The initial running of recon-all autorecon-1 autorecon-2 for a sample scan
resulted in a bad skull strip. I am attempting to troubleshoot the issue
through running just the skull strip portion of the recon-all pipeline again,
followed by adjusting the watershed parameters.
During re-running -s
Dear Douglas
Thank you for your response. I cannot run asegstats2table and
aparcstats2table command outside of qdec.
Best regards,
Duy Nguyen
*--v-- Peace --v--*
*Duy Nguyễn *
*Biomedical Engineering Department- IU HCMC*
*Cell: (+84)90056*
*Email: duy.nguyen...@gmail.com *
On Thu, Mar 23,
Hi Mailing List,
I am fitting an LME model with random effects for B0 and B2, so I am using the
following to fit a spatiotemporal model:
lhstats = lme_mass_fit_Rgw(X,[1 3],Y,ni,lhTh0,lhRgs,lhsphere);
However, prior to this when i am computing the initial temporal covariance
estimates, do the s
Hello Doug, I was able to solve the problem. It had to do with the gtmseg part of the pipeline. I had to re-run gtmseg again and mri_gtmpvc exited without error and produced all output. Thank you Best, Paul
don't know what is going on there. Can you run the asegstats2table
command outside of qdec?
On 3/17/17 8:29 AM, Duy Nguyen wrote:
Dear FS Expert
I am doing analysis from the group_analysis_tutorial data to practice
and learn. However, I come across the error window like it shows on
the att
not sure what is going on there. Can you send the full terminal output?
Also can you email me the mri_glmfit-sim file?
On 3/19/17 11:00 PM, June Kang wrote:
The version downloaded in offical page. 6.0 stable for OS X.
On Mar 20, 2017, at 11:02 AM, Douglas Greve
mailto:gr...@nmr.mgh.harvard.e
Ah I see. Okay, will give this a try. Thank you Doug!
Best regards,
Fred
> On Mar 22, 2017, at 17:04, Douglas Greve wrote:
>
> when you ran mri_glmfit, you had to give it an input (eg, --y
> group1.mgh) with all the subjects from group 1. You would have a similar
> file for group2. You would
FWHM should be the impulse response FWHM for your scanner. This is a
number (eg, the HR+ is about 6), not the string 'FWHM'
On 3/22/17 4:16 PM, Agrawal, Shubhi (NIH/NINDS) [E] wrote:
Hi,
I am trying to run SGTM partial volume correction in Petsurfer by
following the tutorial on the wiki. Ever
Can you tar up the output folder and send it to me at our file drop?
https://gate.nmr.mgh.harvard.edu/filedrop2
Also, please send the following 3 files
/net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.mgz
/net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.ctab
/net/synapse/nt/pau
Hi Doug,
What do you mean by combining all the data (and how would you suggest we go
about this?)?
And also how does one do a two-group test?
Thank you!
Best,
Fred
> On Mar 22, 2017, at 16:51, Uquillas, Federico D'Oleire
> wrote:
>
> Dear FreeSurfer experts,
>
> I’ve been trying to find a
when you ran mri_glmfit, you had to give it an input (eg, --y
group1.mgh) with all the subjects from group 1. You would have a similar
file for group2. You would then combine them into one file, eg
mri_concat group1.mgh group2.mgh --o group1-and2.mgh
you would then create a new FSGD file for bo
t;> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> greve at nmr.mgh.harvard.edu
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>>
>> __
the easiest thing to do is to combine all the data together and do a two
group test
On 3/22/17 4:49 PM, Uquillas, Federico D'Oleire wrote:
Dear FreeSurfer experts,
I’ve been trying to find a way to get a map of the difference between
two independent CTh association maps but can’t seem to fin
Dear FreeSurfer experts,
I’ve been trying to find a way to get a map of the difference between two
independent CTh association maps but can’t seem to find a solution.
I have two maps of independent groups (one is N=15, the other N=20) I would
like to compare. Is there maybe a way to do a sig1.m
Never mind Doug. I was able to solve the problem.
Best,
Paul
On Wed, Mar 22, 2017 at 3:34 PM, miracle ozzoude
wrote:
> Thank you Doug. I am trying to perform pvc for my pet data based on the
> tutorial however, I keep getting this error:
>
> " mri_gtmpvc --i C6_01_001_140813_PET_AV45_coreg_avg.n
Hi,
I am trying to run SGTM partial volume correction in Petsurfer by following the
tutorial on the wiki. Every step preceding mri_gtmpvc has been successful and
the coregistration looks good.
the last step, mri_gtmpvc command gives an error-
Segmentation fault (core dumped)
This is the informa
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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This is the wrapper script that it’ll call, the input formats are explained
here:
http://surfer.nmr.mgh.harvard.edu/fswiki/epidewarp.fsl
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of VA Research
mailto:n.n.di.methyl.tryptami...@gmail.com>>
Reply-To: Freesurfer support lis
Thank you Doug. I am trying to perform pvc for my pet data based on the
tutorial however, I keep getting this error:
" mri_gtmpvc --i C6_01_001_140813_PET_AV45_coreg_avg.nii.gz --reg
C6_01_001_140813_PET_AV45_coreg_avg.reg.lta --psf 6mm --seg gtmseg.mgz
--default-seg-merge --auto-mask PSF .01 --mg
do I have to prepare the mag file and make it radians/s for FreeSurfer?
like you do in FSL? with command fsl_prepare_fieldmap
On Wed, Mar 22, 2017 at 7:35 AM, Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:
> Hi Joseph – You can use fugue as part of the preprocessing in TRACULA.
> Search f
On 3/22/17 2:02 PM, miracle ozzoude wrote:
Hello Doug,
Thank you for the detailed reply. I do have other questions.
1) Can you confirm if this is the correct use of mris_preproc for
Uncached PET data. mris_preproc --fsgd your.fsgd --target fsaverage
--hemi lh --meas Pet --out lh.your.pet.00.
Great! Thank you for taking that time to clarify that.
-Prad
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Iglesias Gonzalez,
Eugenio
Sent: Wednesday, March 22, 2017 11:34 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfie
Hi again, Prad,
In that case, you don’t need the discrete segmentations. Just look at the
posteriors directly.
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 22 Ma
Sorry about that. I should have stated what I was trying to do. I'm trying to
see if the posterior probability changes when using a certain combination of
the different T1 and T2 weighted scans that we have in our lab. I thought using
the binary masks to extract the probabilities as they were th
Hi Prad,
The final probabilities are in the posterior files. There’s no need to binarize
?h.hippoSfLabels if what you’re interested in is the soft segmentations.
Or maybe I’m missing something? What are you exactly trying to do?
Cheers,
/E
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translat
Hello Doug,
Thank you for the detailed reply. I do have other questions.
1) Can you confirm if this is the correct use of mris_preproc for Uncached
PET data. mris_preproc --fsgd your.fsgd --target fsaverage --hemi lh --meas
Pet --out lh.your.pet.00.mgh. This modification was made from the thicknes
Hi Dr. Iglesias,
Thank you for the overview of the labeling rules. I have also tried setting
WRITE_POSTERIORS to 1 to write out the posteriors.
I had a follow up question about obtaining the probabilities for the final
subfield labels as available in the ?h.hippoSfLabels-T1.v10.mgz
I use mr
Thanks for the reply, Doug!
Best,
Feilong
On Wed, Mar 22, 2017 at 1:24 PM, Douglas Greve
wrote:
> I think the motion correction works a little better if done to a reference
> inside each run, and there's probably less interpolation in the end
>
> On 3/20/17 11:04 AM, Feilong Ma wrote:
>
> Hi Fr
I think the motion correction works a little better if done to a
reference inside each run, and there's probably less interpolation in
the end
On 3/20/17 11:04 AM, Feilong Ma wrote:
Hi FreeSurfer Experts,
I was reading the document of preproc-sess, and it seems -per-run is
recommended inste
We don't have something explicitly to do this, but you can run FDR on it
using either mri_fdr (use nomask for the mask) or you can load the
sig.mgh file into matlab and run it there, eg,
sig = MRIread('sig.mgh');
p = 10^-abs(sig.vol);
fdrthresh = fast_fdrthresh(p);
On 3/20/17 9:32 AM, Laura F
On 3/22/17 11:02 AM, miracoo...@gmail.com wrote:
Sent from my BlackBerry 10 smartphone.
*From: *miracle ozzoude
*Sent: *Tuesday, March 21, 2017 7:41 PM
*To: *Douglas N Greve
*Subject: *PETsurfer surface based analysis
Hello,
I am working through the PETsurfer surface based analysis and i h
I don't think this will do it, and I don't think we have anything that
will do this precisely. You can do something like it by running the
xhemi stream http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi, mapping the
lh and rh thickness to the lh for fsaverage_sym, then run the face
parcellation on
If you have the T1 for the mni152 (which is somewhere in the bowels of
the spm distribution), then you just run recon-all on it. I've done this
for myself, so you can just download the result (which I have not
checked thoroughly) from here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mni152
not that I know of. I think you'll have to do it by hand (sorry)
On 3/21/17 11:02 AM, Ahearn, T wrote:
Hello
I need separate grey and white volumes for the frontal and temporal
lobes. I have values for grey volume from
mri_annotation2label --subject 01 --hemi lh --lobesStrict lobar_annotat
copy it to $FREESURFER_HOME/bin and then
chmod a+x mris_apply_reg
then
rehash
On 3/21/17 8:23 AM, Marissa Pifer wrote:
Hi Doug,
I'm not sure how to use this binary. Do I need to install it?
Marissa
On Fri, Mar 17, 2017 at 12:23 PM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrot
Hi Meaghan
it looks like the white surface is pretty accurate but the gm doesn't get
out far enough. I would play with some of the expert options to
mris_make_surfaces like max_gray_at_csf_border. If you upload a subject I
can try it out and see if I can improve things and get back to you.
c
For a skull-stripped anatomical nifti file, What’s the difference between '91 x
109 x 91’ and 2mm x 2mm x 2mm?
[image1.png]
Youssif
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The first is the number of voxels, the second is the size of a single voxel.
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of yusif Al-kheder mailto:yusi...@live.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, March 22, 2017 at
Hi Joëlle – What images do you pass as input to TRACULA? Do you pass the dicom
itself, or a converted file? Happy to look at your dicom, if it’s anonymized.
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Joëlle Ismay Rosanne Van Der Molen
mailto:joelle.vandermo...@etu.
Hi Joseph – You can use fugue as part of the preprocessing in TRACULA. Search
for items with “b0” in the example config file:
https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
Best,
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of VA Research
mailto:n.n.di.methyl.tryptami
Hi Hui
meancurv is the spatially smoothed mean curvature of the surface at each
point (that is, the average of the two curvatures k1 and k2)
cheers
Bruce
On Wed, 22 Mar
2017, 李慧 wrote:
Dear FreeSurfer Group,
Sorry for interrupting.
I am Hui Li, a researcher fron Beijing, China, interesti
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