On 3 Aug 2016, at 12:00, <freesurfer-request@nmr.mgh.harvard.edu>
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Today's Topics:
1. Re: brain mask and T1 are not the same size (Isabelle Deschamps)
2. Re: Coordinates in TRACULA group analysis (Anri WATANABE)
3. Re: mapping error (Douglas Greve)
4. Re: Multiple Comparison Question for surface-based analyses
(Douglas Greve)
5. Re: Coordinates in TRACULA group analysis (Anastasia Yendiki)
6. Re: brain mask and T1 are not the same size (Douglas N Greve)
----------------------------------------------------------------------
Message: 1
Date: Wed, 3 Aug 2016 10:50:30 +0000
From: Isabelle Deschamps <isabelle.deschamps.1@ulaval.ca>
Subject: Re: [Freesurfer] brain mask and T1 are not the same size
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Message: 2
Date: Wed, 3 Aug 2016 20:19:09 +0900
From: Anri WATANABE <z2aanri@koto.kpu-m.ac.jp>
Subject: Re: [Freesurfer] Coordinates in TRACULA group analysis
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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Hi Anastasia,
Thank you for your kind explanation. I can be understanding how TRACULA
tracts white matter pathways.
At each position (in training subjects, not in new subjects of my data)
probability that next goes for which direction to every labels in the
aparc+aseg (not with setting a certain ROI) is computed with use of
training subjects. The prior probabilities are made from training subjects
(your publication in 2011) and they are based on manual labeling (the
manual labeling tracts are referred to Wakana et al. 2007). Then when white
matter pathways are reconstructed in my subjects, TRACULA computes
anatomical priors in each subjects in my data in pre-processing and
probability distributions from anatomical priors and by fitting
ball-and-stick model.
Is this comprehension ok?
Best Regards,
Anri
**********************************************************************
????????????
????????
?? ??
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**********************************************************************
2016-07-31 22:49 GMT+09:00 Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>:
-------------- next part --------------
Hi Anri - Instead of hard-coding some ROIs in the white matter that the
tract is forced to go through, TRACULA uses information like "what is the
probability that this tract goes lateral/anterior/etc to XXX", where XXX
any of the labels in the aparc+aseg. TRACULA computes these prior
probabilities from a set of training subjects, where the tracts have been
labeled manually. So it knows how likely a tract is to go through a certain
aparc+aseg label, or to he left, right, anterior, etc of a certain
aparc+aseg label. This is computed separately at each position along the
tract. It's computed from the training subjects, and then used when
reconstructing the tract in the new subject that you run TRACULA on.
Hope this helps,
a.y
On Sun, 31 Jul 2016, Anri WATANABE wrote:
Thanks, AnastasiaI know that TRACULA use probabilistic tractography but if
ROIs are not...
set how determine the origin and the end of a certain tract? I think that
the first we
have to determine the origin and the end of the tract, the second it
constructs possible
pathway not with the deterministic way (only 1 direction / 1 voxel) but
with the
probabilistic way (considering which direction should be next to). Is
this comprehension
wrong?
Thank you.
Anri
**********************************************************************
????????????
????????
?? ??
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**********************************************************************
2016-07-31 13:22 GMT+09:00 Anastasia Yendiki <
ayendiki@nmr.mgh.harvard.edu>:
Hi Anri - TRACULA does not use deterministic ROIs. It uses a
probabilistic
model of how likely each tract is to go through or next to each of
the labels
of the freesurfer subcortical segmentation and cortical
parcellation, as a
function of position along the trajectory of the tract.
Best,
a.y
On Sun, 31 Jul 2016, Anri WATANABE wrote:
Hi Anastasia,
Thank you! It seems work well!!
I have another question. Are ROIs for automatic tractography
in
TRACULA the same ROIs
presented in Wakana et al. 2007?
Anri
**********************************************************************
????????????
????????
?? ??
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**********************************************************************
2016-07-27 13:17 GMT+09:00 Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu>:
Hi Anri - The problem is in this line:
set cmd = ($cmd --ref $cvstempdir/$cvstemp)
It should be changed to this:
set cmd = ($cmd --ref
$cvstempdir/$cvstemp/mri/norm.mgz)
For this to take effect, you need to run "which
trac-all"
and make the change in
the trac-all file that the which commands shows you.
Hope this helps,
a.y
On Fri, 15 Jul 2016, Anri WATANABE wrote:
Hi, AnastasiaThis is trac-all.local-copy from 1
subject. Thank you!
Anri
**********************************************************************
????????????
????????
?? ??
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University
of
Medicine
**********************************************************************
2016-07-13 6:16 GMT+09:00 Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu>:
Hi Anri - This may be a bug that was fixed
at
some point. Can
you send me the scripts/trac-all.local-copy
from
one of your
subjects? Thanks!
a.y
On Mon, 11 Jul 2016, Anri WATANABE wrote:
Hi Anastasia,There is an error in .log
files of left
corticospinal tract in cvs template
and I
attached
one
of file. In addition .log files of
right
corticospinal tract in cvs template
doesn't exist.
Thanks in advance.
Anri
**********************************************************************
????????????
????????
?? ??
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural
University of
Medicine
**********************************************************************
2016-07-07 20:12 GMT+09:00 Anastasia
Yendiki
<ayendiki@nmr.mgh.harvard.edu>:
Hi Anri - Is there an error in
the
stats/*.log
files for the different tracts?
a.y
On Tue, 5 Jul 2016, Anri
WATANABE
wrote:
Dear Anastasia,
I use TRACULA to obtain
diffusion
measures at each voxel in a certain
pathway for
group analysis, but
there aren't
stats/*.path.mean.txt
files. I found .log files
(<tract>_PP.avg33_mni_bbr.log)
which
exist
1 file per 1 tract, except
corticospinal
tract which has 2 .log files.
Command: trac-all ?stat ?c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.example
Error log: Loading output
reference
volume from
/Applications/freesurfer/subjects/cvs_avg35
corRead(): can't open file
/Applications/freesurfer/subjects/cvs_avg35/COR-.info
ERROR: Could not read
/Applications/freesurfer/subjects/cvs_avg35
I attached dmrirc.example
(configuration
file) and
<subjd>/scripts/trac-all.log.
Thanks in advance,
Anri
**********************************************************************
????????????
????????
?? ??
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto
Prefectural
University of Medicine
**********************************************************************
2016-06-03 9:51 GMT+09:00
Anri
WATANABE
<z2aanri@koto.kpu-m.ac.jp>:
Hi, Anastasia.
There aren't any .log
files
but text
files like
lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt.
I guess text
files complete all
pathways
and
measures.
**********************************************************************
????????????
????????
?? ??
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto
Prefectural
University of Medicine
**********************************************************************
2016-06-02 3:03 GMT+09:00
Anastasia
Yendiki <ayendiki@nmr.mgh.harvard.edu
:
Thanks, Anri. So the
previous
steps seem to have run fine. Are
there any
.log
files
created in the
stats/
folder,
which is created by trac-all -stat?
On Wed, 1 Jun 2016,
Anri
WATANABE
wrote:
Hi
Anastasia, This
is a
<subjid>/scripts/trac-all.log of one
subject of
the group.
Thanks,
Anri
**********************************************************************
????????????
????????
?? ??
**********************************************************************
Anri WATANABE,
M.D.
Department of
Psychiatry,
University
Hospital, Kyoto
Prefectural University of Medicine
**********************************************************************
2016-05-31
22:55
GMT+09:00
Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu>:
Hi Anri
-
Can you also
send your log file
(scripts/trac-all.log)?
I'll need to
see
what
exactly
was
running
when the error occurred. Thanks!
a.y
On Sat,
28
May 2016,
Anri WATANABE wrote:
Hello
Anastasia,sorry for few information
and
let me tell
you
command and
error
log.
Command: trac-all ?stat ?c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.example
Error
log: Loading output reference volume
from
/Applications/freesurfer/subjects/cvs_avg35
corRead(): can't
open file
/Applications/freesurfer/subjects/cvs_avg35/COR-.info
ERROR:
Could not
read
/Applications/freesurfer/subjects/cvs_avg35
dmrirc.example (configuration file) is
attached to
this
e-mail.
Thanks
in
advance,
Anri
**********************************************************************
????????????
????????
??
??
**********************************************************************
Anri
WATANABE,
M.D.
Department of
Psychiatry,
University
Hospital, Kyoto Prefectural
University of
Medicine
**********************************************************************
2016-05-27 22:57
GMT+09:00 Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu>:
Hi Anri -
I do not know what command line you
ran
and
what your
configuration
file looks like, so it is very
hard for
me to suggest solutions.
Best,
a.y
On Fri, 27
May 2016, Anri WATANABE wrote:
Hi
Anastasia,
Thank you for your answer.
There aren't stats/*.path.mean.txt
files and
terminal says
'Could
not
read
/Applications/freesurfer/subjects/cvs_avg35.' I
checked
/Application/freesurfer/subjects/cvs_avg35
folder
and
couldn't find
COR-.info file.
Could you tell me any resolutions,
please?
Thanks,
Anri
**********************************************************************
????????????
????????
??
??
**********************************************************************
Anri
WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural
University
of Medicine
**********************************************************************
2016-05-21 6:48 GMT+09:00 Anastasia
Yendiki
<ayendiki@nmr.mgh.harvard.edu>:
Hi Anri - The FA values are
extracted in
the native
space
of
each subject,
which is why
those are the only
coordinates that you see. If you
want to
display the
results of your
analysis on an average
path, after
running trac-all -stat, you can use
the
stats/*.path.mean.txt files (see also
the
last part
of
the TRACULA
tutorial).
Best,
a.y
On Wed, 18 May 2016, Anri WATANABE
wrote:
Dear experts,
I use TRACULA to examine a
measure
(FA) at each
voxel
in one
pathway.
pathstats.byvoxel.txt files
show
coordinates in
native
space and
after converting
those the new
files don't show any
coordinates
which are in
MNI
space.
Could you tell me how can I
know
MNI
coordinate
values?
Thank you!
Regards,
Anri
**********************************************************************
????????????
????????
?? ??
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto
Prefectural
University of
Medicine
**********************************************************************
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Message: 3
Date: Wed, 3 Aug 2016 09:30:48 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mapping error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <f3f77469-16ad-6fdf-f647-80aee162dbfc@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
what is your command line?
On 8/3/16 6:00 AM, Caroline Beelen wrote:
Dear FS,
An aparc.annot ctab file was created but I got the following error:
Colortable:aparc.annot.ctab
Annotname: myaparc
Nhitsfile nhits.mgh
Nlabels 6
Labeltresh 0 0.00000
Loading freesurfer/fsaverage/surf/lh.orig
1 -1 not found
2 -1 not found
3 -1 not found
Etc?
Mapping unhit to unknown
Found 132101 unhit vertices
Writing annot to freesurfer/fsaverage/lh.myaparc.annot
I guess my ctab file is incorrect? I included an example of a label
with it.
Thanks again for your help.
Caroline
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Message: 4
Date: Wed, 3 Aug 2016 09:41:24 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Multiple Comparison Question for
surface-based analyses
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <dcd38d26-01cd-721e-9b52-81382d318dc3@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
On 8/3/16 3:45 AM, Ajay Kurani wrote:
Hi Doug,I was not planning to. The 809 subjects that I used for thickness do not
Thank you very much for your update regarding this issue.
1)Just curious, will LGI be included in this report as this is another
analysis of interest?
have lGI run on them, but I think it is possible to run it on a subset
without too much trouble. Not sure when I'll get to it.
Sort of. It is the Gaussian assumption that is incorrect, so there is no
2)As for the cortical thickness I originally used 15mm in the analysis
so based on your email I think using 5-10mm may be more prudent in
order to minimize FPR. From your email, I understand that
mris_surf2surf (command I use to convert individual subject to
fsaverage or template and smooth to 10-15mm) assumes an ACF estimation
of smoothness which DOES NOT take into account the long tail
distribution. Does this mean that when using mri_mcsim on my own
template, the cluster extents for a given smoothness will be
undersampled due to the fact that the "true" smoothness is more than
what is estimated in the simulation, correct? For instance, when I
select 15mm in qdec, it would point to the 21mm folder
(fwhm.dat=20.8mm estimate), and I would select a given cluster extent
for p=0.05. However, in this case, 15mm may translate to a larger
FWHM than the estimated 21mm, correct?
one FWHM that is correct (it is not a question of it simply being too
small).
Permutation uses your data and permutes (ie, randomly swaps) the class
3)You mentioned that I can use mri_glmfit-sim which is permutation
testing based. I am struggling a bit in understanding how this
differs from the simulation ran with mri_mcsim/qdec? Does qdec monte
carlo simulation option run mri_glmfit-sim in the background to
estimate the smoothness which looks up the cluster extent within the
mri_mcsim based on the estimated FWHM? If so, is this estimate
incorrect due to the fact that the long tails are not taken into account?
label associated with a subject, the data with this new labeling are
analyzed and clusters computed. Under the null, the label is irrelevant,
so clusters are interpreted as false positives. After several thousand
of these swaps, one builds a list of the probability of seeing a cluster
of a certain size under the null, and this is used to generate the
p-value. Permutation will then naturally take into account all the
non-Gaussian aspects of the data. The monte carlo (MC) simulation is
similar, but it uses smoothed synthesized gaussian noise instead of the
real data and so the gaussian assumption is built into it.
Thanks,
Ajay
On Mon, Aug 1, 2016 at 11:43 PM, Ajay Kurani <dr.ajay.kurani@gmail.com
<mailto:dr.ajay.kurani@gmail.com>> wrote:
Hello Freesurfer Experts,
Recently there were two article published regarding clusterwise
simulations for volumetric fmri analyses and potential errors for
underestimating clusterwise extent thresholds.
1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes
2) biorxiv.org/content/early/2016/07/26/065862
<http://biorxiv.org/content/early/2016/07/26/065862>
One issue pointed out from these articles seems software specific,
however the second issue is determining the proper clustersize.
The heavy-tail nature of spatial smoothness seems to be ignored
and a gaussian shape is generally assumed, leading to an
underestimation of the spatial smoothness which can affect cluster
size calculations. The issues are highlighted in the second
article above.
I created my own monte carlo simulation in Freesurfer for a
specific brain template and I wanted to find out if these concerns
also apply to my surface based simulations? I am not sure if it
does since the monte carlo tool is a GRF simulation as opposed to
an analytic equation, however given that these articles were
highlighted very recently, I wanted to ensure I am running things
appropriately for surface based cortical thickness/dti analyses.
Thanks,
Ajay
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Message: 5
Date: Wed, 3 Aug 2016 10:15:53 -0400 (EDT)
From: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Coordinates in TRACULA group analysis
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1608031015470.22565@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
That's correct!
On Wed, 3 Aug 2016, Anri WATANABE wrote:
Hi Anastasia,
Thank you for your kind explanation. I can be understanding how TRACULA tracts white matter pathways.?
At each position (in training subjects, not in new subjects of my data) probability that next goes for
which direction to every labels in the aparc+aseg (not with setting a certain ROI) is computed with use of
training subjects. The prior probabilities are made from training subjects (your publication in 2011) and
they are based on manual labeling (the manual labeling tracts are referred to Wakana et al. 2007). Then
when white matter pathways are reconstructed in my subjects, TRACULA computes anatomical priors in each
subjects in my data in pre-processing and probability distributions from anatomical priors and by fitting
ball-and-stick model.?
Is this comprehension ok?
Best Regards,?
Anri
**********************************************************************
????????????
????????
?? ??
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**********************************************************************
2016-07-31 22:49 GMT+09:00 Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>:
Hi Anri - Instead of hard-coding some ROIs in the white matter that the tract is forced to go
through, TRACULA uses information like "what is the probability that this tract goes
lateral/anterior/etc to XXX", where XXX any of the labels in the aparc+aseg. TRACULA computes
these prior probabilities from a set of training subjects, where the tracts have been labeled
manually. So it knows how likely a tract is to go through a certain aparc+aseg label, or to he
left, right, anterior, etc of a certain aparc+aseg label. This is computed separately at each
position along the tract. It's computed from the training subjects, and then used when
reconstructing the tract in the new subject that you run TRACULA on.
Hope this helps,
a.y
On Sun, 31 Jul 2016, Anri WATANABE wrote:
Thanks, AnastasiaI know that TRACULA use probabilistic tractography but if ROIs
are not
set how determine the origin and the end of a certain tract? I think that the
first we
have to determine the origin and the end of the tract, the second it constructs
possible
pathway not with the deterministic way (only 1 direction / 1 voxel) but with the
probabilistic way (considering which direction should be next to). Is this
comprehension
wrong?
Thank you.
Anri
**********************************************************************
????????????
????????
?? ??
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**********************************************************************
2016-07-31 13:22 GMT+09:00 Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>:
? ? ? Hi Anri - TRACULA does not use deterministic ROIs. It uses a probabilistic
? ? ? model of how likely each tract is to go through or next to each of the
labels
? ? ? of the freesurfer subcortical segmentation and cortical parcellation, as a
? ? ? function of position along the trajectory of the tract.
? ? ? Best,
? ? ? a.y
? ? ? On Sun, 31 Jul 2016, Anri WATANABE wrote:
? ? ? ? ? ? Hi Anastasia,
? ? ? ? ? ? Thank you! It seems work well!!
? ? ? ? ? ? I have another question. Are ROIs for automatic tractography in
? ? ? ? ? ? TRACULA the same ROIs
? ? ? ? ? ? presented in Wakana et al. 2007?
? ? ? ? ? ? Anri
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ????????????
? ? ? ? ? ? ????????
? ? ? ? ? ? ?? ??
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? Anri WATANABE, M.D.
? ? ? ? ? ? Department of Psychiatry,
? ? ? ? ? ? University Hospital, Kyoto Prefectural University of Medicine
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? 2016-07-27 13:17 GMT+09:00 Anastasia Yendiki
? ? ? ? ? ? <ayendiki@nmr.mgh.harvard.edu>:
? ? ? ? ? ? ? ? ? Hi Anri - The problem is in this line:
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?set cmd = ($cmd --ref $cvstempdir/$cvstemp)
? ? ? ? ? ? ? ? ? It should be changed to this:
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?set cmd = ($cmd --ref
? ? ? ? ? ? $cvstempdir/$cvstemp/mri/norm.mgz)
? ? ? ? ? ? ? ? ? For this to take effect, you need to run "which trac-all"
? ? ? ? ? ? and make the change in
? ? ? ? ? ? ? ? ? the trac-all file that the which commands shows you.
? ? ? ? ? ? ? ? ? Hope this helps,
? ? ? ? ? ? ? ? ? a.y
? ? ? ? ? ? ? ? ? On Fri, 15 Jul 2016, Anri WATANABE wrote:
? ? ? ? ? ? ? ? ? ? ? ? Hi, AnastasiaThis is trac-all.local-copy from 1
? ? ? ? ? ? subject. Thank you!
? ? ? ? ? ? ? ? ? ? ? ? Anri
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ????????????
? ? ? ? ? ? ? ? ? ? ? ? ????????
? ? ? ? ? ? ? ? ? ? ? ? ?? ??
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? Anri WATANABE, M.D.
? ? ? ? ? ? ? ? ? ? ? ? Department of Psychiatry,
? ? ? ? ? ? ? ? ? ? ? ? University Hospital, Kyoto Prefectural University of
? ? ? ? ? ? Medicine
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? 2016-07-13 6:16 GMT+09:00 Anastasia Yendiki
? ? ? ? ? ? ? ? ? ? ? ? <ayendiki@nmr.mgh.harvard.edu>:
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi Anri - This may be a bug that was fixed at
? ? ? ? ? ? some point. Can
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? you send me the scripts/trac-all.local-copy from
? ? ? ? ? ? one of your
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? subjects? Thanks!
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? a.y
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? On Mon, 11 Jul 2016, Anri WATANABE wrote:
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi Anastasia,There is an error in .log
? ? ? ? ? ? files of left
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? corticospinal tract in cvs template and I
? ? ? ? ? ? attached
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? one
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? of file. In addition .log files of right
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? corticospinal tract in cvs template
? ? ? ? ? ? doesn't exist.?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Thanks in advance.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ????????????
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ????????
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ??
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri WATANABE, M.D.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Department of Psychiatry,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University Hospital, Kyoto Prefectural
? ? ? ? ? ? University of
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Medicine
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2016-07-07 20:12 GMT+09:00 Anastasia
? ? ? ? ? ? Yendiki
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? <ayendiki@nmr.mgh.harvard.edu>:
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi Anri - Is there an error in the
? ? ? ? ? ? stats/*.log
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? files for the different tracts?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? a.y
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? On Tue, 5 Jul 2016, Anri WATANABE
? ? ? ? ? ? wrote:
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Dear Anastasia,?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I use TRACULA to obtain
? ? ? ? ? ? diffusion
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? measures at each voxel in a certain
? ? ? ? ? ? pathway for
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? group analysis, but
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? there aren't
? ? ? ? ? ? stats/*.path.mean.txt
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? files. I found .log files
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? (<tract>_PP.avg33_mni_bbr.log)
? ? ? ? ? ? which
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? exist
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 file per 1 tract, except
? ? ? ? ? ? corticospinal
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? tract which has 2 .log files.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Command:?trac-all ?stat ?c
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Error log:?Loading output
? ? ? ? ? ? reference
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? volume from
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? /Applications/freesurfer/subjects/cvs_avg35
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? corRead(): can't open file
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? /Applications/freesurfer/subjects/cvs_avg35/COR-.info
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ERROR: Could not read
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? /Applications/freesurfer/subjects/cvs_avg35
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I attached dmrirc.example
? ? ? ? ? ? (configuration
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? file) and <subjd>/scripts/trac-all.log.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Thanks in advance,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ????????????
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ????????
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ??
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri WATANABE, M.D.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Department of Psychiatry,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University Hospital, Kyoto
? ? ? ? ? ? Prefectural
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University of Medicine
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2016-06-03 9:51 GMT+09:00 Anri
? ? ? ? ? ? WATANABE
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? <z2aanri@koto.kpu-m.ac.jp>:
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi, Anastasia.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? There aren't any .log files
? ? ? ? ? ? but text
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? files like
? ? ? ? ? ? lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I guess text
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? files complete all pathways
? ? ? ? ? ? and
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? measures.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ????????????
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ????????
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ??
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri WATANABE, M.D.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Department of Psychiatry,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University Hospital, Kyoto
? ? ? ? ? ? Prefectural
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University of Medicine
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2016-06-02 3:03 GMT+09:00
? ? ? ? ? ? Anastasia
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Yendiki <ayendiki@nmr.mgh.harvard.edu>:
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Thanks, Anri. So the
? ? ? ? ? ? previous
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? steps seem to have run fine. Are there any
? ? ? ? ? ? .log
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? files
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? created in the stats/
? ? ? ? ? ? folder,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? which is created by trac-all -stat?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? On Wed, 1 Jun 2016, Anri
? ? ? ? ? ? WATANABE
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? wrote:
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi Anastasia,?This
? ? ? ? ? ? is a
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? <subjid>/scripts/trac-all.log of one
? ? ? ? ? ? subject of
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? the group.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Thanks,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ????????????
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ????????
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ??
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri WATANABE,
? ? ? ? ? ? M.D.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Department of
? ? ? ? ? ? Psychiatry,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University
? ? ? ? ? ? Hospital, Kyoto
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Prefectural University of Medicine
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2016-05-31 22:55
? ? ? ? ? ? GMT+09:00
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anastasia Yendiki
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? <ayendiki@nmr.mgh.harvard.edu>:
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi Anri -
? ? ? ? ? ? Can you also
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? send your log file (scripts/trac-all.log)?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I'll need to see
? ? ? ? ? ? what
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? exactly was
? ? ? ? ? ? running
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? when the error occurred. Thanks!
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? a.y
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? On Sat, 28
? ? ? ? ? ? May 2016,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri WATANABE wrote:
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hello
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anastasia,sorry for few information and
? ? ? ? ? ? let me tell
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? you
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? command and
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? error
? ? ? ? ? ? log.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Command:?trac-all ?stat ?c
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Error
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? log:?Loading output reference volume from
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? /Applications/freesurfer/subjects/cvs_avg35
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? corRead(): can't
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? open file
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? /Applications/freesurfer/subjects/cvs_avg35/COR-.info
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ERROR:
? ? ? ? ? ? Could not
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? read
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? /Applications/freesurfer/subjects/cvs_avg35
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? dmrirc.example?(configuration file) is
? ? ? ? ? ? attached to
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? this
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? e-mail.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Thanks
? ? ? ? ? ? in
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? advance,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ????????????
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ????????
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ??
? ? ? ? ? ? ??
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri
? ? ? ? ? ? WATANABE,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? M.D.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? Department of
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Psychiatry,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? University
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hospital, Kyoto Prefectural University of
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Medicine
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? **********************************************************************
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? 2016-05-27 22:57
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? GMT+09:00 Anastasia Yendiki
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? <ayendiki@nmr.mgh.harvard.edu>:
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? Hi Anri -
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I do not know what command line you ran
? ? ? ? ? ? and
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? what your
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? configuration
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? file looks like, so it is very
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? hard for
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? me to suggest solutions.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? Best,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? a.y
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? On Fri, 27
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? May 2016, Anri WATANABE wrote:
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? Hi
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anastasia,?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Thank you for your answer.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? There aren't?stats/*.path.mean.txt
? ? ? ? ? ? files?and
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? terminal says
? ? ? ? ? ? 'Could
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? not
? ? ? ? ? ? read
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? /Applications/freesurfer/subjects/cvs_avg35.' I
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? checked
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? /Application/freesurfer/subjects/cvs_avg35
? ? ? ? ? ? folder
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? and
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? couldn't find
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? COR-.info file.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Could you tell me any resolutions, please?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Thanks,?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? Anri
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? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? WATANABE, M.D.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Department of Psychiatry,
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? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University Hospital, Kyoto Prefectural
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? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? of Medicine
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? ? ? ? ? ? Yendiki
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? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? <ayendiki@nmr.mgh.harvard.edu>:
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? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi Anri - The FA values are extracted in
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? the native space
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? of
? ? ? ? ? ? each subject,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? which is why
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? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? those are the only
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? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? coordinates that you see. If you want to
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? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
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? ? ? ? ? ? last part
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? ? ? ? ? ? ? ? ? of
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? the TRACULA
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? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? tutorial).
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
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? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Best,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ?
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? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? On Wed, 18 May 2016, Anri WATANABE
? ? ? ? ? ? wrote:
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Dear experts,?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I use TRACULA to examine a measure
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? (FA) at each voxel
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? in one
? ? ? ? ? ? pathway.
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? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? MNI
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? coordinate
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? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Thank you!
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Regards,?
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? ? ? ? ? ? ? ? ? ? ?
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? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Anri WATANABE, M.D.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Department of Psychiatry,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? University Hospital, Kyoto
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Prefectural
? ? ? ? ? ? University of
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? Medicine
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
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? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? _______________________________________________
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Freesurfer mailing list
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Freesurfer@nmr.mgh.harvard.edu
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
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? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? The
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? information in this e-mail is intended
? ? ? ? ? ? only
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? for the person to
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? whom
? ? ? ? ? ? it is
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? addressed. If you believe this e-mail was
? ? ? ? ? ? sent
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? to
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? you in error
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? and
? ? ? ? ? ? the e-mail
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? contains patient information, please
? ? ? ? ? ? contact
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? the
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Partners
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? Compliance
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? HelpLine at
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? http://www.partners.org/complianceline .
? ? ? ? ? ? If the
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? e-mail was sent
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? to you
? ? ? ? ? ? in error
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
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? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? does not contain patient information,
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? please
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? contact the
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? sender
? ? ? ? ? ? and
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? properly
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? dispose of the e-mail.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? _______________________________________________
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? Freesurfer
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? mailing list
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Freesurfer@nmr.mgh.harvard.edu
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? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? The
? ? ? ? ? ? information
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? in this e-mail is intended only for the
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? person to whom it
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? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? addressed. If
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? you believe this e-mail was sent to you in
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? error and the
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? contains patient
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? information, please contact the Partners
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Compliance
? ? ? ? ? ? HelpLine
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? at
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? http://www.partners.org/complianceline .
? ? ? ? ? ? If the
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? e-mail was
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? sent to you in
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? error
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
...
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------------------------------
Message: 6
Date: Wed, 3 Aug 2016 10:43:56 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] brain mask and T1 are not the same size
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <57A2032C.4050903@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
Sorry, I did not see that one of the volumes was 256x256x255. I cannot
replicate here on your data using 5.3 under linux. Can you say exactly
what you do in freeview? Also, what version of FS are you using? And
what platform?
On 08/03/2016 06:50 AM, Isabelle Deschamps wrote:
I had the problem before and was told the the output of mri_info
should be 256 x 256 x 256 for the dimensions of the brainmask and T1.
When I run mri_info on the brainmask.mgz that I modified I have 256 x
256 x 255 but the T1 I have 256 x 256 x 256. The zstart and zend are
also different between the brainmask and T1. Could that be the source
of the problem?
*Modified brainmask:*
mri_info
/Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/brainmask.mgz
Volume information for
/Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/brainmask.mgz
type: MGH
dimensions: 256 x 256 x 255
voxel sizes: 1.0000, 1.0000, 1.0000
type: UCHAR (0)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -127.5, zend: 127.5
*T1:*
mri_info
/Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/T1.mgz
Volume information for
/Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S14_FS/mri/T1.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.0000, 1.0000, 1.0000
type: UCHAR (0)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
*Non-modified brain mask:*
mri_info /Users/Isabelle/Desktop/S14/brainmask_orig.mgz
Volume information for /Users/Isabelle/Desktop/S14/brainmask_orig.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.0000, 1.0000, 1.0000
type: UCHAR (0)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
I am not sure why I get this error and why the change in dimensions,
zstart and zend between the brainmask and T1. For all other
participants that do not have an error the information of mri_info for
dimensions, zstart and zend is the same for the brainmask and T1. So I
am very confuse as to why these 4 participants are exiting with the
same error. I am not sure what I am doing wrong in this case.
Thanks,
Isabelle
On 3 Aug 2016, at 06:00, freesurfer-request@nmr.mgh.harvard.edu
<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
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When replying, please edit your Subject line so it is more specific
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Today's Topics:
1. DTI of frontostriatal tracts (Ritobrato Datta)
2. Re: Multiple Comparison Question for surface-based analyses
(Douglas N Greve)
3. Re: brain mask and T1 are not the same size (Douglas N Greve)
4. Save Overlay via Command Line (Jordan Chad)
5. Re: MNI coordinates of all the vertices of fsaverage
(Douglas N Greve)
6. Retinotopy questions (Xiaomin Yue)
7. Re: DTI of frontostriatal tracts (Anthony Dick)
8. Re: DTI of frontostriatal tracts (Ritobrato Datta)
9. Re: Labels to MNI152, SPM compatible (Thomas Yeo)
10. Re: Multiple Comparison Question for surface-basedanalyses
(Ajay Kurani)
11. mapping error (Caroline Beelen)
----------------------------------------------------------------------
Message: 1
Date: Tue, 2 Aug 2016 12:26:43 -0400 (EDT)
From: Ritobrato Datta <ridatta@mail.med.upenn.edu
<mailto:ridatta@mail.med.upenn.edu>>
Subject: [Freesurfer] DTI of frontostriatal tracts
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:
<1643573287.53129960.1470155203784.JavaMail.root@zimbra.upenn.edu
<mailto:JavaMail.root@zimbra.upenn.edu>>
Content-Type: text/plain; charset=utf-8
Hello All,
We are studying adolescents with HIV and are interested in
frontostriatal tracts (anything from frontal cortex to
caudate/putamen/nucleus accumbens) and tracts connected to the amygdala.
Is anyone aware of DTI based atlases where these tracts are defined
in MNI or some other standard space ?
Any suggestions will be very helpful.
Best
Ri
------------------------------
Message: 2
Date: Tue, 2 Aug 2016 12:54:01 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Multiple Comparison Question for
surface-based analyses
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID: <57A0D029.7020303@nmr.mgh.harvard.edu
<http://nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset=windows-1252; format=flowed
I have been doing simulations similar to #1 (Eklund) using
surface-based analysis on both thickness and fMRI. I'll prepare a report
of the results, but the early indications are that the same effect is in
play, though it does not look like the effects are as bad as in Eklund.
For thickness analysis using applied smoothing of 5 or 10 mm FWHM, for a
voxel-wise threshold of .001, the false positives are appropriate (ie,
5%). For a voxel-wise threshold of .01, the false positives is only a
little off (about 7%); for a voxel-wise threshold of .05, the FPR is
about 13%. If the data are not smoothed at all, then the false positive
rates go way up. The reason appears to be the same as found in Eklund
(ie, the autocorrelation function has a heavier-than-Gaussian tail). I
did the analysis by randomly selecting 40 subjects from a homogeneous
data set of 809 subjects aged 18-25. I then made two groups of 20
subjects each and ran a two-group test, then found clusters significant
based on our Monte Carlo (Gaussian) simulations. I repeated this several
thousand times. Any significant clusters were interpreted as false
positives. These results are much better than Eklund, but Eklund was
analyzing fMRI data.
I'm still working on the fMRI data. It is much more complicated because
the results depend on the assumed stimulus schedule (eg, 10 sec blocks
vs 30 sec blocks) and whether a one-group or two-group anaysis is done;
nuisance variables also play a role. At very low cluster-forming
thresholds (ie, .05), the FPR is roughly 20-30%. At a threshold of .01,
the FPR is about 3-13%. At a threshold of .001 are about 1-6%. This is
all for an applied smoothing level of 5mm.
All of these results are preliminary, so don't take them as true and
established yet. As a reminder, you can always do a permutation test
using mri_glmfit-sim. Eklund found that permutation did pretty well in
most cases.
doug
On 8/2/16 12:43 AM, Ajay Kurani wrote:
Hello Freesurfer Experts,
Recently there were two article published regarding clusterwise
simulations for volumetric fmri analyses and potential errors for
underestimating clusterwise extent thresholds.
1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes
2) biorxiv.org/content/early/2016/07/26/065862
<http://biorxiv.org/content/early/2016/07/26/065862>
<http://biorxiv.org/content/early/2016/07/26/065862>
One issue pointed out from these articles seems software specific,
however the second issue is determining the proper clustersize. The
heavy-tail nature of spatial smoothness seems to be ignored and a
gaussian shape is generally assumed, leading to an underestimation of
the spatial smoothness which can affect cluster size calculations.
The issues are highlighted in the second article above.
I created my own monte carlo simulation in Freesurfer for a specific
brain template and I wanted to find out if these concerns also apply
to my surface based simulations? I am not sure if it does since the
monte carlo tool is a GRF simulation as opposed to an analytic
equation, however given that these articles were highlighted very
recently, I wanted to ensure I am running things appropriately for
surface based cortical thickness/dti analyses.
Thanks,
Ajay
_______________________________________________
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------------------------------
Message: 3
Date: Tue, 2 Aug 2016 13:18:09 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] brain mask and T1 are not the same size
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID: <57A0D5D1.20301@nmr.mgh.harvard.edu
<http://nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset=windows-1252; format=flowed
The voxel size and dimensions of all three volumes are the same: 256^3
and 1mm^3. Why do you think they are not?
On 08/02/2016 09:17 AM, Isabelle Deschamps wrote:
Yes, of course. The upload is now active.
Thank you again for your help,
Isabelle
On 2 Aug 2016, at 08:55, freesurfer-request@nmr.mgh.harvard.edu
<mailto:freesurfer-request@nmr.mgh.harvard.edu>
<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
Re: [Freesurfer] brain mask and T1 are not the same size
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
------------------------------
Message: 4
Date: Tue, 2 Aug 2016 14:17:28 -0400
From: Jordan Chad <jchad@research.baycrest.org>
Subject: [Freesurfer] Save Overlay via Command Line
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CA+FdjQX9T0cr50M4awGdW0YJHM3n32FrFcQ9AvGM_+=vMB1JPQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hello,
I am trying to perform between-subject statistics on cortical DTI data in
certain ROIs.
I can do this by overlaying the DTI data on the surfaces on tksurfer,
load
and mask the label with the ROI, and then go to File -> Save Overlay.
After
doing this for all subjects I can perform statistics on the output files.
However, it is not practical to do this for all >200 subjects for
each ROI.
Is there a way to go about this process on the command line?
Thank You,
Jordan Chad
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Message: 5
Date: Tue, 2 Aug 2016 15:40:33 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MNI coordinates of all the vertices of
fsaverage
To: Sabin Khadka <mr.sabinkhadka@gmail.com>,
"Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu>
Message-ID: <57A0F731.9050108@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
By default they are in talairach. But you can get mni305 by adding
--nofixmni to the surfcluster command line
On 08/02/2016 03:36 PM, Sabin Khadka wrote:
Hi Doug, Thanks. Are these coordinates in talairach or MNI space? From
previous post you mentioned these are in mni305 space but if I look at
the log file it say TalX, TalY, TalZ. I am a little confused.
And how can I convert these coordinates to MNI152 space?
thanks for your help.
Cheers,
Sabin Khadka
On Mon, Aug 1, 2016 at 9:24 PM, Douglas Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
ps. you can always just load the xyz in the label into matlab and
compute the centroid
On 8/1/16 10:23 AM, Sabin Khadka wrote:
Anyone?
Cheers,
Sabin Khadka
On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka
<mr.sabinkhadka@gmail.com <mailto:mr.sabinkhadka@gmail.com>> wrote:
Hi Doug, I tried to pick up from the thread below to get MNI
coordinates of each destrieux parcellation region.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html
I created label files from
mri_annotation2label --subject fsaverage --hemi lh(/rh)
--annotation aparc.a2009s --outdir label_destrieux # which
works fine
And I tried to get the coordinates of each labels using
mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness
--clabel <label file> --sum <output file> --centroid --thmin
0 --hemi lh --subject fsaverage
But, all left labels would produce the same coordinates and
so does right labels. (I've attached few example files here
with). Also, it says TalX, TalY, TalZ are these coordinates
in MNI or Talairach?
Thanks for help.
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
------------------------------
Message: 6
Date: Tue, 2 Aug 2016 21:55:38 +0000
From: Xiaomin Yue <yuexm@hotmail.com>
Subject: [Freesurfer] Retinotopy questions
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <BLU406-EAS159BDB45B45CE0F30358A01B3050@phx.gbl>
Content-Type: text/plain; charset="utf-8"
Hi,
I am running a retinotopy analysis using fsfast 5.3. ?The design has
15 TR blank before and after wedge presented for 30 TR with 7
repeats, and ring presented ?for 24 TR with 7 repeats. ?Here is my
analysis:?mkanalysis -s vz -a rtoy.self.rh -fsd bold -fwhm 2 -nskip
15 -TR 1.5 -retinotopy 48 -paradigm rtopy.par.
The data doesn't look right. ?I assume that the analysis does require
the stimuli presentation as a full circle, which means that the last
15 TR blank was accounted as the stimuli presentation time. If I am
correct, ?is there simple way to take care of it in mkanalysis-sess?
Second, the ring and wedge were presented in different frequency. It
seems that the anslysis-sess does not take this into account in the
current configration. Is there a way to specify this??
Thanks very much for the help.?
Xiaomin?
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_______________________________________________
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Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
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------------------------------
Message: 7
Date: Tue, 2 Aug 2016 18:34:53 -0400
From: Anthony Dick <adick@fiu.edu>
Subject: Re: [Freesurfer] DTI of frontostriatal tracts
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <ef9ff21a-e069-a7b7-74e8-04ab84e11840@fiu.edu>
Content-Type: text/plain; charset="windows-1252"; format=flowed
Hello,
See the paper at this link: http://www.ncbi.nlm.nih.gov/pubmed/25086832
Anthony
On 8/2/16 12:26 PM, Ritobrato Datta wrote:
Hello All,
We are studying adolescents with HIV and are interested in
frontostriatal tracts (anything from frontal cortex to
caudate/putamen/nucleus accumbens) and tracts connected to the
amygdala.
Is anyone aware of DTI based atlases where these tracts are defined
in MNI or some other standard space ?
Any suggestions will be very helpful.
Best
Ri
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in
Cognitive Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: adick@fiu.edu
Webpage: http://myweb.fiu.edu/adick
Join the Society for the Study of Human Development:
http://www.sshdonline.org
------------------------------
Message: 8
Date: Tue, 2 Aug 2016 19:41:51 -0400 (EDT)
From: Ritobrato Datta <ridatta@mail.med.upenn.edu>
Subject: Re: [Freesurfer] DTI of frontostriatal tracts
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<1403815860.53391808.1470181311536.JavaMail.root@zimbra.upenn.edu>
Content-Type: text/plain; charset=utf-8
Many thanks.
Best
Ri
----- Original Message -----
From: Anthony Dick <adick@fiu.edu>
To: freesurfer@nmr.mgh.harvard.edu
Sent: Tue, 02 Aug 2016 18:34:53 -0400 (EDT)
Subject: Re: [Freesurfer] DTI of frontostriatal tracts
Hello,
See the paper at this link: http://www.ncbi.nlm.nih.gov/pubmed/25086832
Anthony
On 8/2/16 12:26 PM, Ritobrato Datta wrote:
Hello All,
We are studying adolescents with HIV and are interested in
frontostriatal tracts (anything from frontal cortex to
caudate/putamen/nucleus accumbens) and tracts connected to the
amygdala.
Is anyone aware of DTI based atlases where these tracts are defined
in MNI or some other standard space ?
Any suggestions will be very helpful.
Best
Ri
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in
Cognitive Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: adick@fiu.edu
Webpage: http://myweb.fiu.edu/adick
Join the Society for the Study of Human Development:
http://www.sshdonline.org
_______________________________________________
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 9
Date: Wed, 3 Aug 2016 10:43:40 +0800
From: Thomas Yeo <ythomas@csail.mit.edu>
Subject: Re: [Freesurfer] Labels to MNI152, SPM compatible
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CANZVnTaW8ja0F7NpK9ErqSQpcBHcGxRRvNm7T3WFTQTNyN4Ovw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Matyas,
In freeview, looks fine to me. See attached.
Can you send us your screenshot?
Regards,
Thomas
On Tue, Aug 2, 2016 at 9:39 PM, Maty?? Kuhn <matyas.kuhn@gmail.com>
wrote:
The Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz-------------- next part --------------
comes from
http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011,
and the description says it is the FSL MNI152 1mm template interpolated
and intensity normalized into a 256 x 256 x 256 1mm-isotropic volume
(obtained by putting the FSL MNI152 1mm template through recon-all ). So
I supposed it is in MNI305 after it was processed with freesurfer. When
I overlap the
Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz and
Template_T1_IXI555_MNI152.nii it is really shifted so I think it is not
in MNI152.
When I add the --invertmtx then the result is still the same, empty
image.
I uploaded those images here:
https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question.zip ,
if you want to try yourself.
Thank you,
Matyas
Dne 2.8.2016 v 14:55 Douglas Greve napsal(a):
From the names, it looks like both the seg vol and the template
vol are both in mni152. Where did
Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz
come from? One thing you can try is to invert the registration by
adding --invertmtx to the command line.
On 8/2/16 8:18 AM, Maty?? Kuhn wrote:
Hi Freesurfer experts,_______________________________________________
I just started to use Freesurfer and I was wondering how can I convert
images from MNI305 which uses Freesurfer to MNI152 which is used
by SPM.
We would like to get MNI152 template of Yeo parcelation
( )
so we can overlay with our results from SPM fMRI analysis.
I tried this:
mri_label2vol --seg
/path_to_analysis/Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz
\
--temp
/path_to_analysis/Template_T1_IXI555_MNI152.nii \
--reg
$FREESURFER_HOME/average/mni152.register.dat \
--o /path_to_analysis/output_mni152.nii
which resulted in image full of zeros (so maybe problem with
registration?). The "Template_T1_IXI555_MNI152.nii" is the MNI152
template which is used by Computational anatomical toolbox 12 for SPM
from Christian Gaser and his group.
Thanks in advance for any suggestions,
Matyas
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Compliance HelpLine at
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------------------------------
Message: 10
Date: Wed, 3 Aug 2016 02:45:47 -0500
From: Ajay Kurani <dr.ajay.kurani@gmail.com>
Subject: Re: [Freesurfer] Multiple Comparison Question for
surface-basedanalyses
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CA+uskrDgnhv2SaRJHGHUQQVJseuEKQC6ov-=f7N0DYrTsgeLTg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Doug,
Thank you very much for your update regarding this issue.
1)Just curious, will LGI be included in this report as this is another
analysis of interest?
2)As for the cortical thickness I originally used 15mm in the analysis so
based on your email I think using 5-10mm may be more prudent in order to
minimize FPR. From your email, I understand that mris_surf2surf
(command I
use to convert individual subject to fsaverage or template and smooth to
10-15mm) assumes an ACF estimation of smoothness which DOES NOT take into
account the long tail distribution. Does this mean that when using
mri_mcsim on my own template, the cluster extents for a given smoothness
will be undersampled due to the fact that the "true" smoothness is more
than what is estimated in the simulation, correct? For instance, when I
select 15mm in qdec, it would point to the 21mm folder (fwhm.dat=20.8mm
estimate), and I would select a given cluster extent for p=0.05.
However,
in this case, 15mm may translate to a larger FWHM than the estimated
21mm,
correct?
3)You mentioned that I can use mri_glmfit-sim which is permutation
testing
based. I am struggling a bit in understanding how this differs from the
simulation ran with mri_mcsim/qdec? Does qdec monte carlo simulation
option run mri_glmfit-sim in the background to estimate the smoothness
which looks up the cluster extent within the mri_mcsim based on the
estimated FWHM? If so, is this estimate incorrect due to the fact
that the
long tails are not taken into account?
Thanks,
Ajay
On Mon, Aug 1, 2016 at 11:43 PM, Ajay Kurani <dr.ajay.kurani@gmail.com>
wrote:
Hello Freesurfer Experts,-------------- next part --------------
Recently there were two article published regarding clusterwise
simulations for volumetric fmri analyses and potential errors for
underestimating clusterwise extent thresholds.
1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes
2) biorxiv.org/content/early/2016/07/26/065862
One issue pointed out from these articles seems software specific,
however
the second issue is determining the proper clustersize. The heavy-tail
nature of spatial smoothness seems to be ignored and a gaussian shape is
generally assumed, leading to an underestimation of the spatial
smoothness
which can affect cluster size calculations. The issues are
highlighted in
the second article above.
I created my own monte carlo simulation in Freesurfer for a specific
brain
template and I wanted to find out if these concerns also apply to my
surface based simulations? I am not sure if it does since the monte
carlo
tool is a GRF simulation as opposed to an analytic equation, however
given
that these articles were highlighted very recently, I wanted to
ensure I am
running things appropriately for surface based cortical thickness/dti
analyses.
Thanks,
Ajay
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Message: 11
Date: Wed, 3 Aug 2016 10:00:18 +0000
From: Caroline Beelen <caroline.beelen@kuleuven.be>
Subject: [Freesurfer] mapping error
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<40b86b2ee4c24b96b8d585eb822a02cd@ICTS-S-EXMBX26.luna.kuleuven.be>
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Dear FS,
An aparc.annot ctab file was created but I got the following error:
Colortable:aparc.annot.ctab
Annotname: myaparc
Nhitsfile nhits.mgh
Nlabels 6
Labeltresh 0 0.00000
Loading freesurfer/fsaverage/surf/lh.orig
1 -1 not found
2 -1 not found
3 -1 not found
Etc...
Mapping unhit to unknown
Found 132101 unhit vertices
Writing annot to freesurfer/fsaverage/lh.myaparc.annot
I guess my ctab file is incorrect? I included an example of a label
with it.
Thanks again for your help.
Caroline
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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