What do you mean by one analysis? I don't think it would make sense to average
the images together. If you mean that different subjects have different scans,
then it is not ideal, but you could include scan as part of your statistical
design. Just make sure that different populations are balance
It is not set up to use the subfields. In principle it could be, but I don't
think it would be very accurate because the subfields are so small.
On 11/17/2020 4:27 AM, 蒋袁芳 wrote:
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Hello Freesurfer,
We know that the freesurfer7 has given a new module to separa
Have you checked that the output of each of the stages is correct? Eg, does
mydata_T1.nii.mgz overlay with MNI152 and with ROI_MNI? At the end of
fslregister, there will be a tkregister command to visualize the regsitration.
Do those look ok?
On 11/17/2020 4:48 AM, Alina Rojas wrote:
E
Use mris_fwhm. Run with --help to get info. Make sure to use the --smooth-only
option
On 11/17/2020 5:31 AM, Enrico Collantoni wrote:
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Dear Freesurfer experts,
I computed the gray to white matter signal intensity ratio using the pctsurfcon
command and extrac
We don't have a GUI, if that is what you mean. The default now is to use the
command line stream where you create your own FSGD file and contrast matricies,
then run mri_glmfit and mri_glmfit-sim
On 11/17/2020 10:44 AM, Pagliaccio, David (NYSPI) wrote:
___
You mean that you are getting a different result between the voxel wise
analysis and the ROI-wise analysis? And you created the ROI from the region
that is significant in the voxel-wise analysis? If so, then I think something
is wrong
On 11/17/2020 8:08 PM, 李梦君 wrote:
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I don't understand why WM was cropped out. What command were you trying
to use?
On 11/18/2020 2:39 AM, RENXI LI wrote:
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>
> Hi Freesurfer experts:
>
> I am trying to extract the mean-time series from the functional image using
> mri_segstats. However, the c
tkmeditfv mni152 nu.mgz -surfs -seg aal.nii
On 11/18/2020 6:28 AM, Alberto Del Cerro Leon wrote:
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How can I load the AAL onto the mni152 subject with the surface?
El lun., 16 nov. 2020 a las 17:10, Douglas N. Greve
(mailto:dgr...@mgh.harvard.edu>>) escribió:
Can you send the full terminal output?
On 11/18/2020 6:41 AM, Alberto Del Cerro Leon wrote:
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I tried to run mri_vol2surf with the following command: mri_vol2surf --src
/home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI --projfrac 0.5 --hemi
lh --out /ho
We use partial volume correct. Maybe that is the problem. What version
of FS are you using?
On 11/18/2020 10:37 AM, Vicente Ferrer wrote:
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>
> Hello Freesurfer,
>
> Once I had run reconall, I tried to calculating left hemisphere total grey
> matter volume a
We certainly cannot guarantee that tkmedit will work as that is a pretty old
program. Try using tkmeditfv in a newer version of FS. It will be ok as long as
the analysis (eg, recon-all, preproc-sess, etc) was done in 5.1
On 11/18/2020 12:00 PM, Tracy Riggins wrote:
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Make sure that --meas volume was passed to mris_preproc was passed (this is
the usual way you would do this) in which case it makes a jacobian correction.
The only other thing to do would be to correct for intra-cranial volume. If you
have 7.X, you can just add --etiv to mris_preproc
On 11/18/
It is mris_smooth. Look in the recon-all.log or recon-all.cmd for the exact
command
On 11/13/2020 10:15 AM, Nasr, Shahin,Ph.D. wrote:
Good morning Doug,
I can load ?h.white and rh.smoothwm but not lh.smoothwm to freeview. I
can even load lh.smoothwm.nofix. So apparently, that is the corrup
Sorry, we don't have any tools to convert from PET formats. Not sure where to
go for that ...
On 11/19/2020 8:27 AM, Marina Fernández wrote:
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Dear experts!
I am using PetSurfer and I have a PET dataset that is in ecat format (.v). I
would like to convert th
Can you upgrade to 6 or higher?
On 11/13/2020 1:32 PM, Wei Shao wrote:
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Hi Douglas
I think it's 5.0.11
[weishao@gra-login2 ~]$ module load nixpkgs/16.09 freesurfer/7.1.0
To initialize FreeSurfer,
do (sh, ash, ksh, and bash)
source $EBROOTFREES
Are you talking about outliers across subject? Or across region? I would just
take the FS-supplied value instead of averaging the regions.
On 11/19/2020 2:14 AM, Stephanie K wrote:
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Hi Bruce,
Thanks for the prompt reply. It is my understanding that l_thickne
Yes, that is correct
On 11/19/2020 11:43 AM, Batool Rizvi wrote:
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Hi Dr. Greve,
Sorry to bring this back up, but I didn't fully understand how to calculate the
variance in order to get the confidence intervals for each covariate, so I
wanted to double check
By "volume" do you mean a surface-based, vertex-wise measure of volume or do
you mean volume of an ROI?
On 11/19/2020 11:46 AM, Mora, Jocelyn S. wrote:
Hi Sara,
You may want to use asegstats2table. Follow these links to learn more about
mris_preproc, mri_glmfit, and asegstats2table:
http://sur
If you want the parahippo label on the surface, then convert the lh.aparc.annot
to labels with mri_annotation2label. Run with --help to get examples
On 11/19/2020 11:57 AM, Catherine Tallman wrote:
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Hello,
After running mri_vol2label I created a custom label
I think it will be threads.
On 11/19/2020 10:21 PM, d m wrote:
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Thanks.
Just to confirm, the openmp reflects threads and not cores? In other words, on
we have a 4 core machine with hyperthreading, so with 4 cores we have 8 threads
available.
In that scenar
It is probably easier to just run recon-all on the mni152, then use
mri_segcentroids on aparc.a2009s to extract the centroids
On 11/20/2020 2:50 AM, Hengameh Marzbani wrote:
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Hello Freesurfer developers,
For the purpose of reporting ROIs in my article, I
This might be a bug with the --bg option when 1 is specified. Try it without
--bg or try it with 2 or more threads
On 11/20/2020 10:20 AM, Basavaraju, Rakshathi wrote:
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One way you can do it is to specify all the GM ROIs with --rescale Id1 Id2 ...
Otherwise, you can run fscalc, eg,
fscalc mgx.ctxgm.nii.gz div `cat global.gm.dat ` -mul 100 -o
mgx.ctxgm.rescaled.nii.gz
On 11/20/2020 11:44 AM, Boris Rauchmann wrote:
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Dear al
If you want a cluster table, then you will have to run mri_surfcluster on the
output of the conjunction. Run it with --help and write back if you need more
info
On 11/21/2020 10:03 AM, Paula Maldonado wrote:
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Dear Douglas,
Could you please tell me where can
I think that would be ok, but I would run this instead
mri_surf2surf --hemi lh --srcsubject 1001 --srcsurfval thickness --src_type
curv --cortex --trgsubject fsaverage5 --trgsurfval ./mgh/1001_lh_fs5_thick.mgh
--trg_type mgh –fwhm-trg 10
On 11/23/2020 4:11 PM, Daniel Leopold wrote:
It is, but it can be either easy or hard. The easy way is to draw it on
gtmseg.mgz and add an entry into gtmseg.ctab. Probably, you should copy the
gtmseg.{mgz,ctab} to a new file and edit that. Otherwise, you can edit, eg,
apas+head.mgz, and pass that to gtmseg with the --head option. At some p
For starters, you need to have four classes, HC-Male, HC-Female, CMT-Male,
CMT-Female and not use gender as a variable. Try that. I would also normalize
the age and thickness
On 11/24/2020 12:04 PM, Ambulatorio SNA FEDERICO II wrote:
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Dear Freesurfer team,
Try mris_divide_parcellation
Run with --help to get docs
On 11/25/2020 1:57 AM, Hyon, Justin J. wrote:
> External Email - Use Caution
>
> Hello,
> I am wondering whether there is a way to split a labeled region in a volume
> into 2 labels, perhaps by using the Freeview gui? I just need t
Traditionally, MG analysis is only run on GM. In principle, it is possible to
run it on WM, but we don't offer that as an option.
On 11/25/2020 8:16 AM, Boris Rauchmann wrote:
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Dear all,
How can I run a voxelwise statistic using grey and white matter uptake?
No, probably just an oversight
On 11/25/2020 10:06 AM, Josue Luiz Dalboni Da Rocha wrote:
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No, you'll have to add it as a covariate. Or you can add --etiv when you run
mris_preproc and it will divide the maps by the eTIV
On 11/25/2020 3:23 PM, Sara Lyn wrote:
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Hi Freesurfer experts,
I'm doing a surface based volume analysis and wanted to know if t
Not in FS. Try using dcm2niix
On 11/26/2020 5:07 AM, John Papatriantafyllou wrote:
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Hi freesurfer exps,
last year a recieve dicom 3d as one file (300 dicoms one file)
Is there any program to unpack them or any other way to recon all
John
___
Use mri_label2vol to map the segmentation into the fMRI space, then use
mri_segstats using the --avgwf option to get time courses. Run it with --help
to get examples
On 11/26/2020 9:16 AM, Francesca Strappini wrote:
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Dear FreeSurfer experts,
I'm trying to u
what is your command line?
On 11/29/2020 2:55 PM, RENXI LI wrote:
> External Email - Use Caution
>
> The WM was cropped out by applying a grey-matter mask in SPM, and I am trying
> to extract non-zero voxels with mri_segstats.
>
> Best,
> Renxi
>
>> On Nov 29, 2020, at 11:23 AM, Greve, D
I don't know. I've never seen this type of analysis. I think with and without
would be valid analyses, but they would be answering different questions, so,
as the scientist doing the study, it is more up to you.
On 11/27/2020 8:56 AM, Letitia Schneider wrote:
___
We don't have a centrum semiovale label in FS. You could try using the
(Left,Right)-UnsegmentedWhiteMatter in the wmparc.mgz
On 11/27/2020 9:28 AM, miracle ozzoude wrote:
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Hello Experts,
I did like to create a mask for basal ganglia, deep grey matter, and ce
External Email - Use Caution
The WM was cropped out by applying a grey-matter mask in SPM, and I am trying
to extract non-zero voxels with mri_segstats.
Best,
Renxi
> On Nov 29, 2020, at 11:23 AM, Greve, Douglas N.,Ph.D.
> wrote:
>
> I don't understand why WM was cropped out.
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Hello, what command can map VTK file to fsaverage5 space? I want its vertex
number to be 10242. If you know, please give me an example.
Looking forward to your reply___
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