On 10/8/2021 8:51 PM, Dongyue Zhou wrote:
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Dear FreeSurfer experts:
I want to know cortical thickness in this file
'subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh' is in standard
space or in native space.
standard
Is not the common coordinate
2021 19:52, Annalisa Lella ha scritto:
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Pre-processed with recon all
Il 8 ott 2021 19:50, "Douglas N. Greve"
ha scritto:
What do you mean by "elaborated"?
On 10/8/2021 1:29 PM,
in freeview, and verify
that it is in the correct location.
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Friday, October 8, 2021 10:49 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re
If you have not done manual editing, then just rerun in 7.2 from scratch
On 10/8/2021 1:52 PM, Annalisa Lella wrote:
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Pre-processed with recon all
Il 8 ott 2021 19:50, "Douglas N. Greve" ha
scritto:
W
o actually it doesn't seem that the results
of recon all with version 7 are bugged.
Il 8 ott 2021 18:53, "Douglas N. Greve" ha
scritto:
Sorry, I'm not sure what you are asking when you ask what you
should do. Do about what?
On 10/4/2021 5:30 AM,
one
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Friday, October 8, 2021 9:25 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] glmfit sig file all zeros
what happens if you
You want to measure cortical thickness in standard space? It is not
something we typically do, but I guess you could apply the taliarach
registration to the surfaces and recompute the thickenss, eg,
mris_apply_reg --lta lh.white ../mri/transforms/talairach.lta lh.white.tal
mris_apply_reg --lta
It has been replaced by thalamus now
On 10/8/2021 6:56 AM, Cubillo, Ana wrote:
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Dear Freesurfer community,
I am using the freesurfer version through a singularity container
(*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com"
. The same
unrelated differences occurred for the wm edits and the wm.mgz still
includes the wm edits from before I ran recon-all to correct it.
On Oct 1, 2021, at 11:02 AM, Douglas N. Greve
wrote:
The first thing to do is to re-run you data using different subject
names so that you have
It might be that the format is too new for our code. Have you tried
dcm2niix? We are currently incorporating dcm2niix backend into
mri_convert, but we're not there yet.
On 10/6/2021 2:36 PM, Rizzo, Nolan W wrote:
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Hello FreeSurfer developers,
I am
Sorry, I don't know what h5 format is.
On 10/5/2021 4:30 AM, I. Kelleher-Unger wrote:
> External Email - Use Caution
>
> External Email - Use Caution
>
> Hi there,
>
> I have used fmriprep to preprocess my BOLD data. One of the outputs of this
> pipeline is a T1w-to-MNI
On 10/4/2021 7:09 PM, Giuseppe Miranda wrote:
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Hello,
I have been looking through tutorials on the website and referencing
the freesurfer mail archives, but I am a bit unsure if I am following
the correct procedures for my analysis. The main source of
The frequency of the low pass filter (lpf) must be greater than the high
pass filter. Why did you set it to 0?
On 9/30/2021 8:27 PM, Nasiriavanaki, Zahra,M.D. wrote:
Hi Freesurfer experts,
I was wondering how many seeds we can use in fcseedcor command? I have
more than 100 seeds and when I
?
Thanks a lot in advance!
Annalisa
*Da:* freesurfer-boun...@nmr.mgh.harvard.edu
per conto di Douglas N. Greve
*Inviato:* venerdì 1 ottobre 2021 17:18
*A:* freesurfer@nmr.mgh.harvard.edu
*Oggetto:* Re: [Freesurfer
The volume is the volume of cortex only, not the volume of subcortical
structures. We don't have a VBM-style analysis that would be needed for
subcortical GM. You can always do an ROI analysis, asegstats2table and
mri_glmfit with --table option; this will allow you to analyze the
volume of
If you subtract them, eg,
fscalc vol1.mgz sub vol2.mgz abs gte 0.5 -o diff.mgz
This command will subtract the two, take the absolute values, then
threshold (binarize) the differences.
I'm not sure what you are looking for in terms of aparc+aseg, but you
can do something like
mri_segstats
You need to add matlab to your path. If you type
which matlab
it will indicate whether it is in your path or not
On 10/1/2021 3:51 PM, Camila Fernandes da Silva wrote:
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Hey,
I'm totally new into Freesurfer and I need some help with my Matlab.
I tried to do
The wm.mgz is expected since we added denoising to it; but it does not
matter because wm.mgz is essentially a binary mask of WM. The
brainmask.mgz is created from T1.mgz. The T1.mgz will be affected by
control points, but only if you run it from the beginning. The surfaces
are placed on
Look in the recon-all.log file for the command that creates the
aparc+aseg.mgz. Change the annotation to be the annotation that you want
to use, and change the name of the output file.
On 9/30/2021 10:07 AM, Ahmed Radwan wrote:
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>
> Dear FreeSurfer
Have you seen this page?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
On 9/30/2021 1:08 AM, Abbie Taing wrote:
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Hi all,
I have a between subjects factor (3 groups) and within subjects factor
(3 stimuli type). I am interested in comparing
-0. 1. -0. 3.
-0. -0. -0. 1.
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Thursday, September 23, 2021 10:19 AM
Can you compare the template_coreg.mgz to the input image; they should
be mostly aligned. If not, then the initial registration failed.
On 9/28/2021 2:38 PM, daedalu...@aol.com wrote:
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We have recently installed FS-7.1 and have tested a few “ADNI” images
Check out 1.3 in https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 9/28/2021 4:07 AM, Yu-Chi Chen wrote:
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Dear FreeSurfer experts,
My current analysis is for analyzing the vertices of the cortical
surfaces.
I'd like to have the same vertice numbers of
The first thing to do is to re-run you data using different subject
names so that you have an unedited version. You can then use mri_diff, eg,
mri_diff unedited/mri/wm.mgz edited/mri/wm.mgz
to determine if there is a differenece that you are just not seeing
On 9/27/2021 7:16 PM, Kevin Miller
Yes. Alternatively, if you are using mris_preproc, you can add --etiv to
the command line and it will do the correction by dividing by the eTIV
(rather than using a regressor).
On 9/27/2021 2:51 PM, Wakim, Kathryn-Mary wrote:
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Hi all,
I'm currently
same thing
On 10/1/2021 11:42 AM, Aaron Tanenbaum wrote:
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What about for 7.1?
On Fri, Oct 1, 2021 at 10:23 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
What version are you running? In 7.2, it will automatically set
the t2pia
What version are you running? In 7.2, it will automatically set the
t2pial flag when you specify -t2
On 9/27/2021 11:53 AM, Aaron Tanenbaum wrote:
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What does Freesurfer do with a T2 if you do not use the t2pial flag?
The 7.0.0 release was recalled because the intensity normalization
*sometimes* did the wrong thing. It would not surprise me if you were
not seeing any of these effects, but I can't guarantee that it won't
happen in your data. If it was happening, you would see some big
differences in the
How did you reslice? If you used trilinear interpolation, then that
would mess up the values; use nearest neighbor. Also, check out
PETsurfer https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer which can
do this sort of thing in a principled way
On 9/27/2021 11:17 AM, Ryan Wales wrote:
No, the RAS in fsaverage is in MNI305 space, so no need to do the
conversion.
On 9/27/2021 11:22 AM, Kennedy, Bryan wrote:
Good morning,
We are trying to conduct a meta-analysis by mapping reported MNI
dimensions (by others) on fsaverage. I know that I have to use the
following conversion:
It looks like the mask is the wrong size. What is the dimension of
/autofs/cluster/neuromod/NIFTI/OCD_N
M/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz
you can check with mri_info
On 9/17/2021 8:32 PM, Pedersen, Walker Scott wrote:
Hi,
I am running glmfit on some functional data
. Both of those surfaces should be
tessellated at 1mm, but I just see the white and pial.
Thanks!
Corinna
On Wed, Jul 21, 2021 at 1:49 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
Yes, just run recon-all with the -fill option to regenerated the
fill
Sorry, we don't support that atlas. Have you tried contacting FSL?
On 9/23/2021 7:08 AM, DRON Noramon wrote:
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Dear Freesurfer Team
I have a very naive question. I am in urgent need to get a cortical
region volume base on the Harvard-Oxford Cortical
You don't need the -legacy flag. Just make a copy of your v6 data and
then run recon-all -all -s subject
It will see and apply your previous edits.
On 9/22/2021 2:14 AM, Amanda Boyes wrote:
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Hi FreeSurfer experts,
Just checking whether anyone has any
They are only changed as part of the resampling process (ie, a form of
interpolation). Volume and surface area are jacobian corrected.
On 9/22/2021 1:24 AM, 周冬跃 wrote:
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Dear FreeSurfer experts:
I use the command recon-all qcache to get file
We are no longer supporting qdec
On 9/21/2021 2:15 PM, Fabiola Macruz wrote:
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Dear freesurfer experts,
I have installed the freesurfer version 7.1.1 in my computer (Mac).
After running the longitudinal pipeline in all
Did the size of the defect change?
On 9/19/2021 8:36 PM, Paul, Rahul wrote:
Hi freesurfer experts,
I was using FreeSurfer v6 for my research. Recently, I started move to
FreeSurfer v7.2.
I encountered the following issue:
Some patients, that had extra large error (xL error), were running
value for each input
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Wednesday, September 15, 2021 1:19 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR
Can't see the image. Can you just cut-and-pas
Can't see the image. Can you just cut-and-paste the full terminal output
into the email?
On 9/15/2021 3:02 PM, Tsiknia, Amaryllis wrote:
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Dear Freesurfer Team,
I have been struggling with an error using the mri_gmfit command. I
have been trying to run a
There is not, but you could create your own. By default, it uses this
table to determine which superclass each segment goes into
$FREESURFER/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/sharedGMMParameters.txt
YOu can see that CP is in the CSF glass. You can try creating its
I can't tell what the problem is. Have you looked at your images in
these cases to see if there is anything wrong with them? What
resolution is your data?
On 9/14/2021 1:59 PM, Xiong, Yanyu wrote:
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Hello FreeSurfer Developers,
I'm attempting to run
Sorry, I don't understand what you are trying to do. Extract ROI (eg,
hippocampal) time courses?
On 9/14/2021 4:29 AM, Alice Giubergia wrote:
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Dear Freesurfer's experts,
I am dealing with time course extraction from preprocessed
(prerpoc-sess) task
On 9/13/2021 10:11 PM, Brigitte Pace wrote:
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We are trying to calculate the volume of grey matter of the
significant clusters within each region identified by our initial
analyses. Is there a procedure already written in matlab to accomplish
this
First, make sure you are not running into this problem
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
The global morphometry statistics embedded in aseg.stats and other files
have an error when the input volume has a voxel resolution different
than 1mm^3. See MorphometryStats
You should just make a copy of your subject, then re-run with version
7x. It should automatically see the edits and incorporate them.
On 9/13/2021 3:40 PM, Funk, Quentin wrote:
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Freesurfer experts,
I have a collection of older controls that I have
Try
mri_mask yourcontrast/gamma.mgh sig.masked.mgh yourcontrast/gamma.masked.mgh
gamma is the contrast value (eg, patients minus controls). Is that what
you wnat?
On 9/10/2021 6:20 AM, Graterol Pérez, José Alberto wrote:
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Hello,
I've done a group
can you point me to the data?
On 9/8/2021 12:46 PM, Nasiriavanaki, Zahra,M.D. wrote:
Hello Freesurfers,
I have 6 runs of DTI data per subject in a sample of 50, and I want
to unpack the dicoms, so it outputs the bval bvec values, to use in
dt_recon.
I realized I can use either dcm2nii or
Not sure what is going wrong. Have you looked at your images? Eg, try
freeview orig.mgz aseg.presurf.mgz
It is a bit unusual that it is dying in two different places on the same
data.
On 9/8/2021 3:39 AM, Falko Mecklenbrauck wrote:
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Dear Freesurfer
You'll have to load it as an overlay to a surface, eg,
freeview -f
$FREESURFER_HOME/subjects/fsaverage/surf/lh.inflated:overlay=fmcpr.up.sm5.fsaverage.lh.nii.gz
there won't be much to see :)
On 9/8/2021 5:51 AM, Alice Giubergia wrote:
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Dear Freesurfer's
yes, in the process now of upgrading. We'll use dcm2niix internally.
On 9/7/2021 5:11 PM, Fischl, Bruce wrote:
Our dicom reader is probably too old
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Peled, Noam
*Sent:* Tuesday, September 7, 2021 2:56 PM
*To:* Freesurfer
Find the defect and edit it out of the wm.mgz (or the filled.mgz if
using 7.2). See the tutorial on fixing defects
On 9/6/2021 12:23 AM, Koustav Chatterjee wrote:
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Dear Forum members,
Could you please help me resolve the following issue? The
that is in ventricle, so you don't need to edit it (unless it is
creating such a big topological defect that FS is crashing or taking a
really long time)
On 9/4/2021 1:05 PM, halil ibrahim AKÇAY wrote:
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Hi
My name is Halil Ibrahim akçay. I am a
I think I fixed this in 7.2. Can you try that?
On 9/3/2021 12:11 PM, ChristianBauer wrote:
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Hello freesurfer help team!
I am using the command reg-feat2anat but I get the error message:
tkregister2_cmdl_cmdl: Command not found.
Here is my full command
On 9/3/2021 9:28 AM, Junyeon Won wrote:
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Dear Freesurfer experts,
Could I have a couple of questions regarding visualization?
1) I found significant clusters on the right hemisphere volume after
glm_fit and cluster correction. I would like to extract
What platform are you using (eg, mac?). Can you send the recon-all.log
file? Can you verify that the file actually exists and that you have
read permissions?
On 9/3/2021 4:52 AM, Szulia Agata wrote:
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Hi,
I have a
I don't know about using R. In FreeSurfer you can run asegstats2table
(for aseg.stats) or aparcstats2table (for aparc.stats). Run with -h to
get help or look at our tutorials
On 9/2/2021 7:26 AM, hyeyoung park wrote:
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Hi,
This is hyeyoung Park from Seoul
Not sure whey those are there. Why not just create your WM mask with
mri_binarize --i aseg.mgz --match 2 4 --o wm.mask.mgz
On 9/1/2021 8:37 PM, Ammar Shujaa wrote:
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Hello freesurfer developer,
I have extracted the right and left cerebral white matter
No, this was a situation that we were not anticipating. You'll have to
do it yourself. If you run asegstats2table, it will create a table that
has the BrainSegNotVet and the eTIV
On 9/1/2021 4:19 PM, Fabiola Macruz wrote:
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you can use the --mask or --label options. You can create a single label
by breaking up the yeo annot into individual labels
(mri_annotation2label), then combining the ones you want (mri_mergelabels)
On 8/31/2021 6:13 PM, Haley Park wrote:
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Hello,
I
Not sure. The first step would be to check the affine registration with
freeview template_coregistered.mgz input
where input is the input to samseg
On 8/31/2021 5:27 AM, achille.teil...@chu-lyon.fr wrote:
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Dear experts,
We are working with a large MRI
Are you asking if that is a topological defect? It is impossible to say
from one slice. The surface itself is ok to be there as that is on the
medial well.
On 8/30/2021 8:53 PM, halil ibrahim AKÇAY wrote:
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Hi
My name is Halil Ibrahim akçay. I am a
can you send the recon-all.log file?
On 8/30/2021 3:54 AM, 朱子家 wrote:
> External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> when I run the recon-all command:
>
> $ export SUBJECTS_DIR=`pwd`
> $ cd /lustre/home/acct/zjzhu/project/zzu_MRI/T1/test
> $ ls *nii | parallel --jobs
Not sure what you are trying to do. Usually we do not do voxel-wise
analysis on the asegs (eg, like with a vbm)
On 8/29/2021 2:52 PM, guang wrote:
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At 2021-08-05 08:44:11, "guang" wrote:
Hello FreeSurfer Developers,
I'm trying to analyze
Hi Jim, I know it has been a while, but I have tracked down the source
of the problem with the pial surface. I can go into detail if you want,
but the fix is to add -no-numakeuchar to recon-all. I noticed that there
are some places where the white surface does not extend far enough. This
is
What kind of 7T image is it? Often they have terrible bias fields. Have
you looked at the images with the ?h.orig.nofix surfaces? Also, remember
to send your recon-all.log files.
On 8/27/2021 10:43 AM, Samuel Paré wrote:
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Hi,
I have been trying to
The simple answer is yes with
mri_glmfit --y func.nii.gz --mask yourbrainmask.mgz --osgm --pca --o glm
then look in the pca folder
However, this will only have the mean removed. If you want fancier
detrending, you'll have to work a bit harder.
On 8/27/2021 3:59 AM, std...@virgilio.it wrote:
It looks like label 7 was not in the volume. Where did aparc+aseg.nii
come from?
On 8/26/2021 1:37 PM, A.R. Sekar wrote:
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Hello Experts,
Hope you are well! I am trying to extract ROIs from the aparc+aseg
file after
qdec is deprecated. Use the "command line" stream instead (ie,
mris_preproc, mris_surf2surf, mri_glmfit, and mri_glmfit-sim)
On 8/24/2021 4:44 AM, inbal paran wrote:
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Dear FreeSurfer experts,
I recently started to work with freesurfer and I am now trying
No, it does not.
On 8/23/2021 11:28 AM, Alan Francis wrote:
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Hi Doug et al,
I know that this question may have been asked before, but does the
latest version of FS segment/ parcellate the volume of the
periaqueductal gray (PAG?
Thank you,
Alan
--
you have to be in the same folder as
lh.Yeo2011_17NetworksConfidence_N1000.mgz
On 8/22/2021 5:40 PM, Haley Park wrote:
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Hello,
I got a response to a question I asked earlier to run the following
script:
mri_convert
This is a known issue. See
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
Known Issues: The global morphometry statistics embedded in
aseg.stats and other files have an error when the input volume has
a voxel resolution different than 1mm^3.
Check and see if
That command will re-run the base, but it should respect your edits. Is
that not the case? If you just want to re-run part of it, you can
specify the stage (eg, -autorecon2) instead of -all
On 8/18/2021 8:05 PM, Eszter Boros wrote:
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Thank you for your
, and want to perform cortical surface parcellation
on them to generate label files and .annot files, how can I do it?
Thank you!
*发件人: *Douglas N. Greve <mailto:dgr...@mgh.harvard.edu>
*发送时间: *2021年8月18日5:27
*收件人: *freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.
Hi Lauri, I was able to run this successfully here on 7.2. What version
of FS are you using? Can you send
/tmp/mkcontrast2.28236.m
(if still there)?
doug
On 8/17/2021 3:10 PM, Lauri Tuominen wrote:
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>
> Dear Surfers,
> I am trying to run fsfast
It says that it cannot find
/Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white
does that file exist and readable?
On 8/17/2021 5:12 PM, Lab of Autism and Developmental Neuroscience, Lab
of Autism and Developmental Neuroscience wrote:
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By default, the measure list includes the .K and .H files. You can
specify your own list of measures with the -measure option. Eg, -measure
thickness (you can add more -measure options for more measures)
On 8/13/2021 5:10 PM, Junyeon Won wrote:
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Dear
We don't have post vs ant insula, but have you looked at the
aparc.2009s.annot? It has a much finer insula segmentation. You might be
able to merge some of those labels to get what you want. Otherwise, you
can split the big insula label in the aparc with mris_divide_parcellation
On 8/13/2021
On 8/11/2021 1:17 PM, Erik O'Hanlon wrote:
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Dear FS experts,
I have run the longitudinal pipeline on a dataset with three
timepoints. I am particularly interested in the longitudinal
hippocampal and amygdala data
Yea, I've tried that before. It does not work very well. You can
proceed, but it will not be providing you with a very good correction.
On 8/9/2021 9:30 AM, Shane Schofield wrote:
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Hi Freesurfer Experts,
I am trying to obtain coregister diffusion data b0
On 8/9/2021 5:51 AM, 刘 亚飞 wrote:
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Hello!
In the process of learning freeSurefer, I have two questions:
The first question is that I want to convert a file in .stl format to
a .pial file, but the error "does not apear to be an STL file" appears
when
That is just part of the way the long stream works. When you run a base
subject, you have to spec all the cross tps that go into it. I agree, it
is not elegant.
On 8/8/2021 8:03 PM, Eszter Boros wrote:
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Dear FreeSurfer Team,
I am working on a
On 8/6/2021 6:35 PM, Zeng, Qi wrote:
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Hi Freesurfer experts,
I've done running a longitudinal analysis pipeline for individuals in
3 groups. Now, I need to get prepared for QDEC group analysis. I cp
all groups of individuals to the same directory and
First, try running recon-all on the mni152 template
Find the vertex closest to your seed coordinate
You can create a circle on the surface with something like this (where
vertexno is the vertex number you found above)
mri_volsynth --dim nvertices 1 1 1 --pdf delta --delta-crsf vertexno 1 1
1
Look in /media/sf_T1/recon/demo3/surf
Does lh.white.preaparc.H exist?
If so, does lh.white.H exist?
If not, what happens when you run
ln -s lh.white.preaparc.H lh.white.H
in that folder?
On 8/5/2021 1:41 AM, guang wrote:
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Hello FreeSurfer Developers,
I'm
both.hippo) in the bm+hippo.mgz file
has become black. Is there any way I can do to change the color of
both.hippo segment from back to another color?
Thanks,
Ammar
On Thursday, August 5, 2021, 11:45:12 AM GMT+9, Douglas N. Greve
wrote:
To merge the two hippocampi together in one fi
mgz file having the segmentations
with the brainmask. I want to use this file (hypocampus+brainmask.gmz)
in another software.
Best regards
Ammar
On Wednesday, August 4, 2021, 11:54:48 PM GMT+9, Douglas N. Greve
wrote:
I don't understand what you mean by "join". Can you elaborat
sorry, no idea. They probably merged labels from the aparc or the
aparc+a2009s to create those labels. You might also try
mri_annotatoin2label with the --lobes option
On 8/4/2021 5:28 AM, Sumit Sharma wrote:
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Hi Freesurfer Developers
I am trying to
I don't understand what you mean by "join". Can you elaborate?
On 8/4/2021 1:16 AM, Ammar Shujaa wrote:
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Hello FreeSurfur Developers,
I have used binary mask and got the segmentations: right and
left-hypocampus.mgz.
I just want to know how to join these
This happens because the cached p-values were generated from a
simulation that only went up to 30mm FWHM of smoothing. lGI has lots of
internal smoothness which often pushes it over this level. You can try
not using any smoothing, or, even better, try using permutation instead.
and you can use
mri_binarize --i aseg.mgz --match index1 index2 --o yourmask.mgz
On 8/3/2021 10:07 AM, Fischl, Bruce wrote:
Hi Ammar
In the mri dir there are segmented volumed called aseg.mgz and
aparc+aseg.mgz where every voxel has an index into the
FreeSurferColorLUT.txt lookup file
do you mean you want a binary mask? If so you can run something like
mri_binarize --i aseg.mgz --match 17 --o left.hippocampus.mgz
where 17 is the index for left hippo as found in
$FREESURFER_HOME/FreeSurferColorLUT.txt
On 8/3/2021 4:18 AM, Ammar Shujaa wrote:
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them in
my analyses. I think this is correct, but wanted to check with you as
well, in case I have to calculate the product of demeaned age and IQ
scores instead? please let me know.
Thank you so much,
Avi
On Mon, Aug 2, 2021 at 11:24 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>&
But do you know why it has multiple frames? We collect multi-echo T1
MPRAGEs that will have multiple frames. We then reduce it to one frame
by computing the RMS across frames (actually the scanner can output a
separate RMS series). Check to see whether you got an RMS series in
their. If not,
If you want to test TD vs the mean of the other groups, you'd need
0.5 0.5 -x -x -x -x -x -x 0 0 ...
where x = 1/6
Contrast 2 is the correct test for a multivariate (F) test.
On 8/2/2021 9:56 AM, Avi Gharehgazlou wrote:
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Hi,
I want to investigate lGI
Use rh.hippoAmygLabels-T1.v21.CA.mgz
On 7/30/2021 11:00 AM, Shane Schofield wrote:
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Hi Freesurfer Tema,
I am trying to use vol2subfield to extract DTI measurements like FA
and MD.
For this purpose, should I be using the
Hi Avi, if you want to compute an interaction between two continuous
variables, you have to create a new regressor where you multiply them
together. The contrast you have created would test whether the age slope
is different than the IQ slope. This contrast does not make sense since
the to
You should be able to use asegstats2table specifying the samseg inputs
with --inputs samseg1/seg.stats samseg2/seg.stats samseg3/seg.stats ...
On 7/26/2021 11:12 PM, AJ wrote:
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Hi,
I was wondering if there is a simple command for generating a table
from
I'm not sure what you mean by a QC rating. For white matter, the volume
will depend upon the boundaries with both subcortical and cortical GM,
so, in theory, you must check both. For eTIV, the value is computed from
the talairach registration, not from a segmentation, so you'd have to
check
Can you send your retinotopy.par file (or just the contents of it)?
On 7/21/2021 11:40 PM, Yaoda Xu wrote:
Dear all,
Using FreeSurfer 7.1.1, I made my analysis file with the following (I assume
-nksip should be in the number of TRs and not in seconds):
mkanalysis-sess -analysis
You might be able to run both through longitudinal samseg as samseg will
create a "base" image from both and try to bias correct both with
respect to this image.
On 7/21/2021 1:31 PM, Fischl, Bruce wrote:
There isn’t really anything available for the latter approach. I would
suggest the
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