Hi list,
Is there a way to obtain a map that report the "vertex by vertex" correlation
between the FC (obtained by FS-FAST) and cortical thickness?
Thanks
Stefano___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.
Check and, if necessary, edit the transform. Then re-run recon-all
including the -no-tal-check option
On 2/2/18 9:14 AM, Dijkshoorn, A.B.C. (Aicha) wrote:
Hello free surfer developers,
I am attempting to compute cortical thickness for anatomical ROIs in
neonates, but for some of my subject
Probably just partial volume correction
On 2/1/18 3:37 PM, Maksimovskiy, Arkadiy wrote:
Dear Experts,
I was wondering if anyone might know why the WM hypointensities total
number in aseg does not match the sum of left and right white matter
hypointensities.
Thanks,
Arkadiy
--
Arkadiy L
Can you upload the glmfit folders and the glmfit input (--y file) to our
filedrop?
https://gate.nmr.mgh.harvard.edu/filedrop2/
On 2/1/18 7:46 PM, miracle ozzoude wrote:
Hello Doug,
I have attached a screen shot of the mask.mgh for both right and left
hemispheres. Everything looks yellow. I
Yes, use the --pvr option to mri_glmfit (per-voxel regressor). Search
through the mail archives for an example on how to use it
On 2/3/18 12:10 PM, std...@virgilio.it wrote:
Hi list,
Is there a way to obtain a map that report the "vertex by vertex"
correlation between the FC (obtained by FS
On 2/2/18 7:47 AM, std...@virgilio.it wrote:
Hi list,
in reference to One Group (One Factor), Two Covariates
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx
that has been applied on FS-FAST fcMRI data
I obtain three folder, respectively, for "main", "covariate 1",
"co
On 2/2/18 8:01 AM, Backhausen, Lea wrote:
Dear freesurfer experts,
I started using qdec for comparing cortical measures in adolescent
patients with ADHD versus typically developing adolescents and I have
a few questions concerning the ROI analysis as well as the
Desikan-Killiany versus Destr
Try adding -oc 0 0 0 to the mri_convert command line
On 2/2/18 7:27 AM, Helen Beaumont wrote:
> I am using the command
> mri_convert -at transforms/talairach.xfm brain.mgz brain_in_tal.nii.gz
>
> to convert a native-space skull-stripped T1 image to talairach space. I used
> recon-all to generat
On 1/31/18 8:33 PM, Ben Smith wrote:
Hi all,
I read from the freesurfer discussion archives that when combining FSL
FEAT with freesurfer, one should definitely NOT do spatial smoothing
in the preprocessing when preparing to examine cortical data.
https://www.mail-archive.com/freesurfer@nmr
Can you send the terminal output of one of the runs that fails?
On 1/31/18 4:10 PM, Sims, Sara A wrote:
Freesurfers,
I am trying to use a cortical label to label wm. I am using the
following command line:
mri_aparc2aseg --s $patient --annot 8V1 –labelwm
And most of the time in most subjec
what do you mean by stats? The mean values of the inputs for each
cluster and subject will be in the output ("ocd" file). See
mri_glmfit-sim --help
On 1/31/18 4:48 PM, Shatil, Anwar Shahadat wrote:
Hello Experts:
After running mri_glmfit sim, I got below clusters:
ClusterNo Max VtxMax S
Hi Keishi,
the frame parameter is the frame in the contrast file. Most of the time
this file will only have one frame (-frame 0) unless you have specified
a multivariate contrast. This does not have anything to do with
multiband. What is your intention when looping through from 0 to 19?
doug
Strange. Can you send me the analysis.info file?
On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
> Hello Dr. Greve,
>
> Yes it exists. The output below was with debug option.
>
> Best
> Idil
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun
what version of FS are you using? What is your bbregister command line?
You should not smooth the data before alignment (usually you would use
the template used for MC). You should also make sure that the
deobliquing does not mess up the geometry info in the nifti file. Load
the template file i
Hi Sara, it looks like you are doing a functional constraint. See these
slides
http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.Part2.pptx
(tutorial here
https://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0)
and let me know if you have any questions
doug
On
You need to map the mask into the fsaverage space. Probably the easiest
way to do this is to run recon-all on your template to get surfaces.
Then run mri_vol2surf to map your mask onto the surface, then use
mris_apply_reg to map your surface mask to fsaverage (make sure to
--no-rev since you ar
If you want to just run the recon-all pipeline without using n3, you'll
have to do something else. You can copy orig.mgz to nu.mgz (or create a
symbolic link, which is probably better), then run with -nonuintensitycor
On 1/29/18 7:14 PM, Alexis Moscoso wrote:
Hello Freesurfer developers,
I’m
That file should be in the same dimensions, no?
On 1/30/18 12:19 AM, Ashley Cole wrote:
I just noticed that that file "fmc.odd.sm5.nii.gz" is created after
selxavg3-sess. I was wondering how can I preprocess the functional
image and have the output with the same dimension as the f.nii.gz
with
Hello Doug,
I have uploaded the files you requested. Thank you for your help.
Best,
Paul
On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve
wrote:
> Can you upload the glmfit folders and the glmfit input (--y file) to our
> filedrop?
>
> https://gate.nmr.mgh.harvard.edu/filedrop2/
>
> On 2/1/18 7:4
It should be possible. Just specify the annotation you want to use iwth
the -p flag (run with -help to get more info)
On 1/25/18 12:48 PM, Lisa Delalande wrote:
Dear FreeSurfer expert,
I would like to use the new destrieux atlas for extracting anatomical
data with the aparcstat2table command
Thanks Douglas. Just one more quick question: will -nonuintensitycor work
if I set the -3T flag? As far as I know, -3T changes some parameters of the
N3 correction and makes use of Schwarz atlas. I was wondering whether this
flag interferes with -nonuintensitycor.
El El sáb, 3 feb 2018 a las 21:01
I don't think so
On 2/3/18 3:28 PM, Alexis Moscoso wrote:
Thanks Douglas. Just one more quick question: will -nonuintensitycor
work if I set the -3T flag? As far as I know, -3T changes some
parameters of the N3 correction and makes use of Schwarz atlas. I was
wondering whether this flag inter
Since I'm following the example on the github page, using the ds005
dataset, now with the correct license binding, I am surprised to see
freesurfer exiting with errors (but I don't know much about freesurfer):
I run this:
docker run -ti --rm -v
/Volumes/Main/Working/BIDS_TESTING/license.txt:/lice
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