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Hi FreeSurfer community,
when I run mri_coreg I get the following error.
/XYZ/2123/mri/brainmask.mgz is in the specified location.
Can you help me with this?
Thanks!
Boris
mri_coreg --s 2123 --mov /XYZ/2123.nii --reg 2123.reg.lta
Could not set loca
it says it cannot find /XYZ/2123.nii
probably this file does not exist
On 2/28/19 10:09 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer community,
>
> when I run mri_coreg I get the following error.
> /XYZ/2123/mri/brainmask.mgz is in the specified location.
The betas are averages across subject, so you should not get one for
each subject
On 2/27/19 4:34 PM, Jahan, Bushra wrote:
>
> When I ran the following command (with our data), I got the average
> beta values for each segmentation i.e. only 5 beta values (as opposed
> to 5 beta values for each
need more info
On 2/27/19 9:42 AM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I am trying to do a registration with tkregister but am experiencing
> this type of issue:
>
>
> The image I should fit is the sagittal view instead of coronal.
>
> Is there some way to change it to coronal from
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Hi Douglas,
Thanks for your reply. I am not sure how to do this with design matrix.
I am trying to get higher order fit. Basically I want to see that whether
the cortical thickness varies in a quadratic fashion with the behaviour
score.
Are yo
If you wanted to do a simple analysis looking at the effect of age in a
linear fashion, you'd have a deisgn matrix something like
1 agesubject1
1 agesubject2
...
ie, first column all ones, second column the ages of each subject.
If you think the change is quadratic, then you'd use
1 agesubject1^
Dear Freesurfers
Hi
I was trying to look at the activation in different cortical layers in a single
subject.
I ran my preproc-sess command three times, once without using -projfrac flag,
once -projfrac 0.5 and lastly -projfrac 0.2
The activation patterns are exactly the same.
My voxel size
The projfrac function might not be working in the way that you think. It
might not actually be re-running anything. Did preproc-sess finish
faster than you would have expected? You can try deleting the projfrac
output and re-running. You can also run preproc-sess with -force, but
this will forc
That looks pretty awful. You should check the orig.nofix surfaces. I bet
your data is extremely noisy
On 2/28/19 11:37 AM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
>
>
> Dear Freesurfer devs,
>
>
> I ran the recon-all in one subject and and this process was sto
Hi Doug
Thank you very much for your reply.
I was actually using -force and It did take a reasonable amount of time.
Then I ran the selxavg command to get the first level maps, and I guess It used
the last preprocessd data which was from projfrac 0.2.
Thanks
Mona
__
Did you check the registration? My guess is that the registration failed
because the initial FSL registration failed. I've put a new version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/dt_recon
it has a better initializer. Just copy it over the one in
$FREESURFER_HOME/bin (make a back
I would have thought that it would have changed. Can you look through
the logs and find the mri_vol2surf command and verify that the
--projfrac argument is changing?
On 2/28/19 2:51 PM, Nasiriavanaki, Zahra wrote:
>
> Hi Doug
>
>
> Thank you very much for your reply.
>
> I was actually using -fo
Yes
On 2/27/19 2:00 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> There is no mean diffusivity output with dt_recon. How would you
> suggest to create MD images? Could you simply divide the adc.nii.gz
> map by 3?
>
> Best,
> *Daniel Callow*
> /PhD Student, Neur
sorry, yes, that is right
On 2/27/19 2:18 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Sorry, I just found in a previous post by doug that ADC is the same as MD?
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> Univers
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Thank you!
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
On Thu, Feb 28, 2019 at 2:56 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.har
did you check the registration? Run mni152reg --help to see how
On 2/26/19 2:36 PM, john Anderson wrote:
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> External Email - Use Caution
>
> Hi Dr Greve,
>
> I used --regheader to move PET to T1.
> mni152reg in mri_vol2vol as follows:
> mri_vol2vol --mov PET.nii.gz --mni152reg --targ
> $
On 2/26/19 7:58 PM, Alon Baram wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I have subject's surfaces where I first register the rh to the lh
> using xhemireg, then register both hemispheres to fsaverage_sym using
> surfreg, and then resample the registered surface to the isoc
please include the previous correspondence in your emails
On 2/26/19 11:33 AM, Ella Hanns wrote:
>
> External Email - Use Caution
>
> Dear Bruce,
>
> Thanks a lot for your help!
>
> I now (roughly) ran the following pipeline but still did not manage to
> downsample my functional data in f
no idea. If you want to use tbss, why not use FSL to do the dti analysis
from the start?
On 2/26/19 10:27 AM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am working through dt_recon troubleshooting (One subjects
> registration to anatomical is skewed leading t
which ROIs are different?
On 2/22/19 5:39 PM, Winkelbeiner, Stephanie A wrote:
>
> External Email - Use Caution
>
> Hi Freesurfers,
>
> I’m trying to read out GM and WM values from parcels (ROIs) but get a
> different amount of ROIs for GM and WM.
>
> I use the following commands (embedde
Did you see the line "If you seek help with this problem, make sure to
send:" and then it lists some things to send
On 2/25/19 2:13 PM, Arsenije Subotic wrote:
>
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>
> Dear experts,
>
> I have recently tried to use the command line to examine thickness
> diff
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Dear FreeSurfer supporter,
We are working on a PTSD project and we used FreeSurfer to obtain the
subcortical and cortical volumes for our MRI images in our patients. We ran our
images through the recon-all pipeline. We then extracted the volumes f
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I was also running an ROI analysis based on the recon-all segmentations so
I figured I could use the FA results and skip the process of running
through the whole tbss process. I also found dt_recon's ability to
determine bvals and bvecs from the dcm wit
I did not find mri_vol2surf.
Below is part of a log file, as you see -projrfac has changed to 0.5 but not
to 0.2.
mri_segreg --mov bold/020/tmp.bbregister.43919/template.nii --init-reg
bold/020/tmp.bbregister.43919/reg.init.dat --out-reg
bold/020/tmp.bbregister.43919/bbr.pass1.dat --subsamp-
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Hello,
I am running segmentation of hippocampal subfields in FreeSurfer 6.0 but
one subject failed running the segmentation with the following error
message.
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
This file does n
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