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Dear Freesurfer experts,
May I ask what's the difference between FSFAST and SPM in the 1st level
GLM? Now I use fsfast to pre-process my task-based imaging data, then model
the data with FSFAST and SPM respectively. I expected to get very similar
resul
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Dear Freesurfer experts,
May I ask how could I customize the color scale in TkSufer? The default
heat scale is blue-red. Could I change it to other colors, such as
green-yellow or blue-white-red (like gradient)?
Now I know how to customize the color s
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Thank you very much.
On Wed, 28 Aug 2019 at 00:01, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> correct
>
> On 8/27/2019 11:28 AM, Zhi Li wrote:
>
> External Email - Use Caution
> I see. Hence I ca
ge*weight for group1 and age*weight for group2, then the
> contrast will be [0 0 0 0 0 0 1 -1]. I would suggest demeaning both age and
> weight prior to computing the product.
>
>
> On 8/27/2019 10:12 AM, Zhi Li wrote:
>
> External Email - Use Caution
> Dear Freesur
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Dear Freesurfer experts,
May I ask how to understand the contrast of interaction between covariates
in the example https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V? The
interaction of group x age x weight is:
[0 0 1 -1 0 0
0 0 0 0 1 -1]
Why the i
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Dear Freesurfer experts,
Now I would like to calculate the distance between two vertices. However,
when I tried "mris_pmake --subject fsaverage --hemi lh --surface0 smoothwm
--curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind
--mpmArgs
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Dear Freesurfer experts,
May I ask how to create a slice delay file for slice timing in fsfast? Is
there an example? The slice order of my data is [33:-2:1 32:-2:2], how
could I convert this vector to time fraction of TR? I have checked the help
inform
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
> > You did not say which MNI space you were dealing with (we use mni305,
> not 152).
> >
> > On 7/15/2019 12:02 PM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Thank you v
/ReconAllOutputFiles
> [2]
> http://www.grahamwideman.com/gw/brain/fs/fsunderstanding/fssampleimages.htm
>
> Best,
>
> Tim
>
> > On July 12, 2019 at 9:30 PM Zhi Li wrote:
> >
> >
> > External Email - Use Caution
> >
> > Dear Fr
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Dear Freesurfer experts,
Now I have an annotation file in fsaverage space and a MNI voxel coordinate
of one subject. May I ask how could I know if this coordinate is in one
parcel of the annotation file? There are many coordinates that I cannot
check i
nal mask. If you run isxconcat-sess,
> it will create a file called masks.nii.gz with all the masks in them. You
> can load it up in freeview (or spm) and scroll through them.
>
> On 7/11/2019 12:15 PM, Zhi Li wrote:
>
> External Email - Use Caution
> It is group level
-stable-pub-v6.0.0-2beb96c.
Best,
Lizhi
On Thu, 11 Jul 2019 at 11:55, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> is this an individual or group? what version of FS are you running.
>
> On 7/11/19 11:10 AM, Zhi Li wrote:
> >
> > External Email
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Dear Freesurfer experts,
Now I am using both FSFAST and SPM to preprocessed my functional image
data. In FSFAST, I replaced the subcortical template with the whole brain
in the folder "mri.2mm", to get the whole brain volumetric data. I have
also dilut
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Hi Bruce,
Thanks. I found a command from a previous post which seems capable of
generating a surface data file in which all the vertices = 0 except the
peak vertex:
mri_volsynth --temp $SUBJECTS_DIR/yoursubject/surf/lh.curv --pdf delta
--delta-crsf ve
> version of freeview to dilate it 4-5 times.
>
> cheers
> Bruce
>
> On Wed, 5 Jun 2019, Zhi Li
> wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts,
> >
> > Now I would like to find the peak vertex showe
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Dear Freesurfer experts,
Now I would like to find the peak vertex showed significant group effect in
a given ROI (e.g. left insula), then draw a 5-mm-radius circle mask centred
this peak point. May I know whether it is applicable and how should I do it
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Thanks.
On Wed, 15 May 2019 at 16:42, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Right, with -fwhm 0, it will not smooth the data.
>
> On 5/14/19 2:21 PM, Zhi Li wrote:
> >
> > External Emai
e (ie, surface-based smoothing instead of volume-based).
> Volume-based smoothing in the subcortical regions is automatically done
> when you specify a FWHM in preproc-sess
>
> On 5/14/19 1:02 PM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> &g
you would like
> to smooth the data then resample, do you mean smooth on the surface? and do
> you mean resample to the standard surface or volume space?
>
> On 5/13/2019 11:26 AM, Zhi Li wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts.
>
> Now I
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Dear Freesurfer experts.
Now I am using preproc-sess to preprocess functional MRI data. I would like
to smooth the data first and then resample them into the standard space.
Hence I run 'preproc-sess -s sub001 -fsd func -stc odd -fwhm 0 -per-run'
first
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Dear Freesurfer experts,
I would like to investigate the overlap between two contrasts with
conjunction analysis. May I know how should I use mri_glmfit-sim to correct
the combined sig.nii.gz of contrast A and contrast B?
Another question is if I want
n the file
'perm.th30.pos.sig.voxel.nii.gz'?
Thanks and regards,
Lizhi
On Thu, 25 Apr 2019 at 12:05, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
>
>
> On 4/25/19 10:54 AM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> &
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Dear FreeSurfer experts,
I am reading your work 'False positive rates in surface-based anatomical
analysis' and having several questions about multiple test correction in
mri_glmfit-sim:
1. The permutation is permuting the design matrix, but how to pe
ectly. Any suggestions would be much
appreciated.
Thanks,
Lizhi
On Wed, 3 Apr 2019 at 12:39, Greve, Douglas N.,Ph.D.
wrote:
> why not just map the fmri volume into the anatomical volume
> (mri_vol2vol)? Why go through the surface at all?
>
> On 4/3/19 12:34 PM, Zhi Li wrote:
> >
wandering if there is a way to sample/map the 2D
raw fmri time series to 3D volume?
On Wed, 3 Apr 2019 at 12:26, Zhi Li wrote:
> Sorry for my confusing explanation. I mean cortical grey matter. How could
> I map the left and right surface fmri data to volume? For example, how to
--o
> subcortgm.mgz, then mask the fmri time series (fmcpr.nii.gz) using
> mri_mask.
>
>
>
> On 4/3/19 10:23 AM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > I see and thank you very much. May I know If I could transform the
> >
y changing the subcortical mask in folder
'mri.2mm' to the whole brain mask, but I do not need the part of white
matter. See if it is applicable?
Thanks,
Lizhi
On Tue, 2 Apr 2019 at 17:32, Greve, Douglas N.,Ph.D.
wrote:
>
>
> On 4/2/19 4:23 PM, Zhi Li wrote:
> >
>
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Dear Freesurfer experts,
I would like to transform the task-based surface data to volume. May I know
if it is applicable? I tried "mri_surf2vol --o test.nii.gz --subject sub002
--so fs/sub002/surf/lh.white
fMRI/sub002/task/001/fmcpr.odd.sm5.fsaverage.l
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Hello Freesurfer experts,
I would like to extract time series of pre-processed data from each vortex
of ROIs in a annotation file, may I ask how could I achieve this? I tried
'mri_segstats' which only generated the mean time series of each ROI. I
also
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Hello Freesurfer experts,
May I know if it is possible to transform the FS-FAST pre-processed data
(left surface + right surface + subcortical region) to SPM-readable format?
How could I combine the three pre-processed data together and transform
them
N.,Ph.D.
wrote:
> Whitening is done by default (you can turn it off with -nowhiten to
> mkanalysis-sess). It uses an AR1 model.
>
> On 3/4/19 12:46 PM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Hello Freesurfer Experts,
> >
>
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Hello Freesurfer experts,
I would like to use mri_segstats with two different masks and thresholds,
such as:
mri_segstats --mask mask1 --maskthresh thresh1 --mask mask2 --maskthresh
thresh2
This command can run smoothly with our any error. However, I
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Hello Freesurfer Experts,
May I ask if there is a whitening/weighting matrix used to give weighted
least squares estimates (WLS) and whiten the data during the 1st-level
model estimation in FSFAST? If so, how could I get it?
Many thanks and kind regar
s.
> Eg, the name of the analysis (--analysis analysisname) is independent of
> the subject. Maybe you are confusing the analysisname and the paradigm?
>
>
> On 2/25/19 9:50 AM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Th
me across runs and
> subjects, the contents paradigm file can be different. That should be able
> to handle what you are doing
>
> On 2/22/19 3:42 PM, Zhi Li wrote:
>
> External Email - Use Caution
> Hello FreeSurfer experts,
>
> It seems that all the subjects
External Email - Use Caution
Hello FreeSurfer experts,
It seems that all the subjects adopt a single same paradigm file in FsFast,
am I correct? So how to handle it if each subject has different paradigm
files, e.g., different onset time and duration? I could do the first-level
an
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I see. Thank you very much.
Best wishes,
Lizhi
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27;lh.BA1_exvivo.thresh.label'.
Thanks and best wishes,
Lizhi
On Thu, 14 Feb 2019 at 13:43, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> did you try looking in the output to see if those files are actually there?
>
> On 2/13/19 1:11 PM, Zhi Li wrote:
> >
> &
External Email - Use Caution
Hello FreeSurfer experts,
I am trying recon-all in a SGE cluster. However, the size of of the results
was smaller than that executed in a local CentOs system. I did not found
error in the recon-all log file which ended with "recon-all -s sub001
finishe
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Thank you very much, Douglas. It works now. How could I know the ROI index
of each column in the .dat file? And if it is available to use pca during
extracting time series as fcseed-config?
Best,
Zhi
___
Fre
External Email - Use Caution
Thank you for your kind reply. Sorry for the confusing question. Now I have
an annotation file in fsaverage space. And I want to extracted mean time
series from each roi in this annotation file from preprocessed fMRI data,
e.g. fmc.odd.sm5.fsaverage.lh.
anatomical volume first:
mri_aparc2aseg --s fsaverage --annot test --o test.mgz
It seems I cannot do it to the left and right surface respectively, right?
How should use this .mgz file next? Any suggestions would be appreciated.
Best wishes,
Zhi Li
ation for you. If not, then you don't need a paradigm file
>
> On 11/07/2018 02:14 PM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Great! So I also need to subtract 8 seconds from the onset time of
> > each stimulus when I make the /para
deign?
On Wed, 7 Nov 2018 at 13:51, Greve, Douglas N.,Ph.D.
wrote:
> First run
> mri_convert --nskip 4
> fmcpr.up.sm5.fsaverage.lh.nii.gzfmcpr.up.sm5.fsaverage.lh.skip4.nii.gz
> then concat the skip files
>
>
> On 11/07/2018 01:42 PM, Zhi Li wrote:
> >
> >
gz
>
>
>
>
> On 11/07/2018 12:30 PM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Hi Dougles,
> >
> > Thank your for your reply. Now I am using FSFAST, but I didn't find
> > flags in prepro-sess which can be used
me a
example?
Thanks and best,
Zhi
On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D.
wrote:
> Are you using FSFAST? If you run the preprocessing (preproc-sess), then
> it will get you most of the way there.
>
> On 11/05/2018 10:16 AM, Zhi Li wrote:
> >
> >
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Hello FreeSurfer experts,
May I ask how can I modify the surface-based fMRI data, such as combing two
independent sessions into one or dividing one 4D into a series of 3D
surface-based fMRI files in which each one denotes a single volume/TR?
Thank you
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Hi FreeSurfer Experts,
Now I am trying FS-FAST in analyzing task-based fMRI data. We have two runs
for each participant. However, there were not enough events in some runs of
some participants. Hence we'd like to concatenate the preprocessed images
of
rs
> Bruce
>
> On Tue, 23 Oct 2018, Zhi Li wrote:
>
> >
> > External Email - Use Caution
> >
> > I see. Thank you very much. Another question is if I can use other
> template for parcellation when I
> > use recon-all?
> >
> > On
avg3-sess to use. Otherwise, it will
> try to look for things that have been preprocessed.
>
> On 10/23/18 12:17 PM, Zhi Li wrote:
>
> External Email - Use Caution
> Thank you. May I ask what do we use the flag -funcstem for? I found that
> there are similar flags in pr
mkanalysis-sess.
On Tue, 23 Oct 2018 at 11:09, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Yes. When you run mkanalysis-sess, you may still have to use the -funcstem
>
> On 10/23/18 10:06 AM, Zhi Li wrote:
>
> External Email - Use Caution
> I see. Can I
denoised data as f.nii.gz, then run
> preproc-sess it should do ok. It will do motion correction, but it should
> not really do any thing if MC is already done. Just make sure that the
> image has a proper baseline so that the registration will work.
>
> On 10/22/1
d proceed as norm.
>
> On 10/22/2018 04:08 PM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Hi FreeSurfer Experts,
> >
> > I am trying surface-based analysis of task-fMRI with FS-FAST. However,
> > I would like to apply ICA-based de
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Hi FreeSurfer Experts,
I am trying surface-based analysis of task-fMRI with FS-FAST. However, I
would like to apply ICA-based denoising and wavelet-despiking which can be
not done with the 'preproc-sess'. I wonder if I can do the preprocessing
with oth
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