Maybe it is running out of memory? Can you try it reducing the number of
inputs?
On 6/29/2022 2:42 PM, Benjamin Deck wrote:
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Hi there,
I am attempting to concat a number of volume files that are filled
cortical ribbons from a series of label files.
My w
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Hi there,
I am attempting to concat a number of volume files that are filled cortical
ribbons from a series of label files.
My workflow is to take the following steps:
*Convert overlay file to label file*
mri_vol2label --i
${inDir}/Indi_Matched_ROIs/
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Hi Douglas!
Thanks for the reply. Apparently, this error was due to a lack of license
file in freesurfer folder. I downloaded a license, put it in the right
place. When I try to process a subject, it works well, but when I try to
analyze my data with q
Hard to say. This is one reason we are not supporting qdec anymore. Was
there anything printed to the terminal?
On 2/3/2022 8:27 AM, Mateus Aranha wrote:
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Dear all,
I'm constantly getting the following error and I have no idea where
the problem is...
im
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Dear all,
I'm constantly getting the following error and I have no idea where the
problem is...
[image: image.png]
Thanks for your help,
Mateus
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Hello Doug,
I fixed it. Thank you
Best,
Paul
On Thu, Jul 20, 2017 at 11:11 AM, Douglas N Greve wrote:
> it cannot open that file meaning that it does not exist or you do not
> have read permisssions
>
>
> On 07/20/2017 11:01 AM, miracle ozzoude wrote:
> > Hello Freesurfer,
> >
> > I am trying to
it cannot open that file meaning that it does not exist or you do not
have read permisssions
On 07/20/2017 11:01 AM, miracle ozzoude wrote:
> Hello Freesurfer,
>
> I am trying to average out all the time frames for my pet images by
> using mri_concat. However, I am getting an error (see below).
Hello Freesurfer,
I am trying to average out all the time frames for my pet images by using
mri_concat. However, I am getting an error (see below). How can I resolve
this issue? Thanks.
Best,
Paul
My command = mri_concat frame1.nii.gz frame2.nii.gz frame 3.nii.gz
frame4.nii.gz --o Aveframe.nii.g
You cannot simply concatenate the thickness files. Use mris_preproc,
which will sample them to fsaverage space and then concatenate them
On 07/14/2017 12:49 PM, Dev vasu wrote:
> Dear all,
>
> I have 115 subjects , and I would like to perform average cortical
> thickness ,pial surface .
>
> I h
Dear all,
I have 115 subjects , and I would like to perform average cortical
thickness ,pial surface .
I have used mri_concat for this and i am getting dimension mismatch
*" mri_concat k***/surf/lh.thickness --mean --o
/media/vasudev/vkirsch4/Data_Driven/Thickness_Pial/lh_thickness/lh.thic
Hi Doug,
There is a bit of movement across the 3 acquisitions. How may I align
everything together before running mri_concat?
1. Run bbregister or mri_coreg to register 1 acquisition to T1
2. Use the reg file to move the remaining 2 acquisitions ?
Is there a quicker way?
Thank you.
--
Shane
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
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
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
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.
Please advise.
Thanks!
--
Shane Schofield
On 8 March 2017 at 22:31:06, Douglas Greve (gr...@nmr.mgh.harvard.edu) w
No, the template is a within subject template used for registration. If
your pet data only has one frame (eg, FDG SUV), then you don't need to
run mri_convert or mri_concat, just use your pet image as the template
On 3/8/17 11:11 AM, Shane S wrote:
Hello Freesurfer,
I have 3 PET images per i
Hello Freesurfer,
I have 3 PET images per individual. I am learning PetSurfer based on the Greve
et al., 2014 paper.
On the PetSurfer link, there are 2 methods.
mri_convert pet.nii.gz —frame frameno template.nii.gz
or
mri_concat pet.nii.gz --mean —0 template.nii.gz
What are the differences?
oops, sorry again.It will give the maximum p-value, not the min. This
implements Nichols. If you threshold the map at a given level, it will
show you what you would have gotten had you applied that threshold to
both mapsand then computed an AND. Doing this way means that you can
choose your thr
Hi Doug,
I also have a tendency towards correcting the conjunction map.
Regarding mri_concat: If I understand the results correctly, it does
not exactly implement Nichols. It seems to give voxels even if they
are only significant in one contrast, which is exactly what Nichols et
al argued against.
oops, sorry, mri_concat takes the smallest p-value (and so implements
Nichols). I think I'd to the multiple comparisons correction after
conjunction (but I'd like to hear opinions). Not sure about the FWHM,
probably take the max of the contrasts that go into it.
doug
On 05/24/2013 03:02 PM,
Hi Doug,
just to make sure I understand you right:
No matter whether I want to test a conjunction a la Friston (any voxel
significant, this is what mri_concat gives) or a la Nichols (both
voxels significant), I would take the maximum p-value, correct?
What about multiple comparisons? Would you thre
The way to do it is to take the maximum p-value at each voxel (this is
what mri_concat does).
doug
On 05/24/2013 02:10 PM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> I am trying to implement something like the MS/CN conjunction
> suggested by Nichols.
> For that, I am finding the voxels that sho
Hi Doug,
I am trying to implement something like the MS/CN conjunction
suggested by Nichols.
For that, I am finding the voxels that show a significant effect at a
given threshold in both contrast maps.
I have one question about the resulting p-value.
In principle, I would tend to think that the con
Hi Caspar, I think the 4.x should be the same as 5.x. I'm not sure about
your fsfast question. There is nothing to automatically do it (ie,
you'll need to run mri_concat)
doug
On 05/23/2013 03:06 PM, Caspar M. Schwiedrzik wrote:
> Hi!
> I am trying to do a conjunction analysis using mri_concat --
Hi!
I am trying to do a conjunction analysis using mri_concat --conjunct
with 2 to three sig.nii as input.
It seems to me that the resulting map is what Nichols et al. refer to
as MS/GN, i.e., a test against the global null (at least one effect).
Is that correct, and does that depends on v4.5 / 5.x
Hi Cooper, try using the --f option to mri_concat. This takes a text
file in which you can list all the files you want.
doug
On 10/13/11 5:40 PM, Cooper Roddey wrote:
> I think my problem is not with mri_concat after all, but with matlab's
> 'unix' function. In any case, reading a list of input f
Hi,
Thank you for your help! I think there might be something wrong just with
the display, as in fact more brains looked strange. I have re-run the
concatenation with the same commands after killing many processes on my
computer and now all brains look correct and in the expected order.
Cheers,
Hi Aga, that does sound strange. mri_concat does no processing at all,
so if that subject looks ok before you run mri_concat, it should look
fine afterwards. Try running just that subject through mri_concat (so
there's no real concatenation). Also, make sure that the bad subject in
the mri_co
It matters. It will order them in the same order that you have them on
the command line. If you want to order them based on modification time,
you can do something like
mri_concat --o out.nii `ls -t *.nii`
doug
Rita Loiotile wrote:
> For a series of nifti fMRI images does it matter in what ord
For a series of nifti fMRI images does it matter in what order I list
the images for my input? Or does MRI_concat get the time series info
from the files themselves?
Sent from my iPhone
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Hi Lars,
mri_concat does not have that kind of option. What specifically do you
want to concat? If it is just something in the subjects' mri dir (eg,
orig.mgz), then you can just:
mri_concat $SUBJECTS_DIR/subj*/mri/orig.mgz --o all.orig.mgz
Alternatively, you can use mris_preproc which does al
Hi,
I am wondering if it is possible to use some kind of a list of subjects to
specify input for mri_concat, like you can use --f filename, where filename
refers to a list of subjects, for mri_surf2surf ?
It seems that using e.g.: mri_concat subj*-lh.mgz --o allsubjs-lh.mgz
is an alternative to:
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