Dear experts,I am kind of new at working with freesurfer.recon-all process has
completed without error, but when I look at brainmask volume on freeview, one
of the issues is that lateral ventricle is completely excluded. I have tried to
edit it with editing the white matter volume, but no succes
Hi Bruce,
Thanks for the reply, I attempted to direct Subjects_dir to the folder with
my data but I received the following error.
Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ export
SUBJECTS_DIR=/Desktop/Brain_Child_subs
Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd
/Deskt
Dear Freesurfer community,
I am working on an ROI analysis using qdec. I have created all aseg and
aparc stats files and would like to determine if there are any differences
in volume, surface area, and thickness for certain structures between two
groups. I was wondering with the analysis, would i
We are in the process of preparing a grant to support FreeSurfer
development and maintenance:
Title: FreeSurfer Development, Maintenance, and Hardening.
PIs: Greve and Fischl.
Grant reviewers need to know that FreeSurfer is useful to a lot of
people, so we encourage you to do one of two things:
sure, but I think Doug wins this round (curse you Greve!)
Bruce
On Mon, 25 Jan
2016, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Bruce and Doug,
>
> Both methods sound great. Thank you both for your help!
>
> Best,
> Panos
>
>> I don't think there is a single command line to do it, but if you can
>
Hi Bruce and Doug,
Both methods sound great. Thank you both for your help!
Best,
Panos
> I don't think there is a single command line to do it, but if you can
> get the centroid voxel from somewhere else (eg, fsl), then you can run
> mri_volsynth --template template.nii.gz --pdf delta -delta-crs
I don't think there is a single command line to do it, but if you can
get the centroid voxel from somewhere else (eg, fsl), then you can run
mri_volsynth --template template.nii.gz --pdf delta -delta-crsf col row
slice 0
where col row and slice are the voxel coordinates
On 01/25/2016 03:49 PM,
Hi Panos
why not just write a matlab script to do it? It would be easy enough. I
don't think we have a binary that will quite do what you want
Bruce
On Mon, 25 Jan
2016, pfot...@nmr.mgh.harvard.edu wrote:
> Dear FS Community,
>
> I was wondering whether there is a way to create a binary volumet
Dear FS Community,
I was wondering whether there is a way to create a binary volumetric file
of just the centroid of a binary volume (represented maybe as a dot of
1x1x1 mm^3 voxel size).
I know how to find the coordinates of the centroid (through either the
fslstats command or MATLAB), but I didn
No one command, but you could
mri_annotation2label choosing the --seg as the output
mri_binarize --i seg.mgz --match NN --o seg.NN.mgz -- NN is the index
of your chosen seg
mri_surfcluster --in seg.NN.mgz --thmin 0.5 --olab seg.NN
this should create a seg.NN-.label for each contiuous element
Hi,
I want to separate each label in the Yeo parcellations into each of
their separate contiguous labels. Is there a command, which can do
this in Freesurfer?
Example lh.yeo7.annot
the network 7 label has 5 non-contiguous components
Is there a command to separate these into 5 separate labels?
T
Hi Martin,
We’ve got the tcsh installed and seems to be working. Can’t find a similar
report on the list serve, so I’ve attached the bug report info below plus the
orig_nu.log output, which is where the script is crashing. Please help!
Cheers,
Daniel
Output from buggr:
FREESURFER_HOME: /home/fr
Hello Experts,
We used the brainstem segmentation that is built into FS 6.0, to interrogate
midbrain volumes. My question was: the way FS segments the midbrain, does it
include the cerebral peduncles?
cheers,Cat___
Freesurfer mailing list
Freesurfer@nm
not necessarily. For FSL, the determinant must be less than 0 (see
mri_info output). Having said that, even if the det<0, it may still show
up funny in fslview
On 01/25/2016 12:11 PM, Yang, Daniel wrote:
> Dear FreeSurfer experts,
>
> I find that mri_convert will convert DICOM of structural scan
Dear FreeSurfer experts,
I find that mri_convert will convert DICOM of structural scan to neurological
orientation by default.
For example, mri_convert --in_type dicom --out_type mii
Thus, the NII may need to be swapped in x for use in FSL.
In this the case?
Many thanks,
Daniel
--
Daniel Y
Please give an example of the command line.
I have performed fdr correction by tksurfer. Should I save that map?
Thanks
Stefano
>Messaggio originale
>Da: Douglas N Greve
>Data: 25-gen-2016 17.30
>A:
>Ogg: Re: [Freesurfer] R: Re: FDR map: hide very little cluster
>
>just use the FDR th
use --o instead of --vwsig
On 01/25/2016 11:31 AM, std...@virgilio.it wrote:
>
> mri_surfcluster --in intercept/sig.nii.gz --hemi rh --sign abs
> --no-adjust --fdr 0.05 --minarea 5 --sum summaryfile --subject
> fsaverage --annot aparc
>
>
> produces only summary.txt
>
>
> mri_surfcluster --in in
mri_surfcluster --in intercept/sig.nii.gz --hemi rh --sign abs --no-adjust
--fdr 0.05 --minarea 5 --sum summaryfile --subject fsaverage --annot aparc
produces only summary.txt
mri_surfcluster --in intercept/sig.nii.gz --hemi rh --sign abs --no-adjust
--fdr 0.05 --minarea 5 --sum summaryfile --su
just use the FDR thresholded input and set --thmin to 0.5
On 01/25/2016 11:21 AM, std...@virgilio.it wrote:
> Thanks. But I do not know how I can obtain a corrected sig.nii.gz.
> In this way I have obtained only summary.txt.
> If I add --vwsig vwsig cds file is request.
>
> Stefano
>
> Mes
Thanks. But I do not know how I can obtain a corrected sig.nii.gz.In this way I
have obtained only summary.txt.If I add --vwsig vwsig cds file is request.
Stefano
Messaggio originale
Da: Douglas Greve
Data: 25-gen-2016 17.10
A:
Ogg: Re: [Freesurfer] FDR map: hide very little clust
Please could you suggest me an example of command line.I'm trying from several
day without results.Thank you very much.
Stefano
Messaggio originale
Da: Douglas Greve
Data: 25-gen-2016 17.10
A:
Ogg: Re: [Freesurfer] FDR map: hide very little cluster
Use the --minarea
Use the --minarea option to mri_surfcluster (not the CSD).
On 1/25/16 10:39 AM, std...@virgilio.it wrote:
Hi list,
please, could you help me because from several days I'm trying to have a
solution.
I have performed a seed-based fcMRI analysis by FAST.
After mri_glmfit, I have obtained a sig.nii
please remember to include previous correspondences. We can't remember
every post ...
On 1/25/16 3:39 AM, Erik Lindberg wrote:
Dear Douglas and Freesufers,
You suggested:
mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 =
-log10(.05)
I tried this and was expecting that I
Research Coordinator Position in Psychiatric Neuroimaging at the
MGH-Martinos Center:
We are looking to hire a college graduate with at least one year of research
experience and strong organizational and interpersonal skills as a full time
research coordinator. The position involves working
Hi list,please, could you help me because from several days I'm trying to have
a solution.I have performed a seed-based fcMRI analysis by FAST.After
mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I
have corrected by FDR using the graphical interface provided in tksur
yes, but do you want to do the fMRI analysis on the surface or in the
volume? There are lots of advantages to doing it on the surface. If your
sig.cluster.mgh was a surface overlay then the threholded.mgh might be
exactly what you want. Load it on an inflated surface and take a look
cheers
Bru
Dear Bruce and Freesurfers,
I probably then go about this in the wrong way. My aim is to create a
binary mask for regions that I found differences in - in a
group-comparison. I then want to export the mask so I can use it as
seed area in an fMRI analysis.
Can this be done
Thanks
Eric
Hi Er
Hi Erik
what is the dimensionality of sig.cluster.mgh? You can tell this with
mri_info. It is problaby a surface overlay (so nvertices in one dimension),
and can't be viewed in the volume but only on the surface.
cheers
Bruce
On Mon, 25 Jan 2016, Erik Lindberg wrote:
Dear Douglas and Fre
Hi Jasmin
you need to create a directory where you have write permission and room
for the subject reconstruction to be written to, then set the SUBJECTS_DIR
environment variable to point to it. At the moment you are trying to use
the subject directory we distribute, which is in some system (a
Ciao Luigi,
I haven't tried FLAIR for images the subfields, but if you sent me a high-res
FLAIR acquisition of the hippocampus, I could take a look.
If you are doing T2, you could implement the procotol used in ADNI: coronal
slices with 0.4x0.4 in plane resolution, with 2mm slice separation (id
Dear members,
in our center we are evaluating whether to introduce a T2 into a protocol
that, among others, already includes a T1 and a FLAIR sequences.
Our main concern is to to maximize the information-to-duration ratio of the
entire protocol.
In order to improve the subfields' segmentation w
Dear Douglas and Freesufers,
You suggested:
mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 =
-log10(.05)
I tried this and was expecting that I would get a three-dimensional mask in
which the statistical significant part would be white and the rest black.
This seems not t
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