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I think it should work ok. If you want to run it in native space, add
-conform-dc (but this should be done for everyone in your study).
Conforming like this was started in FS 25 years ago and for
reprodicibility purposes, we've kept it there by
Mob.:- +91-8899605552
On Tue, 20 Jun, 2023, 6:58 pm Douglas N. Greve,
wrote:
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I have not used mri_cc for that. I would use mri_sclimbic_seg;
that will also segment the fornix and create a stats files that
you can use as normal
On 5/26/2023
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recon-all died immediately after trying to create a symlink. Might be
because it is on a VBox. Rob, can you help figure this out?
On 6/21/2023 11:55 AM, Varun Chandran wrote:
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p.s. I am wondering whether this
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There is nothing that allows it from freeview. The easiest thing to do
is probably to split the annot into labels (mris_label2annot), then load
the label you want with :label=your.label
You can take snapshots automatically with freeview using the -ss
in the
mri_convert --conform by adding options -odt short -ns 1. Freesurfer
6.0 ran well until its default skull stripping, attached below.
Screenshot from 2023-06-20 10-20-03.png
Best,
Ruifeng
On Tue, Jun 20, 2023 at 9:59 AM Douglas N. Greve
wrote:
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FS 7.4.1 is now available here
to apply in 2 thousand subjects. I would
like to know if there is any way to improve the performance.
Em ter., 20 de jun. de 2023 às 11:15, Douglas N. Greve
escreveu:
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For 1mm data, FS will generally run in 5-10 hours. Are you talking
about high
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For 1mm data, FS will generally run in 5-10 hours. Are you talking about
high resolution data?
On 6/20/2023 10:11 AM, Michelle Diniz wrote:
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Hey guys. I'm using FMRIprep on the OASIS3 database and I've noticed
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Does this page help
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You can also use something like
mri_segstats --seg aparc+aseg.mgz --id 1027 --mask overlay.nii.gz --sum
summary.dat
you can set a threshold to the mask with --maskthresh
On 6/17/2023 7:45 AM, John Anderson wrote:
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You might be able to convert it to a nifti (eg, with mri_warp_convert
--outfsl), do your optionations, then convert it back to m3z
On 6/14/2023 4:08 PM, Proulx, Jean Sebastien wrote:
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Hello,
I produced an m3z
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This was done a long time ago to conserve space/memory. There is a
rescaling that is done, so it should not affect the bias correction much
On 6/14/2023 3:35 PM, Ruifeng Dong wrote:
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Hi Yujing,
Thanks. I am
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that is fine
On 6/2/2023 11:42 AM, Nikolaidou, Sofia wrote:
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Good morning,
I would like to aggregate the measurements for average cortical
thickness across the two hemispheres. I read on the FAQ of the
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does it happen if you don't use --cache-in? Also, can you send the full
terminal output?
On 5/30/2023 6:46 PM, Akansha Mahesh Naraindas wrote:
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Hi
I am attempting to create a group file using MRIS PREPROC
My
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On 5/28/2023 1:32 PM, Ruifeng Dong wrote:
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Hi all,
I am running freesurfer 7.3.2 for segmentation of T1 data. It seems
like still using the old skull stripping tools by default. How should
we change it to
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On 5/26/2023 5:39 PM, Andrew Dedinas Geoly wrote:
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Hello Freesurfer experts!
I am conducting a longitudinal GMV and CT analysis of mTBI
participants who received an experimental single-dose pharmacological
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you cannot run tksurferfv with a tcl script. tksurferfv is just a
frontend for freeview that will take tksurfer-like options.
On 5/26/2023 9:54 AM, Robert Terziev wrote:
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Hello,
I am trying to run an old script
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I have not used mri_cc for that. I would use mri_sclimbic_seg; that will
also segment the fornix and create a stats files that you can use as normal
On 5/26/2023 3:37 AM, Ahsan Ali wrote:
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Dear Sir/Madam,
I
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That map is whatever you are studying. Eg, lh.thickness
On 5/25/2023 1:30 PM, Carlos Alcocer wrote:
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Hello,
I am trying to do an asymmetry analysis using steps detailed in
*MailScanner has detected a possible
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I can't remember why I removed it, but there was some problem with it.
You can do the conjunction with
mri_concat contrast1/sig.nii.gz contrast2/sig.nii.gz --min --o
conjunction.nii.gz
You can have as many contrasts as you want
This will do an "AND"
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Use the cespct.nii.mgz file
On 5/24/2023 10:18 AM, Maria Czarnecka wrote:
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Dear experts,
I struggle with the functional analysis in Freesurfer. How can I
calculate the percent signal change in a specific
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you should ask the authors of fmriprep
On 5/24/2023 9:32 AM, Michelle Diniz wrote:
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Can I use fmriprep to analyze only the anatomical part?
--
Michelle Diniz Lopes
ly let me know how I can rectify the issue.
Thanks and regards,
malav
--------
*From: *"Douglas N. Greve"
*To: *"freesurfer"
*Sent: *Monday, May 22, 2023 3:32:28 PM
*Subject: *Re: [Freesurfer] Cortical thickness of elephant brain
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For the sclimbic, you can find it in $FREESURFER/models/sclimbic.ctab
For the brainstem, the labels are in the main FS table,
$FREESURFER/FreeSurferColorLUT.txt
I think there are only three labels in the brainstem, so you can load it
into freeview to
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Hi Malav, try
mris_diff --min-dist lh.wm.smth5 lh.pial.smth5 1 lh.thickness
The output will be on the pial surface. Reverse the surface order to get
it on the white surface
doug
On 5/22/2023 5:48 AM, Malav Shah wrote:
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you can make individual surface files (mri_binarize --match 16 --i
aseg.mgz --surf brainstem.surf --surf-smooth 2), but there is not a
registration target to register the surface to
On 5/21/2023 3:41 AM, t...@ms36.hinet.net wrote:
External
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what is roi_in_MNI152.mgz? If that is an binary ROI mask, then that will
certainly fail. Try something like
mri_coreg --mov orig.mgz --dof 12 --reg reg.mni152.lta --targ
mni152-template.nii.gz
where mni152 template is an intensity volume in
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oh, you should have used --fwhm 3 on that first command, and if you want
5mm then use --fwhm 5
On 5/19/2023 7:15 AM, Andy Kim wrote:
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Dear Dr. Douglas N. Greve,
Thanks to you, I could have a binary disk
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The algorithm works by projecting the average face inward and outward.
In which direction is the problem occurring? Can you send me the log file?
On 5/18/2023 12:16 PM, Hermann, Jacob wrote:
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We have
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So the same input volume will sometimes succeed and sometimes fail
depending upon the platform?
On 5/17/2023 12:05 PM, Patrick Sadil wrote:
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Hello,
I am trying to process several images with |MiDeFace| but
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I don't know about recon-all-clinical, but you can get a decent
cerebellum seg with mri_synthseg. I don't think anything will give you
great GM/WM segmentation in cblum as that requires super high resolution.
On 5/15/2023 2:11 PM, Nathan Santana
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try fixing your qform first
On 5/15/2023 3:28 PM, Nadia Kane wrote:
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Hi,
I tried using mri_synthmorph in FreeSurfer on synthetic mouse brain
data, but my output moved image is just black pixels.
Thanks,
Nadia
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Does this help
ehiwR96EIeUGWr7_fuZ7GXKf4z9OMOtq-eeHNVNbugrrg8g6w0I1T56XXUf_XncJ8ZPG7n23Rr_D5UmCI5ebupLdDhVQNkoq4G0gR5G4r7RLCDYqObteTCYE6XOT2JrhWrdmWqCFW9ZLSNOz2wJuxXirkxrAms2Qoz0EW/https%3A%2F%2Fmed.umn.edu%2Fuic>
On Mon, May 15, 2023 at 8:50 AM Douglas N. Greve
wrote:
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I don't see why not. I think the only reason it might fail is if it
makes some assumptions about the voxels size. You can also try
mri_coreg; I wrote this so I'm pretty sure there are no such assumptions
(but robust reg might work as well)
On
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* 12 May 2023 21:37:21
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] [FreeSurfer] Process terminated when
talairach was running
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That is a lot of non-FreeSurfer code. We only support FreeSurfer code.
If this is a question about FS code, then please distill it down to that.
On 5/15/2023 8:25 AM, bong516612 wrote:
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Greetings esteemed
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That's weird. In the echo below, is that from your shell or on the HCP?
When you source the FS environment, that variable will be set.
On 5/12/2023 5:33 AM, Krystal Xiwing Yau wrote:
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Dear FreeSurfer expoerts,
label overlaps
in the new space.
Thank you,
Negin
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Monday, May 8, 2023 10:47 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subjec
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what version are you using? This is not a problem in the last two
versions ...
On 5/10/2023 3:43 AM, 朱筱 wrote:
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Hi Freesurfer Develpers,
I am attempting to preprocess fMRI by running preproc-sess based on
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I think you would need an interaction term with age as well (ie,
multiplying age by the ROI). You are starting to get into complicated
territory with complicated interactions between continuous variables. In
theory, you would need to have each
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No, there is not an easy way to tweek the arguments to N4. I can add
something in dev. You can also hard code it by editing
mri_nu_correct.mni (line 126)
On 5/9/2023 4:06 AM, 刘梦醒 wrote:
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Hello FreeSurfer
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It is not corrected for eTIV. You can compute eTIV as you suggest, ie,
running autorecon1 then running mri_segstats --xfm2etiv
subject/mri/transforms/talairach.xfm etiv.dat
On 5/9/2023 8:01 AM, Asmin Alam wrote:
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FYI, there is also a make_folding_atlas script, though you won't be able
to fine tune the parameters when it runs mris_register
On 5/8/2023 10:12 AM, Fischl, Bruce R.,PHD wrote:
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Hi Jan
If you create a family
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No, it is not there explicitly. You can compute it yourself using these
measures
# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter
volume, 226058.544078, mm^3
# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter
availability,
Federica Di Antonio
Il giorno lun 27 feb 2023 alle ore 14:30 Federica Di Antonio
ha scritto:
Thank you so much!
Il giorno gio 15 dic 2022 alle ore 16:24 Douglas N. Greve
ha scritto:
I have something called the adaptive GTM that is currently a
"h
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I don't understand what you are referring to. Can you elaborate?
On 5/5/2023 7:53 PM, Nadvar, Negin wrote:
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Hello,
I have a general question about handing atlas ROIs after applying
recon-all on a T1W image.
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can you be more specific?
On 5/4/2023 1:34 PM, Rosalia Dacosta Aguayo wrote:
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Dear Freesurfer's experts,
Why is this happening?
Kind regards,
Rosie
*
*
___
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If you download the dev version, you can run something like this:
mri_binarize --dilate-vertex vtxno lh.white 10 lh.white.circle10.mgz
where vtxno is the vertex no where you want the circle to be centered,
10 is the radius of the circle in mm
It will
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what do you mean that you won't want to do any resampling? How else
would you apply a transform? Or do you mean that you want to use nearest
neighbor resampling (so no interpolation)? If so, you can use
mri_vol2vol with the --interp nearest option
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what is the error you are talking about? The area around the stroke? In
theory, you could edit to WM where the WM is now gone, but you'd have to
wait for the next version of FS, and even then I'm not sure it would
work. Or are you talking about the
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The current versions of FS require an intensity normalization step be
run on 7T data prior to running it through FS. I have used SPM VBM for
this, but I think samseg should work too, eg,
samseg --i t1.mgz --o samseg
Then use
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no plans for a new gui. you might look up qdecr. this is a 3rd party
altenative that uses R; I've never used it myself, so I don't know how
well it works on voxel-wise analysis or if there is a gui
On 5/1/2023 2:00 PM, Lauren Stephens wrote:
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I'm not sure what you mean that you created conditions in an osgm file;
this does not make sense to me at the first level. Please elaborate on
your design
On 4/17/2023 12:25 PM, Maria Czarnecka wrote:
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Dear
), controlling for eTIV, the contrast
would be the following?
[ 0 0 0 0 0.5 -0.5 -0.5 0.5 0 0 0 0]
All the best,
Fred
On Apr 28, 2023, at 10:30 AM, Douglas N. Greve
wrote:
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The method you describe is only for discrete variables, not
continuous ones
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sorry, we don't have an SN segmentation. I think there are some other
tools out there that will do this though.
On 4/28/2023 10:33 AM, Lund, Anina wrote:
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Hi,
Is it currently possible to extract metrics
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I'm not sure the parallel flag works any more. But you can specify
multiple threads with -threads N
On 4/27/2023 5:45 AM, Michael Mc Laughlin wrote:
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That is a single command. How can you run a single command
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The method you describe is only for discrete variables, not continuous
ones. The traditional method for continuous variables is to create a new
variable where you multiply them together. You should normalize you
continuous variables too (ie, subtract
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The UK biobank runs FS on all their scans. The HCP has hundreds
(thousands?) of cases as well with FS segmentations.
On 4/20/2023 2:44 PM, Keith E Moore wrote:
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Hi,
First samseg and mri_reg are amazing
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You can move your ADC volumes into the output synthseg space with
mri_vol2vol --mov adc.mgz --regheader --targ synthseg.mgz --o
adc.synthseg.mgz
Then they will be voxel-for-voxel alignment
On 4/24/2023 10:16 AM, bar gen wrote:
External
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Can you send the matrix Xg.dat?
On 4/21/2023 12:59 PM, Resnick, Patricia wrote:
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Tricia Stefancin
Lab manager
Z-lab
Department of Psychology
The Ohio State University
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you mean you want to map the aparc+aseg.mgz from the subject space to
the cvs/mni152 space using the cvs transform? Try this
mri_convert aparc+aseg.mgz -at cvs.m3z aparc+aseg.from-subject-to-cvs.mgz
where cvs.m3z is the cvs nonlinear registratiopn
On
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What form are your labels in? If in freesurfer .label format, then you
can convert them to an annotation (mris_label2annot), then use annot2std
to create an average annotation in fsaverage (standard) space using your
subject, you can then map the
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When you do the corrections for multiple comparisons, you will get a
file with "ocn" in the name. This is the output cluster number where the
vertices have values 0 to NumberOfClusters. You can use this with mri
_segstats to extract the values from
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I'm not sure what you are trying to do exactly. It looks like you want
to get cortical volumes of regions in BN_Atlas. Please elaborate.
On 4/20/2023 12:52 AM, Garrett Tan wrote:
> External Email - Use Caution
>
> Hi FreeSurfer Experts,
>
>
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do you mean you want a list of vertices and their uncorrected p-values
from a given cluster that is significant after corrections for multiple
comparisons? The easiest way is probably matlab, eg
ocn = MRIread('ocn.mgh');
ind = find(ocn.vol ==
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I've attached a new version of dcmunpack. Try running this with
-keep-scouts and without -keep-scouts
Let me know if this runs successfully in both situations (I'm using you
as my tester:)
On 4/18/2023 10:51 AM, Proulx, Jean Sebastien wrote:
Sorry
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No, it does not affect it. The ICV is actually and *estaimated* ICV
derived from the registration of the T1 to MNI305 space, so the T2 does
not come into play.
On 4/17/2023 2:11 PM, Steven Meisler wrote:
> External Email - Use Caution
>
>
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if you set up the data in the fsfast format, eg, subject/rest/001
subject/rest/002 etc, then it will handle it automatically
On 4/26/2023 12:30 PM, Elmira Hassanzadeh wrote:
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Hi,
How do we analyze multiple
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it will also handle the concatenation
On 4/26/2023 12:30 PM, Elmira Hassanzadeh wrote:
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Hi,
How do we analyze multiple resting state runs for a subject at once?
- do we need certain folder structure/naming?
-
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Yes, this is the expected behavior, ie, it should cover only subcortical
GM regions. It is expected that cortical regions will be handled with
the surface based analysis. You can recombine the results at the end
with vlrmerge.
On 4/26/2023 12:22
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Forwarded Message
Subject: Re: Turku PET Centre Brain Imaging Course / September
19th-21st 2022
Date: Mon, 17 Apr 2023 06:34:32 +
From: Lauri Nummenmaa
To: petpub...@tyks.fi
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We don't currently segment the STN, sorry.
On 4/12/2023 7:30 AM, Abhishek Prabhu wrote:
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Dear Freesurfers,
I am a neuroscience master's student and new to free surfer. I had a
task of segmenting deep brain
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I can't see anything wrong with what you have done (just use 1/6 instead
of 1.6, but that won't change your sig values). How was the aparc.stats
analysis done? Did you use the same FSGD file?
On 4/10/2023 10:09 AM, Christoph Aster wrote:
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I think it should mostly work. There might be a few places where the
pial surface includes a vessel because it is bright.
On 4/7/2023 1:49 PM, Carlos Alcocer wrote:
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Can you use T1 with contrast in freesurfer or
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not sure what you mean. It will accurately reflect the volume inside the
boundaries, but if the boundaries are off then the volume will be off
On 4/6/2023 1:52 PM, Carlos Alcocer wrote:
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Hi,
I am interested in
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It only ignores them if you use -auto-runseq Is that what you are doing?
On 4/5/2023 11:00 AM, Proulx, Jean Sebastien wrote:
Dear Freesurfer Team,
The help of dcmunpack says it will ignore scout scans. Is there
perhaps a hidden flag to avoid that
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QDEC has been deprecated in FS 7+, but you can have multiple versions of
FS on your computer, just make sure to source the version you want when
you want it. I'll leave the password to Rob.
On 4/8/2023 8:05 AM, mariangela asimina wrote:
Forwarding on an interesting job working Jessica Turner!
Forwarded Message
Subject:Research scientist positions at OSUMC!
Date: Fri, 7 Apr 2023 13:42:55 +
From: Turner, Jessica
To: Douglas N. Greve
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https://osu.wd1
t; Best,
> Chris
>
> ________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Douglas N. Greve
>
> Sent: Thursday, March 30, 2023 09:29
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] -gcareg dropped from -autorecon
specified in the "--annot" option. Thanks again
On Wed, Apr 5, 2023 at 10:46 PM Douglas N. Greve
wrote:
What is h.all.suvr.sm05.proj0.5.nii.gz? Where did it come from?
The name looks like it might be a voxel-wise map, but you say
something about ROIs. mri_glmfit does not
You do not need to re-run; all 7.X are designed to give the same answer
on automatic processing.
On 4/4/2023 6:03 PM, Lauren Stephens wrote:
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Hello,
We have been using Freesurfer v7.1.1 to process our data. We want to
update to the v7.3.2. Can we
What is h.all.suvr.sm05.proj0.5.nii.gz? Where did it come from? The name
looks like it might be a voxel-wise map, but you say something about
ROIs. mri_glmfit does not correct for multiple comparisons. For
ROI-based analyses, you can use bonferroni or FDR. For maps you can use
mri_glmfit-sim.
If you know what the vertex number is, you can do something like
mri_volsynth --dim-surf fsaverage/surf/lh.white --pdf delta --delta-crsf
vertexno 0 0 0 --o delta.mgh
mris_fwhm --i delta.mgh --o delta.sm3.mgh --s fsaverage --hemi lh
mri_binarize --i delta.sm3.mgh --min 0.5 --o delta.sm3.bin.mgh
With the dev version, you can convert the annoation to a simple surface
segmentation, like,
mri_convert lh.somthing.annot lh.something.mgz
Then binarize it like
mri_binarize --i lh.somthing.mgz --match SegId ... --o lh.binary.mgz
Then run mri_surfcluster on lh.binar.mgz setting the --thmin to
The regressors have been demeaned; other than that, they should be the same.
On 3/31/2023 6:59 PM, Andy Kim wrote:
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Dear Douglas N. Greve,
But the 3 additional columns in X.mat file (which is result of
-mcextreg option in mkanalysis-sess command
Hi Jennifer, remember to send questions to the freesurfer list, thanks!
Answers below
On 4/3/2023 4:01 AM, Jennifer Kilmer wrote:
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Hi Douglas,
Thank you for your response. I have a few more questions;
We can do the analysis in the surface space, but how
this area.
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Friday, March 31, 2023 8:43 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] White matter exclusions occurring in
v7.3.2 but not v5.3
** External Email - Caution **
oh, it won'
I have not tried that, but I wanted to point out that you can also use
samseg, eg,
samseg --i yourvolume.nii.gz --o samseg
samseg/seg.mgz will be a segmentation that includes skull
You can also use simnibs
https://simnibs.github.io/simnibs/build/html/index.html
This uses samseg under the hood.
If you are going to do the analysis in volume space, then it does not
make any sense to do any part of it in surface space. Why not map the
individual to fsaverage space and do the comparison there?
On 3/31/2023 8:26 AM, Jennifer Kilmer wrote:
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Hello—
I
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Date: *Wednesday, March 29, 2023 at 8:58 AM
*To: *freesurfer@nmr.mgh.harvard.edu
*Subject: *Re: [Freesurfer] White matter exclusions occurring in
v7.3.2 but not v5.3
** External Email - Caution **
Frm an automated
They should be the first 3 columns of mcprextreg.dat which are the first
3 PCA components I mentioned below. The actual motion correction
parameters are in the .mcdat file
On 3/30/2023 11:39 PM, Andy Kim wrote:
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Dear Douglas N. Greve,
Thank you. I
why are you doing this with modulation instead of just designating 3
different conditions?
On 3/28/2023 1:36 PM, Gillian Grennan wrote:
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Hi Freesurfer Developers,
I am analyzing a fear conditioning imaging study and am attempting to
regress out the
you did not specify to include any motion correction regressors in the
design. If that is what you want, then include -mcextreg
On 3/29/2023 11:29 PM, Andy Kim wrote:
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Dear Douglas N. Greve,
My experiment design is block design with 2 conditions.
Here
Hi Louis, yes, meanfunc is after all regresssions, etc.
doug
On 3/28/2023 12:08 PM, Vinke, Louis N.,PHD wrote:
Hello,
After running a seed-based connectivity 1^st level analysis on an
individual subject, is it possible to pull out the mean BOLD
activation (across all time-points; all runs)
_______
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Douglas N. Greve
>
> Sent: Monday, March 27, 2023 11:16
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] -gcareg dropped from -autorecon2-volonly
>
> In 7.2 it appears to
These are not the basic translations and rotations, rather:
mcprextreg - text file of the motion correction parameters assembled
into an orthogonalized matrix that can be used as nuisance regressors
I don't know what your design is, please send your mkanalysis command lie
On 3/29/2023 12:45
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Monday, March 27, 2023 10:06 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] White matter exclusions occurring in
v7.3.2 but not v5.3
** External Email
at 11:19 AM Douglas N. Greve
wrote:
Can you try it with --dcm2niix ?
On 3/25/2023 9:43 AM, John Anderson wrote:
External Email - Use Caution
Dear Dr Doug Greeve,
For each participant in my dataset, I have 8 mosaic volumes with
36 slices each. I am trying
...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Date: *Monday, March 27, 2023 at 10:54 AM
*To: *freesurfer@nmr.mgh.harvard.edu
*Subject: *Re: [Freesurfer] Using the Desterieux Cortical Atlas to
Extract PET SUVs
I think all you have to do is convert the aparc.a2009s+aseg.mgz to
nifti
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