Dear Freesurfer Experts,
I am wondering if the cortical reconstruction is possible for the
quantitative mri images (R1, MT, PD...) obtained with the multiparameter
sequences .
If yes which image should i use?
Many thanks in advance,
Mohamed
--
Dr. Mohamed Ali Bahri,
1er Logisticien de Recher
Dear Douglas,
Just one more question : by default mri_gtmpvc uses pons for computing rSUV,
but is this intensity normalization done before or after partial volume
correction ? What file is used in input for intensity normalization ?
Thanks in advance !
Best regards,
Matthieu
2015-12-18 18:26 GM
Hello,
Does anybody have an idea ?
Thanks in advance !
Best regards,
Matthieu
2016-01-08 16:59 GMT+01:00 Matthieu Vanhoutte :
> Dear FS's experts,
>
> Projecting volumic data onto native surface (brain mask:
> "Unknown_S_calcarine_ROI_mask.jpg"), I observed that a thin region in the
> S_calcar
Dear Andrew,
sorry for the late reply.
Aren't there any error outputs for the two cases?
If not, would you mind uploading the subjects so I can take a look?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Le
Dear FreeSurfers,
I am editing a paper on subcortical volumes in deficit schizophrenia after
some reviewers' comments.
On of them suggested me to correct the volumes of subcortical structures
for whole brain volume instead of intracranial volume. In the reviewer's
opinion ICV estimated by FreeSur
Hi Mohamed
you can use mri_synthesize to create a flash image with good T1 contrast
from quantitative maps and run it through recon-all.
cheers
Bruce
On Mon, 11 Jan 2016,
Mohamed Ali Bahri wrote:
> Dear Freesurfer Experts,
>
> I am wondering if the cortical reconstruction is possible for the
>
Hi Pietro
ICV (or eTIV) is computed using Randy Buckner's method, so you can cite
his paper. Correcting for whole brain volume is certainly a reasonable
thing to do but note that then you are testing a somewhat different
hypothesis (that local atrophy is faster than whole-brain atrophy, as
op
Thanks a lot Bruce.
Cheers
2016-01-11 14:43 GMT+01:00 Bruce Fischl :
> Hi Pietro
>
> ICV (or eTIV) is computed using Randy Buckner's method, so you can cite
> his paper. Correcting for whole brain volume is certainly a reasonable
> thing to do but note that then you are testing a somewhat differ
Hi Pietro,
One additional thing to consider is that the ICV (eTIV) is entirely
dependent on the Talairach transform. Frequently, the accuracy of
Talairach transform isn¹t explicitly checked by users, because the
surfaces, aseg, etc can be accurate even if the Talairach transform isn¹t.
cheers,
-
I see.
This is very helpful.
Thanks
2016-01-11 15:15 GMT+01:00 Harms, Michael :
>
> Hi Pietro,
> One additional thing to consider is that the ICV (eTIV) is entirely
> dependent on the Talairach transform. Frequently, the accuracy of
> Talairach transform isn¹t explicitly checked by users, becaus
No, it is not. Have you tried using -fslhrf option in mkanalysis-sess?
On 01/09/2016 12:13 AM, LiTuX Sol wrote:
>
> Hi,
>
> I’m working on some fMRI data processing these days. In order to
> construct a HRF, I find this Matlab function in fsfast. But after some
> careful comparison, it seems tha
Hi Neha, I've attached a file called load_nifti.m. Put this in
$FREESURFER_HOME/matlab (after making a backup of what is there). Then
re-run and let me know if that fixes the problem.
doug
On 01/09/2016 06:00 AM, neha hooda wrote:
Hii
I am using freesurfer to find the resting state connectiv
Use mri_vol2label to create a label file. If you want the label on the
surface, then use mri_label2label with the --paint option
On 01/09/2016 03:11 PM, Jae Cho wrote:
> Dear FreeSurfer Experts,
>
> Could someone help me with a pipeline for creating a label from an
> edited existing label? I hav
On 01/10/2016 12:20 PM, Andrea Bozoki wrote:
> Plus, the
> minute you take an ROI created by Freesurfer to analyze a PET image (which
> cannot be surface-rendered accurately due to its inherent low resolution),
> you are forced to ³translate² the borders of ROIs from FS to a
> coordinate-based
The km.hb.tac.nii.gz is not a volume. It is a single voxel of data
stored in nii format. This format is needed to input to mri_glmfit. Try
loading it in matlab, eg,
hb = fast_vol2mat( MRIread('km.hb.tac.nii.gz'));
plot(hb)
if that is all 0s then it will surely cause mrtm1 to fail.
doug
On 01/
If you want to use partial volume correction, then you are better off
using mri_gtmpvc with the bbr registration, something like
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 reg
Hi Freesurfer experts.
Is there any tool to perfom volume calculations? Such binarize a volume,
intersect two volumes, sum volumes etc?
Thanks.
___
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Hi FreeSurfer experts,
I recently ran a simple fMRI analysis in FSL and now generating images of the
activation in freesurfer using reg-feat2anat to register the functional
activation to the freesurfer recon-all files, and generating the images using
tksurfer:
tksurfer pilot_3 lh inflated -ann
The pons intensity used to normalize has been PVC'ed. The file used is
the input file.
On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
> Dear Douglas,
>
> Just one more question : by default mri_gtmpvc uses pons for computing
> rSUV, but is this intensity normalization done before or after p
Hello,
I have a question regarding volume-correction for the morphometry stats
obtained via recon-all. I’ve noted that eTIV is derived using the atlas scaling
factor in order to account for head size. I’m wondering whether the other
volumes given, e.g. TotalGray or lhCorticalWhiteMatter, have a
Dear Douglas,
If the pons intensity used to normalize has been PVC'ed, couldn't we have
an output of mri_gtmpvc with the whole brain PVC'ed ?
Because the only files on output of mri_gtmpvc are :
mgx.ctxgm.nii.gz - pvc'ed cortex gm only
mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
mgx.gm.nii.g
Hi Christina
we don't correct any volumes for head size - we just provide the
information for you to do it yourself. I think including it as a
regressor is more common than dividing it out, but perhaps others can
comment.
cheers
Bruce
On Mon, 11 Jan 2016, Christina van den Brink wrote:
Hel
I'm not sure exactly what you mean. I guess you could set all voxels in
a given ROI to be the value of that ROI? This is not really a voxel-wise
correction and probably would not do what you want. You can use the mgx
data (corrected with muller-gartner method). There is also a --rbv
(region-bas
There is another parameter called -fmid. The final mapping is a
complicated combination of all three (fthresh, fmin, fslope). I usally
use the -fminmax option which is easier to explain. -fminmax 2 5 means
that the threshold is set to 2 and that at 5 the color will saturate.
doug
On 01/11/2016
Dear Douglas,
Sorry if I wasn't clear. With the PVC, voxels intensities are modified,
right ? So, in the case of anatomical intensity normalization based on
gray matter of cerebellum, is the mean activity of gray cerebellum taken
from the original PET image or from the PVC'ed PET image ?
Best
Thanks Doug! This is very good to know. Is there a ratio or relationship
between the fmin and fmax that is optimal, as in, should we keep a 2 to 5 ratio?
Gabriella
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf
no, it is a matter of taste. Note that 2 is the threshold. If you are
looking at sig maps, then the threshold may be important. The p-value
threshold is 10^-fthresh
On 01/11/2016 02:19 PM, Hirsch, Gabriella wrote:
> Thanks Doug! This is very good to know. Is there a ratio or relationship
> bet
OK, thanks!
Gabriella
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, January 11, 2016 2:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fMRI activation color
On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote:
> Dear Douglas,
>
> Sorry if I wasn't clear. With the PVC, voxels intensities are modified,
> right ?
Not necessarily. The GTM does not work this way. MG and RBV do. For an
ROI analysis, the GTM is by far the preferred method.
> So, in the case o
Le 11/01/2016 20:33, Douglas N Greve a écrit :
On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote:
Dear Douglas,
Sorry if I wasn't clear. With the PVC, voxels intensities are modified,
right ?
Not necessarily. The GTM does not work this way. MG and RBV do. For an
ROI analysis, the GTM is by far
Yes with MGPVC the voxel values are rescaled by the MG formula. Note
that MG (and RBV) use GTM as a preprocessing step. If you average the MG
output over an ROI, then it comes close to the GTM value.
On 01/11/2016 02:39 PM, Matthieu Vanhoutte wrote:
> Le 11/01/2016 20:33, Douglas N Greve a écrit
Dear FS Community,
I am currently using FreeSurfer 5.3 to conduct a longitudinal analysis of
atrophy in Semantic Dementia. Because of the profound temporal pole atrophy in
these patients, I have been making a lot of manual edits (mostly control points
and wm edits) to the baseline scan, and the
Hi list,
I have resolved my issue on the previous point 2 by downloading matlab file
on:
https://sites.google.com/site/kittipat/mvpa-for-brain-
fmri/convert_matlab_nifti
after the command that you suggesedt:
fdrthresh = fast_fdrthresh(p,0.05);
the script produce p=0.053
Therefore, coming back t
For binarization use mri_binarize. For intersecting, you can use
mri_binarize with the --mask option. If you want to add to volumes, you
can use fscalc, eg
fscalc vol1.mgh sum vol2.mgh -o sum.mgh
fscalc has a bunch of options. Run it with -help to see
On 1/11/16 11:30 AM, Julio Alberto González
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