Hi Doug,
thank you veru much for the answr.
Please what do you mean by " an emperical question that depends on your data"? For example:
I have two groups of participants. I ran cortical thickness analysis in Qdec to study the differnce between the groups in cortical thickness:
1. Monte car
Dear FS experts,
I have PET image "pet.anat.mgz" in subject space. I want to calculate the mean
PET signal for every parcellate and segment in the atlas "wmparc.mgz".
Which one of the following commands is more accurate?
1. mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab
$F
what do you mean isolate? what do you mean export? You can create a
binary mask in nifti format with mri_binarize --i aseg.mgz --match 10 49
--o thalamus.mask.nii.gz
On 07/06/2016 04:46 PM, Dorsa Haji Ghaffari wrote:
>
>
>
> Hi,
>
> I was able to segment the MRI successfully, now I am trying to
Hi,
This is a repost. Would anyone have a solution to this problem ?
Thanks for your help.
Best,
Ismail
> On Jul 5, 2016, at 11:24 AM, Koubiyr, Ismail wrote:
>
> The file has not been anonymized.
>
> Thanks,
>
> Ismail
>
>> On Jul 5, 2016, at 11:20 AM, Douglas N Greve
>> wrote:
>>
>> c
Hi Doug,
Thank you so much! Because I will do the analysis using SPM, I need the
coordinates in MNI152 space. I found a transformation between them:
M = [0.9975 -0.00730.0176 -0.0429
0.01461.0009 -0.00241.5496
-0.0130 -0.00930.99711.1840
Hi,
I was able to segment the MRI successfully, now I am trying to isolate the
thalamus and export it out of FS as a volume. Is there a way to do that in
FS?
Thank you
Dorsa
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Hi Baojuan, that coordinate will be mni305 space. Is that what you want?
On 07/06/2016 04:17 PM, Li, Baojuan wrote:
> Dear Freesurfer experts,
>
>
> I am using MNE (with MEG data) to define my ROIs for a connectivity
> analysis. I am going through the following steps to get the MNI
> coordinates
Dear Freesurfer experts,
I am using MNE (with MEG data) to define my ROIs for a connectivity analysis. I
am going through the following steps to get the MNI coordinates of the regions:
1. Morph the subject's brain to fslaverage;
2. Load the inflated surface of fslaverage to MNE analyze;
3. Lo
Hi Rito
the control points you have look like they are in voxels that contain
some gray matter, which will probably make things worse. YOu need to
identify why you are missing that part of the surface. Is the dark stuff
there labeled as white? Maybe it's a topological defect that gets filled
i
Hi Doug,
I just wanted to make sure that we were on the same page. I may have
been a little unclear in what I would ideally like to do.
For #2 what I would like to do is take into account age slopes and
total intracranial slopes for gender, and age slopes and total
intracranial slopes for diagnos
Hi,
The missing sulcus may be a consequence of the topology correction going awry. Check the “nofix” surface to see the surface before topology correction. If the topology correction is the problem, you’ll need to edit the wm.mgz. There is an example on
the FS tutorials.
ch
Freesurfer Support,
I have seen previous message threads on extracting LGI measurements across
ROIs, however I have yet to find anything which would provide a summary LGI
across an entire hemsphere.
Other measurements like cortical thickness have a measurement like this. Is
there a measurement lik
The output L_parahipp_seed.surf.lh/L_parahipp/sig.nii.gz is already on
the surface.
if you need the output as text, you can run mri_convert sig.nii.gz
output.txt --ascii
or use --ascii+crsf
--ascii
save output as ascii. This will be a data file with a
single
I did not get the same matrix. Here's how I would do it
Columns 1-16 model the intercepts for all your classes
Columns 17-20 model the ages for your gender-x-diagnosis subclasses
Columns 21-24 model the ICV for your gender-x-diagnosis subclasses
On 07/06/2016 02:04 PM, Timothy Hendrickson wrote:
Ah, the problem is with using an lta with 5.3 mris_preproc. I've put
version 6 mris_preproc here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc
try that and see if it works. Alternatively, you could convert the lta
files to register.dat files
On 07/06/2016 02:02 PM,
Freesurfer Support,
Thank you for your support with my previous line of questions
regarding design matrix creation.
I have manually created another design matrix and want to ensure that
I designed it correctly.
An example of my FSGD file is as follows below:
Class SITE 1-Male-Control
Class SITE 1
What is the problem with the orientation? The little letters indicate
that the orientation is correct. fslview ignores the orientation when
displaying so it might come out upside down.
On 07/05/2016 01:35 PM, Sabin Khadka wrote:
>
> Hi Doug, As you suggested I mapped fmri into the anatomical spa
Hmm, it says that there is one frame in each of the subjects.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 06, 2016 1:54 PM
To: freesur
that looks right. You might want to call the output something else so
that you don't overwrite the default FS output
On 07/06/2016 01:55 PM, Sabrina Yu wrote:
>
> Hi,
>
>
> Thanks for the quick reply. I just want to confirm that my command is
> correct for changing the input volume to orig.mgz:
Hi,
Thanks for the quick reply. I just want to confirm that my command is correct
for changing the input volume to orig.mgz:
mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/orig.mgz
--excludeid 0 --brainmask mri/brainmask.mgz --in mri/orig.mgz
--in-intensity-name orig --i
It must be that one of the ces files has multiple frames. Try running
mri_info --nframes ces.nii.gz
on all of the ces files to see how many frames are in each
On 07/06/2016 01:39 PM, Raney, Talia L. wrote:
> mris_preproc --target fsaverage --hemi lh --iv
> WADG77j/restingstate/fc.lh-entorhinal.sp
It would be something like
mris_apply_reg --src lh.data-from-fsavgsym.mgh --streg
$SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg
$SUBJECTS_DIR/yoursubject/surf/lh.fsaverage_sym.sphere.reg --o
lh.data-from-fsavgsym-on-yoursubject.mgh
On 07/04/2016 10:34 AM, Ali-Reza Mohammadi-Nejad wrote:
> De
There is no recommendation between FDR and monte carlo. The question of
which one is "better" is an emperical question that depends on your data.
On 06/29/2016 06:38 AM, John Anderson wrote:
> Dear FS experts,
> I will re post this thread again looking for your help and support:
> I ran cortical
use mri_vol2vol to map the pet into the anatomical space
On 06/28/2016 01:48 PM, Pradeep wrote:
> Hello All,
>
> I am trying to extract the SUV values a PET image
>
> mri_segstats --seg wmparc.mgz --sum petsuv.segstats.dat --i rPET
> --ctab-default
>
> since rPET is supposed to be coregistered to
try this version and let me know if it works.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
If not, please send me the dicom via filedrop below
On 06/30/2016 05:45 AM, Leonardo Tozzi wrote:
>
> To Whom it may concern,
>
>
> I have tried to run the recon-all pipeline on
mris_preproc --target fsaverage --hemi lh --iv
WADG77j/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz
WADG77j/restingstate/bb.register.lta --iv
WADG77k/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz
WADG77k/restingstate/bb.register.lta --projfrac 0.5 --out lh.c
The subject name is the FreeSurfer subject name assigned when you ran
recon-all to analyze the T1 anatomical MRI images. BTW, you need
everything in native space to run the pipeline.
doug
On 06/30/2016 12:25 AM, Lee Subin Kristine wrote:
> Dear FreeSurfer experts,
>
> Hello,
> I am trying to use
Trisanna, has this issue been resolved?
doug
On 06/30/2016 01:26 PM, Trisanna Sprung-Much wrote:
> Hi Bruce
>
> here is the output of my mri_vol2surf for a volumetric spam created in
> minc tools. When I then overlay this result in Freeview, it displays a
> Min of 127 and a Max of 255.
>
> trisa
Is this problem resolved? There is a new version here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg
On 06/16/2016 11:05 AM, Leila Reddy wrote:
> Hi FS Experts,
>
> I'm trying to use the mni152reg command but I get an error that --lta
> is not recognized.
>
> It appears t
On 07/06/2016 01:05 PM, Sabrina Yu wrote:
>
> Hello,
>
>
> I have a couple of questions about the wmparc.stats file generated.
> What volume is the data based on?
>
norm.mgz
>
> Has the intensity of the volume been corrected?
>
Yes
>
> I just need the average voxel intensity over the ROIs, but a
can you send the terminal output?
On 07/06/2016 11:32 AM, Raney, Talia L. wrote:
> Hi FreeSurfer users,
> I'm trying to use mri-preproc to do a group fMRI analysis(based on the
> tutorial). However, I keep getting an error that the number of input volumes
> does not equal number of subjects. It
Hi Rito,
I just read this today myself "Select a few control points around your
trouble areas, space them out throughout the brain and on different
slices. You want to pick points in a region where the wm intensity is
lower than it should be (that is, having a voxel value less than 110)."
fro
Hello,
I have a couple of questions about the wmparc.stats file generated. What volume
is the data based on? Has the intensity of the volume been corrected? I just
need the average voxel intensity over the ROIs, but am unsure if this intensity
is based on an intensity normalized brain volume.
Dear Freesurfers,
I am looking for a way to add a colorbar to my p-value tract cores
generated through TRACULA.
When I load up the images as described in the tutorial here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
I only get a colorbar from 0 to 28.5 which cannot r
Hi FreeSurfer users,
I'm trying to use mri-preproc to do a group fMRI analysis(based on the
tutorial). However, I keep getting an error that the number of input volumes
does not equal number of subjects. It seems one volume is counted as 4
subjects. I'm wondering what the command determines to b
Thanks. Only for FS 6.0 and later, correct?
Jim
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias, Eugenio
Sent: Wednesday, July 06, 2016 9:47 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields command
Not yet, sorry. But it’s on my todo list.
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 6 Jul 2016, at 14:39, Hibert, Matthew Louis
mailto:mhib...@mgh.harvard.edu>> wrote:
Hi Eugenio,
Have you had a chance
Hi Jim,
the latter command uses a new, higher resolution atlas based on ex vivo scans.
Cheers,
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 6 Jul 2016, at 15:39, Alexopoulos, Dimitrios
mailto:alexop
A quick question re: hippocampal segmentation.
I have processed 1mm isotropic T1 data with 5.3 using the following command:
recon-all -qcache -all -hippo-subfields
How is this this different than using the following command I have found here:
https://surfer.nmr.mgh.harvard.edu/fswiki/Hippocamp
Dear Bruce,
Thanks a lot for clarifying.
Best wishes,
Barbara
On 06/07/2016 15:57, Bruce Fischl wrote:
> Hi Barbara
>
> yes, this is intentional and shouldn't be a problem. The hippocampus has
> lots of internal structure that we don't model with the surfaces (but we do
> with the subfield stu
Hi Mahtab
you should look them up in a differential geometry textbook. Essentially,
a 2D surface has two curvatures at each point, one in the direction of
maximum folding (k1) and one in the direction of minimum folding (k2). The
Gaussian curvature is then k1*k2 and the mean is (k1+k2)/2
che
Hi Doug,
Yes. Dr. Yeo Thomas helped me figuring out ways to extract ROI values from
Buckner 2011 7 Cerebellar network. Please see below for the steps I
performed to extract time series from Buckner 2011 7 Cerebellar networks.
If you could give your thoughts on the steps/process that'd be great.
*
Hi Barbara
yes, this is intentional and shouldn't be a problem. The hippocampus has
lots of internal structure that we don't model with the surfaces (but we do
with the subfield stuff), but we exclude it from our analyses so you should
be fine
cheers
Bruce
On Wed, 6 Jul 2016, Barbara Kreilkam
Hi Abbie
you might check out Matti Hamalainen's MNE software. He does both boundary
and finite element analysis. We distribute a test subject named "bert" you
can use
cheers
Bruce
On Tue, 5 Jul 2016, Abbie McNulty wrote:
Hello,
Just a couple more questions that would be great if you could
See if this page helps
http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
On 7/6/16 9:07 AM, Kaiming Yin wrote:
Dear experts,
Could I ask which value in the stats/aseg.stats represents the volume
of the cerebrum (including the subcortical structures while excluding
the ventricles and
Hi,
There is nothing to solve — that is the expected behavior around the
hippocampus/amygdala.
See this FAQ:
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Thesurfac
esnearthemedialwall.2Chippocampus.2Candamygdalaaren.27taccuratelyfollowingt
hestructuresthere.HowcanIfixthis.3F
use this program
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr
On 7/6/16 9:22 AM, tom parker wrote:
Dear Freesurfers,
I ran a comparison between different groups using mri_glmfit.
Now I would like to correct the results in sig.mgh by multiple
comparisons using FDR.
Hi Eugenio,
Have you had a chance to look into the possibility of combining the -hires flag
with the hippocampal subfield segmentation?
Thanks,
Matt
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias, Eugen
Dear Freesurfers,
I ran a comparison between different groups using mri_glmfit.
Now I would like to correct the results in sig.mgh by multiple comparisons
using FDR. I tried using tksurfer but it doesn't work so well on my
computer and I read that freeview does not allow to do that yet.
I'm now t
Dear experts,
Could I ask which value in the stats/aseg.stats represents the volume of
the cerebrum (including the subcortical structures while excluding the
ventricles and brain stem)? I'm not sure whether the
"SupraTentorialNotVent" can be the value for this measurement, and could it
be a bit bi
Dear FreeSurfer,
I am using the mris_anatomical_stats output to calculate the curvature and
thickness indices for different brain areas. However, I am not sure what
the mean and gaussian curvatures mean. I could not find a complete
description on these two. Would you please guide me what principle
Dear all,
We are working on this; I'll write again when the problem is solved (hopefully
soon!)
Cheers
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: freesu
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