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Hello,
When was the wm-hypointeisities label added to the Freesurfer segmentation? Is
there any paper that explicitly mentions this, or should I just cite the 2002
paper?
Thanks,
-Eli
Houston Methodist. Leading Medicine. Houston Methodist is ranked
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I've noticed an issue when trying to manually input values into fields with
Qdec. This problem has been reported before. I thought perhaps it was because
Qdec is deprecated, so I loaded the results into tksurfer, and I can't change
fields in this pro
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Hello, it's possible I found a bug in freeview:
I'm using the overlay_color option with freeview. Specifically I am trying to
use both the "truncate" and "inverse" options in a command line call to
freeview for a pipeline I am building. The documenta
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Hello,
with Qdec, there was an option to "remove" positive (or negative) results from
the displayed overlay...
Is it possible to do something similar with the results of mri_glmfit, but
displaying with freeview instead? For instance, if I wanted to
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Hello,
Are the WM-hypointensities segmented in the same way as the rest of the
subcortical regions? i.e., using the probablistic atlas referenced in the 2002
Fischl et al paper?
Thanks,
- Eli
Houston Methodist. Leading Medicine. Houston Methodis
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Hello,
I have a subject with two MRIs and surface reconstructions, several years
apart. I would like to directly compare these surfaces if possible, for
instance, to subtract (new - old) to see a "difference surface" or something
similar. Is there
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Hi Andrew,
Looks like that cleared the errors.
Thank you both,
-Eli
From: Hoopes, Andrew
Sent: Tuesday, July 31, 2018 3:09 PM
To: Freesurfer support list
Cc: Rockers, Elijah D.
Subject: Re: [Freesurfer] Surface
, 2018 2:14:18 PM
To: Freesurfer support list
Cc: Rockers, Elijah D.
Subject: Re: [Freesurfer] Surface editing: recon-all exited with errors
h, maybe -make all has changed (or my memory of what it does is
incorrect). I'll find someone else here to help you out
cheers
Bruce
On Tue, 31 Jul 2018,
Bruce
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Hello.
I manually edited the brainmask.mgz file for three subjects. This was done to
prevent the pial surface from extending into non-cortical areas, in particular
the soft-tissue near the brain stem, and some cerebellar areas. Usually this
type of
Hello,
I noticed that recon-all automatically segments hypointesities in the white
matter regions. Is there any possibility of using Freesurfer to segment T2
FLAIR WMH?
I did not see anything in the Wiki documentation about it.
Thanks,
- Eli
Houston Methodist. Leading Medicine. Houston Me
Hello,
I am using mri_convert to convert my standard T1-weighted structural images
into nifti format.
The conversion works, but it might be somewhat delayed due to spamming the
console with the following message
ERROR: don't know how to get DWI parameters from --Philips Healthcare--
ERROR: Get
amount?
On Thu, 11 Jan
2018, Rockers, Elijah D. wrote:
Thanks Bruce.
I went over some more images with our PI and he was mostly satisfied with the
pial/white
segmentations. The real problem here is that our results look correct, except
for they seem to be
translated vertically by a small amount
check to make sure
everything is lining up correctly?
- Eli
On Thu, 2018-01-11 at 08:08 -0500, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Message: 5
Date: Wed, 10 Jan 2018 20:26:11 +
From: "Rockers, Elijah D."
mailto:edrock...@houstonmethodist.org>>
Subject: [Freesurfer
Hello,
We have some images that reflect severe atrophy in some subjects, in which gray
matter is virtually undetectable on the MRI in some regions. However, upon
checking the segmentations visually, the white/pial surfaces are reflecting a
significant cortical thickness in these areas.
Is ther
Hello,
I was hoping to get some clarification on how exactly the cortical thickness
number is calculated. In the videos, Doug says it's "the distance between the
vertex on the white to the vertex on the pial, and you go backwards and
forwards to compute the average thickness", and the 2000 pape
7b7a7-cdc3-46f1-8e1b-098142fd3...@nmr.mgh.harvard.edu<mailto:54b7b7a7-cdc3-46f1-8e1b-098142fd3...@nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset="us-ascii"
That defect is so big you probably ran out of memory.
> On Aug 23, 2017, at 11:21 AM, Rockers, Elijah D.
>
We encountered a hard failure, below is the tail of the log. We are currently
running Freesurfer 6 again locally to see if it succeeds on a desktop machine
(this is the first time encountering a hard failure on the XNAT server). Any
suggestions?
-merging segment 180 into 178
160 defects t
Hello,
The Freesurfer segmentation for hypointensities is very good, but misses on
some subjects, i.e. it does not include large chunks of hypointense regions in
some subjects. It does fantastic picking up the periventricular
hypointensities, but appears to fail on some deep WM regions. I just
I am attempting to create a volume from a surface. My ultimate goal is to
obtain a mask that includes everything "inside" the white matter surfaces.
wm.mgz is close, but it would nicer to just get a mask from lh.white and
rh.white. I would like these masks to be in the subject's native space. Ho
From what I understand, the --cortex flag is simply supposed to zero out any
signal in the medial wall with a mask, I checked mask.mgh, it is 0 on the
medial wall and 1 everywhere else as expected... however when I analyze the
data without this flag, the resulting sig.mgh file has completely cha
Hi,
We like using Qdec to display cortical thickness results. The only drawback is
that we are unable to manually input values into the boxes for threshold
values, FDR rate, etc.. We are running Centos7. We thought the graphics drivers
were the problem, but even after buying a whole new GFX car
Hello FS,
I am attempting to run a monte carlo simulation on some cortical thickness data
in Qdec 1.5, but I get the following error:
ERROR: CSDread(): could not open
../freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm4/abs/th40/mc-z.csd
I thought it might be a permissions issue s
Hello,
We have a large number of subjects processed with the default settings of
recon-all. Unfortunately the presence of white matter creates problems when
creating the white matter surface. There are large hypo-intensities in the
white matter which badly distort the surfaces in multiple areas
Hello all,
Again, I tried to modify the white matter surface by adding voxels to
the wm.mgz file, and performed the reconstruction by doing the
following.
-Opened brainmask.mgz for reference
-Opened wm.mgz on top of that
-Click the voxel edit button
-Check the recon editing checkbox
-Fill in voxe
gt; Also, in general it is hard for us to help you unless you include more
> information. What exact command did you run? What was the screen output?
> What was in the recon-all.log?
>
> cheers
> Bruce
>
>
> On Wed, 1
> Mar 2017, Rockers, Elijah D. wrote:
>
gt; Also, in general it is hard for us to help you unless you include more
> information. What exact command did you run? What was the screen output?
> What was in the recon-all.log?
>
> cheers
> Bruce
>
>
> On Wed, 1
> Mar 2017, Rockers, Elijah D. wrote:
>
Couple of questions:
1)
I edited wm.mgz following the instructions in the wiki guide, but it did
not change anything after reconstruction. I am still using 5.3 right
now, so maybe the guide is wrong for me. What is the brush value
supposed to be? I used 255 but it did not extend the white matter
> You can reach the person managing the list at
> freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
>1. Manual ed
Hello,
I could not find any information on changing the cursor via command
line. My goal is to persistently change the default cursor style/color,
I was going to create an alias on my system.
Thanks,
Eli
Houston Methodist. Leading Medicine.
U.S. News & World Report has recognized Houston Method
Is there something I can do to extend the pial surface to include cortex
that it ignored? In some places there are rather large chunks of cortex
not included in the pial surface.
http://imgur.com/a/FnAgj
Link is to a screenshot, notice the top of the brain. It's fairly
pronounced, visible in 12 a
OK, sorry for spamming the list. I fixed the the faulty skullstrip by using
recon-all -skullstrip -clean-bm -no-wsgcaatlas -subjid
Currently redoing the surface reconstructions, but it should be OK now.
Thanks for the nice documentation.
Eli
On Fri, 2017-02-24 at 15:30 -0600, Elijah Rockers wr
As far as I can tell, everything looks OK up until brainmask.mgz. The
skullstrip step seems to have cropped out the brain and left the neck...
On Fri, 2017-02-24 at 12:58 -0600, Elijah Rockers wrote:
> Hello all,
>
> I recon-all'd ~40 different subjects. I have been going through all the
> images
Hello all,
I recon-all'd ~40 different subjects. I have been going through all the
images to make sure they were processed correctly. Most required no no
editing and recon-all did a very good job.
But for one scan in particular, it looks like Freesurfer thinks the top
of the spinal cord is the br
Nevermind. I discovered if I just change ftp to https in the download
link, it works fine.
- Eli
On Wed, 2017-02-22 at 12:22 -0500, Elijah Rockers wrote:
> Is there by any chance another way to download Freesurfer? My
> institution does not allow FTP connections (HIPPA...) Same goes for the
> tuto
Is there by any chance another way to download Freesurfer? My
institution does not allow FTP connections (HIPPA...) Same goes for the
tutorial data, but obviously Freesurfer is the priority here... thanks.
- Eli
Houston Methodist. Leading Medicine.
U.S. News & World Report has recognized Houston
ting the PET after setting this env var
>
> setenv FS_SLICE_LIN_SCALE 1
>
> This causes mri_convert to read 28,1052 (intercept) and 28,1053
> (slope). the output value should be
>
> dicomvalue*slope + intercept
>
> Is 2005,100e accompanied by an intercept ?
>
>
>
y.
>
> On 11/10/2016 12:40 PM, Douglas N Greve wrote:
>> What is the dicom tag for the scale?
>>
>>
>> On 11/10/2016 01:29 PM, Rockers, Elijah D. wrote:
>>> As far as I can tell, mri_convert doesn't apply the scaling factor, and
>>> also doesn&#x
gt;
> On 11/10/2016 01:29 PM, Rockers, Elijah D. wrote:
>> As far as I can tell, mri_convert doesn't apply the scaling factor, and
>> also doesn't copy over the slope scale header entry, when converting
>> from dicom to nifti.
>>
>> By contrast, dcm2nii does n
r software (eg
Freeview..) to apply the scaling..
Hope this clarifies. Thanks for checking into this.
On 11/10/2016 12:18 PM, Douglas N Greve wrote:
> Sorry, is it a scale in the dicom file or the nifti file that is not
> being applied properly?
>
>
> On 11/10/2016 11:01 AM,
, so including it in the output would be
> inappropriate. On 11/09/2016 03:03 PM, Rockers, Elijah D. wrote:
>> >Hello,
>> >
>> >We have been using mri_convert to convert our dicoms into .nii niftis.
>> >There is an entry in the .nii header for the slope scal
Hello,
We have been using mri_convert to convert our dicoms into .nii niftis.
There is an entry in the .nii header for the slope scale, but
mri_convert appears to discard this value instead of copying it into the
header (whereas mricron retains this value) We prefer to use mri_convert.
Is ther
Is it possible for freesurfer to parcellate the substantia nigra from a T1?
--
Elijah Rockers
Research Data Analyst
Houston Methodist Research Institute
O: 713-363-7729
Houston Methodist. Leading Medicine.
U.S. News & World Report has recognized Houston Methodist as one of the
nation’s top 20
Hello,
Doing a recon-all -all yields some deprecation warnings.
defined(@array) is deprecated at
/freesurfer/mni/bin/nu_estimate_np_and_em line 165.
Use of ?PATTERN? without explicit operator is deprecated at
/freesurfer/mni/bin/sharpen_volume line 153.
I think my results should still be OK b
After much scouring, this appears to be a problem with XQuartz. I spoke to
someone on the XQuartz team and they are basically on life-support. It looks
like support for this may be going down the toilet, and migration to an
entirely new architecture is needed. I am not the only person experienci
Hello freesurfers,
Running a Mac Pro, OS X El Capitan 10.11.4
With ATI Radeon Graphics card, and XQuartz v 2.7.9
I am able to run Qdec and freeview perfectly fine on my machine. The problem
comes when I attempt to SSH into another machine and use these programs (it
used to work fine, but I am w
Trying to integrate freesurfer data with our XNAT database.
Are there any freesurfer schemas for XNAT available, or is it pretty much I
have to try to make my own?
Thanks,
--
Elijah Rockers
Research Data Analyst
Houston Methodist Neurological Institute
O: 713 363 7729
Houston Methodist. Leadin
Hello,
The Houston Methodist Research Institute is hiring for a research
assistant position. Please see the attached document for details. Please
also note that candidates must be able to work in the city of Houston
day-to-day.
If you are interested in applying, please follow the instructions
Hello,
The Nantz National Alzheimer Center, in Houston, TX is looking to fill two
positions pertaining to neuroimaging and analysis.
Be aware that we cannot accept remote employment, the candidate would have to
work day-to-day in the city of Houston.
Any interested person is encouraged to revi
Great thank you!
On 11/25/2015 11:54 AM, Douglas Greve wrote:
> You can use fscalc, something like
> fscalc input.nii mul 10 -o output.nii
> I think you can use fslmaths as well
>
> On 11/25/15 12:08 PM, Rockers, Elijah D. wrote:
>> I am interested in finding a way to
I am interested in finding a way to apply a slope scaling factor to the
voxel values in a NIfTI image.
I have done this in MATLAB and PMOD so far, but for some reason both
methods change the origin or otherwise distort the dimensions of the
image and render it impossible for me to process furth
Alternatively, all of our tools accept the extension # so you could do:
mri_convert file.nii#5 file.frame5.nii
cheers
Bruce
On Mon, 26 Oct 2015, Rockers, Elijah D. wrote:
Hello again,
I have a large time series in dicom or .nii format. I am interested in
extracting a single time frame from it. I
Hello again,
I have a large time series in dicom or .nii format. I am interested in
extracting a single time frame from it. I did this before, I believe
with freesurfer, but I have somehow forgot the name of the command, and
I can't seem to find it. I believe it could be used to specify
partic
Hello,
We are interested in finding a way to use particular parcellations from
Freesurfer in a separate program. For instance, we are very happy with
the way Freesurfer parcellates the Choroid Plexus and separates the
Cerebellum into white and gray matter regions, and would like to import
thes
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