Try adding --invertmtx to the mri_label2vol command
On 11/28/2019 4:35 AM, Zoro wrote:
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Thanks for your reply and sorry to bother you again. The problem is that the
volume converted from label which drew by freeview does not match T1.
Happy Thanksgiving day!
It sounds like it would be a one-group, two-variable situation, like this
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V
Is that not correct?
On 11/28/2019 5:24 AM, Ferraro, Pilar wrote:
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Hi,
I apologize if I did not explain my issue properly.
I'm inter
In the bold directory, it looks like you have one run directory called "1".
Change this to "001"
On 11/29/2019 1:48 AM, Renew Andrade wrote:
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Dear FreeSurfer experts:
I have some issues with "preproc-sess" because I cannot seem to get the setup
of the direct
On 11/29/2019 4:27 AM, 于倩倩 wrote:
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Hello,
I have some questions about the command of mri_vol2surf and mri_surf2surf
1. For fMRI data, I find previous paper reported that they used standard SPM8
preprocessing routines, no normalize to standard MNI152 templa
Try using mri_vol2surf to sample your fMRI onto the surface, then load it as a
surface overlay in freeview
On 11/29/2019 3:35 AM, 朱青 wrote:
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Dear madam or sir,
I'm a student in China who use the Freesurfer to analyse my fMRI data and
overlay some results
That will use the pre-computed ("cached") CSD files distributed with
FreeSurfer. This used 10,000 iterations.
On 12/1/2019 11:34 PM, Ting Li wrote:
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Dear Freesurfer Expert:
I have used the simulation code as show below:
mri_glmfit-sim \
--glmdir lh.gende
Can you send the log file for each of the gtmseg runs?
On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
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Thank you! I have a gca for subcortical and two gcs (lh/rh) for cortical
structures.
I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_lab
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Dear Dr. Douglas,
Thank you so much for your quick response! You saved my half life.
From the introduction of clusterwise correction for multiple comparisons, I
have a few questions.
1, What is the null hypothesis here ?
2, What is a z map? Do you me
On 12/2/2019 11:58 AM, Ting Li wrote:
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Dear Dr. Douglas,
Thank you so much for your quick response! You saved my half life.
From the introduction of clusterwise correction for multiple comparisons, I
have a few questions.
1, What is the null hypothesis he
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In this example tried it with only the subcortical segmentations from my
atlas. Please find the logfile attached. It gives me back: "tissue type is
not set" but I set it to 2 in the LUT.txt
In principle look the following commands right to you?
xcereb
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Dear Dr. Douglas,
Thank you so much for your detailed response.
The simulation here is to get the probability of a maximum cluster that
size or larger in the cached CSD files. It checks the probability of the
cluster size but have nothing to do with
Correct. This is no different than, eg, a t-test. Look in the back of a stats
book from the 1950s and you will find a table of t-ratios and corresponding
p-values. Obviously, they did not have access to any of the data being analyzed
today:), but the tables are still valid.
On 12/2/2019 2:03 P
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Hi,
I have a statistical question about how to approach reporting results from
FreeSurfer analyses containing three groups. I ran a group effect (F-test)
and then post-hoc tests looking at pair-wise comparisons between the three
groups. My question is
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Dear Dr. Douglas,
Thank you so much for your explanation. You really helped me a lot!
Best regards,
Ting
On Mon, Dec 2, 2019 at 1:59 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Correct. This is no different than, eg, a t-test. Look
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Hello Experts,
I ran the PETsurfer pipeline using AV45 pet and performed pvc using pons as
reference point. When i looked at the gtm.stats.dat file for one of my
subjects, the SUVr for right and left nucleus-accumbens areas were in the
negative (left =
It may or may not be something that needs to be fixed. The PVC is just a linear
model where the regression coefficients are the uptake in each ROI. As with any
model, it adjusts the regression coefs to minimize the error in the fit. If
some end up being less than zero when you really expect all
I don't think there is a standard way to do this. A vertex-wise analysis is not
the same thing as a averaging over a group of vertices. I guess you could
constrain your post-hoc analysis to be within the main effect cluster; that
would be most consistent. But I don't think you'd have any problem
On 12/2/2019 7:12 PM, Joëlle Ismay Rosanne Van Der Molen wrote:
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Dear Freesurfer experts,
After running the -qcache option to extract thickness data for every subject, I
tried pulling all the data together in order to get a matrix of subjects x
vertices c
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