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:
>
> External Email - Use Caution
>
> How can I discard the first 4 time points of each run during
> concatenating
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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 in combing or dividing fMRI data. Using
the following code I could get three files for each run (left cortical
surface, right
If you just want to concatenate you can use something like
mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz
002/fmcpr.up.sm5.fsaverage.lh.nii.gz
003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o
all.fmcpr.up.sm5.fsaverage.lh.nii.gz
On 11/07/2018 12:30 PM, Zhi Li wrote:
>
> External Email -
are you trying to use FSFAST to do the entire fmri anlaysis? If so, then
follow the tutorial as it will handle the skipped TRs and the
concatenation 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
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I see. Thank you very much.
On Wed, 7 Nov 2018 at 15:18, Greve, Douglas N.,Ph.D.
wrote:
> are you trying to use FSFAST to do the entire fmri anlaysis? If so, then
> follow the tutorial as it will handle the skipped TRs and the
> concatenation for
It is probably trying to use a default bval and bvec file, but it can't
find it. If you have your bvals and bvects, try passing them explicitly
to dt_recon
On 11/07/2018 11:56 AM, Anwar Shatil wrote:
>
> External Email - Use Caution
>
> Hello Doug:
>
>
> My dti_recon is getting stuck at
Can you send the terminal output that includes the error?
On 11/06/2018 06:36 PM, James Michael Roe wrote:
> External Email - Use Caution
>
> Hi Bruce
>
> I realise that my last message made it sound as though the problem was fixed.
> However, I was only confirming that the files load
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Great! So I also need to subtract 8 seconds from the onset time of each
stimulus when I make the *paradigm file*, right? If the duration of
stimulus is smaller than 1 second, such as 0.05 second, do I need to change
its duration to 0 in a event-related
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How can I discard the first 4 time points of each run during concatenating
several runs? I know I can skip the first 4 time points with the flag *-nskip
4* in configuring a analysis, but this condition can be only applicable
when each run is modelled
Sounds like you need an F-test, eg, create a contrast like
1 1 -1 -1 0 0 0 0 0 0 0 0
1 1 0 0 -1 -1 0 0 0 0 0 0
This tests the null hypothesis that p1==p2==control
On 11/07/2018 10:11 AM, 13181786167 wrote:
>
> External Email - Use Caution
>
> Thanks for your reply. Using the first
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Hello Freesurfer expert, I am brand new to Freesurfer, my apology for the
basic question, I kept trying to figure out my mistake in installation for
last week and could not find a solution to it.
Here is my output, my problem with subject_DIR keeps
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Hello Freesurfer Developers,
I was going to reconstruct MPRAGE images from GE 3T machine.
First I used this command:
*dcmunpack -src . -scanonly scan.log*
It made just *scan.log* file for me. Then I used this command:
*unpacksdcmdir -src / -targ
You have to specify an output directory with -targ and the runs you want
to unpack with -run. See the help (ie, run dcmunpack with -help)
On 11/07/2018 05:38 PM, Maryam Tayebi wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer Developers,
> I was going to reconstruct MPRAGE
On 11/03/2018 02:20 AM, Vikas Bandalli wrote:
>
> External Email - Use Caution
>
> Dear freesurfer team.
>
> I am running an analysis betweene two groups Normal and Patients.
> Here is an example of my particular design
> diagnosis :- Normal vs Bipolar
> Co-variate :- Age
> Nuisance
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Hello Freesurfer devs,
Is there available any Desikian-Killiany and Destrieux atlas template or
image downloadable with all brain labels of the atlas? I would to use this
image to show my results in a lab meeting? I would need somethig similar
that
Hi Miguel
I think we distribute parcellations of the fsaverage subject (and of bert
and ernie), so if you have any of those you can use them to show the
atlas labels. The atlases themselves are more complicated and store other
information that isn't easily visualizable
cheers
Bruce
On Wed,
I'm not sure what you mean. The atlas is distributed with FS.
On 11/07/2018 05:09 PM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
>
>
> Hello Freesurfer devs,
>
>
> Is there available any Desikian-Killiany and Destrieux atlas template
> or image downloadable with
External Email - Use Caution
Hello Freesurfer devs,
Is possible segment the brain ventricles using Freesurfer in terms of mm3
or ml? I would be interested in study the ventricular enlargement. Is
possible with Freesurfer or other toolbox.
Any help would be appreciated. Thanks
Hi Miguel,
yes, we report ventricular volume in mm^3 in the stats files.
cheers
Bruce
On Thu, 8 Nov
2018, Miguel Ángel Rivas Fernández wrote:
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Hello Freesurfer devs,
Is possible segment the brain ventricles using Freesurfer in terms of mm3 or
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Hello Zainab,
The first 2 commands you list are,
export FREESURFER_HOME=/usr/local/freesurfersource
$FREESURFER_HOME/SetUpFreeSurfer.sh
and the output from the source command shows you what has been setup in
your environment...
FREESURFER_HOME
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Hi Freesurfer experts,
The cerebellar 7 and 17 networks parcellation cannot be downloaded.
The link to cerebellar parcellation in SUIT is out of date too.
so, if you can kindly share the cerebellar 17-network parcellation and
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I tried this way, but I got lots of errors, as the attached file. What is
the problem? Is there anything wrong with my data? Because I am using the
online databases which I think it might be back to 2009 ish.
Thanks
On Thu, 8 Nov 2018 at 11:55,
You can use the per-voxel regressor (--pvr) option to mri_glmfit. Search
through the mail archives for how to use it
On 10/23/2018 06:34 AM, Damien MARIE wrote:
>
> External Email - Use Caution
>
> Hi Matt,
>
> Many thanks for your prompt reply, you are right.
>
> Any tips on how I could
When you ran mkanalysis-sess, did you specify two event types? You only
have one non-null event in your paradigm file.
On 10/28/2018 08:57 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> Thanks! Now it's loading correctly my event file.
> However, when I run
Hello Freesurfer Experts,
I am wondering whether it is possible to apply the same manual edits (removing
GM/WM or adding CPs) to multiple scans. I have a dataset with ~100 scans per
subject acquired in quick succession and, interestingly, Freesurfer appears to
have the same issue in almost
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Thanks for your time and the clarification.
Tim
--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
On 10/24/2018 09:45 PM, srishti goel wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am trying to perform a paired analysis for a data set that has
> subjects' who belong to either group1 or group2 and have data at time
> point1 (tp1) and time point2 (tp2). I am following all
On 10/25/2018 11:31 AM, ts...@rcmd.org wrote:
> External Email - Use Caution
>
> Dear Douglas,
>
> thanks for your answer.
>
> Did you by any chance mean mris_preproc instead of preproc-sess? The latter
> seems to have no --meas flag according to the help (and a quick grep through
>
Hi Ryan
it would be pretty trivial to do in matlab, so probably that is best,
although I don't understand what multi-frame volume you are using
cheers
Bruce
On Wed,
7 Nov 2018, Nillo, Ryan Michael R wrote:
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Hi FreeSurfer users,
I want to
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:
>
> External Email - Use Caution
>
> Hello FreeSurfer experts,
>
> May I ask how can I modify the surface-based fMRI data, such as
>
On 10/26/2018 10:53 AM, Zhi Li wrote:
>
> External Email - Use Caution
>
> 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
If you are using output froom mri_segstats, then you need to use
asegstats2table, not aparcstats2table. It can be confusing ...
On 11/01/2018 05:06 PM, Figueiro Longo, Maria Gabriela wrote:
>
> Hi,
>
>
> I extracted some volumes using mri_annotation2lable --> mri_aparc2aseg
> --> mri_segstats .
Use the first one. Not sure what you mean by your multiple comparisons
question
On 11/01/2018 11:20 PM, 郑凤莲 wrote:
>
> External Email - Use Caution
>
> Hi experts,
>
> I am using FS 6.0 for analyzing the cortical thickness difference
> between 3 groups: patient1, patient2 and control.
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Hello Doug:
My dti_recon is getting stuck at the "Fitting Tensor" stage. I was wondering if
there is any solution to the problem "MatrixReadTxT: could not scan value
[1][1]". My log file is attached here and the problem can be found right at the
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