Hi Bruce,
In regard to ?h.curv. i extrated the meancurv from aparcstats2table
(https://surfer.nmr.mgh.harvard.edu/fswiki/aparcstats2table). Howver, when i
run long_mris_slopes, it does not seem to find ?h.meancurv. But i think i need
to try ?h.curv instead.
a) What were the thoughts behind usi
Dear FS experts
we constructed a customized template (using make_average_subject) to register
the individual surfaces on that template instead of the fsaverage template.
we recognized that there are, at least, two ways to do this either using
mris_register or using surfreg.
Is there any differe
Hi Bronwyn
I defer to Martin :)
Bruce
On Fri, 18 Aug 2017, Bronwyn Overs wrote:
Hi Bruce,
Please find attached both the command line output and the recon-all log. The
command line I ran was:
recon-all -long BASEID_001 TPID_001 -all
I have already run and reviewed the cross-sectional and base
actually you can just do it with mri_convert -sc
as long as the intensity isn't too low you should be fine. Try specifying
so that the average white matter intensity is around 100
On Thu, 17
Aug 2017, Dino Digma wrote:
Hi Bruce,
I'm having very similar to this thread. How do I know the
Hi Patricia
try using the subject's rh.thickness instead (it is in subject space, as
I think is your label)
cheers
Bruce
On Thu, 17 Aug 2017, Patrícia Klobušiaková wrote:
Dear Freesurfer experts,
I have labels representing clusters that I created using mri_surfcluster on
sig.mgh file using a
Thanks for that Doug!
Cheers,
*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.
Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney
*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
Hi,
We are currently doing longitudinal FreeSurfer analysis on subjects some of
whom are scanned over a period of 6 years. There were 2 groups. One was the
control group and the other was mTBI group. The hypothesis was the control
group would have a fairly stable cortical and sub-cortical volume (
Hi Bruce,
I'm having very similar to this thread. How do I know the proper value to
re-scale them by? Sorry if this is a basic question - I'm very new to
FreeSurfer.
Thanks!
Best,
Dino
you need to scale them. WHy do you have negative values? I would scale them
so that the min is 0 and the mean
Hi Doug,
I'd like to use the registration matrix from bbregister to transform
functional data into a cropped FOV that corresponds with the anatomy.
I thought that bbregister outputs a ras2ras transform, so if I could crop
the anatomical volume with a correct header vox2ras, things should be fine.
Dear Freesurfer experts,
I have labels representing clusters that I created using mri_surfcluster on
sig.mgh file using a specific threshold. Now I want to use these labels to
extract average thickness values for every subject. I tried to use
mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/clla
selxavg uses scenario #1, which corresponds to the 2nd image below, ie,
all the task regressors are in a single column and not pulled out on a
run-by-run basis. The nuisance regressors are specific to each run.
>
On 08/16/2017 08:24 PM, Kevin Aquino wrote:
> Thanks for that Doug,
>
> [I was ho
I would just use
tkregister --mov mov.nii --targ targ.nii --reg reg.dat --ltaout reg.lta
--noedit
On 08/17/2017 03:03 PM, Bruce Fischl wrote:
> not sure, maybe it doesn't work for what you are trying? I defer to
> either Martin or Doug on this
> On Thu, 17 Aug 2017, John Anderson wrote:
>
>> T
Sorry, I don't know if that info is in PET dicom files
On 08/16/2017 07:14 PM, Shane Schofield wrote:
> Okay I understand.
>
> So I ideally would like to do the PetSurfer before actually working
> on the BPND but I already got them in the BPND format as well as the
> raw dynamic images. I trie
I'm coming into this a little late, but it seems very complicated. If
understand correctly, you have a volume created in another software
package that you want to map into the freesurfer space. Is that right?
Do you want it in the "native" space of the anatomical or the
"conformed" space?
On
Hi!
We are processing images using
recon-all -all -3T -mprage -qcache -hippocampal-subfields-T1
-brainstem-structures
We've encountered an issue when we're trying to use multiple inputs (acquired
at the same timepoint and with comparable quality). The issue is due to the two
images having sl
not sure, maybe it doesn't work for what you are trying? I defer to
either Martin or Doug on this
On Thu, 17 Aug 2017, John Anderson wrote:
Thank you Dr Bruce,
I tried
lta_convert --inreg reg.dat --outlta reg.lta
but I am getting error message
This REGISTR_DAT is only valid for volume betwee
Thank you Dr Bruce,
I tried
lta_convert --inreg reg.dat --outlta reg.lta
but I am getting error message
This REGISTR_DAT is only valid for volume between COR type c_(r,a,s) =0
Please what I am doing wrong?
> Original Message
> Subject: Re: [Freesurfer] dat to lta
> Local Time:
sorry, I still don't understand what it is you are trying to do. What are
you trying to mask out? What is the source of the mask? Is the target of
the mask a FreeSurfer volume?
On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote:
> I looked at their orientation differences using mri_info and used this
I think lta_convert will do the trick. Check out the help
cheers
Bruce
On Thu, 17 Aug
2017, John Anderson wrote:
> Hi FS experts,
> Is there any way to convert the registration matrix reg.dat to reg.lta?
>
> Thank you
> John
>
>
___
Freesurfer mailin
I looked at their orientation differences using mri_info and used this command;
mri_convert --in_orientation LIA --out_orientation AIL native.template.mgh
native.corrected.nii
But still there is an alignment problem. Looks like the xform info differs so
can I use the mri_mask command with specif
Hi FS experts,
Is there any way to convert the registration matrix reg.dat to reg.lta?
Thank you
John___
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Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail
Dear Antonio,
“-norm3diters“ are the iterations of mri_normalize, whereas “-nuiterations”
refers to the number of cycles of mri_nu_correct.mni. I suppose they both work
in v6. If not you can simply create a file with expert options.
Hope this helps!
Best,
Falk
Von: freesurfer-boun...@nmr.mgh.
Hi,
I have a question regarding -nuiterations and -norm3diters. I would like to
get a feel for the options available for fine-tuning the intensity
normalization in FreeSurfer 6.0.
I've seen mention of -nuiterations on some posts. Is this still an option
in FreeSurfer 6.0?
The reason I ask is bec
Hi Mateus,
Could you clarify your original post for me:
By "nothing changed," do you mean that the brainmask.mgz is the same as before
even though you used the new watershed threshold? Or that this changed but
nothing downstream (like the aseg.mgz) changed?
Thanks,
Emma
Yes; sorry. The mask is created by an applied docker image which produced
volume and surface files of the template in both the brain's native and
freesurfer origin orientation. MW_IIHC_aTAL.nii is the brain file of the same
subject I exported from another software-I am hoping to export the templ
Hi Idil
you need to give us much more information to be able to help you. How did
you create the mask? Why volume to you expect it to be in register with?
What are the volumes MW_IIHC_aTAL.nii native.template.mgh and
native.orientation.mgh ?
Bruce
On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote
Hi Martin,
Sorry for delayed response and thank you so much for looking into it. I will
follow the steps as described to get their thickness maps.
For qdec, can we do analysis for single subjects? I believe I had tried it
earlier but it failed with dof = 0. Can I set up qdec table as below to
if you want to reslice the mask to be like a template volume, use "-rl"
instead of "-at"
cheers
Bruce
On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote:
> I do not have a transform file I can use so I was wondering if I can simply
> use the volume file I am trying to adapt the mask to as the transfo
I do not have a transform file I can use so I was wondering if I can simply use
the volume file I am trying to adapt the mask to as the transform file in the
-at option. But looks like I cannot;
mri_convert -at MW_IIHC_aTAL.nii native.template.mgh native.orientation.mgh
mri_convert.bin -at MW_II
sorry, I don't understand
Bruce
On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote:
> Thank you!
>
> Then I guess I would use the volume as the transform file to convert my mask.
>
> Best,
> Idil
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-bou
Thank you!
Then I guess I would use the volume as the transform file to convert my mask.
Best,
Idil
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Thursda
ok, but your mri_mask command line has the string "%s" in it, which is
not correct. You need to specify an actual file name. I also think you
are better off using mri_convert -at to map
the mask into the right coordinate system so that you can then view it in
freeview to make sure it is c
The mask in volume format was created using a docker image and it works well
both with my freesurfer origin and native volume files; the one that it doesn't
align with is the volume file I am trying to adapt to/from a different
software. The command line I used for transforming is this;
mri_vo
Hi Idil
how did you create the mask and the transform? Also, you can't specify "%s"
on the command line - you need an actual name of a transform file.
cheers
Bruce
On Thu, 17 Aug 2017, Yagmur Ozdemir
19 wrote:
Hello freesurfer experts,
A volume file I want to save as a mask(the orange
Hi Rose,
you should post to the list as you will get better and faster answers
(although this time I know it didn't work so well for you).
I believe Martin published these numbers
Bruce
On Thu, 17 Aug 2017, Van Der Deijl, Rosanne wrote:
Dear Bruce,
I think my message might have gotten los
Hi Bronwyn
can you send us the full command line you ran, screen output and
recon-all.log? And maybe a description of where you are in the process?
You already ran all the tps through the cross? And created the base?
cheers
Bruce
On Thu,
17 Aug 2017, Bronwyn Overs wrote:
Hi again list,
So
Hi Emma,
Could you take a look at the recon-all.log file I sent you?
Best
Mateus
Enviado do meu iPhone
> Em 11 de ago de 2017, às 11:18, Boyd, Emma escreveu:
>
> Hi Mateus,
>
> Please attach the recon-all.log file for your subject and I will take a look.
>
>
> Best,
>
> Emma
>
>
>
>
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