Dear Freesurfer,
1) I would like to investigate the possible outcomes of my functional group
analysis after smoothing with 5 FWHM and 10 FWHM. My functional data is already
mapped onto the fsaverage. Which command would you suggest for smoothing this
data?
2) In the functional group analysis tut
if it's saved as a surface you can get it from mris_anatomical_stats. If
you want only a region within the surface, create a label and use the -l
option
cheers
Bruce
On Tue, 8 Sep 2015, Jockwitz, Christiane wrote:
Dear all,
I would like to extract the surface area from the outer smoothed
Hi Yun
1. No, the surfaces are not binary. They exist in in a continuum, so aren't
limited by the resolution of the underlying volumes. You should be able to
visualize them over the volumes using
freeview -v -f
2. mri_compute_layer_fractions computes the volume fractions of each
compartme
Thanks for your answer! Truly help me a lot!
> On Sep 8, 2015, at 07:17, Bruce Fischl wrote:
>
> Hi Yun
>
> 1. No, the surfaces are not binary. They exist in in a continuum, so aren't
> limited by the resolution of the underlying volumes. You should be able to
> visualize them over the volu
Dear Michael,
Thank you very much for your fast reply. Sorry for bothering you, I had not
seen the FAQ entry.
Sorry and thank you again,
Leonardo Tozzi
Research Fellow
Discipline of Psychiatry
Trinity College Institute of Neuroscience
College Green
Dublin 2
Ireland
Office: +35318964234
Mobile
Thanks Doug,
Is there a way to do this for surface clusters as well?
Tracy
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, September 02, 2015 4:02 PM
T
I need to see the log file. Based on the output files that you sent me,
it ran further along this time, so you must be running into a different
error now. I can't guess what the problem is without seeing the log.
On Mon, 7 Sep 2015, andrea cristina Lima wrote:
-- Forwarded message
Hi all,
I'm trying to generate an ROI mask from the Freesurfer label lh.MT.label of a
specific subject. I've browsed the documentation and the archives and it seems
the best command to use is mri_label2vol. However, I can only seem to produce
the "outline" of the label, if that makes sense (as
Hi,
We are using mri_robust_register in one of our pipelines to register two 2D
T2 images from the same patient (2 different timepoints). We resample both
volumes into halfway space to then perform image subtraction.
Both T2 volumes are 2D images, each with 44 slices. However when volumes
are resa
It is masked in, ie, it only uses the vertices that are in the label.
On 09/03/2015 04:26 PM, Sebastien Proulx wrote:
>
> Quick question :
>
> When using --label with bbregister, does the specified label file mask
> in or out (is the the voxels that are out or in of the label file that
> are exc
they are the files named like "fmcpr.odd.nii.gz"
On 09/04/2015 08:17 AM, std...@virgilio.it wrote:
> Hi using Philips scanner (interleaved)
> Therefore, I'm running
>
> preproc-sess -sf sessid -fwhm 5 -surface fsaverage lhrh -mni305-1mm
> -fsd rest -per-run -sliceorder odd
>
> However, as you c
Run recon-all on the mni152 T1 template that comes with SPM, project
your VBM results to the surface of that (mri_vol2surf), binarize it if
not already (mri_binarize), create a surface label (mri_cor2label with
--surf option and --id 1), then use mri_label2label to map it to each
subject, then
It is expecting it in mgz format, so just
mri_convert MRS_MASK.nii.gz MRS_MASK.mgz
On 09/04/2015 01:08 PM, std...@virgilio.it wrote:
> Hi list,
> I'm performing FS-FAST using as seed MRS voxel (MRS_MASK).
> MRS_MASK shows a god overlap with orig and both of these are located
> in $SUBJ/mri.
> F
what is different?
On 09/07/2015 07:02 PM, Jacek Manko wrote:
> Dear All,
>
> In your entry on corical parcellation:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
>
> You enumerate a certain list of cortical labels obtained in that procedure.
> If I run aparcstats2table I got
What are you using to do the functional analysis? In general, use
mri_surf2surf to do the smoothing (or mris_fwhm). cesvar.nii.gz is
something produced by FAFAST. If you are not using FSFAST then you'll
have to find the equivialent (it is the variance of the contrast,
VARCOPE in FSL I think)
O
Hi Leorah,
in order to do a 3D registration you really need 3D information, so
intrinsically the registration works in isotropic spaces. That is why
the midspace has isotropic voxels. Maybe try writing out the two
transforms to midspace and then use mri_convert with the -rl flag
(passing one
Try it with --fill-ribbon
On 09/08/2015 11:01 AM, Hirsch, Gabriella wrote:
> Hi all,
>
> I'm trying to generate an ROI mask from the Freesurfer label
> lh.MT.label of a specific subject. I've browsed the documentation and
> the archives and it seems the best command to use is mri_label2vol.
> H
Hi Freesurfer experts,
I am trying to create a label from Talairach coordinates. I loaded the
fsaverage brain in tkmedit (tkmedit fsaverage orig.mgz) and entered the
coordinates 0 -16 -6 (our coordinates of interest). From here I saved the label
using "save label as". However, when I try to loa
Hi FS experts,
In FS development package I see that there have been tools added for
partial volume correction of PET data, but I was wondering if there were
also kinetic modeling tools similar to those described in Doug's 2014
paper? If you could let me know what PET processing tools have been
inc
Thanks Doug - I tried adding it but got an error:
ERROR: Option --fill-ribbon unknown
Does the order matter/should some other flag be removed?
Thanks,
Gabriella
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on b
Yes there are both. For KM we have MRTM1 and MRTM2 so far. They are not
well documented yet.
1. To start, run
gtmseg --s subject
This will take a couple of hours and produces some files needed for GTM
PVC (which is used for GTM, MG, RBV).
2. You'd then register the PET to the anatomical with
try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol
On 09/08/2015 02:30 PM, Hirsch, Gabriella wrote:
> Thanks Doug - I tried adding it but got an error:
>
> ERROR: Option --fill-ribbon unknown
>
> Does the order matter/should some other flag be removed?
>
Not as easily. You can use mri_segstats again with the --annot option.
Create a new surface overlay by masking ?h.area with your cluster and
use this as the input; also add --accumulate. Run it a second time (with
diff output) and use the ?h.area as input (instead of the masked area).
If you di
There are no points in the label. I'm not sure that you actually created
a label. Did you have tkmedit configured to draw labels? Actually, I
think it open that way... Did you see a colored dot where your label was?
On 09/08/2015 02:04 PM, Rodriguez-Thompson, Anais wrote:
> Hi Freesurfer experts
Ah, running into a slight snag. I placed the new version in the freesurfer/bin
folder but I'm running into permission issues:
/usr/local/freesurfer/bin/mri_label2vol: Permission denied.
Tried chmod-ing it but still didn't work:
chmod +x mri_label2vol
chmod: changing permissions of `mri_label2vo
You probably don't have permissions on your network. Are you local to
the Martinos? If so, then use the dev version (but only for this).
Alternatively, you can copy it into your path somewhere. You probably
don't want to overwrite the version in your distribution.
On 09/08/2015 03:05 PM, Hirsch
Hi Doug,
I didn't see a colored dot. Unlike tksurfer, I didn't see a fill option to
create a label from a point. Is there something I should do other than moving
the cursor to my point of interest and then "save label as?"
Thanks,
Anais
From: freesurfer-
use the middle mouse button to create the label, then save it
On 09/08/2015 04:27 PM, Rodriguez-Thompson, Anais wrote:
> Hi Doug,
>
> I didn't see a colored dot. Unlike tksurfer, I didn't see a fill option to
> create a label from a point. Is there something I should do other than moving
> the c
Use "abs" not ""
On 09/04/2015 03:20 PM, Xiaomin Yue wrote:
> Hi,
>
> I got this error when run mri_glmfit-sim: missing name for redirect.
> I am running freesurfer 5.3. the command is: mri_glmfit --glmdir
> ces.nii --cache 2 --sim-sign . The ces.nii was generated from
> group level analysis
no, use mri_concat with the --conjunct option
On 09/04/2015 12:08 PM, std...@virgilio.it wrote:
> Hi list,
>
> is possible to obtained a conjunction map from vlrmerge command on
> FS-FAST (resting state) results?
>
>
> Stefano
>
>
> ___
> Freesurfer mai
Thanks
Xiaomin
On Tue, Sep 8, 2015 at 2:03 PM -0700, "Douglas N Greve"
wrote:
Use "abs" not ""
On 09/04/2015 03:20 PM, Xiaomin Yue wrote:
> Hi,
>
> I got this error when run mri_glmfit-sim: missing name for redirect.
> I am running freesurfer 5.3. the command is: mri_glmfit --glmdir
> ces
Hi Freesurfer experts,
I'm trying to run a functional connectivity analysis using a label that was
created in the volume (vta.label). I have a few questions about how I would do
this (compared to a label created on surface).
Usually, we create a smoothed mask using the commands
mri_label2labe
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