External Email - Use Caution
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:
External Email - Use Caution
Hi
I am attempting to create a group file using MRIS PREPROC
My
External Email - Use Caution
On 5/28/2023 1:32 PM, Ruifeng Dong wrote:
External Email - Use Caution
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
External Email - Use Caution
On 5/26/2023 5:39 PM, Andrew Dedinas Geoly wrote:
External Email - Use Caution
Hello Freesurfer experts!
I am conducting a longitudinal GMV and CT analysis of mTBI
participants who received an experimental single-dose pharmacological
External Email - Use Caution
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:
External Email - Use Caution
Hello,
I am trying to run an old script
External Email - Use Caution
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:
External Email - Use Caution
Dear Sir/Madam,
I
External Email - Use Caution
That map is whatever you are studying. Eg, lh.thickness
On 5/25/2023 1:30 PM, Carlos Alcocer wrote:
External Email - Use Caution
Hello,
I am trying to do an asymmetry analysis using steps detailed in
*MailScanner has detected a possible
External Email - Use Caution
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"
External Email - Use Caution
Use the cespct.nii.mgz file
On 5/24/2023 10:18 AM, Maria Czarnecka wrote:
External Email - Use Caution
Dear experts,
I struggle with the functional analysis in Freesurfer. How can I
calculate the percent signal change in a specific
External Email - Use Caution
you should ask the authors of fmriprep
On 5/24/2023 9:32 AM, Michelle Diniz wrote:
External Email - Use Caution
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
External Email - Use Cauti
External Email - Use Caution
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
External Email - Use Caution
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:
External Email - Use
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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:
External Email - Use Caution
Dear Dr. Douglas N. Greve,
Thanks to you, I could have a binary disk
External Email - Use Caution
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:
External Email - Use Caution
We have
External Email - Use Caution
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:
External Email - Use Caution
Hello,
I am trying to process several images with |MiDeFace| but
External Email - Use Caution
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
External Email - Use Caution
try fixing your qform first
On 5/15/2023 3:28 PM, Nadia Kane wrote:
External Email - Use Caution
Hi,
I tried using mri_synthmorph in FreeSurfer on synthetic mouse brain
data, but my output moved image is just black pixels.
Thanks,
Nadia
External Email - Use Caution
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:
External Email - Use Cautio
External Email - Use Caution
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
External Email - Use
External Email - Use Caution
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:
External Email - Use Caution
Greetings esteemed
External Email - Use Caution
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:
External Email - Use Caution
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
External Email - Use Caution
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:
External Email - Use Caution
Hi Freesurfer Develpers,
I am attempting to preprocess fMRI by running preproc-sess based on
External Email - Use Caution
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
External Email - Use Caution
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:
External Email - Use Caution
Hello FreeSurfer
External Email - Use Caution
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:
External Email - Use
External Email - Use Caution
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:
External Email - Use Caution
Hi Jan
If you create a family
External Email - Use Caution
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
External Email - Use Caution
I don't understand what you are referring to. Can you elaborate?
On 5/5/2023 7:53 PM, Nadvar, Negin wrote:
External Email - Use Caution
Hello,
I have a general question about handing atlas ROIs after applying
recon-all on a T1W image.
External Email - Use Caution
can you be more specific?
On 5/4/2023 1:34 PM, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Dear Freesurfer's experts,
Why is this happening?
Kind regards,
Rosie
*
*
___
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
The method you describe is only for discrete variables, not
continuous ones
External Email - Use Caution
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:
External Email - Use Caution
Hi,
Is it currently possible to extract metrics
External Email - Use Caution
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:
External Email - Use Caution
That is a single command. How can you run a single command
External Email - Use Caution
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
External Email - Use Caution
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:
External Email - Use Caution
Hi,
First samseg and mri_reg are amazing
External Email - Use Caution
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
External Email - Use Caution
Can you send the matrix Xg.dat?
On 4/21/2023 12:59 PM, Resnick, Patricia wrote:
External Email - Use Caution
Tricia Stefancin
Lab manager
Z-lab
Department of Psychology
The Ohio State University
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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,
>
>
External Email - Use Caution
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 ==
External Email - Use Caution
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
External Email - Use Caution
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
>
>
External Email - Use Caution
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:
External Email - Use Caution
Hi,
How do we analyze multiple
External Email - Use Caution
it will also handle the concatenation
On 4/26/2023 12:30 PM, Elmira Hassanzadeh wrote:
External Email - Use Caution
Hi,
How do we analyze multiple resting state runs for a subject at once?
- do we need certain folder structure/naming?
-
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
External Email - Use Caution
We don't currently segment the STN, sorry.
On 4/12/2023 7:30 AM, Abhishek Prabhu wrote:
External Email - Use Caution
Dear Freesurfers,
I am a neuroscience master's student and new to free surfer. I had a
task of segmenting deep brain
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
Can you use T1 with contrast in freesurfer or
External Email - Use Caution
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:
External Email - Use Caution
Hi,
I am interested in
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
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
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 to convert the DICOM files to Nifti format
using the mri_convert
In 7.2 it appears to be there (and in 7.3 and in dev and in 7.0 and 7.1)
case "-autorecon2-volonly":
set DoGCAReg = 1;
set DoRemoveNeck = 0;
set DoSkullLTA = 0;
set DoCANormalize = 1;
set DoCAReg = 1;
set DoCALabel
Does this describe the problem?
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
Bug fix: improve surface placement in inferior frontal area near
putamen. There are some cases where the white surface is not placed well
in these areas because of the close proximity of putamen to cortex; it
You can create a point set. I would recommend creating an initial point
set in freeview, saving it (json), then looking at that to get the
format, then create a new json with your points. If you have them as a
binary map in nifti, you can load that with your anatomical (assuming
the nifti
The scale is much different between columns 1 and 8, you may want to
normalize by subtracting the mean and dividing by the standard deviation.
On 3/21/2023 1:53 PM, miracle ozzoude wrote:
External Email - Use Caution
Hello,
Any idea how to solve this problem? I have tried the
The easiest thing is probably just to use matlab to load in the data
(MRIread.m) and pull out the vertices you need. Alternatively, you can
convert an mgh/mgz file to ascii with mri_convert --ascii or
--ascii+crsf and then do what you want with it.
On 3/21/2023 12:38 PM, Maria Czarnecka
It is a little complicated, but the GTM just sets up a general linear
model where the value at a given vertex is model as a weighted sum of
regression coefficients (the uptake in an ROI). Once you have set the
ROI boundaries, then it tries to fit the data by finding the regression
coefficients
I think all you have to do is convert the aparc.a2009s+aseg.mgz to nifti
(mri_convert something.mgz something.nii.gz
On 3/20/2023 4:50 PM, Bues, Hannah Francesca wrote:
Good afternoon all,
I was hoping to get some advice on how to approach this. Any and all
feedback is much appreciated.
Yes, all the 7.X versions will give the same answer unless you
explicitly use a new feature
On 3/20/2023 2:45 PM, mariangela asimina wrote:
External Email - Use Caution
I see now this is an issue addressed stable 7.2.0 version of FreeSurfer:
*MailScanner has detected a possible fraud
It might not be a registration issue. When you look at the orig.mgz
compared to the rawavg.mgz, are parts of the head cut off in orig.mgz?
Can you send a pic of the head orientation?
On 3/17/2023 1:32 PM, Aaron Tanenbaum wrote:
External Email - Use Caution
We acquired some data this
In theory you could, but you'd have to map the tp1 brainmask to tp2.
Note that it might not matter that much because the cross surfaces are
not used during the base creation. I would see how things look in the
base, then edit the brainmask in the base if needed. The base brainmask
will then be
I noticed that your DOF is 1290, so it is possible that you are maxing
out the float computation. By coincidence, I just reprogrammed this to
use double instead of float precision. You can get it from here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit
username guest
pwd collab
giorno lun 6 mar 2023 alle ore 16:31 Douglas N. Greve
ha scritto:
can you send an example?
On 2/17/2023 9:38 AM, Federica Di Antonio wrote:
External Email - Use Caution
Dear experts,
I hope this email finds you well.
I run the pvc correction with mri_gtmpvc
301 - 400 of 8964 matches
Mail list logo
