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Is this for PPMI project? We can provide total hippo volumes if needed.
> On Jul 31, 2019, at 1:48 AM, eric f wrote:
>
> I don't think it will take 20h, probably more like 10-12h, so that's
> only 1.5 years:). Most people who are running it that
I don't know what is in the NODDI maps. The way mri_glmfit works is that
if any subject has a 0-value at a vertex, then it will mask out that
vertex for all subjects. Is NODDI something that might have a lot of
0-values? It also may be that one subject has all 0s (eg, if the
regitration was
Right, you can't use both --fsgd and --iv. You have to use --iv, so make
sure the order is the same as in the fsgd file.
On 7/30/19 8:44 AM, Reza Rahmanzadeh wrote:
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>
> Thanks Doug,
>
> The script works well for projfrac-avg. but the problem is: when i use
I don't think it will take 20h, probably more like 10-12h, so that's
only 1.5 years:). Most people who are running it that many data sets
have access to a computational cluster (on ours it would only take a few
weeks). Alternatively, you can try buying cloud-based computational
power (eg,
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Hi,
Now I have T1 and T2 images (dcm files) and want to calculate the
hippocampal volume. I find it takes ~20h to run recon-all -all and then
~40min to run -hippocampal-subfields-T1. However, I need to calculate the
hippocampal volume for more than
I don't know anything about fsleyes or fsl command to extract data. In
FS, you can use mri_segstats after resampling the PET to the anatomical
space (mri_vol2vol). Use the PET as the --i and the aseg+aparc as the
--seg. Alternatively, you could use PETsurfer
Dear Rudolph,
Thanks a lot for your reply! Do you know why does it fail on
holes/edges? Does the algorithm require each triangle vertex to have
1-ring neighbours?
Also, do you by chance know how to use the -a parameter correctly? I did
not observe any difference nor in the results nor in runtime
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Hi Doug,
Yes that is exactly the concern that we have.
--
Brian Biekman
Graduate Student, University of Houston
Clinical Psychology, Neuropsychology Concentration
Laboratory of Early Experience and Development (LEED)
bdbiek...@uh.edu
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*Please direct all submission materials and inquiries to Dr. Michal Assaf @
michal.as...@hhchealth.org *
*Postdoctoral Research Associate Position *
The Olin Neuropsychiatry Research Center is seeking to fill a postdoctoral
researcher/fellow position
Dear FreeSurfers,
I would like to use fsleyes for imaging. Does anybody know how to source it?
And what fsl command I should use if I want to extract all ROIs in aparc+aseg
file and get their uptake value from PET image? I know how to do it for a
single ROI. I am just wondering if there is
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Thank you! And glad to hear it’s in the works for the newest version.
Best,
Daniel
On Tue, Jul 30, 2019 at 12:50 PM Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:
> Hi Daniel - It'll be easier to just preprocess the data before passing
> them
Hi Daniel - It'll be easier to just preprocess the data before passing them to
trac-all. Topup will be incorporated to the preprocessing for the next version
release. Of course you can replace that part of the script yourself if you
prefer - you'll have to also combine the AP and PA outputs etc
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(sorry for bombaeding you with e-mails)
It seems that the error happens only when i use NODDI diffusion image e.g. NDI
map i get that error, but for MWIs the new mris_preproc works well.
Should i do anything special for NODDI images? BTW, the
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... One problem when i use the new mris_preproc:
Always the output of mri_glmfit when the input is the result of new
mris_preproc is:
Found 0 voxels in mask
ERROR: no voxels found in the mask
make sure at least one voxel has a non-zero value for
Hi Brian, I'm looking at your data. For the most part, it looks like the
surface placement is accurate. I do find a few places where the white
surface "leaks" into the cortex like in the attached picture just to the
left of the cursor. Is this the type of thing you are worried about? If
not,
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Hello,
After running recon-all, and attempting to run freesurfer (using the command
"checksurfswmflair") the following error message appears for number of studies:
Failed to load MRI
OK -- looked again -- and I need to fix the in-line help obviously.
Anyway, this works:
mris_pmake --subjecttestSubject \
--hemi lh \
--surfacepial\
--curv
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Dear Rudolph,
Thank you for following up.
I changed flags and tried it again with this command line:
mris_pmake --subject cvs_avg35_inMNI152_temp --hemi lh --surfaceFile pial
--curvatureFile
sulc --mpmOverlayArgs euclidean --mpmProgID pathFind
Hi Maria --
If there are holes/edges in the surface `mris_curvature_stats` it will
fail.
On Wed, 2019-07-24 at 10:03 +0200, Maria Kalemanov wrote:
> Hello FreeSurfer developers,
>
> I have three issues with mris_curvature_stats:
>
> 1. I attempted to compute curvature on a *noisy sphere*
Apology if this is a repeat email. I used the wrong email address in my
reply. I was one of the original
authors of `mris_pmake` although it's been (quite) a few years now. I
do remember that at some point the CLI changed, and given the FS
release cycle it took a while for this to make it into
I would segment the T2s, but using the longitudinally processed T1s/subjects.
Unless the T1s are high-res. Then, segment the T1s ;-)
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Daniel Callow
Reply-To:
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In that case, would you suggest one to use segmentHA_T1_long.sh instead of
segmentHA_T2.sh (cross-sectional) if one has longitudinal data and T2
high-resolution data? Would one be expected to provide superior results?
Best,
*Daniel Callow*
*PhD
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Thank you for the prompt answer!
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
On Tue, Jul 30, 2019 at 9:18 AM Iglesias
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Dear Daniel,
Such a script doesn’t exist yet (it’s in the to-do list). The reason why it’s
not a straightforward extension of segmentHA_T1.sh is that resampling the
anisotropic T2s to a common space is not a good idea, given the differences in
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Hello,
I have previously used field map correction for b0 inhomogeneities when
running TRACULA, however my new data set has A>P and P>A encoding. I know
that topup has been shown to perform slightly better than filed map
correction. I wonder if it
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Thanks Doug,
The script works well for projfrac-avg. but the problem is: when i use
mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is
only the order of my controls and subjects and i would have the inflated cortex
of MWI
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Dear experts,
I have a segmentation file of all the tissues in the brain and the ribbon
file which were extracted by another toolbox rather than freesurfer. Also, I
have created the annotation file using "write_annotation.m". Now, I wanna
create a
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