Hi list, this error occurs during selxavg3-sess in FS-FAST fcMRI
meanval --i stem2fname stem Looks for stem.fmt where fmt is mgh mgz nii nii.gz
bhdr img w, then returns stem.fmt. See also stem2fmt, fname2stem The file needs
to exist on disk. --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.da
There is usually three different approaches to analyze longitudinal data
(and yours is longitudinal as you have 2 time points and are interested
in change).
- linear mixed effects models (matlab), recommended
- 2 stage approach (long_mris_slopes), old approach, and superseded by
LME. Can be s
Hi Matthieu,
one option is to replace time with score in the model. That should be
straight forward.
The other option is to include score as a time-varying covariate. If
your score is not varying much across time and you are more interested
if the average score (or baseline score) affects at
Dear FSers
I extracted left thalamus as ROI volume from aseg.mgz by this command:
mri_binarize --i control001/mri/aseg.mgz --match 10 --o
control001/roi/l_thal.nii
I overlaid l_thal.nii to control001.nii in MRIcro software in a Macbook and
it looks well.
However, when I overlai
Hi gAbE
you could try using mris_fill, or even mris_compute_volume_fractions
cheers
Bruce
On Mon,
15 May 2017, Gamaliz wrote:
My idea is to convert the registered white surface into a volume, so it can
be shown in a volume viewer (not a surface viewer). I need to display a DTI
image and m
thanks Doug! I will give this a shot!
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Mon, May 15, 2017 at 9:56 PM, Douglas Greve
wrote:
> you can do something like
>
> a = MRIread('map1.mgz');
>
> b = MRIread('map2.mgz');
>
> c = MRIread('map3.m
Dear Freesurfer experts,
I would like to obtain perirhinal cortex volumes from structural images that
have undergone recon-all.
I see that the label subfolder contains left and right perirhinal cortex labels
but the stats file does not. So a first step seems to be "converting" the label
to a
If you run it with --help, it will print out examples. Did you try that?
On 5/16/17 9:26 AM, Bruce Fischl wrote:
Hi gAbE
you could try using mris_fill, or even mris_compute_volume_fractions
cheers
Bruce
On Mon, 15 May 2017, Gamaliz wrote:
My idea is to convert the registered white surface
On 5/15/17 10:34 PM, Kevin Aquino wrote:
Hi all,
First of all, Freesurfer V6 is working like a dream, my 0.7 mm
segmentations are running really well and in comparisons to
hi-resrecon in 5.3 and early beta, I'm having to do fewer manual
corrections!
Now for my questions,
1. I'm running
you can't really do permutation at the first level because the temporal
autocorrelation and non-orthogonal design matrix violate the permutation
assumptions.
On 5/15/17 11:23 PM, Kevin Aquino wrote:
Actually,
would would be preferable would be running a permutations test
something that you
not sure what is going on. Is the script stem2fname in your path? If so,
run selxavg3-sess with -debug as the first option and send the terminal
output
On 5/16/17 3:08 AM, std...@virgilio.it wrote:
Hi list,
this error occurs during selxavg3-sess in FS-FAST fcMRI
meanval --i stem2fname stem L
no idea. you'll proably have to contact the MRIcro group
On 5/16/17 8:28 AM, Cong wrote:
Dear FSers
I extracted left thalamus as ROI volume from aseg.mgz by this command:
/ mri_binarize --i control001/mri/aseg.mgz --match 10 --o
control001/roi/l_thal.nii/
I overlaid l_thal.nii to contro
The 2nd is the correct matrix
On 5/15/17 12:36 PM, Sahil Bajaj wrote:
Hi everyone,
From FreeSurfer manual and discussion forum, I found that volume and
LGI can be correlated using mri_glmfit command with -pvr flag.
For that, my fsgd file has age, gender as covariates and the file is
as fo
You can do FDR or you can co cluster correction, but you can't do both.
It looks like that paper only did FDR. If you want to do FDR, you can
use mri_fdr. Run with --help for more info
On 5/15/17 12:33 PM, Martin Juneja wrote:
Thanks Dr. Greve.
Regarding 2nd question, I am not sure how autho
We do not report those regions because the volume-based approach
(counting up voxels labeled 2 and 41) is less accurate than the
surface-based approach (this is the CorticalWhiteMatterVol).
On 5/15/17 1:10 PM, Gamaliz wrote:
Regions 2 and 41 are labeled as
Left-Cerebral-White-Matter
Right-Cer
On 5/11/17 3:25 PM, John Anderson wrote:
Hi Doug,
Why Qdec offer "volume, area, thickness ,...etc " in the drop down
menu "measures"?
In this menu there are many measures and I understand that I can run
surface based analysis depending on the choice of this drop down menu.
Is this Correct?
selxavg3-sess -s subj067_GROUP -a fc.lamgseed.surf.lh -debugset echo = 1
;breakswbreaksw
endendwhile ( $#argv != 0 )while ( 0 != 0 )goto parse_args_return ;goto
parse_args_return
foreach grp ( $grpdefs )foreach grp ( )
goto check_params ;goto check_params
if ( $#SessList == 0 ) thenif ( 1 == 0 )
Bruce,
I tried mris_fill, but it gives me a filled white matter volume (I already
have that in the mri directory. I need the contour only.
Douglas, Looking into the --help gave me a few ideas. I think the help page
(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol ) should include
this infor
Bruce,
I tried mris_fill, but it gives me a filled white matter volume (I already
have that in the mri directory. I need the contour only.
Douglas, Looking into the --help gave me a few ideas. I think the help page
(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol ) should include
this infor
Does this file exist ?
/Applications/freesurfer/subjects/fMRI/subj067_GROUP/001/masks/brain.e3.nii.gz
You can try deleting the
/Applications/freesurfer/subjects/fMRI/subj067_GROUP/001/masks folder
and re-running.
On 5/16/17 11:53 AM, std...@virgilio.it wrote:
selxavg3-sess -s subj067_GROUP
Try visualizing it in freeview instead of fslview.
On 5/16/17 12:11 PM, Gamaliz wrote:
Bruce,
I tried mris_fill, but it gives me a filled white matter volume (I
already have that in the mri directory. I need the contour only.
Douglas, Looking into the --help gave me a few ideas. I think the
Yes, the file exists.Additionally, please take in account that I have run other
FC analysis on this subj using other seed as ROI.
Messaggio originale
Da: "Douglas Greve"
Data: 16-mag-2017 18.21
A:
Ogg: Re: [Freesurfer] R: Re: selxavg3-sess error
Does this file exis
Dear Doug
I think my problem may caused by that extracted ROI have different
coordination to original
T1 image, although they match well in freeview. For example, one voxel is
[148,144,131] in
extracted left thalamus but [71,130,89] in original T1.nii and T1.mgz. So how
to extract a ROI havi
Hi Douglas,
I am using the cortical surface for MEG time series reconstruction. I need
to know which vertices belong to a specific area, i.e. vertices that
belong to the PCC, AG... I got the surfaces from the HCP which has 4.002
vertices in each subject, then I decimated with mris_decimate 0.25,
just erode it once using mri_morphology, then subtract it from the
un-eroded volume
On Tue, 16 May 2017, Gamaliz wrote:
Bruce,
I tried mris_fill, but it gives me a filled white matter volume (I already
have that in the mri directory. I need the contour only.
Douglas, Looking into the --help
Rerunning it is ok
Messaggio originale
Da: "Douglas Greve"
Data: 16-mag-2017 18.21
A:
Ogg: Re: [Freesurfer] R: Re: selxavg3-sess error
Does this file exist ?
/Applications/freesurfer/subjects/fMRI/subj067_GROUP/001/masks/brain.e3.nii.gz
You can try delet
Hello Freesurfer Developers,
I want to perform texture analysis on the CA1 subfield of the hippocampus.
Thus, I am using the recon-all command to generate the subfields. However, I
want to perform texture analysis on the CA1 subfield only and I need to extract
it from the original T1 image... H
The thalamic seeds from 8001-8014 are available in FS 6.0 and, specifically for
FS-FAST for functional connectivity.Thanks.Regards,Stefano___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesur
Please I wonder whether the thalamic seeds from 8001-8014 are available in FS
6.0 and, specifically for FS-FAST for functional
connectivity?Thanks.Regards,Stefano
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard
Please I wonder whether the thalamic seeds from 8001-8014 are available in FS
6.0 and, specifically for FS-FAST for functional
connectivity?Thanks.Regards,Stefano
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard
Try something like
mris_apply_reg --src overlay4k.mgh --trg overlay1k.mgh --streg surf4k surf1k
On 5/16/17 12:41 PM, Dorothy Sincasto wrote:
Hi Douglas,
I am using the cortical surface for MEG time series reconstruction. I
need to know which vertices belong to a specific area, i.e. vertices
No, not yet
On 5/16/17 1:10 PM, std...@virgilio.it wrote:
Please I wonder whether the thalamic seeds from 8001-8014 are
available in FS 6.0 and, specifically for FS-FAST for functional
connectivity?
Thanks.
Regards,
Stefano
__
try this https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 5/16/17 12:34 PM, Cong wrote:
> Dear Doug
> I think my problem may caused by that extracted ROI have different
> coordination to original
> T1 image, although they match well in freeview. For example, one voxel is
>
Hi Martin,
Thank you for this detailed answer.
Are replacing time by score or include score as time-varying covariate
leading to the same result because of looking at the same effect ?
My willing would be to find patterns of atrophy rate/progression correlated
with cognitive score. In context of
Dear Freesurfer experts,
I also have this problem and can't seem to find the script. Would it be
possible to get access to it?
Thank you in advance,
Mikael Novén
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.e
Hi Douglas,
Thanks, that worked. However, for future reference, if it's necessary to
keep the original values then put --no-rev
Thanks
Dorothy
On Tue, May 16, 2017 at 10:31 AM, Douglas Greve
wrote:
> Try something like
>
> mris_apply_reg --src overlay4k.mgh --trg overlay1k.mgh --streg surf4k
Hello Freesurfer Developers,
I want to perform texture analysis on the CA1 subfield of the hippocampus.
Thus, I am using the recon-all command to generate the subfields. However, I
want to perform texture analysis on the CA1 subfield only and I need to extract
it from the original T1 image... H
not sure what you're talking about
On 5/16/17 2:55 PM, Mikael Novén wrote:
Dear Freesurfer experts,
I also have this problem and can’t seem to find the script. Would it
be possible to get access to it?
Thank you in advance,
Mikael Novén
___
Fre
Hi Freesurfer list,
I have a statistical map (.nii format) produced from analysis performed in
BrainVoyager that I'd like to register with the anatomical model produced with
Freesurfer's recon-all, this is on a single-subject basis from the same raw
data. I have several questions with respect t
Hi Stephanos,
The easiest way is to extract label 206 (CA1) from
[lr]h.hippoSfLabels-T1.v10.FSvoxelSpace.mgz using mri_extract.label, and then
apply the resulting mask on the original (orig.mgz) or normalized (norm.mgz)
volumes.
From the subject’s mri directory:
mri_extract_label lh.hippoSfLa
Hello Douglas,
Sorry for the delay. I converted this file from a .csv format in order to
keep the column format ideal. Although QDEC is correctly reading the number
of factors, it is only reading three subjects which is incorrect. I have
attached the document to this email for clarification.
Ben
that file has a bunch of carriage returns instead of new lines (obscure
unix vs windows problems). Did you convert the csv under windows?
On 5/16/17 3:53 PM, Benjamin Ubani wrote:
Hello Douglas,
Sorry for the delay. I converted this file from a .csv format in order
to keep the column format
Yes, I used Windows to convert initially then also tried it over Libre
Office.
Ben
On Tue, May 16, 2017 at 3:09 PM, Douglas Greve
wrote:
> that file has a bunch of carriage returns instead of new lines (obscure
> unix vs windows problems). Did you convert the csv under windows?
>
> On 5/16/17 3
Hi
I run the commands listed below and I was wondering if there is a way to get
the average pc1 for each group. I get an average for the entire sample. What
should I use instead of --osgm?
long_stats_slopes --qdec ./qdec/long.qdec.table.dat --stats aseg.stats --meas
volume --sd $SUBJECTS_DIR
Hi Doug,
Thanks for that! with regards to your last point
Unfortunately, it does not help much. Much was made of the bug that Eklund,
et al, found in the alphasim program (the AFNI mc simulator), but even
after fixing it, the volume-based analyses still had very high false
positive rates. This is
Dear Expert,
I have come across that I have freesurfer support cuda version 5, but I
have already installed latest version.
Can I use latest version for freeesurfer or should I install version 5?
Since I am not expert in this field I need guidance to remove latest
version of cuda and installing an
46 matches
Mail list logo
