystart: -115.0, yend: 115.0
zstart: -55.5, zend: 55.5
TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
Yendiki,
Anastasia<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.ed
an 15, 2017 at 1:27 PM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Derek - It sounds like the programs that you used to convert from dicom to
nifti and to resample from anisotropic nifti to isotropic nifti don't copy the
TE and TR info in the header correctly. This in
ader fixed.
Curious to see if that one works!
mri_convert --in_type nii --out_type nii --out_orientation RAS dwi.nii.gz -tr
1000 dwi_TRfixed.nii.gz
On Sun, Jan 15, 2017 at 1:44 PM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Derek - It looks like it fails, but I suspect that it
Hi Prad - mri_aparc2aseg assigns WM voxels to the nearest cortical region from
the cortical parcellation. Which cortical region would you want to assign the
corpus callosum to? What's labeled as corpus callosum in the aseg is the part
of the corpus callosum between the 2 hemis.
Best,
a.y
_
,
-Prad
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Tuesday, January 17, 2017 5:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] WM lobes and Corpus Callosum
Hi Prad - mri_aparc2aseg assigns WM voxels to the
Hi Barbara - If you take out the "set baselist" part, you'll run the
cross-sectional TRACULA stream, i.e., analyze each time point independently. So
you want to leave that in to use the longitudinal TRACULA stream.
The base template itself (i.e., the median of the T1s of the time-points) may
no
rking with version 5.3 so I'll send attach the
trac-all.local-copy for that if that’s OK. Once again, thank you!
On 20 Jan 2017, at 23:52, Yendiki, Anastasia wrote:
Hi Barbara - If you take out the "set baselist" part, you'll run the
cross-sectional TRACULA stream, i.e., a
Thanks for the tip, Peter. Someone has had this issue in past. These were
adapted from old FSL scripts and the goal is to phase them out eventually.
Right now trac-all has a new option to print out the commands to be
submitted to a cluster, so that the user can handle that herself. It would
be impr
e again, thanks, I'm super grateful!
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
on behalf of Yendiki,
ommand line, can I simply run it for each timepoint separately as if it was
cross-sectional or is there an extra step?)
Many thanks!
On 26 Jan 2017, at 14:51, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Glad to hear it, thanks for checking! If the final 6.0 works,
Hi Qiuyun - You can use orientLAS instead.
Hope this helps,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fan, Qiuyun
[qiuyun@mgh.harvard.edu]
Sent: Tuesday, January 31, 2017 6:03 PM
To: freesurfer@nmr
Hi Graham – Have you tried mri_convert? The 6.0 version should be able to
extract diffusion gradient tables and b-value tables from most standard recent
dicoms.
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Warner, Graham Cary"
mailto:gwar...@mgh.harvard.edu>>
Reply
raham
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia
[ayend...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 10:15 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix
Hi Graham – Have you
raham
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia
[ayend...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 1:55 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix
Old versions of mri_convert (before 6.0) us
Hi - Running topup is not a problem. Just make sure that there's as many
entries in the gradient table and b-value table as there are frames in the DWI
file. So if with topup you're combining 2 sets of DWIs (collected with opposite
phase-encode directions), you also have to combine the correspon
Hi Adarsh – Is that a space there in between “--“ and “input”?
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Adarsh Nellore
mailto:adarsh.nellore...@gmail.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, February 10, 2017 a
Hi Abby – When you say you have successfully processed a subject on that
machine before, what FS version was that with? What has changed since then? The
last I remember memory allocation issues, they were years ago in a very old
version of OSX that we don’t even distribute binaries for any more,
Hi Adarsh - It should be --inputs.
Best,
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Adarsh Nellore
mailto:adarsh.nellore...@gmail.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, February 10, 2017 at 5:02 PM
To: "freesur
updated to FS 6. The only thing that was altered
was the directory structure in the dmrirc text file, and the subjects.
Thanks!
Best
Abby
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia
[ayend
Can you please send the correct command line and the output of the command in
full? Thanks.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Adarsh Nellore
[adarsh.nellore...@gmail.com]
Sent: Saturday, February 1
urfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia
[ayend...@mgh.harvard.edu]
Sent: Sunday, February 12, 2017 9:39 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Is the data size different for the new subjects than the old subject? Is th
Hi Adarsh – The command works fine with our data. When you open your input
file, does it look like the example in the tutorial below?
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics#Anisotropyanddiffusivityaveragedoveranentirepathway
Thanks,
a.y
From:
mailto:freesurfer-bo
_
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
on behalf of Yendiki, Anastasia
[ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>]
Sent: Monday, Februa
Hi Adarsh – What operating system are you running this on? It runs fine for me
with this input file when I test it on both a mac and a linux computer.
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Adarsh Nellore
mailto:adarsh.nellore...@gmail.com>>
Reply-To: Freesurfe
This is of course a possibility but the script has been around for years, so
it's been run with a range of versions.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Antonin Skoch
[a...@ikem.cz]
Sent: Wednesday,
ttached the log.
Thanks!
Abby
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
on behalf of Yendiki, Anastasia
[ayend...@mgh.harvard.edu<mailto:ayend.
Check out the ROI analysis tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials
It's highly recommended that you upgrade to a more recent version of freesurfer
- 5.0 is a decade old.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.
-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia
[ayend...@mgh.harvard.edu]
Sent: Wednesday, February 15, 2017 4:57 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Hi Abby – Interesting, this means that it was the update and not
Hi Joëlle - I highly recommend using the TRACULA version in 6.0, because it
tries to detect the cases that need to be reinitialized and reruns them
automatically. (It's ok if the anatomical segmentations come from the 5.3
version of recon-all.) Of course, like with any automatic method for dete
One potential difference is that TRACULA does not need the gradient vectors to
be flipped. It needs to get them the way they are stored in the DICOM header,
and that's what mri_convert outputs.
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-
Hi Heidi - It's up to you. As long as the N of subjects at each point is
included in the statistical test, this will adjust the corresponding p-value
accordingly.
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on
Hi Heidi - TRACULA does not use deterministic constraints like pre-defined ROIs
to reconstruct the tracts. For each point along a tract (and not just the end
points), it has a prior probability (that it has computed from the atlas
subjects) that a tract goes through each of the aparc+aseg labels
Hi Jürgen - If your subjects' freesurfer directories have the standard
structure as it comes out of recon-all, then you probably have a different
problem than the one in that older thread. Have you changed the recon-all
output directories in some way?
Best,
a.y
Hi Joseph – You can use fugue as part of the preprocessing in TRACULA. Search
for items with “b0” in the example config file:
https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
Best,
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of VA Research
mailto:n.n.di.methyl.tryptami
t,
Joëlle van der Molen
De :
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
de la part de Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>>
Envoyé : jeudi 16 mars 2017 22
The first is the number of voxels, the second is the size of a single voxel.
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of yusif Al-kheder mailto:yusi...@live.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, March 22, 2017 at
le and make it radians/s for FreeSurfer?
like you do in FSL? with command fsl_prepare_fieldmap
On Wed, Mar 22, 2017 at 7:35 AM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Joseph – You can use fugue as part of the preprocessing in TRACULA. Search
for items with “b0” in
They're under $base/mri/transforms/*.lta.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Matthieu Vanhoutte
[matthieuvanhou...@gmail.com]
Sent: Friday, March 24, 2017 10:43 AM
To: Freesurfer support list
Subject
Hi Michael - Have you tried fscalc?
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Michael Kranz
[mbkr...@gmail.com]
Sent: Wednesday, March 29, 2017 3:03 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Free
Hi Batool - Yes, it would be a problem. It'd be similar to having some scans
with one spatial resolution and some with another, or administering one
questionnaire to some of your subjects and a different one to the others and
then trying to compare the answers. If the 16 directions are a subset
files, would you use the first 16
directions in the file, or the most evenly distributed 16 directions?
Thanks again!
Batool
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia
[ayend...@mgh.har
See the group analysis tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0
The tutorial uses age and gender, but you can add any other variables you want
to the design matrix.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-
surfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
on behalf of Yendiki, Anastasia
[ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>]
Sent: Wednesday
vard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
de la part de Yendiki, Anastasia
<mailto:ayend...@mgh.harvard.edu>
Envoyé : mercredi 22 mars 2017 15:40
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstruction
Hi Joëlle – What images do you pass
boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
de la part de Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>>
Envoyé : jeudi 30 mars 2017 15:20
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstruction
Hi Joëlle - Can you please send t
Hi Amelia - This means that it can't find any of the tracts that you've
specified (or any tracts period, if you haven't specified a list) for the
subjects that you've specified in your config file. It'd be looking under:
/data/dprojects/BIOS/tracula/$subj/dpath/
Best,
a.y
_
ssage-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 12, 2017 5:04 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all -stat
Hi Amelia - This means that it can't find any of th
Hi John - Unless someone else has a better idea, the aseg (subcortical
segmentation) contains left and right cerebral and cerebellar white matter
labels. You can look at the ROI analysis tutorial for how to extract stats from
aseg labels.
Best,
a.y
From: freesu
gradient tables, so
I think I'm probably doing something wrong in the configuration of the dmrirc
file... Would you mind sending me the dmrirc file you would use to run this
subject?
Best,
Joëlle
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la part d
Hi Quentin - Yes, this is possible! You can use the info in the
pathstats.byvoxel.txt files to do that. The -stat step of TRACULA (see last
part of tutorial) will put together all the point-wise, along-the-tract stats
of all the subjects into a table. Each element in the table will be one
posit
2017 20:21:29 +
From: "Yendiki, Anastasia"
Subject: Re: [Freesurfer] TRACULA anterior/posterior {Disarmed}
To: Freesurfer support list
Message-ID:
Content-Type: text/plain; charset="windows-1252"
Hi Quentin - Yes, this is possible! You can use the info in the
path
st
Subject: Re: [Freesurfer] TRACULA tract reconstruction
Of course, here it is. Thank you for taking a look at it!
Best,
Joëlle
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la part de Yendiki, Anastasia
Envoyé : mardi 25 avril 2017 10:25
À : Freesurfer su
t: Re: [Freesurfer] TRACULA tract reconstruction
Hi Anastasia,
I added a screenshot of what I get when I run that command.
Thanks again!
Joëlle
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la part de Yendiki, Anastasia
Envoyé : samedi 29 avril 2017 02
Hi Joelle - See my previous email, you should download the 6.0 version. In this
version TRACULA will attempt to detect which tracts require reinitialization,
so hopefully you'll see an improvement in this.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[frees
Hi Yong - If you do not have diffusion data, you won't be able to map your
subjects' white matter tracts. In a T1 scan there is no contrast between white
matter tracts that would allow you to segment them, as white matter looks
uniform. All you could do is transform some generic labels from an a
Hi Stephanie - The arcuate fasciculus is reconstructed when you run TRACULA on
your diffusion data, but it is not an ROI. Please refer to the tutorial for how
to run TRACULA and how to visualize the tracts:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
a.y
__
Hi Lauren - I suspect that TRACULA is not using your corrected bbregister
registration file. That's because the -intra step in TRACULA doesn't just run
bbregister, but also does a bunch of other things with the output of
bbregister, like transform, invert, and compose a bunch of registration fil
and I'm afraid I got the same erroneous result. Do you
have any other ideas as to where the problem could be coming from?
Lauren
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia
[ayen
: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia
[ayend...@mgh.harvard.edu]
Sent: Tuesday, May 30, 2017 6:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [TRACULA] Issue with registration to diffusion space
Hi Lauren - Can you
Hi John - You can read more on how to use the motion measures in our paper:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029882/
The gist of it is that it's not easy to set a hard threshold on the motion
measures so that everything above the threshold is good data and everything
below is ba
Hi Katrina - Most likely the problem occurred earlier in the process, so the
real error is hiding earlier in the log file. Can you please the entire
scripts/trac-all.log file?
Thanks,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.
attached. Let me know if you think you need anything
else.
Best
Katrina
On Jun 6, 2017, at 9:33 PM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Katrina - Most likely the problem occurred earlier in the process, so the
real error is hiding earlier in the log file. C
, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Katrina - It looks like the last stage of the pre-processing did not run for
some reason. You can run that one stage only with trac-all -prior. If that
runs, then you can run trac-all -path (no need to rerun trac-all -bedp).
Bes
atsi...@sas.upenn.edu<mailto:katsi...@sas.upenn.edu>]
Sent: Wednesday, June 07, 2017 1:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA -path issue
Hi Anastasia, thanks for your response.
The entire log file is attached. Let me know if you think you need anything
els
Hi Fatima - mri_aparc2aseg is the right command, but you should specify
the name of your annotation instead of aparc.a2009s (which is one of the
standard freesurfer annotations). So if your annotation is lh.mine.annot
and rh.mine.annot, then you need "--annot mine².
Anastasia.
On 6/14/17, 3:42 PM
Hi Marissa – Those things are not all required simultaneously. You should
either specify a single file (if it’s the same for all scans you’re processing)
or a list of files, but not both at the same time.
As far as errors go, there’s no way of guessing what’s going on without seeing
the error.
Hi Yong – Your 6 directions are on the low end for tractography. I’d recommend
using TRACULA with 30 directions or more. TRACULA doesn’t use the tensor model,
which you can fit with just 6 directions, but a model that can capture multiple
bundles per voxel, so you need a few more directions for
Yep, you can use the dmri_motion command. Run it without any arguments to see
usage info. It needs:
* Your original, unprocessed DWIs
* b-value table
* Output from your FSL eddy correction (*.ecclog from eddy_correct or
*.eddy_parameters from eddy)
Hope this helps,
a.y
From:
mail
Hi Daniele - A main feature of the freesurfer longitudinal stream is that it is
unbiased, i.e., it treats all the time points in the same way, regardless of
their order in time.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.m
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