#@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011
/home/virtualuser/freesurfer/subjects/test005/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
I am receiving the error (pasted below) on about half of my scans, despite
all cans using same protocol. I detect no obvious issue
Small Update: Error Disappears if Using Freesurfer version 5.0 instead of
5.1. However, since I am keenly interested in the hippocampal-subfield
segmentation capabilities of the most recent version, I am loathe to
regress to an earlier version of FreeSurfer
-
Joshua Lee
Graduate Student
Center for
Dear FreeSurfer experts,
I have a question regarding pial area analysis.
What is commonly used as a nuisance variable to correct for brain size
difference between groups (e.g men vs women)? Can you suggest any
article where this is discussed or has been done?
Thank you,
Tanja.
can you send us an example that works in 5.0 and fails in 5.1?
thanks
Bruce
On Wed, 2 Nov
2011, Joshua Lee wrote:
Small Update: Error Disappears if Using Freesurfer version 5.0 instead of
5.1. However, since I am keenly interested in the hippocampal-subfield
segmentation capabilities of the
Typically one uses either a measure of brain volume or an estimate of
intracranial volume -- the choice depends on whether or not you want to
control for whole brain atrophy when making your interpretations, in
which case you would use brain volume rather than ICV. There have
been numerous posts
Thank you Michael,
I was wondering about a nuisance specific to area analysis. I
understand using ICV or brain volume in volumetric analysis, but for
area analysis something like overall pial area seems more logical to
me. That is why I am curious if there is any literature about area
(surface)
Oops -- I missed that aspect of your question. Yes, that would make
sense, and is precisely what we did in a 2010 paper in Brit J Psychiatry
(196:150-7). Although the measures in that paper were not FS-based, we
used appropriate global volume, area, and thickness measures to covary
for each
Thank you very much Michael for an extensive answer.
I am doing analysis in QDEC, thank you for pointing that, I will check the list.
On Wed, Nov 2, 2011 at 2:52 PM, Michael Harms mha...@conte.wustl.edu wrote:
Oops -- I missed that aspect of your question. Yes, that would make
sense, and is
Hello Bruce et al,
I have a dataset processed in 5.0. Can I use the Hippocampal Sub-Field
Segmentation tools of 5.1 to process these?
thanks so much,
Alan
BIDMC/ Psychiatry
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
I believe so, but Koen is the one who would know for sure
Bruce
On Wed, 2 Nov
2011, Alan Francis wrote:
Hello Bruce et al,
I have a dataset processed in 5.0. Can I use the Hippocampal Sub-Field
Segmentation tools of 5.1 to process these?
thanks so much,
Alan
BIDMC/ Psychiatry
Dear FS users,
I would like to use FS to calculate WM hypointensitis (so-called black
holes) for patients with multiple sclerosis, but
1. I don't know which stat file I should use to report the volumes, such as
total WM, WM hypointensities, etc
2. which editing tool I must use when the lesion is
Thats an interesting suggestion, givien my recently reported issues with
the talairach in FreeSurfer 5.1.
-
Joshua Lee
Graduate Student
Center for Mind and Brain
Department of Psychology
University of California, Davis
530.747.3805
On Wed, Nov 2, 2011 at 11:41 AM, Bruce Fischl
Dear experts,
We have recently encountered processing errors (during recon-all and
-autorecon23) due to the creation of symbolic links within our SUBJECTS_DIR.
Since our data were located on a data mount, the system somehow could not
source the linked file. We have addressed this issue by
One more thing I noticed... When I run mri_anatomical_stats on the annot file,
it tells me this:
reading colortable from annotation file...
colortable with 207 entries read (originally
/home/leila/freesurfer/mycolortables/original_color_P1_16_R.txt)
I don't find this txt file anywhere though.
Hi David, an easy way is to load the segmentation as both a segmentation
and as the auxiliary volume (not aux segmentation). When you click on a
point, you'll see the number of the segmentation in the aux field of the
control window.
doug
David Grayson wrote:
Hi Doug,
I made good progress
no, it saves the actual color table in the annot file.
doug
David Grayson wrote:
One more thing I noticed... When I run mri_anatomical_stats on the annot
file, it tells me this:
reading colortable from annotation file...
colortable with 207 entries read (originally
Carolina Valencia wrote:
Dear FS users,
I would like to use FS to calculate WM hypointensitis (so-called black
holes) for patients with multiple sclerosis, but
1. I don't know which stat file I should use to report the volumes,
such as total WM, WM hypointensities, etc
Use aseg.stats
2.
joshua,
try adding -use-mritotal to the end of your recon-all command. it will
use an alternate way to compute the talairach.xfm which works better on
some data.
the change from v5.0 to v5.1 in the talairach stage was that in v5.1,
the talairach.xfm is needed to compute nu.mgz, so the talairach
Thanks Nick,
Is use-mritotal equivalent to what version 5.0 does by default?
Also, any suggestions on why this talairach error would occur only on a
portion of my data, despite all being collected with the same imaging
protocol, same conversions from dicom, etc?
-
Joshua Lee
Graduate Student
your solution of copying fsaverage and the EC_average dirs to your
SUBJECTS_DIR is the proper one in this case. symlinks are used only to
save space.
this data (fsaverage and EC_average) is used only during recon-all, and
doesnt need to 'travel' with the subject data (unless you intend to
no, v5.0 uses nu.mgz as input to the talairach_avi routine, whereas v5.1
uses orig.mgz.
its hard to say why it would fail for some subjects but not others,
other than head positioning and to some degree ventricle size makes a
difference.
n.
On Wed, 2011-11-02 at 16:10 -0400, Joshua Lee wrote:
OK, now I understand better.
One further question: Would the use of MRI-total degrade quality of the
Freesurfer segmentations substantively, and would using it only on a
portion of my data introduce a systematic bias to the data set?
Josh
On Wed, Nov 2, 2011 at 4:15 PM, Nick Schmansky
it should not change the quality of the subcortical or cortical streams
at all. the talairach.xfm is used for reporting purposes in the gui
tools, and for group averaging (in some instances, qdec not being one of
them). so i would not worry about introducing a bias. if you are
concerned about a
Thank you for the response Nick. Knowing that these are the only symlinks is
reassuring. However, we do plan on running group analyses. The symbolic link
within the subject directories already point to the local directory while my
data are on the server (the folders were copied to the server
i dont think the symlinks in the group analysis instance should be an
issue either. the only time it would be is if the 'fsaverage' used to
create the group analysis files (say, using recon-all -qcache) did not
match the fsaverage found in your subjects dir, which would be the case
if fsaverage
Hi,
What was the reason for this switch? Intuitively it seems that a
bias-corrected image is likely to get a better registration (since I assume
the target has essentially uniform intensities).
Michael
On Wed, Nov 2, 2011 at 1:15 PM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote:
no, v5.0
Hi guys,
We have a sample of 150+ pediatric brains that we pumped through FS 5.1,
and in an easy majority of them the white/pial surface accuracy in the
anterior temporal lobe is poor.
I know that this is an area where problems have frequently been
reported. What is it about that area in
Hi Michael,
It might have something to do with low myelin content there in general (will
make grey matter harder to tell from CSF) and late myelination (at least
part of the anterior temporal cortex has its white matter myelinate quite
late in development), which would reduce grey/white contrast.
Hello,
What is the difference between the mris_ms_surface_CNR and mri_cnr
functions? (I couldn't find any descriptive info for either). And are
either of them useful for identifying datasets with poor
gray/white/csf contrast?
thanks,
-MH
--
Michael Harms, Ph.D.
Hi Michael
we found that the conversion to unsigned character sometimes compressed
the brain into only a couple of bits of the dynamic range. We know use
the talairach xform to locate the center of the brain and make sure that
a ball centered at the tal origin occupies a lot of the histogram.
Hi Mike,
I would guess it's because of incomplete myelination there. Is the
darkening predominantly in the wm?
cheers
Bruce
On Wed, 2 Nov 2011, Michael Harms wrote:
Hi guys,
We have a sample of 150+ pediatric brains that we pumped through FS 5.1,
and in an easy majority of them the
Hi,
I have converted a custom-made annotation file to a volume, and now I am trying
to find a table with the labels and their corresponding label codes (index
values which are created when the annotation file is converted to a volume). I
only have the “annotation values” or color codes for
Michael,
I had a similar problem with about 10% of pediatric datasets I used.
In my case the problem also often included anterior and ventral
surface of the frontal lobes. Much like you I looked at possible
explanations and a medical physicist and a radiologist I worked with
blamed inaccuracies
Hi Anastasia,
I am trying to run Tracula for the first time in our lab and
I'm getting errors during step 2 that seem to involve how the program wants
to be launched via grid. I've attached the configuration file I'm using and
the error message is below...
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