Yes, that all looks right to me.
On 3/14/2023 6:00 PM, mariangela asimina wrote:
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Dear experts,
I am looking into the covariance of the volume of subcortical
structures with cortical vertex-wise volume, comparing between two groups,
correcting for the
You should not use either T1.mgz as that has been highly processed for
other purposes. The brainmask has also been processed, skull stripped
and bias correction. I have not looked at what has to happen to get the
most correlation between the methods; they are different methods and are
supposed
On the PETsurfer wiki,
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer, I had recommended
using mri_coreg to register your PET to the FS anatomical using the
following command line:
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta
This works well for PET scans that do
This is just straight-forward GLM, ie,
beta = inv(X'*X)*X'*y (y is the input time series after preproc)
yhat = X*beta
residual = y - yhat
residualstd = sum(residual.^2)/DOF (DOF = rows of X - cols of X)
t = C*beta/sqrt(C'*inv(X'*X)*C*residualstd)
where C is the contrast matrix
On 3/10/2023 4:50
It is probably a scaling problem with using age^2. Try normalizing the
age^2 column (ie, remove the mean and divide by the sum of the squares)
On 3/9/2023 3:30 PM, Triebswetter, Curtis wrote:
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Hello Freesurfer experts,
I am attempting to run the command
--- Original Message ---
On Monday, March 6th, 2023 at 11:16 PM, Douglas N. Greve
wrote:
If you are using 7.X, you can run
tkmeditfv subject norm.mgz -defects
This will load a "segmentation" with the defects in the volume, an
annotation (surface segmentation) sh
You can pass it a --mul SCALE option to multiply the output by any
scaling factor
On 3/7/2023 1:16 PM, John Anderson wrote:
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Dear Freesurfer community,
Please forgive me for the basic nature of my question.
I was wondering whether there is an argument that
or use mris_apply_reg with the --m3z option
On 3/4/2023 10:56 AM, Fischl, Bruce R.,PHD wrote:
You can try mris_transform, although you might need to convert the
nonlinear warp to our format. I’m pretty sure others have done this,
so maybe someone else can comment?
Cheers
Bruce
*From:*
probably something wrong with your stimulus schedule (paradigm). Can you
send the X.mat (or Xtmp.mat)?
On 2/28/2023 12:12 PM, Caspar M. Schwiedrzik wrote:
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Hi!
I am running into an issue with fast_selxavg3b.
I am attempting a first level PPI analysis.
The
We do not have a way to generate surfaces for hippocampus. You could
play with the subfields, eg, like
mri_binarize --i subfields.mgz --match M1 M2 ... --surf lh.hippo
--surf-smooth 2
This will build a surface around segments M1, M2, ...
you can then view with freeview
On 2/28/2023 8:42 AM,
You probably don't have write permission to that folder.
Also, you can try
mri_segstats --qa-stats subject subject.qa.dat
Run mri_segstats with --help to understand what is in the qa.dat file
On 2/17/2023 7:43 PM, MANSON ERIC NAAB wrote:
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Thank you once
Yes, but you have to get it started in about the right place.
On 2/23/2023 9:47 AM, Fischl, Bruce R.,PHD wrote:
Hi Sebastien
I believe that Doug has had success using bbregister for this. You
might give it a try
Cheers
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of
Under "Render" select "Mesh"
Under "Annotation" hit the View/Edit button. From there you can turn any
annotation on or off.
On 2/22/2023 2:34 PM, Leonardo Tozzi wrote:
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Dear Experts,
I would like to use Freeview to achieve the following.
I would like to
If you are using 7.X, you can run
tkmeditfv subject norm.mgz -defects
This will load a "segmentation" with the defects in the volume, an
annotation (surface segmentation) showing them on the surface, and a
point set that you can go to any of the points.
On 2/21/2023 7:21 PM, KennethSPrice
These are segments in the wmparc.mgz file. Originally, I called these
centrum semiovale, but I realized that, while they might overlap heavily
with CS, it they were really just voxels left unsegmented by the main
process and I did not really know that they were a good segmentation of CS.
On
You'll probably have to use matlab, eg,
[vertices, label, colortable] = read_annotation(filename)
ind = find(label==yourlabel);
beta = fast_vol2mat(MRIread('beta.nii.gz'));
yourlabelbeta = beta(:,ind);
On 3/6/2023 10:08 AM, Huang, Yujing wrote:
Hi Andy,
Can you try the mask option?
can you send an example?
On 2/17/2023 9:38 AM, Federica Di Antonio wrote:
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Dear experts,
I hope this email finds you well.
I run the pvc correction with mri_gtmpvc for subjects data obtained
with two different PET tracers.
In gtm.stats.dat, for every
On 2/17/2023 9:21 AM, Federica Di Antonio wrote:
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Dear Freesurfer experts,
I'm using PETsurfer. I've done the standard pipeline for all my
subjects, using the cvs registration.
I was wondering (maybe it's very stupid) when the standard pipeline
"uses"
when you say that it is better cortex segmentation, do you mean better
than the aseg.mgz=aparc+aseg.mgz or better than the aseg.presurf.mgz? Do
you mean in general or just near the WMH? The aseg/aparc+aseg use the
surfaces to refine the gray/white boundary, and usually the surfaces do
a much
On 2/15/2023 5:35 PM, Antonio #30 wrote:
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Hello again,
I would like to ask one last thing.
How can the class averages computed from csdbase.y.ocn.dat not match
the gamma.mgh values in the cluster?
e.g. How can gamma show +29 in a vertex that is part of
I think it is basically the same procedure as the other segmentations,
ie, a set of 40 subjects' whole brains were manually labeled, many of
them had WMH, then it is just the normal Bayesian labeling as in Bruce
Fischl's 2002 Neuron paper.
On 2/13/2023 12:37 PM, Alberto Del Cerro Leon wrote:
That one looks like there was a massive failure of the registration. One
thing you can try is to add -samseg-reg to the command line. This will
use samseg to do this registration, which may be more robust. Is there
anything amiss with your image?
On 2/13/2023 10:25 AM, Goeckner, Bryna wrote:
Hi Philipp, by default, those parameters are not used anymore as we are
using ANTS N4 (though this is not obvious). There is no separate
parameter set for for 3T for N4. It is still possible to use the old
MNI N3 code, so we have kept it in there.
On 2/25/2023 2:58 PM, Saemann, Philipp
Hi Zuha, I'm not the person who can give permission. I think the license
allows you to use the software in the way that you are describing. I'm
cc'ing Heonick Ha, one of the MGH licensing lawyers, who should be able
to tell you definitively.
best
doug
On 3/3/2023 3:30 AM, Zuha Junaidi wrote:
This is actually a very obscure feature of freesurfer that takes some
explaining. In FS, all p-values are computed with a two-sided test (so
the sig.mgh represents a signed p-value). When you pass --sign pos to
mri_surfcluster, it sees that you want to do a signed test instead of an
unsigned
It looks like you are doing the right thing. You indicated not to use a
contrast matrix. If you want to test a contrast, I think the matrix
would be [0 1] (I think it adds an offset regressor)
On 2/10/2023 4:50 PM, Finn, Quentin wrote:
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Freesurfer
That looks like a GM lesion (maybe some kind of stroke). I don't think
we have a way to fix it.
On 2/7/2023 10:34 AM, Aaron Tanenbaum wrote:
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I have this subject that has holes in the insula. Please see
attached. I was wondering what should freesurfer
you would add them as task regressors and set up first level contrasts
as you describe. I'm not sure of your last question (ie, second-level
comparison of their effect). Do you want to compare, eg, respiration vs
motion? I'm not sure how you would do that.
On 2/6/2023 5:18 AM, Marilena
was not very clear. My purpose is to generate new .mgz files
(e.g., scalp.mgz and CSF.mgz, etc.) that are not in the MRI folder.
Bset regards,
Yichuan Jiang
-- Original --
*From: * "Douglas N. Greve";
*Date: * Wed, Feb 1, 2023 11:00 PM
*To: * "freesurfer&q
everything except skull and scalp are in the aseg.stats file. You can
get skull by running samseg, eg,
cd subject/mri
samseg --i orig.mgz --o samseg
there will be a stats file in the samseg folder with skull volume in it
On 2/1/2023 5:00 AM, 江一川(JIANG Yichuan) wrote:
External Email -
In my experience, the issues that Matt is describing are mostly unique
to the HCP data, but I have not tried it on much other hires data.
On 1/30/2023 1:54 PM, Glasser, Matt wrote:
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Issues with surface placement in harder areas (e.g., white matter
surface
I think it will but I don't have a reference
On 1/30/2023 10:22 AM, Lee, Sang Hoon wrote:
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I understand that from Version 7.0, better high resolution surface
reconstruction with -hires is done.
My question is, if we use higher resolution T1, such as
You will have to run from the beginning. Make sure to include your
watershed parameters on the command lie.
On 1/30/2023 4:03 AM, Rakshathi Basavaraju wrote:
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Dear FS people,
A few of my brains were excessively skull stripped and I used
watershedding to
Pass your mask to recon-all with -xmask
On 1/30/2023 1:13 AM, Boa Sorte Silva, Narlon wrote:
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Hi there,
I just wanted to follow-up on this.
Thanks!
Nárlon Cássio
*Nárlon Cássio Boa Sorte Silva* PhD (He, Him, His)
CIHR and MSHR BC/PARF Postdoctoral
didn't I answer this last week?
On 1/27/2023 8:52 PM, David wrote:
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Hi Freesurfer experts,
I'm very sorry to bother you, but I am very confused with the
following questions:
My experimental design includes two discrete factors:
with three
You can manually edit them to restore the parts that have been stripped
(using the clone feature in freeview). See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview
On 1/27/2023 5:21 AM, Rakshathi Basavaraju wrote:
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Dear FS,
A
In any case, please let
me know what you think.
Best,
Siamak
On Thursday, January 26, 2023 at 07:13:32 AM PST, Douglas N. Greve
wrote:
Does this happen on every volume or just with this one. If just this
one, then it is probably a problem with the volume itself and not the code
On 1/25/
You can use the --pvr (per-vertex regressor) option in mri_glmfit. But
if you are testing for a difference between groups, there is no valid
way to do correction for multiple comparisons. Look through the archives
as I have explained how to do it several times through the years.
On 1/26/2023
Does this happen on every volume or just with this one. If just this
one, then it is probably a problem with the volume itself and not the code
On 1/25/2023 9:15 PM, Siamak Sorooshyari wrote:
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Dear FreeSurfer,
I am using the FieldTrip software to process
environment and
define a path to the application? If so what should i include in my
bash profile.
On Wed, Jan 25, 2023 at 11:00 AM Douglas N. Greve
wrote:
I have not idea, try it and see.
On 1/25/2023 9:25 AM, Justin Oh wrote:
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Is the student
That basically looks right. One thing to note is that you are sampling
onto the average surface (fsaverage); this is not really doing
surface-based analysis, it will be about the same as registering you
individual subject to the mni152, then sampling your ROI atlas onto the
individual
to work.
Best,
Justin Oh
On Thu, Jan 12, 2023 at 9:38 AM Douglas N. Greve
wrote:
Just the basic is ok. Although I have not done it in a while, you
should also be able to use octave (which is free). Once you get
octave install and in your path, set the env variable
FS_USE_OCTAVE to 1
I assume you mean on an ROI basis. They are usually correlated in some
way because volume = thickness*area. The only way they could not be
correlated is if the area were to change opposite to thickness -- but
almost always they are both moving in the same direction, down:(
On 1/25/2023 10:25
Probably not. What do you mean by "suboptimal"?
On 1/25/2023 5:50 AM, Michele Valotti wrote:
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Dear Freesurfer experts,
Should I expect Freesurfer 7 to significantly improve segmentation of
the Temporal Lobe when compared to Freesurfer 6? I often see
No, it is not
On 1/20/2023 2:26 PM, Aaron Tanenbaum wrote:
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Hello FreeSurfers,
I just need to know if the FSL is used in the recon-all scripts.
Basically if FSL_DIR is different will the recon-all produce different
values.
Thank you
Aaron.
James, what do you mean by restrict the analysis within lobes? An ROI
analysis? Adding --label will not give you an ROI analysis.
On 1/20/2023 9:32 AM, Huang, Yujing wrote:
Hi James,
Did mri_annotation2label commands create lh.lobes.annot and
rh.lobes.annot in fsaverage/labels directory?
Hi Sarah, sorry, I don't know where that code came from; it is not being
supported. Over the years, things find there way into FS, often from a
postdoc or visiting fellow, then they leave and the program becomes
orphaned.
On 1/18/2023 5:31 PM, Sarah Lavelle wrote:
External Email -
When you load it into freeview, use the aux/bbpet2anat.lta , eg,
freeview orig.mgz aseg.mgz mgx.ctxgm.nii.gz:reg=aux/bbpet2anat.lta
On 1/17/2023 12:46 PM, Marina Fernández wrote:
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Dear experts,
I am trying to do PVC on FBB-PET images using the following
Hi Bram, there is not a way to do it with a single command. You could
use the aparc+aseg, merge the two hemi labels into one, then run
mri_segstats. If you want to stick with pure surface-based analysis,
then you'd have to run mri_segstats twice, then just compute a weighted
mean of the two
You have to register the atlas to each individual person's space. You
can do this with
mri_coreg --mov atlas-template-brain.nii.gz --targ brain.mgz --dof 12
--reg reg.lta
Then map the atlas to the subject's space
mri_vol2vol --mov atlas.nii.gz --targ brain.mgz --reg reg.lta --interp
nearest
Try
1 -1 0 -1 1 0 ...
0 1 -1 0 -1 1 ...
The first row look for the interaction between dm and fm, the second for
mh and fm, then using both will test for an interaction in either
On 1/16/2023 12:21 AM, David wrote:
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Hi Freesurfer experts,
I'm very
!
Sean
On Thu, Jan 12, 2023 at 11:29 PM Douglas N. Greve
wrote:
Can you send your command line and full terminal output?
On 1/8/2023 9:37 PM, Shao-Min (Sean) Hung wrote:
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Dear Doug,
I have been having the following issue and haven't
If you are looking for the difference in the correlation between the
groups then you have to use DODS and 0 0 1 -1. The way to understand it
is that you have four regression coefficients and each means something.
The way you have it set up in the fsgd file is that they are
1. group 1 intercept
Not really. I think that 3 mostly spanned the space but I did not do any
systematic tests. In general, I think you should be careful when adding
regressors so 3 is more conservative than 6.
On 1/12/2023 4:40 AM, Andy Kim wrote:
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Dear FreeSurfer
Just the basic is ok. Although I have not done it in a while, you should
also be able to use octave (which is free). Once you get octave install
and in your path, set the env variable FS_USE_OCTAVE to 1. Like I said,
I have not used it in a while, but it I think it should still work.
On
yes, you are correct. I just fixed that, so it will be in the next release.
On 1/10/2023 4:14 PM, Aaron Tanenbaum wrote:
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I should have said I am using FS 7.3 on Ubuntu 20.04
On Tue, Jan 10, 2023 at 12:23 PM Aaron Tanenbaum
wrote:
Hello,
FYI, I
FS does not filter prior to segmentation
On 1/10/2023 12:35 PM, Ruifeng Dong wrote:
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Dear Freesurfer community,
I wonder if Freesurfer uses any filter to deal with the noise in the
image, before segmentation. If so, is the filter spatially local or
Can you send your command line and full terminal output?
On 1/8/2023 9:37 PM, Shao-Min (Sean) Hung wrote:
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Dear Doug,
I have been having the following issue and haven't figured out a way
to get around it. I have also searched the archive and did not find
Not that I know of. Ruopeng would know for sure.
On 1/7/2023 5:00 PM, Aaron Tanenbaum wrote:
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Hello,
Is there a way to set a loaded volume as read only in freeview on the
command line?
___
Freesurfer mailing
Oh, I see what you mean. Can you try putting the line "DOSS" (no quotes)
into your FSGD file?
On 1/3/2023 11:51 AM, miracle ozzoude wrote:
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Hello Doug,
Thanks for the quick response. I did see the error. However, I
specified doss in the mri_glmfit
I think it has to go through the whole recon as it uses wmparc.mgz and
that is one of the last things created
On 1/5/2023 4:16 AM, Verónica E wrote:
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Dear all,
I am planning to run the thalamic segmentation (as implemented on
FreeSurfer 7.1). The data
On 1/4/2023 8:00 PM, Yoonho Hwang wrote:
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Dear Douglas N. Greve,
Thank you for quickly replying.
Although I ask many questions, To reply to the mail kindly and quickly
is very grateful for me.
It became clear how to analyze it. Nevertheless, *_there
no, it is not
On 1/4/2023 9:20 AM, Rosalia Dacosta Aguayo wrote:
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Dear Freesurfer team,
I have found a warning about not using amygdala, hippocampus and
brainstem volumes from asegstats file.
I wonder if that is true.
Best wishes,
Rosie
*
*
Is the error message not clear what the problem is?
On 12/30/2022 6:37 PM, miracle ozzoude wrote:
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Hello,
I have 2 groups (group 1 = 3 members, group 2 = 12 members) and I did
like to regress out the effects of groups + other variables by using
doss.
not sure what you mean. is this python code? what package? what is the
error? what is xxx?
On 12/23/2022 12:33 PM, Kalluvila, Aryan wrote:
Good morning Freesurfer Team,
Is there a certain freesurfer version that needs to be installed in
order to get the image attribute? For example, I have
yes, you can copy that. I'm cc'ing Rob in case he has any insights. @
Renew, you should try running the whole recon-all in a single platform.
If you copied it from Mac to ubuntu, it is possible that those links
weren't created in Mac or did not survive the copy.
On 12/22/2022 10:28 AM, Huang,
Try
mri_segstats --seg Cluster1_R.nii.gz --id 1 --sum sum.R.dat
That will give you the number of voxels that have a value=1 times the
size of the voxel (so the volume). It will not be in MNI space unless
the nifti files you sent are in MNI space.
On 12/21/2022 5:42 PM, Beatriz Cavendish
what are you not getting?
On 12/21/2022 10:11 AM, Rosalia Dacosta Aguayo wrote:
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Maybe is -qcache ?
*
*
On Wed, Dec 21, 2022 at 4:10 PM Rosalia Dacosta Aguayo
wrote:
Dear Freesurfer group,
Could you tell me which is the flag I need to use
Douglas N. Greve rašė:
Why not samseg?
On 12/20/2022 12:50 PM, Donatas Sederevičius wrote:
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Hi, is there a tool to make a tetrahedral mesh of the brain from
the MRI T1w image and/or its whole-brain segmentation? I need
Why not samseg?
On 12/20/2022 12:50 PM, Donatas Sederevičius wrote:
External Email - Use Caution
Hi, is there a tool to make a tetrahedral mesh of the brain from the
MRI T1w image and/or its whole-brain segmentation? I need it for the
finite elements method.
-Don
On 12/20/2022 12:22 PM, James Brown wrote:
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Dear Freesurfer experts,
I have 2 questions about the command mri_glmfit and I appreciate your
help.
1- Are there any settings or flags that can be used in mri_glmfit to
restrict statistical comparison of
: @BoaNarlon
On Dec 15, 2022, at 11:46 AM, Douglas N. Greve
wrote:
[CAUTION: Non-UBC Email]
I recently found a bug in the pial placement refinement with FLAIR
images (recon-all -flair ...) that affects version 7.{0,1,2,3}. This bug
caused the pial surfaces to not extend nearly far enough. It has been
and then it could not work. How to solve this problem?
Best regards
Mingyang Xia
Douglas N. Greve 于 2022年12月12日周一
上午7:40写道：
regressing out is the analysis. You'll have to create an
"analysis" with mkanalysis-sess, then run selxavg3-sess with
-svres to save the residual.
On 12/7/202
I recently found a bug in the pial placement refinement with FLAIR
images (recon-all -flair ...) that affects version 7.{0,1,2,3}. This bug
caused the pial surfaces to not extend nearly far enough. It has been
fixed in the development version of FS and so will be in future
versions. If you
you can also do it with mri_volsynth
mri_volsynth --temp yourfile.mgz --pdf const --val-a your val --o
yournewfile.mgz
On 12/15/2022 9:12 AM, Huang, Yujing wrote:
Hi Aaron,
I think you can do this using mri_binarize
(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize).
‘—min’ and
On 12/15/2022 2:00 AM, Yoonho Hwang wrote:
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Dear FS developers,
Hi, I'm Yoonho.
I know that new features, such as SynthSeg, SynthStrip,
segment_subfields (beta version), etc, based on deep learning have
been added after the FreeSurfer 7.3.2.
Here I have
please send your command line and recon-all.log file
On 12/13/2022 10:18 PM, Brooklyn Wright wrote:
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Hi there
I am running into repeat difficulty with reconstructing ultra-high
resolution T1w .nii images (0.25mm^3 voxel size). These have been
submitted
FreeSurfer does not segment extracerebral CSF. You can use samseg
(samseg --i orig.mgz --o samseg) and look at the samseg/seg.mgz file
On 12/13/2022 1:46 AM, priya padma wrote:
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Dear Team,
I have tried creating binary CSF mask from
# CSF:
# - 4:
ec 2022 10:34:15 -0500
From: "Douglas N. Greve"
Subject: Re: [Freesurfer] Creating and analyzing combined ROIs,
combining different FreeSurfer versions
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <8e7e390b-bbef-00cd-29c6-bda799bfd...@mgh.harvard.edu>
Content-Type: text/plain;
I have something called the adaptive GTM that is currently a "hidden"
feature in mri_gtmpvc as it has not been published yet. You can try it
by adding the following flags --opt 1 --opt-tol 4 10e-6 .02 --opt-seg-merge
When this is done, there will be a file called gtmdir/aux/opt.params.dat
The
fsfast does not work with topup in this way. You can do a couple of
things (1) do the preprocessing yourself and then turn it off for fsfast
(2) create your own B0 map and put it in to sessid/fsd/b0dcmap.nii.gz
and specify -b0dc in mkanalysis-sess
On 12/8/2022 9:50 AM, Asa Borzabadi
need more info
On 12/7/2022 1:39 PM, Ngo, Nathan Xi wrote:
Hello,
I have several flash volumes that I am able to open using stable5 but
not with the current version of freesurfer. Is there a way to convert
these volumes into the current freesurfer format?
Best,
Nathan
It means that no such voxels were found in the aseg (not uncommon for
these segs)
On 12/7/2022 12:35 PM, Eszter Boros wrote:
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Dear FreeSurfer Team,
I am writing because I was extracting the aseg values using Freesurfer
7.1.1 and much to my surprise,
the those multiple dat files into one excel or csv file.
regards
Amar Shukla
On Mon, 17 Oct 2022 at 2:56 AM, Douglas N. Greve
wrote:
yes, but how are you combining them? And what features after you do?
On 10/16/2022 10:18 AM, Amar Shukla wrote:
External Email - Use
regressing out is the analysis. You'll have to create an "analysis" with
mkanalysis-sess, then run selxavg3-sess with -svres to save the residual.
On 12/7/2022 12:04 AM, Mingyang Xia wrote:
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Dear Freesurfer expert:
After I used ' fcseed-config' to get
Or just use the --split option
On 12/6/2022 12:10 PM, Wighton, Paul wrote:
Oh that's perfect, thanks Bruce!
-Paul
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fischl, Bruce
R.,PHD
*Sent:* Tuesday,
It all must be done.
There is no tissue type segmentation per se. You can get it from the
aseg.mgz
The 3rd question is about FSL commands. you should contact FSL
On 12/5/2022 5:50 PM, Zeng, Qi wrote:
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Hi Freesurfer experts,
If I just want to normalize,
change what?
On 12/5/2022 9:27 AM, Sarah Lavelle wrote:
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Hi Doug,
Thank you for your help! Yes, I have followed the points using vertex
indices but there were some that didn't match up. It could be because
of the 1-based indexing. Where would I change
not clear what the problem is, can you be more specific?
On 12/4/2022 11:40 PM, 白晨 wrote:
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Hello FreeSurfer Developers,
I'm attempting to analyze the T1 imaging of children aged 2–7 years, a
problem with the segmentation occurred,the pial surface of many
On 12/2/2022 12:35 PM, Trolle, Carl wrote:
Dear FreeSurfer team,
1. We're trying to focus our cortical analysis following suggestions
here
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23939.html.
The
FS ROI tutorial page mentions that labels should be drawn or
It looks like the anatomical analysis is out of sync with the functional
analysis. Is is possible that you ran the functional analysis, then
edited the subject, then tried to rerun the analysis? If so, try running
preproc-sess with -force to redo all the preprocessing.
On 12/1/2022 12:45 PM,
It looks like it is missing WM extending into the temporal pole. If it
is not in the filled.mgz, then edit the wm.mgz and/or add control points
in the WM in that region.
On 12/1/2022 11:34 AM, Alessia Sepe wrote:
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Hi FreeSurfer Developers,
I have a
did mri_glmfit create a file called pcc.mgh? If so, that is the partial
correlation coef (R).
On 11/30/2022 6:31 AM, Lyna Mariam El Haffaf wrote:
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Hi!
I'm taking the liberty of writing another email on this subject, as I
didn't get a reply to my previous
freeview will show the coords of the white surface for the inflated
surface since those of the inflated surface are not meaningful. why not
just get the vertex no and reference that in matlab? Note that matlab
will use 1-based indexing vs freeview uses 0-based
On 12/3/2022 12:27 PM, Sarah
You don't need a different template for the surface-based analysis. I'm
not sure about the volume-based analysis. I'm cc'ing Lilla in case she
wants to weigh in.
On 11/24/2022 11:53 AM, Olivier Brown wrote:
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Dear Freesurfer experts,
I am using a
When you run selxavg3-sess, add the -svres flag. This will save the
residuals (ie, the time series without the nuisance variables)
On 11/24/2022 4:16 PM, std...@virgilio.it wrote:
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Hi list,
I would extract the rs-fMRI time-series from spitted components
that is quite strange. Does it happen every time? What is the
mri_glmfit-sim command line and terminal output?
On 11/23/2022 2:47 PM, Vicente Ferrer wrote:
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>
> Dear Freesurfer users,
>
> I was trying yo use mri_glmfit-sim after using mri_glmfit that run
>
you can just rerun preproc-sess. it will see that the reg file has
changed. As a precaution, I would change the permissions of that file to
read-only, otherwise it could get overwritten (not likely, but possible)
On 11/21/2022 7:45 PM, Asa Borzabadi Farahani wrote:
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please send the recon-all.log file
On 11/23/2022 5:10 PM, Christopher Mcnorgan wrote:
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A student and I have independently been trying to reconstruct a
dataset. We've tried it a couple different ways using either an
additional FLAIR or a T2 image and
yes, that should work. make sure to use DOSS.
On 11/23/2022 11:50 AM, Olivier Brown wrote:
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Dear FreeSurfer experts,
I would like to confirm my FSGD file format and mtx contrasts prior to
continuing with my analyses. Here is some background information: I
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