perations that can be
executed independently ?
I hope to have explained myself correctly
Thanks in advance.
Cheers
2018-05-03 18:28 GMT+02:00 Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>:
No, not currently
On 05/03/2018 11:26 AM, M Janani wrote:
>
> Hi Team,
>
>
External Email - Use Caution
Hi Team,
I have one doubt. Can I input T2 weighted images for recon-all
command?
Regards,
Janani
::DISCLAIMER::
--
External Email - Use Caution
Hi Team,
We would like to compute the CSF value from the MRI data. We
have both T1 and T2 weighted images.
Have processed the T1 images and obtained the CSF
value(summation of ventricular system and CSF value). But it
Thanks andrew... I will try this
From: Hoopes, Andrew
Sent: Tuesday, February 20, 2018 8:55:47 PM
To: M Janani; Freesurfer support list
Cc: Sasikala Sethu
Subject: Re: [Freesurfer] Error in running make_average_subject
Hi Janani,
We have a patch for this bug
Dear FreeSurfer Experts,
I’m recently getting an error in make_average_subject and can’t find
the reason.
Please see the following for the error log from recon-all.log:
mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel
mri/norm.mgz mri/transforms/tala
found? What is the terminal output?
On 09/13/2017 07:07 AM, M Janani wrote:
> No.
> When we ran the unsetenv FS_LOAD_DWI, we got command not found error.
>
> Thanks,
> Janani
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
&
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault
Do you mean that the error is still there even after running the unsetenv
command? And you ran them from the shell, one after the other?
On 09/12/2017 02:27 AM, M Janani wrote:
> Hi Douglas,
>
>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault
Try running
unsetenv FS_LOAD_DWI
then re-running recon-all
On 09/11/2017 12:57 PM, M Janani wrote:
>
> Hi Team,
>
> Am getting segmentation erro
Hi Team,
Am getting segmentation error during the reconstruction process.
Please help in resolving the error.
I have attached log for reference.
Thanks,
Janani
::DISCLAIMER::
---
Hi Team,
Could you please tell me how to modify this command to perform
SGTM
mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM
--seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o
gtmpvc.output
I have tried with -sg
Hi team,
Could anyone please tell how to create the time.dat file in the
Kinetic Modelling MRTM1 step
mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1
--no-est-fwhm --nii.gz
Regards,
Janani
::DISCLAIMER::
-
Behalf Of Douglas N Greve
Sent: 15 August 2017 00:12
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer PIB PET image processing
If you use mri_gtmpvc, then the gtm.stats file will have the intensity values.
On 08/11/2017 02:37 AM, M Janani wrote:
> Thanks for your supp
esurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer PIB PET image processing
>
> We do not have any thing to specifically analyze PiB. You can look at
> the PETsurfer page for more general instructions
>
>
> On 08/09/2017 02:15 AM, M Janani wrote:
>&
] Freesurfer PIB PET image processing
We do not have any thing to specifically analyze PiB. You can look at the
PETsurfer page for more general instructions
On 08/09/2017 02:15 AM, M Janani wrote:
>
> Hi Team,
>
> I apologize, I am new to Freesurfer.
>
> Currently we are process
. I would not trust the 2nd formula since we don't
compute actual ICV
On 8/2/17 2:22 AM, M Janani wrote:
Hi Douglas,
Thanks for your support.
From the below conclusion, can I say
Total ventricular CSF = (lh + rh) Lateral-Ventricle + = (lh +
rh)Inf-Lat-Vent
Hi Team,
I apologize, I am new to Freesurfer .
Currently we are processing PIB PET images.
When we compare the SPM data along with FREESURFER outputs. We
were able to see a large variation in the values.
Could you please guide us in processing PI
Douglas
Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22>
Mon, 31 Jul 2017 07:48:02
-0700<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20170731>
On 7/31/17 3:12 AM, M J
Hi Team,
Could you please confirm whether the below mentioned formulas
to compute Total WM and ventricular CSF are correct
1. Total White Matter = CerebralWhiteMatterVol + (lh+rh) Cerebellum
White Matter
2. Total ventricular CSF = (lh + rh) Lateral-Ventricle + =
07/25/2017 08:33 AM, M Janani wrote:
>
> Hi Team,
>
> I would like to create mask for Total Gray matter and
> white matter volume.
>
> I was able to get the total white matter volume using the below
> mentioned command
>
> mri_binarize -i ap
Hi Team,
I would like to create mask for Total Gray matter and white
matter volume.
I was able to get the total white matter volume using the below mentioned
command
mri_binarize -i aparc+aseg.mgz --wm --o wm.mgz
But I couldn't find any option to create the mask for Total Gray
u get exactly the same error?
On 07/14/2017 02:05 AM, M Janani wrote:
>
> Hi Douglas Greve
> <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22>,
>
> Thanks for your support.
>
> I tried with the --resh
Regards,
Janani
---
How did you create the segmentation? You can change the shape of the seg with
mri_surf2surf --reshape 6 --s fsaverage --hemi lh --sval seg.mgh --tval
seg.reshape.mgh
On 7/7/17 10:15 AM, M Janani wrote:
Hi Team,
I'm attempting
Hi Team,
I'm attempting to extract cortical thickness values for a region-of-interest
(ROI) defined in volume spacesubject for PiB MRI.
I got the below mentioned error while computing the stats value
cwd
cmdline mri_segstats --seg
freesurfer/subjects/fsaverage/surf/lh.fsaverage.CBLROI.mgh --in
Hi Team,
Currently I'm working on ROI analyses. I saw one article
related to VolumeROICorticalThickness in Free surfer wiki.
Could anyone please tell me what is the anatomical
file(TT_avg152T1.nii) they are referring to?
I took AAL ROIs from SPM.
Hi Team,
Currently I'm working on ROI analyses. I saw one article
related to VolumeROICorticalThickness in Free surfer wiki.
Could anyone please tell me what is the anatomical
file(TT_avg152T1.nii) they are referring to?
I took AAL ROIs from SPM.
Hi freesurfer team,
I apologize, I am new to freesurfer.
I'm doing analysis on PiB. I have successfully got my .stats
files by running the recon-all command.
When I checked for Left Cerebellum Exterior and Right
Cerebellum Exterior value in the
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