Make sure that you are looking at the surfaces though. It looks like the
image you attached was the aseg.mgz, and you should not be using the
"cortex" as defined in the aseg.mgz because that is based on the
volume-stream segmentation. Either overlay the surfaces, or take a look
at the aparc+aseg
FreeSurfer will preserve your previous edits (e.g., brainmask.mgz edit, or wm.mgz edits, among others) when you run a newer version on top of an older version. However, that is no guarantee that there won't be any issues following the re-processing with
the newer version, so it is best to a
Is this perhaps the same issue that I reported in this thread?:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38258.html
If so, it is due to a "bug" of sort in the recon-all in v5.3
It appears that some of our followup conversation occurred off list, so
for others benefit, I'm
e, or
just white/pial crossing?
cheers
Bruce
On Fri, 24 Apr 2015, Harms, Michael wrote:
>
> Is this perhaps the same issue that I reported in this thread?:
>
>http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38258.html
>
> If so, it is due to a "bug" o
Your analogy just has to be interpreted in the context of the winter of
1936-1937 or more recently 2011-2012, not 2014-2015!
http://www.erh.noaa.gov/box/climate/bossnw.shtml
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of M
Hi Anastasia,
We are looking at running TRACULA on some data, where we were attracted by the longitudinal component of TRACULA. Is a paper on the longitudinal aspect of TRACULA in the works?
If we have multiple dMRI runs/series
per imaging session, do we need to merge/concatenate thos
y School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110Email: mha...@wustl.edu
On 7/6/15 12:00 PM, "Anastasia Yendiki"
wrote:
Forgot to reply re: merging. You have to merge them yourselves, sor
Hi Chris,
I would generate some scatterplots of some of the various "summary" type measures available in aseg.stats. That will quickly show you if you indeed have some pronounced outliers that don't fall near the regression line.
e.g., compute a 4 x 4 panel scatterplot of CortexVol, SubCo
As an add-on to this, since the ICV (eTIV) is based solely on the
"talairach transform", you should really QC the accuracy of the talairach
transform itself if you intend to use ICV as a covariate. In particular,
the talairach transform can be off, and thus your estimated ICV would be
wrong, but
y aseg.stats file
Thanks!
AS
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Harms, Michael
[mha...@wustl.edu]
Sent: Thursday, July 30, 2015 11:23 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Frees
ampus size , controlling for brain size, means you
are interested in testing if the hippocampus is relative small for
someone with that brain size. While the brain size is affected by both
head size and disease.
Cheers, Martin
On 07/30/2015 11:58 AM, Harms, Michael wrote:
> Sure, that would
Hi Emma, Martin,
I'd like to offer a different perspective. Based on what you showed, I thought that the motion related ringing wasn't too bad, and I'd expect that FS would handle that data quite well, which is what you indicated was indeed the case. If we all started
excluding data of th
.
Cheers, Martin
On 08/05/2015 05:44 PM, Harms, Michael wrote:
Hi Emma, Martin,
I'd like to offer a different perspective. Based on what you showed, I thought that the motion related ringing wasn't too bad, and I'd expect that FS would handle that data quite well, which is
Sounds like you had a clinical scan and got a copy of a sagittal scan series and an axial scan series. Those would be "2D" acquisitions in which the slice thickness is probably considerably thicker than the in-plane resolution. That kind of data isn't
ideal for FS. Rather, data for FS is
Hi,
I would sum up the set of labels you have in (2) if you want the best estimate of ventricular volume.
See the following page for additional info on the various measures:
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
In particular, I would expect your measure in (2) would
That depends on a number of complicated, potentially inter-related factors such as:
1) What exactly is Philips putting into that field in its DICOMs
2) Is mri_convert returning a NIFTI with the same orientation as Philips is using for its gradient directions.
3) Importantly, if the acquisitio
I'm a fan of using global mean thickness as a covariate for thickness analyses, and total surface area as a covariate for surface area analyses. That way you directly covary for possible global effects using the same type of measure that you are analyzing.
cheers,
-MH
--
Michael Harm
surfer-boun...@nmr.mgh.harvard.edu]
On Behalf Of Harms, Michael
Sent: 29 September 2015 04:30
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] total grey matter volume
I'm a fan of using global mean thickness as a covariate for thickness analyses, and total surface area as
Hi,
You can simply rerun 'recon-all -all’ on top of your already processed/edited subject, and it will respect your previous edits. Of course, it is a good idea to still review/QC the results afterwards, to make sure that the outcome of those edits is satisfactory
under the new FS v
ain
Kx
On 22 June 2016 at 14:48, Harms, Michael
<mha...@wustl.edu> wrote:
Hi,
You can simply rerun 'recon-all -all’ on top of your already processed/edited subject, and it will respect your previous edits. Of course, it is a good idea to still review/QC the results
Hi,
When running TRACULA with longitudinal data, is it necessary for all scan waves of a given subject to be included in a single dmrirc file? My initial thought was “no”, that it would be fine to run one scan wave
per subject per dmrirc file (as long as the “baselist” variable is set
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Harms, Michael" <mha...@wustl.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
se that, unless
there's a systematic bias, you might expect that these changes will be in
different directions for different subjects and would then average out.
But it's a tricky issue.
Best,
a.y
On Fri, 1 Jul 2016, Harms, Michael wrote:
>
> Hi Anastasia,
> Looking throu
Hi,
Why not use total surface area to control for analyses involving area, and
mean cortical thickness to control for thickness? I’ve posted to the list
before regarding this, so you should be able to find those posts.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Hi,
There is nothing to solve — that is the expected behavior around the
hippocampus/amygdala.
See this FAQ:
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Thesurfac
esnearthemedialwall.2Chippocampus.2Candamygdalaaren.27taccuratelyfollowingt
hestructuresthere.HowcanIfixthis.3F
Hi,
The missing sulcus may be a consequence of the topology correction going awry. Check the “nofix” surface to see the surface before topology correction. If the topology correction is the problem, you’ll need to edit the wm.mgz. There is an example on
the FS tutorials.
ch
Hi Anastasia,
I was wondering what the resolution to this thread was:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42734.html
It sounds like a new version of dmri_paths was deemed necessary to appropriately process single time points in the longitudinal T
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Harms, Michael" <mha...@wustl.edu>
Reply-To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, July 20, 2016 at 11:59 AM
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Cc: Dillan Ne
Hi Michael - Which build of freesurfer do you use? I can send you the new
version of dmri_paths so you can try it out.
Best,
a.y
On Wed, 20 Jul 2016, Harms, Michael wrote:
>
> Hi Anastasia,
>
> I was wondering what the resolution to this thread was:
>
>http://www
Thanks for clarifying. Is the same true for the --pthr option of
dmri_pathstats as well?
i.e., --pthr is specifying the portion of the 99th percentile, not the
strict maximum?
thx,
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscie
FYI: I supplied a version of the “Gordon” parcellation in .annot format to Bruce a while back. He had expressed an interest in possibly including it as part of FS 6.0.
cheers,
-MH
--
Michael Harms, Ph.D.
---
<freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, August 18, 2016 at 8:55 AM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST ROI atlas
Hi Michael- Thanks very much for the file. Is there
Hi Anastasia,
My interpretation of the “reinit” parameter is that it is for situations
where a narrow probability distribution is assumed to be incorrect. But
how do you know whether it is indeed incorrect, or whether in fact the
true equilibrium distribution is (correctly) very narrow?
In parti
bout the initial path if it doesn't
move at all.
Best,
a.y
On Tue, 23 Aug 2016, Harms, Michael wrote:
>
> Hi Anastasia,
> My interpretation of the “reinit” parameter is that it is for situations
> where a narrow probability distribution is assumed to be incorrect. But
> how do
Hi,
You might want to check out FSL’s PALM tool, which has a bit more sophisticated permutation framework, and allows for permutation in the context of non-orthogonal covariates.
cheers,
-MH
--
Michael Harms, Ph.D.
---
te carlo simulations.
>
>
> Thanks, Maaike
>
>
> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu
> namens Harms, Michael
>
> *Verzonden:* vrijdag 26 augustus 2016 01:00:13
> *Aan:* Freesurfer support
on-orthogonal designs are wrong. There
>are ways to try to compensate for it, which is what PALM is doing. Sorry
>to be nit-picky!
>
>
>On 08/29/2016 06:12 PM, Harms, Michael wrote:
>> Hi Maaike,
>> Why not just use PALM? Then you don¹t have to worry about this (since
n parametric methods. Anderson tested them on a wide
range of designs, but it was, of course, not exhaustive. The accuracy of
his results may not extend to other designs, so it is a buyer-beware
situation (as with all neuroimaging).
On 8/29/16 10:16 PM, Harms, Michael wrote:
> Hi,
> I wouldn
FWIW, we’ve had good success with including the T2w scan as part of the FS 5.3-HCP release.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University S
Hi,
One comment: I don’t know about the details of these particular scripts,
but users should be aware that different SMS/MB implementations (e.g.,
CMRR vs. Siemens/MGH) do not necessarily use the same slice ordering. The
safest thing to do is confirm the timing from the DICOMs.
cheers,
-MH
--
Hi,
Even if the two sites are the same Siemens model, you are going to have difficultly convincing people that any differences you find might not just be a site effect. In my opinion, this falls into the “not possible at all” category.
cheers,
-MH
--
Michael Harms, Ph
Hi,
I remember looking into this — all the time points for a given subject need to
be specified in the same configuration file, otherwise you don’t get the
longitudinal aspect of the processing.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Con
Hi,
Is this just an exercise to try to duplicate the HCP processing? Because we’ve
already run all subjects (with released structural data) through FreeSurfer for
users.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neurosc
To clarify, in that post, Matt wasn’t saying that FS was going to incorporate
myelin maps. Rather, the new (v6) version of FS, with its support of data
acquired with < 1 mm resolution, may eliminate the need for some of the steps
that are currently the HCP Pipelines that are there to take full
Hi Martin,
I’ve addressed this in your query to the FSL list. Please see my response
there.
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry
That would be yet another way.
For those that are curious, the field is “MosaicRefAcqTimes”.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department o
Wow, that’s a terrible correlation between two putative measures of head size.
What does the scatterplot of FS’s “eTIV” vs “SupraTentorialVol” look like? The
latter is based on the surfaces, so a scatterplot of the two can be a good way
to identify cases where the talairach.xfm file (from whic
We are not using the -washu_mprage option in the HCP pipelines.
My understanding is that flag dates way back to when WashU was running a
"non-standard" MPRAGE.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Me
Hi Vinke,
In the QAtools_v1.1 package, should the supplied DefaultAsegMeans.txt file have "0 +/- 0" as all its entries?
More generally, I was wondering what aspects of the QAtools package you've found most useful? In particular, do the results from wm-anat-snr relate to data quality in a me
To add to this thread, I have this same problem (upside-down display in tksurfer, with mismatch with the reported annotation labels in the Tools window) when using a CentOS 6.4 system, using both FS 5.1 and FS 5.3, but not when using a CentOS 5.5 system.
If there is an easy fix for this (e
ce Fischl" wrote:
>Hi Mike
>
>what kind of mismatch do you mean?
>Bruce
>On Mon, 13 Jan 2014, Harms, Michael
>wrote:
>
>>
>> To add to this thread, I have this same problem (upside-down display in
>> tksurfer, with mismatch with the reported annotation l
BTW: If you download the structural preprocessed data, the HCP data
already includes aparc+aseg.nii.gz in both "native" space and transformed
to MNI152 space. If you want the data values contained in the native
space aseg.stats file of FreeSurfer, you can quickly get that as part of
the spreadshe
Hi,
I see that the links off of
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
now provide instructions for editing via Freeview rather than Tkmedit.
I found the older instructions for editing via Tkmedit still available by appending "_tktools" rather than "_freevi
Hi Chad,
Why do you say the Segmentation step overwrites your WM edits? We've just run WM edits under FS 5.3 very recently and it worked fine. Also, a glance at the recon-all script indicates that the Segmentation step is testing for the presence of existing
edits.
cheers,
-MH
--
Mic
Hi Ed,
If you want to avoid the rotation (e.g., to avoid an interpolation at the
conform step) then you need to manually alter the input so as to remove
the off-diagonal elements. That is in fact what we do as part of our
DICOM2NIFTI conversion in the HCP.
cheers,
-MH
--
Michael Harms, Ph.D.
-
rm,
>
>Thanks for the trick. Will this, however, give not rise to conversion to
>Talairach
>coordinates?
>
>Cheers,
>Ed
>
>
>On 6 Feb 2014, at 15:38, Harms, Michael wrote:
>
>>
>> Hi Ed,
>> If you want to avoid the rotation (e.g., to avoid an interpo
Hi guys,
I was wondering if someone could take a look at a subject that I just uploaded (L217_100908.zip).
An RA was editing wm.mgz to attempt to fix a topology problem in the LH visual cortex. The edited wm.mgz that she created looks fine to me, but after re-running FS, the surfaces still ar
You must have already run this subject once with an expert-options file?
Once you've already run recon-all once on a subject with an expert-options file, you don't include it again in future invocations of recon-all. The expert options that you've previously used will automatically get used
Hi Caspar,
I can't address your question regarding a specific tool, but wanted to mention a note of caution.
You need to make sure that you scrub any identifying info from Siemen's custom DICOM fields (not just the obvious public DICOM fields).
The challenge of doing that is why the safest th
Hi Elizabeth,
The measure called "CorticalWhiteMatterVol" *is* the total cerebral white
matter.
See this page:
http://freesurfer.net/fswiki/MorphometryStats
The values for the "{lh,rh}CorticalWhiteMatterVol"measures in aseg.stats
used to be the same as that returned by the 'mris_wm_volume' functi
Hi Doug,
Is 'pctsurfcon' intended to supersede 'mri_cnr'? If not, what are the
intended situations in which one would be used over the other?
thanks,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Wa
Is the brain merely shown "sideways" in FSLview? What matters is that the A/P/S/I/L/R labels are correct in FSLview, in which case the orientation info is read just fine, and it is solely a matter of how FSLview choses to display data that doesn't have
an RAS/LAS orientation.
cheers,
-MH
;
Reply-To: "std...@virgilio.it" <std...@virgilio.it>
Date: Tuesday, April 29, 2014 1:52 PM
To: "Harms, Michael" <mha...@wustl.edu>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: R: Re: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in
...@wustl.edu
From: "std...@virgilio.it" <std...@virgilio.it>
Reply-To: "std...@virgilio.it" <std...@virgilio.it>
Date: Tuesday, April 29, 2014 2:09 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, "Harms, Michael&q
lio.it>
Date: Tuesday, April 29, 2014 2:09 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, "Harms, Michael" <mha...@wustl.edu>
Subject: R: Re: [Freesurfer] R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL
I'm trying to d
rfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, "Harms, Michael" <mha...@wustl.edu>
Subject: R: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL
Please, see the snapshot attached. A/P/S/I/L/R labels seem correct. What do you think
about
Hi Simon,
Since you are using the HCP data, this may be more appropriate for the HCP-Users list.
If you look at the current HCP pipeline code, you'll see that after converting FS surfaces to .surf.gii (using 'mris_convert'), an affine transform is then
applied based on the c_ras contents (
Hi,
FWIW, I've looked at a number of these measures in 500+ subjects from HCP
data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
relate to each other, and whether they correlate with mean cortical
thickness, white matter surface area, or number of SurfaceHoles (prior to
topolo
is has been my experience as well. Not much seems to predict which
scans will need to be edited.
On 10/19/15 10:23 AM, Harms, Michael wrote:
> Hi,
>
> FWIW, I've looked at a number of these measures in 500+ subjects from HCP
> data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr --
anover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
Sent: Monday, October 19, 2015 at 12:24 PM
From: "Harms, Michael" <mha...@wustl.edu>
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MPRAGE SNR
A
In my experience, none of the quantitative "SNR/CNR" metrics available
through various FS tools (some of which may be part of the QATools)
replace the need to manually inspect the results. Some truly awful data
may show up as "outliers", but you can't count on those values to flag all
the data w
It seems problematic to me to use a nightly dev build for publication.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatr
Hi Pietro,
One additional thing to consider is that the ICV (eTIV) is entirely
dependent on the Talairach transform. Frequently, the accuracy of
Talairach transform isn¹t explicitly checked by users, because the
surfaces, aseg, etc can be accurate even if the Talairach transform isn¹t.
cheers,
-
As an add-on to this, note that using a single table for all subjects is probably only appropriate if the DWI was acquired with a fixed orientation relative to the scanner gradient axes (e.g., strictly axial) for all subjects. If the orientation was customized
individually for each s
Hi,
Why not use a measurement of brain size rather than “eTIV”?
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 S
, Angela Favaro wrote:
>>>
>>> > Hi, thank you
>>> > I think this would test something different: 'how much a brain
>>> area is
>>> > atrophic controlling for the average brain atrophy' and not
>>>
Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110Email: mha...@wustl.edu
On 2/22/16, 10:19 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Harms, Michael" wrote:
Even assuming one had a true measure of TIV, if you get meaningfully
different results
Just an aside: if you acquire oblique (e.g. AC/PC aligned), and don’t want
FS to rotate the volume back into the native scanner space as part of its
“conformation” step, you can edit the s/qform of the NIFTI header to
appear as a non-oblique acquisition. As Bruce noted, this isn’t a big
deal, alth
That looks very similar in principle to something I posted back in Oct.
2014 (“pial surface crossing white”).
I think some of the subsequent back-and-forth with Bruce and Nick was off
the list, so I’ve included the key email (where Bruce diagnosed the
problem) below.
Has this been fixed in the f
Hi,
There are certainly papers in which thickness is corrected using global mean thickness, and surface area is corrected using total surface area. It is a valid approach, and one that I think is preferable to correcting by using a somewhat arbitrary adjustment
to a non-like measure
Hi Josh,
The WU-UMN HCP outputs provide the thickness values already aligned to a common mesh in the *thickness.{32,164}k_fs_LR.dscalar.nii files (both 32k and 164k mesh version available). You should be able to run a nice, permutation-based group analysis on
those using the FSL PA
chwiedrzik" <cschwie...@mail.rockefeller.edu>
Date: Friday, May 31, 2013 2:50 PM
To: "Harms, Michael" <mha...@wustl.edu>, "Freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mprage flag in recon-all
yes, but recon-all
Hi guys,
We have some longitudinal scans in which the time1 (T1) scans were processed with FS 5.1, and the T2/T3 scans haven't been processed yet.
I'm trying to assess whether the differences between FS 5.1 and 5.3 warrant us re-running the T1 scans under FS 5.3.
I see two possible optio
Hi,
There seem to be a couple small bugs in recon-all (FS 5.3) regarding the interface of trying to do a "clean" run on top of processing that used an expert-options file:
1) The "-xopts-clean" flag doesn't work. It sets XOptsClean = 1, but doesn't set XOptsUse = 0. Consequently, because
Hi again,
Not sure if this is intentional or not, but I noticed that 'mris_curvature_stats' (FS 5.3) appends to Xh.curv.stats on successive invocation, rather than overwriting the existing file.
I noticed this in the context of comparing the stats results from a "-clean" run vs. a fresh run fr
Are you saying that edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are not showing up as affecting the actual pial surfaces themselves?
I would focus on whether the pial surfaces are fixed, not whether edits to brain.finalsurfs.manedit.mgz are "back-propagated" to brainmask.mgz. (I
From: Francesco Siciliano <sici...@nyspi.columbia.edu>
Date: Wednesday, August 28, 2013 12:36 PM
To: "Harms, Michael" <mha...@wustl.edu>
Subject: RE: [Freesurfer] pial surface editing
My main issue is that the edits I make to brain.finalsurfs.manedit.mgz are not being incorpo
onvert output?
>
>Thanks very much,
>pt
>
>
>
>
>On Thu, Sep 12, 2013 at 4:50 PM, Harms, Michael wrote:
>>
>> Were these oblique acquisitions?
>> By default, dcm2nii and MRIConvert rotate the bvecs according to the
>> orientation info for oblique acquis
Were these oblique acquisitions?
By default, dcm2nii and MRIConvert rotate the bvecs according to the
orientation info for oblique acquisitions, whereas it sounds like
mri_convert might not be doing that.
cheers,
-MH
--
Michael Harms, Ph.D.
--
Hi,
A reasonable definition of TBV would be TotalGrayVol +
CorticalWhiteMatterVol from the aseg.stats file.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medic
That subjects looks like a candidate for exclusion, because the SNR anteriorly
is much less than posteriorly. It looks to me like there is either a problem
with your head coil, or the anterior coil elements were not active.
cheers,
-MH
--
Michael Harms, Ph.D.
-
dcm2niix with the -s flag will allow you to convert a single DICOM that is
part of a directory with other DICOMs
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of
The HCP Pipeline scripts use ‘bash’. (setenv is for the csh shell).
The equivalent for bash is:
export OMP_NUM_THREADS=2
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medi
Hi,
I converted a surface to GIFTI
e.g.,
mris_convert lh.white lh.white.gii
lh.white and lh.white.gii align when they are both loaded in 'tkmedit'.
However, they do not align when loaded simultaneously in 'freeview'.
Of possible relevance: When I loaded lh.white.gii into 'freeview', I got
FWIW: In FS 5.3, -autorecon2-cp and -autorecon2-wm invoke the exact same
set of flags. (This wasn't the case in earlier versions).
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington Un
Hi,
The recon-all based striatal parcellations are based on the anatomy of each particular subject, guided by a probabilistic atlas. That is inherently likely to be more accurate that just taking a set of ROIs/parcellations defined in some (non-probabilistic)
atlas and warping them to each
Actually, if you run 'recon-all' a second time (from scratch) on the same
subject, on the same platform/architecture, and you use the default
recon-all settings (i.e., don't use the -randomness flag, or specify your
random seed via the -rng-seed flag), then you should get identical
results, becaus
FS uses FSL tools under the hood, so you want to use the bvecs that are rotated into the axes of the scan.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School
to correct this kind of thing
>
>cheers
>Bruce
>
>
>On Thu, 7 Aug 2014, Harms, Michael wrote:
>
>>
>> Hi,
>> An astute RA, while reviewing the aparc+aseg.mgz of brains processed
>>with FS
>> 5.3, noticed a fair number of instances, where the
Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110Email: mha...@wustl.edu
On 8/7/14 2:52 PM, "Bruce Fischl" wrote:
>so that region really is cortex? It's not filled in ventricle or
>anyt
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