can you send the terminal entire output that includes the error?
On 3/9/17 7:57 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote:
Dear Freesurfer Experts,
I want to customize the directory so I can run the following command
mris_preproc --fsgd gender_age.fsgd --cache-in
thickness.fwhm10.fsaver
Dear All,
A simple issue of precedence. In the recon-all pipeline, wm edits take
precedence to pial edits.
If there are both wm and pial defects, should one apply edits sequentially,
say on brainmask.mgz (first wm edits, rerun recon-all say recon-all
-autorecon2 -wm, then do pial edits, rerun reco
Hi Experts,
I am trying to inflate the brains with lesions in the LHs. The inflation
failed because of those lesions. I need the RH data from the files
"mri/wmparc.mgz" and "stats/rh.aparc.stats". Here are what I did:
1. Use "recon-all -hemi rh" to inflate the RH only but the inflation
stopp
Dear Freesurfer Experts,
I want to customize the directory so I can run the following command
mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage
--target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh
However, after running this command it keeps checking
you could create a mask that is the AND of all your subject masks I suppose
On Thu, 9 Mar 2017, Dorian P. wrote:
Thanks. I created a video to loop through all my 170+ subjects in template
space:
https://drive.google.com/open?id=0BxHeqEv37qqDeGFWVnpSVkVobkk
I see some cases that have dramatic
Dear Sahil,
I would suggest at first to make check of your GLM PALM setup by comparing
mri_glmfit and PALM output files (using the same design and contrast):
1. values of gamma.mgh should correspond to values of *cope.mgh
2. values of F.mgh should be (*dpv_tstat.mgh) ^2.
3. values of sig.mgh
Thanks. I created a video to loop through all my 170+ subjects in template
space:
https://drive.google.com/open?id=0BxHeqEv37qqDeGFWVnpSVkVobkk
I see some cases that have dramatic problems. I will need to check those
more carefully and probably do an inspection of each one in individual
space. Be
Hi Dorian
you can load the aparc.annot for each subject and use it to chek if the
spherical registration worked ok. It's easy enough to write a script to
load these for each subject, then write a tif file with a medial view, and
zip through them all with nmovie
cheers
Bruce
On Thu, 9 Mar 2017,
Thank you Bruce, Douglas.
Yes, I think thicknesses were obtained with v 5.3.0. There might be errors
as Bruce pointed out, I am going now through all maps to check them. This
makes me think of a question. Volumetric template registrations sometimes
go wrong. Does this happen also to surface regist
Hi Doug,
This is the final line with "cost" in it:
MinCost: 0.862331 7440.183178 7411.264107 -1.819400
We're switching from FLIRT BBR (two-pass) to bbregister when there's a
reconstructed subject available, so I'm using `--init-fsl` to try to
minimize the differences in the pipeline in the two c
that should have worked. what was the bbregister final cost function? It
could have been that fsl did not provide a good initial registration. If
you have v6, you can leave off --init-fsl and it will use mri_coreg
(which is more robust).
On 03/09/2017 03:24 PM, Christopher Markiewicz wrote:
>
Hi all,
Suppose you have a sub-pipeline:
$ recon-all -s $SUBJ -i $T1 -all
$ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat --fslmat
fsl.mat
Now `bbreg.dat`/`fsl.mat` is registered to
`$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to register to $T1?
I've tried:
$ tkregi
Thank you very much!!
--
Shane S
On 9 March 2017 at 17:01:28, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote:
If the 3 volumes are in register (ie, no motion between them), then I
would just run the mri_concat command to create a single volume which is
the average of the 3, then proceed
didn't I respond to this earlier this week? the images appear to be
binarized regions of interest and not whole (or ever partial) brain. To
run the registration, you will need an actual brain. If you created the
ROI from a brain image, then use that image to create the reg, then run
vol2surf us
The design matrix does not match the FSGD file. It could be because you
have commas (i,e ",") instead of decimal points (ie, ".") in the FSGD
file. Try replacing and rerunning.
On 03/08/2017 04:32 AM, teodora petrova wrote:
> Hello,
>
> I am trying to test for the effect of different variables
Hi Doug,
I want to derive a single averaged PET volume from the three reconstructed 5
min acquisitions, expressed in detected counts. Then we will divide the counts
based on the cerebellum. Following that, I want to use PetSurfer for partial
volume correction and GLM comparisons. May I upload t
If the 3 volumes are in register (ie, no motion between them), then I
would just run the mri_concat command to create a single volume which is
the average of the 3, then proceed as described.
On 03/09/2017 11:58 AM, Shane S wrote:
> Hi Doug,
>
> I want to derive a single averaged PET volume fro
This was done to clear up a misunderstanding when using a target subject
other than fsaverage. The way that 5.3 worked is that the data were
actually sampled onto fsaverage through the ?h.sphere.reg. The target
subject was only used in the smoothing process (if you even specified
that as part o
On 03/08/2017 09:27 PM, Dorian P. wrote:
> Hi Freesurfers,
>
> I am using R to perform thickness analyses. All subjects are
> transformed in fsaverage space and all values are placed in a matrix
> with 327684 columns (163842 for each hemisphere). I put the results
> back in a surface file (.as
How did you create lh.fsaverage.ROI5.mgh and lh.thickness.fsaverage.mgh?
On 03/08/2017 08:15 PM, Elodie Boudes wrote:
> Hello FreeSurfer community,
>
> I am trying to extract the cortical thickness from a specific ROI.
> I followed the pipeline: cortical thickness of a volume-defined ROI.
> But
How are you planning on analyzing the different time points?
On 03/08/2017 05:33 PM, Shane S wrote:
> Dear Doug,
>
> My PET data is 3 x 5 minute acquisitions. Each subject has
> subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am
> supposed to align and average them.
>
> Pleas
Hi Dorian
that is a bit worriesome. Typically the surfaces are "frozen" at the
midline and hence the thickness is 0, so there should be no difference. I
guess if a single subject had an incorrect CC segmentation you would be 0
variance within one group and hence significant results or something
Hi Joshua
hmmm, label2vol takes our text label file format as input, not a .gii
file. You probably need to ask the Wash U HCP folks how to do this
conversion as I believe there should be a step before label2vol
cheers
Bruce
On Thu, 9 Mar 2017,
Burks, Joshua D (HSC) wrote:
Hello FreeSurf
Dear FS experts
we are trying to run statistics in FS6 Linux. Everthing worked fine until we
applied the command
mris_preproc that called mri_surf2surf and produced the following error:
#
---
Hi,
Following previous discussions on the mailing list, I am using
mri_surfcluster to extract MNI (or Talairach) coordinates of a label using:
mri_surfcluster --in $SUBJECTS_DIR/fsaverage/surf/lh.area --clabel
lh.G_cingulate-Isthmus.label --sum ~/Desktop/pract3 --centroid --thmin 0
--hemi lh --su
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