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Hi,
Thank you so much , it works.
BRG,
Nazanin
On Wed, Oct 10, 2018 at 9:41 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> if you want to mask the thickness, then use mri_mask
>
> On 10/10/2018 10:30 AM, N Saf wrote:
> >
> > E
It could make sense to apply it to WM. CSF I'm not so sure. Are you
really trying to measure the signal in CSF?
On 10/10/18 6:08 PM, David.Mackarthy wrote:
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>
> Dear Dr Greve, thank you for the response
> This is for a map-based study. Absolutely, this is cl
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Dear Dr Greve, thank you for the response
This is for a map-based study. Absolutely, this is clear, I appreciate the
response. I just have one additional question and I appreciate your patience.
Is it recommended to apply PVC on white matter or csf? d
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[Apologies for cross-posting]
The Brain Dynami
what do you mean by FreeSurfer space?
On 10/02/2018 10:11 AM, Sarosh, Cyrus wrote:
>
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>
> Hello FreeSurfer Experts,
>
> I’m trying to find the best method and command to move a hand drawn
> VOI in original MRI space to FreeSurfer space. These scans have
> al
Which subject did you load it on? It must be fsaverage. Can you send the
terminal output and command line?
On 10/03/2018 11:31 PM, Ting Li wrote:
>
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>
> Dear Freesurfer Expert,
>
> I have figured out the problem is that I didn’t specify lh before the
> annot
Probably so
On 10/10/2018 03:41 AM, Caroline Beelen wrote:
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>
> Few clusters survive glm fit. No clusters seem to survive glm-fit-sim (when
> visualizing). However, I'm not sure if I should also see this in a text file.
> Opening cache.th40(or 30).abs.sig.c
I think this was a bug in 5.3. Try running recon-all like
recon-all -s subject -parcstats -parcstats2 -parcstats3
to regenerate the stats files
On 10/09/2018 11:19 PM, Jianzhong Chen wrote:
>
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>
> They are different. I attached two screenshots of lh.thickness
Is this for an ROI-based study or a map-based study? For ROI, we use the
GTM, and it PV corrects for all structures (including WM and CSF). For
map-based, we use MG. MG removes WM (and CSF) entirely. In theory, it
can be run in a way to keep WM and throw GM and CSF away, but that is
not impleme
I think they are probably the same thing. Can you run
mri_diff lh.area.fsaverage.mgh lh.area.fwhm0.fsaverage.mgh
On 10/10/2018 11:12 AM, ts...@rcmd.org wrote:
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>
> Dear FreeSurfer experts,
>
> what is the difference between the following 2 files found in a
if you want to mask the thickness, then use mri_mask
On 10/10/2018 10:30 AM, N Saf wrote:
>
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>
> Dear Douglos,
>
> as you recommended, I used the --outmask and create the binary mask of
> a label in mgh format. as I use the mri_binarize command with this
> m
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Dear FreeSurfer experts,
what is the difference between the following 2 files found in a subject's surf/
directory:
* file #1: lh.area.fsaverage.mgh
* file #2: lh.area.fwhm0.fsaverage.mgh
I see in the logs (/scripts/recon-all.log), that file #2
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Thanks, Niels.
It is definitely a matter of hyperintensity of voxels close to the lateral
boundary, particularly in the anterior region (which has a fuzzy boundary with
the white matter in first place). Whether these hyperintensities are due to MS
pa
It depends on exactly what you mean. Transforming it into MNI space is
fine if you keep it on the surface. If you try to sample it to a voxel mesh
you will lose effective resolution. I believe we distribute lh.aparc.annot
and rh.aparc.annot files for the fsaverage subject (in the label dir).
Th
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Dear Douglos,
as you recommended, I used the --outmask and create the binary mask of a
label in mgh format. as I use the mri_binarize command with this mask and
?h.thickness; the output is binary too or if I use --match flag or --min
--max flag the out
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Thanks, Niels.
I suspect the problem is that, for some reason, such voxels have much brighter
intensity than their surroundings, and are classified as white matter /
reticular nucleus. But that shouldn’t be happening that far from the lateral
boundar
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Hi Eugenio,
Thank you again for the fantastic thalamic nuclei segmentation tool!
I'm going through and QC'ing a batch of subjects that were processed
through the pipeline. Data was originally processed with freesurfer-6.0.0
and then processed through t
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POSTDOCTORAL FELLOWSHIPS IN TRAUMATIC STRESS DISORDERS
Collaborating research groups at the VA Boston Healthcare System anticipate up
to two NIMH-funded postdoctoral fellowships to begin by September 2, 2019.
These two-year training positions are desi
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Dear Dr Greeve,
I am following petsurfer pipeline to do surface based analysis of PET-FDG data
and I have interest in doing partial volume correction. I would like to inquire
about:
1) Can partial volume correction be applied on white mater, or just
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Dear Miguel Angel,
Ideally, one would always run all the subjects on the same platform. If this is
completely impractical due to computational limitations, then it is very
important to:
- spread the groups across platforms, e.g., avoid running all co
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Hi everyone,
Here a question and an answer of FreeSurfer experts that would be for
interest.
- Could there be any difference in accuracy when the recon-all is executed
on two Mac computers that have a different processor? that is, it is
preferable
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Dear All,
I am a master student in Turkey. For my thesis; I have to do exactly this;
Desikan atlas (which I have in the tailarach space) in the MNI space, as a file
(Desikan_mni.nii). I am aware that transforming from one space to the other is
not a
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We are seeking an enthusiastic PhD student with a particular interest in
neuroscience of auditory (speech) perception. The PhD position is part of the
Chair of Cognitive and Clinical Neuroscience led by Prof. Dr. Katharina von
Kriegstein at the TU Dr
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Few clusters survive glm fit. No clusters seem to survive glm-fit-sim (when
visualizing). However, I'm not sure if I should also see this in a text file.
Opening cache.th40(or 30).abs.sig.cluster.summary it seems to have found no
clusters. At least,
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