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Hello,
When trying to post to the freesurfer listserv with this account my emails
don't seem to go through. When using my university email dcal...@umd.edu it
works. Unfortunately, I don't get and can't respond to responses to emails
I submit from that
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Hi Douglas!
Thank you for the response. I figured out it was simply an issue with the
pathing to the register.dat file!
Thanks,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland,
wow, that looks pretty bad. Can you send us the recon-all.log (or upload
the entire subject and we will investigate)?
On Tue, 19 Feb 2019, mara alves
wrote:
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Hi there,
I ran the recon -all command in two samples, one of young participants and
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Yes, one more question where can I get the example of mri glimfit for ROI
analysis
---Original---
From: "Greve, Douglas N.,Ph.D."
Date: Tue, Feb 19, 2019 22:47 PM
To: "freesurfer@nmr.mgh.harvard.edu";
Subject: Re: [Freesurfer] commends of GLM
You can get the volumes of structures, eg, hipocampal volume, for each
structure and subject using asegstats2table, then mri_glmfit can read in
that table. But it is an ROI analysis, not a voxel-wise analysis. Is
that what you want to do?
On 2/19/19 5:20 PM, ?? wrote:
>
>
I have not really stressed the code with --pargs (it is a relatively new
program), but if it produces the same output, then it should work
On 2/19/19 5:01 PM, Daniel Leopold wrote:
>
> External Email - Use Caution
>
> Thank you, Doug. I'm aware of fspalm, but stayed with palm in order to
You can use mri_surf2surf or mris_apply_reg to do the transferring
On 2/19/19 4:51 PM, Bruce Fischl wrote:
> Hi Alex
>
> yes, the vertices of the lower res fsaverage representations come
> first in the ordering. So the first 12 are ico0, then the first 42 are
> ico 0 and ico 1, etc
>
>
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Or I can not use mri to do the Glm for subcortical volume analysis ?
---Original---
From: "Greve, Douglas N.,Ph.D."
Date: Tue, Feb 19, 2019 21:29 PM
To: "freesurfer@nmr.mgh.harvard.edu";
Subject: Re: [Freesurfer] commends of GLM for volume
IIs
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Hi,
Thanks for your reply. it is a just a normal mri analysis, but I want to
compare the subcortical volume and Cortical thinkness between PD dementia
patient and healthy control group. I only got the t1image.
---Original---
From: "Greve,
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Thank you, Doug. I'm aware of fspalm, but stayed with palm in order to take
advantage of NPC and exchangeability blocks because I've got twins and
singletons in the sample. Does --pargs allow for all palm functionality,
including things like TFCE,
Hi Alex
yes, the vertices of the lower res fsaverage representations come first in
the ordering. So the first 12 are ico0, then the first 42 are ico 0 and ico
1, etc
cheers
Bruce
On Tue, 19 Feb 2019, Alexander
Samir Hatoum wrote:
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Hello,
I am currently working with the fsaverage7 parcellation and would like to
move to a lower resolution brain parcelltation (fsaverage4, 5, or 6 for
example). I was wondering if there is a simple way to translate my data
without rerunning
You can create an annotation with mris_seg2annot (you basically have a
surface-based segmentation). Run it with --help to get more info
including examples. You will need to create your own color table
On 2/19/19 3:21 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I have a 3D volume mask
IIs this an fMRI analysis? If so, you should use permutation for both
surface and subcort. See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLevelPerm
On 2/19/19 6:00 AM, ?? wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> Hello Greve,
> I am
Not sure exactly what you mean by a template or what you would want to
do with such a thing. You can run make_average_subject to create a
folding atlas.
On 2/19/19 3:24 AM, Vivek Sharma wrote:
>
> External Email - Use Caution
>
> I'm working on source reconstruction using MEG data. For
what are the artefacts exactly? It looks like the back of the brain was
not segmented. Is there something in the raw data? Otherwise, look
though the trouble shooting tutorial.
On 2/18/19 12:19 PM, Backhausen, Lea wrote:
>
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>
> Dear FreeSurer experts,
>
>
Sorry, qdec is not really being supported anymore. You'll have to use
the "command line" stream (ie, creating an FSGD file, running
mris_preproc, mri_surf2surf, mri_glmfit). See the group analysis tutorial
On 2/18/19 2:21 AM, Hua, Jessica wrote:
>
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>
> Hi
yes, run it twice. The second time specify the output of the first run
with --merge
On 2/17/19 3:29 PM, Bruce Fischl wrote:
> sorry, I'm not sure what your question is. You probably have to run it
> twice - once for each hemi
> cheers
> Bruce
> On Sun, 17 Feb 2019, Barletta, Valeria wrote:
>
>>
see this page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm
On 2/16/19 6:48 PM, Daniel Leopold wrote:
>
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>
> Hi all,
>
> Do you have any suggestions on how I could extract stats (e.g.,
> thickness, area, LGI, etc.) from a cluster(s) identified via palm?
On 2/16/19 2:54 PM, Matthieu Vanhoutte wrote:
>
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>
> Dear Douglas,
>
> I wanted just to compute rescaled PET image without any PVC but
> following the same process as if I would have applied PVC. Moreover, I
> didn’t want to reduce FOV with auto mask
I'm not sure what you are trying to do here. Ico7 is just a 7th order
icosahedron and does not "belong" to any subject. What belongs to
fsaverage or fsaverage_sym is the atlas of curvatures and registrations
derived from them (eg, lh.sphere.reg). It might be easier to use
mris_apply_reg
A tmap is not produced. You can get one with
fscalc gamma.nii.gz sign -o gamma.sign.nii.gz
fscalc F.nii.gz sqrt mul gamma.sign.nii.gz
doug
On 2/15/19 4:12 PM, Lauri Tuominen wrote:
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>
> Dear freesurfers,
> I am trying to find a t-map for my group level test.
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Hello developer,
I am glad to tell you that after 3 hours, something did print more on terminal.
when I was doing the GLM follow the tutorial, it only provided the example of
the cortical thickness. And I did not know how to transfer it into volume.
Check the lh.orig and lh.inflated surfaces
On 2/15/19 3:34 PM, ?? wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> For more than 3 hours
>
> ---Original---
> *From:* "Greve, Douglas N.,Ph.D."
> *Date:* Fri, Feb 15, 2019 20:03 PM
> *To:* "freesurfer@nmr.mgh.harvard.edu";
did you analyze them with different versions of FS?
On 2/15/19 3:28 PM, Morgan Botdorf wrote:
>
> External Email - Use Caution
>
> Thanks for taking a look at the file I sent! I think I have figured
> out the issue for the most part. While it shows that there is data in
> the
what do you get when you run
ls -l /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat
On 2/19/19 8:44 AM, Daniel Davidson Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I ran a successful dt_recon and then wanted to use
>
> mri_vol2vol --mov
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Hi,
I am trying to run freeview in the linux subsystem (Ubuntu 18.04) for windows
10 but keep getting the following error:
failed to get the current screen resources
QXcbConnection: XCB error: 170 (Unknown), sequence: 170, resource id: 90, major
When you say it stopped running, do you mean that it exited or that it
kept running but nothing printed out and it did not proceed to further
steps?
On 2/15/19 12:42 PM, ?? wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> when i was
I would average the R values across run
On 2/15/19 11:34 AM, Nasiriavanaki, Zahra wrote:
>
> Dear Freesurfer experts
>
>
> I have asked this question before and I really do appreciate if you
> could please reply whenever you had a chance.
>
> I have been doing seed to seed connectivity analysis
yes
On 2/12/19 11:28 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> Thank you! Unfortunately, I don't have any whole brain scan.
> I registered the template and all the runs with tkregisterfv and the I
> run bbregsiter.
> Now, should I just re-run selxavg3-sess?
>
>
If you want to use a target other than fsaverage, then you need to
register each subject to that target (eg, with surfreg). If you have
found a problem with mris_make_subject, please document it in a separate
post.
On 2/12/19 6:38 AM, Bunting, Emma wrote:
>
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Dear Freesurfers,
I have a 3D volume mask of cortical lesions with 8 different clusters (8
cortical lesions).
I projected this mask to the cortex and obtained a .mgh file with the command
vol2surf:
mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out
It sounds like you will just need to create your own design matrix and
then feed it into mri_glmfit with --X (and not include --fsgd)
On 2/12/19 12:03 AM, Abhinav Yadav wrote:
>
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>
> Hello,
>
> I am trying to do GLM analysis for cortical thickness with a
>
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---Original---
From: "??"<646102...@qq.com>
Date: Tue, Feb 19, 2019 11:00 AM
To: "Greve, Douglas N.,Ph.D.";
Subject: Re: commends of GLM for volume
Hello developer,
I am glad to tell you that after 3 hours, something did print more on terminal.
Hi Morgan
can you send us some pictures? Control points can sometimes help the pial
also, but it depends on what the cause of your inaccuracy is.
cheers
Bruce
On Tue, 19 Feb 2019, Morgan Botdorf wrote:
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Dear Freesurfer Experts,
We have come
what format did you save your estimates in? If you want to overlay it on
the surface, it has to be a "volume" where the first dimension is the
number of vertices in the surface, and the others are all 1. Unless it is
nifti in which case you have to split up the first dimension since it is
too
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Dear Freesurfer Experts,
We have come across several subjects where the pial boundary line does not
extend far enough outward and misses some gray matter. We know that control
points can be used to fix a similar issue with white matter boundaries. Are
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Dear FreeSurfer list,
I'm wondering if there is any way to input different starting
segmentations for the hippocampus into the hippocampal subfield
segmentation? We've got a hippocampus specific segmentation algorithm
which we'd like to try as
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Hello Freesurfer Community,
I want to view my cortical thickness estimates (I calculated standard
deviations for different subjects) on a 3D file.
I thought I could replace the lh.thickness part in the following code by
my own estimations:
freeview
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Hello Freesurfers,
I was wondering if anyone has access to a Qdec tutorial, other than the one
on the Freesurfer website. The one on the website only covers the basics
and it does not have a video component. In case you have a better tutorial
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Dear Bruce
Thanks a lot for this very helpful explanation! This is much appreciated and it
is now much clearer to me what I have to do.
Thank you,
Stephanie
> On Feb 19, 2019, at 11:09 AM, Bruce Fischl wrote:
>
> External Email. Use Caution.
>
Hi Stephanie
if you have an annot named lh.myannot.annot you could use:
freeview -f lh.inflated:annot=lh.myannot.annot -ss filename.tif
where of course you will need paths to the various files and will want to
change the filename for each subject
cheers
Bruce
On Tue, 19 Feb 2019,
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Hi Bruce,
Thank you for your quick and helpful reply.
Unfortunately, I wasn't able to figure out what comes between -f and -ss...
Would you mind explaining what you meant with ... ?
Thanks a lot,
Stephanie
-Original Message-
From:
Hi Daniel
do you have a mixed version of binaries? This works fine for me:
/usr/local/freesurfer/stable6_0_0/bin/mri_relabel_hypointensities -all-info
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info
ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/19-16:01:28-GMT
freesurfer-6.0.1/bin/recon-all line 630 calls:
mri_relabel_hypointensities -all-info
However, -all-info is not a valid option:
$ mri_relabel_hypointensities
usage: mri_relabel_hypointensities [options]
This program measures a variety of anatomical properties
valid options are:
-l
will do
On Tue, 19 Feb 2019, Matthieu VANHOUTTE wrote:
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Hi Bruce,
I don't see major thing that could be wrong.
I uploaded on the FileDrop the subject directory compressed. Could you have a
look at it and tell me
what you think ?
Best,
Matthieu
Hi Viktor
it is a 3D erosion, and a cubic 3x3x3 structuring element.
cheers
Bruce
On Tue, 19 Feb
2019, Viktor Domazetoski wrote:
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Dear FreeSurfer experts,
I would like to enquire about the command mri_extract_label. More specifically
I am
yes, because the differences in their morphology don't change the average
very much. You can try it both ways to verify this is true for your
subjects.
cheers
Bruce
On Tue, 19 Feb 2019,
Laboratorio de Neurociencia Funcional wrote:
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Thank,
Hi Julia
did you upload the entire subject dir (gzipped and tarred)? And what
happened with ftp? We can help you get that working. I would think the
whole subject dir would be too big for the filedrop, but feel free to
send me the link
cheers
Bruce
On Tue, 19 Feb 2019, Julia Ströhlein
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Hello,
I ran a successful dt_recon and then wanted to use
mri_vol2vol --mov $subj_dir/dtrecons/${subj}.${cond}/lowb.nii.gz --targ
$subj_dir/diffusion_recons/${subj}.${cond}/mri/aparc+aseg.mgz --inv
--interp nearest --o
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Dear community,
anyone out there who can give me some information regarding how valid a volume
detection of the choroid plexus is?
I used fs 6.0.
Kind regards,
Ben
___
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Hello Greve,
I am glad to tell you that after 3 hours, something did print more on terminal.
when I was doing the GLM follow the tutorial, it only provided the example of
the cortical thickness. And I did not know how to transfer it into volume.
Here
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Hi Bruce,
I don't see major thing that could be wrong.
I uploaded on the FileDrop the subject directory compressed. Could you
have a look at it and tell me what you think ?
Best,
Matthieu
On 18/02/2019 15:56, Bruce Fischl wrote:
Hi Matthieu
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Dear FreeSurfer experts,
I would like to enquire about the command mri_extract_label. More specifically
I am looking for information about the -erode argument. Therefore I have a few
questions:
1. Is a 3D erosion of the entire brain or a 2D
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Thank, Bruce. So the final message is that I should use the same average
subject to display results of cortical thickness even when samples to be
compared have highly different brain morphology. Is that correct?
El lun., 18 feb. 2019 a las 23:37,
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I'm working on source reconstruction using MEG data. For which segmented T1
images of MRI scans are required. I use recon -all for individual subjects.
Can we have a common average template made from MRI scans of all subjects.
If I have MRI scans from
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Hi Bruce,
I created a link with the Martinos File Drop System, because ftp upload did
not work.
It's probably the best idea to send the links to your personal mail address?
Best
Julia
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