Hi Hsiang-Yuan,
I do not know how color file works for MRIcron, so I am unable to help.
Regards,
Thomas
On Tue, Jul 5, 2016 at 2:41 AM, Hsiang-Yuan Lin wrote:
> Hi Thomas,
>
> Thanks for swift instruction. It works well. However, I have further
> question: could I write the color lut into heade
Also when I run mir_convert on the DICOMs I get the same error as the one I got
when I used DICOMs :
WARNING: file
/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
does not contain a Siemens ASCII header
has this file been anonymized?
ERR
It says 1 … I don’t understand why I get that knowing that when I open the
nifti I can go through the frames …
Ismail
> On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki
> wrote:
>
>
> I do not know why the dicoms do not work. When you run mri_info on your
> nifti, what is the number of frames
I do not know why the dicoms do not work. When you run mri_info on your
nifti, what is the number of frames that shows up?
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia,
This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So
this shouldn’t be the reason.
A
Hi Anastasia,
This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So
this shouldn’t be the reason.
Also why the DICOMs wouldn’t work at the beginning ?
Thanks,
Ismail
> On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki
> wrote:
>
>
> Hi Ismail - You can see from the log
Hi Ismail - You can see from the log file that the command that causes the
error is this:
mri_convert --frame 31
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz
It's trying to extract the 32nd fram
Hi Thomas,
Thanks for swift instruction. It works well. However, I have further
question: could I write the color lut into header? Because I used your
suggested Colorlut information to create a new .lut file and put them into
MRIcron templates folder with the correctely oriented Yeo2011_7network
t
Hi Anastasia,
Here it is.
But how could the problem be related to the nifti volume since I have errors
when using the DICOMs too ?
Thanks again,
Ismail
> On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
> wrote:
>
>
> Hi Ismail - It sounds like the error has to do with the nifti volume, not th
yes, just note that they are somewhat different hypothoses that you are
testing as noted by Mike in the past. If you use average surface
area/thickness you are testing the hypothesis that part of the brain is not
changing/different relative to the average. If you control for TIV (or the
2/3 roo
Hi Clara,
Yes- my apologies. I misunderstood your initial analyses description.
Sounds right to me as well.
- Arkadiy
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The informati
Hi Ismail - It sounds like the error has to do with the nifti volume, not
the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
Thanks,
a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia,
Thank you for getting back to me.
Here are more details about my problem, I t
Hi Michael - There is no bvec file associated with the base template. The
base template is a structural (the median of a subject's structural time
points) and not a diffusion scan.
The way you'd want to account for different amounts of motion across
subjects in a cross-sectional analysis, yo
Hi,
I am doing a research about the uterus, in this research I am trying to
define the geometry of this organ, so I want to use freesurfer to mapping
the uterus into a sphere; as far as I understand I don't need all the brain
image processing. I have already a FEM model of the uterus in matlab, a
yup, that is a reasonable approach
Bruce
On Mon, 4 Jul 2016, Harms, Michael
wrote:
Hi,
Why not use total surface area to control for analyses involving area, and
mean cortical thickness to control for thickness? I’ve posted to the list
before regarding this, so you should be able to find th
Hi,
Why not use total surface area to control for analyses involving area, and
mean cortical thickness to control for thickness? I’ve posted to the list
before regarding this, so you should be able to find those posts.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Hi Anastasia,
Thank you for getting back to me.
Here are more details about my problem, I think it should help you understand
more.
I run trac-all -prep -c on some DICOM files but I had the following error :
WARNING: file
/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.36800
Dear Freesurfer experts,
Based on the FS wiki, I calculated the cortical thickness difference between
the lh and rh of a subject.Now, I want to use the “mris_apply_reg” command to
map the “left-right difference” from fsaverage_sym back to the subject's
native surface.Unfortunately, I did not fi
Do you know, if there are any publications concerning this matter? So far I've
found only this
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0148852 that
controls for tGM only for area and not CT.
Cheers Clara
- Ursprüngliche Mail -
Von: "Bruce Fischl"
An: "Freesurf
Ok, thanks!
- Ursprüngliche Mail -
Von: "Bruce Fischl"
An: "Freesurfer support list"
Gesendet: Montag, 4. Juli 2016 15:37:57
Betreff: Re: [Freesurfer] controlling for total gray matter volume
sounds right to me
Bruce
On Mon, 4 Jul 2016, Clara Kühn wrote:
> I have decided now to not con
sounds right to me
Bruce
On Mon, 4 Jul 2016, Clara Kühn wrote:
I have decided now to not control for ICV or total gray matter volume when
looking at cotrical thickness but to control for total gray matter volume when
looking at surface area. Does that sound about right?
Cheers, Clara
- U
Hi Lee
that is the correct option, I just haven't gotten around to putting it in
the help text yet.
Bruce
On Mon, 4 Jul 2016, Lee Subin Kristine wrote:
>
> Dear FreeSurfers,
>
>
> Is it possible to get tissue probability maps (for the purpose of using them
> in spm DARTEL, PVElab, etc) out
I have decided now to not control for ICV or total gray matter volume when
looking at cotrical thickness but to control for total gray matter volume when
looking at surface area. Does that sound about right?
Cheers, Clara
- Ursprüngliche Mail -
Von: "Arkadiy Maksimovskiy"
An: freesurfe
So, what bvec/bvec file should be associated with the BASE scan? It isn’t
clear to me how the bvec/bval in the BASE scan get used in trac-paths.
I see the point of your note of caution, but unless someone moved the same
amount (and for the same frames) for their sessions in a longitudinal
study,
Hi Hsiang-Yuan,
That's because the header information is different. You can do the following:
>> mri_vol2vol --mov Yeo2011Parcellation.nii.gz --targ
>> FSL_MNI2mm_template.nii.gz --regheader --nearest --o Yeo2011_FSL2mm.nii.gz
The output file "Yeo2011_FSL2mm.nii.gz" should have an orientation
c
Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals
and dmri/bvecs files that get generated look fine too?
a.y
On Sat, 2 Jul 2016, Lars M. Rimol wrote:
Hi,
Trying to run trac-all -c dmric_file -prep, I get an error message stating
that there are different numbers of
Hi Derek - Are you by any chance using the dev version of freeview?
a.y
On Fri, 1 Jul 2016, Derek Pisner wrote:
Dear Anastasia,
I am running into an issue with the trac-all -stat option on our longitudinal
TRACULA data.
Everything runs smoothly through all earlier stages, and I checked ind
Hi Michael - Indeed it should not be too difficult to add the feature of
specifying the b-value table for each scan and I can add this in the next
version.
However, I would be a bit careful with removing different DWI volumes for
different time points. The acquisition should be as consistent
Hi Ismail - Are you passing the nifti volume as input to trac-all? It's
hard to tell without looking at your configuration file.
Best,
a.y
On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
> Hi everyone,
>
> I have some problems trying to run TRACULA on some DWI data. It is a mosaic
> Siemens DWI.
Hi Yang - Have you followed the instructions on how to set up the
freesurfer environment?
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configuration
Best,
a.y
On Mon, 13 Jun 2016, yangfuxing wrote:
Hi professor?? When I finished setting up the configuration file "
Hi Shashwath - It looks like you have modified the directory structure of
the output files. Normally the dpath/ directory is right under the
directory with subject's name. From your file of inputs, it looks like
you've created some other subdirectories and now dpath/ is a few levels
down the
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