See this page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
On 2/7/2020 9:52 PM, Kim, Gwang-Won wrote:
Hi there,
I ran “mri_glmfit-sim –glmdir g2v3.wls –2spaces –perm 1000 1.3 abs”.
But, there was error message as follow: “design matrix is not
orthogonal,
On 2/11/2020 9:26 AM, Benjamin Ineichen wrote:
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Dear Freesurfer experts,
I ran recon-all on 100 subjects. Around 20 of them needed manual
corrections of the pial surface on the brainmask.mgz.
1.) Can I run the command: "recon-all -make all- s " on all
On 2/12/2020 2:46 PM, Faizan Anwar wrote:
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Hello,
My name is Faizan Anwar. I am currently a undergraduate student at
UCLA. I had two questions regarding freesurfer:
* Is FSAVERAGE file a universal template that could be used with any
set of
Try running it as a single line (ie, without the backslashes and the >)
On 2/6/2020 6:26 AM, FRILEUX Solene wrote:
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Good morning,
I am writing to you in order to ask you some help about optseq.
I am struggling using the command cmx .
I need to save the
What tool are you trying to use to load the label? What happens when you
try?
On 2/7/2020 10:11 PM, Tien Pham wrote:
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Thank you for your email. I run exactly the command mri_label2label as
you suggested, and the command finished without any problem.
But
Even if you use the same subjects, you are performing three different
analyses, so it is not surprising that you are getting different
results. As to why they are wildly different, I don't know. I suspect
that you need to demean your continuous variables.
On 2/10/2020 11:26 AM, Wang, Lily
You could do it, but I would just use fsaverage. I don't understand
what the relationship would be between the number of vertices on the
surface and the number of voxels in the PET volume or the rational for
using the 5th order ico
On 2/12/2020 8:03 AM, Marina Fernández wrote:
Hi Lara, I think that is right, but I don't use gii much
doug
On 2/12/2020 2:05 PM, Lara Foland-Ross wrote:
> External Email - Use Caution
>
> Hello Freesurfer experts,
>
> I'd like to convert my subjects' thickness mgh files to gii format for use in
> an analysis with a separate
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@Chris:
I recently needed exactly what you want in Matlab, feel free to use it:
https://github.com/dfsp-spirit/comp_neuro_science/blob/master/matlab_utility_functions/mesh_neighborhood.m
A usage example is included (see script). It's not terribly
Hi Kirill
I think this is a question for Matti (now ccd)
cheers
Bruce
On Fri, 14 Feb 2020, Kirill
Elin wrote:
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Hallo everybody,
I am not entirely sure whether this is FreeSurfer error actually.
I am doing first recon all which completes without
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I think one way to do this would be to split the atlas into a set of label
files using `mri_annotation2label`. I would do it for the fsaverage subject.
This will give you one label file per atlas region. Something like this:
cd
Is the hV5+MT label already a binary volume in the FS conformed 1mm
space (ie, same space as orig.mgz)? And what do you mean by "constrained"?
On 2/13/2020 11:04 AM, Star Xi wrote:
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FS experts,
Commonly, I can use mri_vol2vol -> mri_segstats to extract
You need to register your subjects to the new average subject with
surfreg --s subject --t 0_1
On 2/11/2020 12:36 PM, Vyacheslav Yarkin wrote:
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I got the idea but faced an issue with mris_preproc, the command is:
mris_preproc --target 0_1 --s
Is the image in the wrong orientation (ie, is it not truly in PIR) or do
you want to change the orientation? doing a left-right swap is more than
changing the orientation
On 2/11/2020 4:06 PM, Miguel Ángel Rivas Fernández wrote:
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Dear Freesurfer experts,
You'll have to use read_surf.m to read in the fsaverage surface. The
surface will neighbor info
On 2/13/2020 1:51 PM, Mcnorgan, Christopher wrote:
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I’m interested in working with data mapped to the .sphere
icosohedrons. I understand from a response from
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Dear Douglas,
My image is in the correct orientation. The reason is that am using a
software to detect brain lesions that only works in left hemisphere and my
subject have the lesion in the right hemisphere. I tried it with the
following command and
You should try the analysis but with the data in the something.y.ocn.dat
output by mri_glmfit-sim. This data contains a nsubjects x nclusters
table of the input data (y) to the glm. If that does not show up as
significant, then something is wrong.
doug
On 2/5/2020 11:30 AM, Hooren, Roy van
On 2/10/2020 11:20 AM, Christian O'Reilly, Dr wrote:
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Hi,
How can I convert a LTA file type 0 (LINEAR_VOX_TO_VOX) to a type 1
(LINEAR_RAS_TO_RAS)?
Use lta_convert
Also, given a volume x.nii.gz and a file y.lta, how do I obtaijn
z.nii.gz as the
On 2/9/2020 10:19 PM, Soo-Jong Kim wrote:
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Thank you, Dr. Greve
I checked all about your comment.
I have questions more.
1. I found that volumes or counts in gtm.stats.dat are for native PET
space.
If co-registered PET onto corresponding MRI(i.e. MRI
See this page
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
On 2/11/2020 2:54 PM, Tegan Hargreaves wrote:
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Hi all,
I am fairly new to FreeSurfer and am implanting the
hippocampal/amygdala subfields script in our
Hi Valeria, I've never used PALS12 before and could not open your
attachements (unknown file type).
doug
On 2/6/2020 1:31 PM, Barletta, Valeria wrote:
Dear Freesurfers,
Is there a way to visualized the PALS12 atlas in the same view with
this overlay (attachments) on tksurfer or freeview?
Sorry, can you include the previous emails, otherwise I don't know what
the context is
On 2/12/2020 3:06 AM, Marina Fernández wrote:
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The error was shown after running tkregisterfv.
Marina.
___
Freesurfer
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Ok, thank you!
I'll try in this way and let you know if it works.
Best,
Valentina
Da: freesurfer-boun...@nmr.mgh.harvard.edu
per conto di Tim Schäfer
Inviato: venerdì 14 febbraio 2020 13:15:29
A: Freesurfer
You don't need to specify a mask when you run mri-glmfigt-sim. When you
ran mri_glmfit, you already specified the mask and that gets stored in
the glmdir and then read by mri_glmfit-sim. Your mri_glmfit-sim command
line look right (but you don't need the --bg 1 unless you really want to
yes, please do
On 2/14/2020 11:17 AM, Varun Chandran wrote:
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Dear Freesurfer committee,
I would like to use the freesurfer mailing list to post my doubts
about the cortical thickness analysis pipeline. Therefore, could you
please provide me the access to
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Dear Freesurfer committee,
I would like to use the freesurfer mailing list to post my doubts about the
cortical thickness analysis pipeline. Therefore, could you please provide
me the access to post my doubts on the same?
Hi
I would like to follow up on this question and would appreciate if you could
reply.
Thanks!
Mona
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
You can try,
mri_convert --in_orientation PIR t1_flip.nii t1_flip_flip.nii
but I'm not promising anything
On 2/14/2020 11:03 AM, Miguel Ángel Rivas Fernández wrote:
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Dear Douglas,
My image is in the correct orientation. The reason is that am using a
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Yes, it works!.
Thank you so much.
El vie., 14 feb. 2020 a las 17:22, Douglas N. Greve ()
escribió:
> You can try,
> mri_convert --in_orientation PIR t1_flip.nii t1_flip_flip.nii
> but I'm not promising anything
>
> On 2/14/2020 11:03 AM, Miguel
Dear Douglas N. Greve,
Thank you very much for your email.
I ran mri_glmfit without --wis. Then I tried to ran mri_glmfit-sim as
following: mri_glmfit-sim -glmdir g2v3.wls -2spaces -perm 1000 1.3 abs.
But there is an error message “ERROR: design matrix is not orthogonal, cannot
be use with
See if this tutorial will help
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
On 2/14/2020 3:28 PM, Kim, Gwang-Won wrote:
Dear Douglas N. Greve,
Thank you very much for your email.
I ran mri_glmfit without --wis. Then I tried to ran mri_glmfit-sim as
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Hi, I just wanted to check in on the progress of this thread. Could you let
me know if you had the chance to take a look at the scan I sent? I'm
unfortunately having the same problem with multiple scans so if I could get
some help, I'd really
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Hallo everybody,
I am not entirely sure whether this is FreeSurfer error actually.
I am doing first recon all which completes without errors. Then I need to
create BEM surfaces using the FreeSurfer watershed algorithm for MEG data
analysis using
We are planning on releasing a beta version 7 next week with a final
version 7 in the middle of March
On 2/7/2020 12:30 PM, Dan Fitch wrote:
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Hi folks! I checked the wiki and github, but couldn't find anything
about milestones or plans for the next major
Your can run
mni152reg --s subject
This will create a file calledsubject/ mri/transforms/reg.mni152.2mm.lta
Then use mri_label2vol to map the aparc+aseg.mgz into the mni152 space
using the --aparc+aseg flag and specifying the mni brain as the
--template and the reg.mni152.2mm.lta as the --reg
Any software package will do the inference on images with different
characteristics, the question is whether the inference is valid. If you
use different types of images, you will get different results (all
software packages). If you try to compare two groups each with image
types, you will
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Dear Freesurfer experts,
we used the Desikan and Killiany atlas to build individual head models in order
to project surface EEG data in the inverse space.
We would like to plot on the cortical surface the regions of the D atlas
where we find a
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Hi Valentina,
Just to be sure I get what you are asking: do you want a visualization like
subfigure B in this image?
https://raw.githubusercontent.com/dfsp-spirit/fsbrain/master/web/fsbrain_vis_overview.jpg
So you have one value per Desikan
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Hi Tim,
yes, exactly something like subfigure B but if possible without the colorcode
(i.e. some regions yellow and some others in red) having just one value.
This is because it would not be super correct to use a "summary measure" that
doesn't
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Hello everyone,
I’m currently working on a longitudinal FreeSurfer pipeline in order to compare
cortical thickness changes across the time. I’m using FreeSurfer version 6.0.0
(OS: Scientific Linux 7.3). I already processed the recon-all, -base and
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