Thank you doug. Is there a command for normalising in fsgd file. I know
DeMeaning is DeMeanFlag 1.
Best,
Paul
Sent from my BlackBerry 10 smartphone.
Original Message
From: Douglas N Greve
Sent: Friday, July 22, 2016 6:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Reply To: Freesurfer support lis
Try demeaning and normalizing your continuous covariates in the FSGD file.
On 07/22/2016 06:17 PM, miracle ozzoude wrote:
>
> Hello doug,
>
> while running the mir_glmfit problem, i encountered this problem “
>
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>
> Continuous Variab
Hello doug,
while running the mir_glmfit problem, i encountered this problem “
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 39.9375 17.3312
1 Education 15.5625 1.99902
2 Firstscore 1.03375 0.341785
3 Secondscore 1.03906 0.3706
That version may have had a bug. Try this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit
btw, you should not be using the dev version of recon-all
On 07/22/2016 02:01 PM, Nicola Toschi wrote:
> Hi,
>
> it's a dev version downloaded on Jan 17th 2016.
>
> As mentioned
I did that. The command I use is:
mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C
group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir
lh.group_diff_g2v0.glmdir
On Fri, Jul 22, 2016 at 2:09 PM, Douglas N Greve
wrote:
> then you need to add --surface fsaverage lh
then you need to add --surface fsaverage lh to the mri_glmfit command
line, otherwise it thinks it is a volume-based analysis
On 07/22/2016 01:58 PM, Mihaela Stefan wrote:
> It's surface-based analysis.
>
> On Fri, Jul 22, 2016 at 1:43 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wr
Hi,
it's a dev version downloaded on Jan 17th 2016.
As mentioned in my other mail, I have uploaded a full glmdir at
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=akbem4mthlv
thanks for your time,
Nicola
On 7/22/2016 6:35 PM, Douglas N Greve wrote:
> what version does it fail on? If a dev versi
It's surface-based analysis.
On Fri, Jul 22, 2016 at 1:43 PM, Douglas N Greve
wrote:
> Are you doing volume or surface-based analysis? If volume, then you'll
> need a volume mask and the --label is not appropriate.
>
> On 07/22/2016 01:36 PM, Mihaela Stefan wrote:
> > I tried that, too and it se
Hi,
I am trying to import and recon-all -i my subject files and am getting
these strange errors that I have never encountered before.
Iteration 1 Tue Jul 19 19:21:54 EDT 2016
nu_correct -clobber ./tmp.mri_nu_correct.mni.83022/nu0.mnc
./tmp.mri_nu_correct.mni.83022/nu1.mnc -tmpdir
./tmp.mri_nu_cor
Are you doing volume or surface-based analysis? If volume, then you'll
need a volume mask and the --label is not appropriate.
On 07/22/2016 01:36 PM, Mihaela Stefan wrote:
> I tried that, too and it seemed to work. I extracted the ROIs from
> ?h.aparc.annot and merged them into a single label wi
I tried that, too and it seemed to work. I extracted the ROIs from
?h.aparc.annot and merged them into a single label with mri_mergelabels
then I ran mri_glmfit. Now I am not sure I used the correct command to mask
the search:
mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C
group
Hi Bruce,
Yes, I agree it doesn't seem right. They're LAG and ACG (I'm using
spectroscopy voxels as my ROIs). The surfaces look reasonable when I'm running
through the suggested steps on the freesurfer website for getting the surface
thickness when using an roi as a mask, but when I look
Hi,
I have uploaded it and the link should be
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=akbem4mthlv
Thanks!
Nicola
On 7/22/2016 6:31 PM, Douglas N Greve wrote:
> Can you tar up the glmdir and send it to me on our filedrop? The first
> warning is not a problem. Not sure about the 2nd.
> do
what version does it fail on? If a dev version, when did you download it?
On 07/22/2016 12:15 PM, Nicola Toschi wrote:
> Hi Again,
>
> (apologies for the many posts): I should add that none of this
> happens (and everything works fine - no warning and small clusters
> which look reasonable) if
What was your visualization command? You should probably run
mri_vol2surf with --projfract 0.5 and --interp nearest to get a surface
map. But it begs the question as to why you would do binarize the
aparc+aseg to get surface ROIs (you should just use the ?h.aparc.annot).
doug
On 07/22/2016 10:3
Can you tar up the glmdir and send it to me on our filedrop? The first
warning is not a problem. Not sure about the 2nd.
doug
On 07/22/2016 08:10 AM, Nicola Toschi wrote:
> Hi,
>
> thanks - I tried using "abs" as well as a higher threshold, however
> the large, whole-brain cluster (as well as th
Hi Again,
(apologies for the many posts): I should add that none of this happens
(and everything works fine - no warning and small clusters which look
reasonable) if I use version 5.3.
Thank you,
Nicola
On 7/22/2016 2:10 PM, Nicola Toschi wrote:
> Hi,
>
> thanks - I tried using "abs" as wel
glad it worked out
Bruce
On Fri, 22 Jul 2016, vars...@cns.iisc.ernet.in wrote:
> Hi Bruce,
>
> Thank you for your suggestion. I managed to figure out how to generate the
> right look-up table. I realised that the indices for the left and right
> hemispheres have 1000 and 2000 added to them. I crea
HI Varsha
we need more information - what was the explicit list of commands you ran
and what was their output? You probably have to change all the indices
first if you want them to be different.
cheers
Bruce
On Fri, 22 Jul 2016, vars...@cns.iisc.ernet.in wrote:
>
>
>
>
>> Message: 17
>> Date
Hi Bruce,
Thank you for your suggestion. I managed to figure out how to generate the
right look-up table. I realised that the indices for the left and right
hemispheres have 1000 and 2000 added to them. I created a look-up table
with the right indices and it worked fine. Thank you.
Regards,
Varsh
Hi,
thanks - I tried using "abs" as well as a higher threshold, however the
large, whole-brain cluster (as well as the warning messages) still remains.
Do the warnings:
WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
WARNING: 251446 NaNs found in volume
give any clues?
The strange
Dear freesurfer experts,
Thank you for guiding me on how to create average volume of all subjects of
depression patients. I later binarized the average volume generated to
extract the amygdala and hippocampus volume(Right and left). Please find
attached. How do I superimpose the extracted amygdala
"PhD position in structural imaging in First Episodes of Non-Affective
Psychosis"
A four years funded full-time PhD position will be available at the
Neuroimaging Unit – Health Research Institute Valdecilla (IDIVAL) headed by
Professor Benedicto Crespo- Facorro from October 2016.
We
> Message: 17
> Date: Thu, 21 Jul 2016 09:31:57 -0400 (EDT)
> From: Bruce Fischl
> Subject: Re: [Freesurfer] Combined parcellation of the left and right
> hemispheres
> To: Freesurfer support list
> Message-ID:
>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Hi
if I start a mris_glmfit via the command line the terminal outputs a line that
it couldn't detect the DeMeanFlag and therefore will not do any demeaning.
Cheers
Clara
- Ursprüngliche Mail -
Von: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Montag, 18. Juli 2016 23:46:
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