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Dear all,
I would like to use the Hippocampal Subfields and Nuclei Of Amygdala tool
concomitantly with the Brainnetome Atlas for a resting-state analysis.
For this purpose, I need the hippocampal/amygdala nuclei to be in the same
space as the
Dear Jessica,
There is no intensity image associated with the atlases, so this is not trivial.
I guess you could register your subjects to the atlas, and propagate the hard
segmentations?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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Got it. Thanks a lot doug. If i have to correct for multiple comparison in
surface based pet analysis and mutlimodal analysis (pet and thickness),
should i use --3spaces?
Thank you.
best,
Paul
On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. <
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I tried to log in with the username and password you mentioned, but logging in
failed. Could you please have a look into the file already i attached to my
previous email, or let me know why i could not log in to transfer the file,
Thanks,
Reza
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Hello Martin,
I was wondering - how solved the "Unmatched" error ?
In our case, this error appears for both 5.3, 6.0 and dev, on 2 different
clusters.
All folders exist, are filled with data and reecon-all finished without
error, plus hippocampus
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Yes, i checked -projfrac 0.5 with old or new mris_preproc but didn’t work. I
checked all registration, they are perfect.
> On 7 Aug 2019, at 17:29, Greve, Douglas N.,Ph.D.
> wrote:
>
> If you do not specify --projfrac-avg, does it come out as
Hi Rachel
all processing is done in the subject's native space. If you want to
downsample probably the easiest thing to do is map to one of the
lower res fsaverage subjects (e.g. fsaverage3 or fsaverage4) using
mri_surf2surf/mri_label2label and the like after running recon-all.
cheers
Bruce
If you do not specify --projfrac-avg, does it come out as non-zero? If
so, I would think that it is a problem with the registration. Have you
checked the registrations?
On 8/7/19 11:25 AM, Reza Rahmanzadeh wrote:
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>
> It means that for any given subjects
no idea until you tell me what you did, including command lines and
terminal output
On 8/7/19 11:08 AM, Reza Rahmanzadeh wrote:
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>
> Thanks, I saw that before, what could be the reason for that and how could i
> do mris_preproc correctly for NDI maps?
>
>
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Yes, for mris_preproc:
mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out
lh.NDI_inflated.avg.mgh --iv
> On 7 Aug 2019, at 17:14, Reza Rahmanzadeh wrote:
>
> mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25
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Hello freesurfer developers,
I am trying to get the user defined segmentation for a subject generated in
here (https://github.com/mattcieslak/easy_lausanne) . After recon-all, I
have the pial surface with ~250k vertices. My first question is about the
Run mris_preproc with a single subject and send the terminal output
On 8/7/19 11:47 AM, Reza Rahmanzadeh wrote:
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>
> Yes, i checked -projfrac 0.5 with old or new mris_preproc but didn’t work. I
> checked all registration, they are perfect.
>
>> On 7 Aug
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Dear Juan Eugenio,
Thanks a lot for your quick response.
I don't understand what you mean exactly by "propagate the hard segmentations".
And when you say to register the subjects to the Brainnetome, do you mean
replace the atlas used by
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Hi,
We are in the midst of designing a short course on Advanced Statistics in
Neuroimaging and Genetics. We would like to get a sense of the interest.
If you don’t mind, please take a moment to fill out this short survey.
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Dear Freesurfer,
Could you help me to resolve this error? I looked up the previous postings, but
the recommendation (copying files in the same folder etc.) did not help.
Thank you.
$ recon-all -base template -tp 002_S_0295_S32678 -tp
The 3 spaces is for left hemi, right hemi, and subcortical, so, if you
are using all three then correct for all 3
On 8/7/19 9:26 AM, miracle ozzoude wrote:
>
> External Email - Use Caution
>
> Got it. Thanks a lot doug. If i have to correct for multiple
> comparison in surface based pet
That mris_preroc commad is incomplete.
On 8/7/19 11:13 AM, Reza Rahmanzadeh wrote:
>
> External Email - Use Caution
>
> My command lines:
>
> My command lines sequentially for the analysis are: ( I have done just
> the same command lines for MWF maps and it worked very good, but for
>
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It means that for any given subjects i’ve had one -iv argument and then for
mri_glmfit i used .fsgd file with the same order.
> On 7 Aug 2019, at 17:23, Reza Rahmanzadeh wrote:
>
>External Email - Use Caution
>
> Yes, for
Dear Jessica,
You can register your image to the atlas, and then apply the same transform to
the segmentations (“propagate”). That will bring the segmentations to atlas
(Brainnetome) space.
I hope this helps,
/E
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL
You should only pass one of --seg, --annot, or --slabel to
mri_segstats. I don't understand how you are trying to use this in the
context of your permutation. Is this something that you are running on
each iteration? If so, it is probably not what you want to do. Probably
you want to run
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Hi exports,
I am using FS6.0 to segment hippocampus. I run "recon-all -s bert
-hippocampal-subfields-T1" and it said "recon all bert finished without error".
However, in mri directory, there is no l(r)h.hippoSfLabels-T1.v10.mgz file. And
in tmp
Dear Zheng,
Can you please send us the log files?
Kind regards,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of 郑凤莲
Reply-To: Freesurfer support list
Date: Wednesday, 7 August 2019 at 21:19
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