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Dear freesurfer experts,
I want to create an equivolumetric surfaces (using the tool from:
https://secure-web.cisco.com/1RxQBNBh7QLlgBP46WWIONAGLCrtuooPBalXpNMTOlsF1eoOQXja0KaogvHBx39bkqpnP1Qnz5FuZhT-DTLRXZLIQWp64WXTSgyrwspQMNHWCVzQPv1cqguMDF7AiGzYh01
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Hello Freesurfer experts,
i am doing some editing after recon-all. I have the issue that one gyrus is
not captured by the pial surface. There is no wm that is wrong and that i
could correct. It looks like this gyrus has a weird angle so there is
actua
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Hello FreeSurfer Developers,
I am brand new to using freesurfer, just learning for the first time. I
have freesurfer installed and sourced on linux Ubuntu 18.04.5 LTS. My NfTI
files are stored on a windows share drive which I mount to the linux
machine
I have not seen anything of that magnitude. I do see a systematic drop
in the thickness with v7 relative to v6, but it is on the order of 1 or
2%. It might be something specific to the pulse sequence that you are
using. Try looking at the surfaces of the subject that has the largest
discrepancy
On 2/25/2021 9:43 AM, Jayachandra Raghava wrote:
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Hello Douglas,
Thank you for your advice.
As you have suggested, I have now used orig.mgz from the recon-all
longitudinal processing stream as an input to Samseg longitudinal
processing stream. For compa
There would be a lot more (if running to the end). You can look at the
recon-all.cmd file for a list of commands in the order that they are run
On 3/18/2021 4:19 PM, Jaiashre Sridhar wrote:
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Hello,
I am using FreeSurfer version v7.1.1. For few subjects who
If it came from running recon-all, then it is corrected for bias fields.
Note that B1 is a particular type of bias field (often quite minor at 3T
and below).
On 3/18/2021 2:25 PM, Arman Avesta wrote:
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Hi FreeSurfer gang,
I'm using ADNI's pre-processed dat
Yes, skullstrip will create that file
On 3/18/2021 12:42 PM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:
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Hello Freesurfer Developers,
am trying to use run freesurfer that is configured inside
smriprep.workflow.anatomical.py under init_anat_preproc_wf pipeli
sounds like you need mri_vol2surf (use --projfrac 0.5)
On 3/18/2021 11:38 AM, Karan Desai wrote:
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Hi Freesurfer List,
I am running fMRIPrep and getting the first two FS output files (aseg
and aparcaseg seen above in the screenshot), but not the actual file
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Hi FreeSurfer gang,
I'm using ADNI's pre-processed data to train a neural network. Specifically,
for each included subject I'm using FreeSurfer Cross-Sectional brainmask.mgz
(as input).
My question is: are these ADNI pre-processed brainmask.mgz volum
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Hi Anastasia
It is working!-thanks so much for your help.
Regards,
Shanika
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Thursday, March 18, 2021 12:26 PM
To: Freesurfer support
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Hello Freesurfer Developers,
am trying to use run freesurfer that is configured inside
smriprep.workflow.anatomical.py under init_anat_preproc_wf pipeline. this
workflow, does the following:
1. T1w reference: realigning and then averaging T1w im
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Hello,
I am using FreeSurfer version v7.1.1. For few subjects who have already been
through the complete recon-all pipeline, I would like to re-run the recon steps
downstream of “-fill”. I am using the following commands to do so. Can an
expert chec
Hi Shanika - Can you try separating the "=" signs from the variable names in
the config file with a space?
Best,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Shanika Jayakody
Sent: Thursday, March 18, 2021 9:55 AM
To: Freesurfer support
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Hi Freesurfer List,
I am running fMRIPrep and getting the first two FS output files (aseg and
aparcaseg seen above in the screenshot), but not the actual file I need which
is the one where it is resampled to the mesh. I have run fMRIPrep and have
th
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Thanks a lot Martin.
Regards
Suzan
On Thu, 18 Mar 2021 at 9:09 pm, Reuter, Martin,Ph.D. <
mreu...@mgh.harvard.edu> wrote:
>
> Hi Suzan,
>
> actually it uses rigid within-subject registration.
> The transformation files should be in ./mri/transforms (i
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Hi Anastasia
Thanks so much for your reply. I have attached herewith the scripts/log file
-please let me know if you need anything else.
Regards,
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, A
Hi Suzan,
actually it uses rigid within-subject registration.
The transformation files should be in ./mri/transforms (in long and in base).
Best, Martin
On 17. Mar 2021, at 23:05, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
Where is the non-linear registration coming from? Our lo
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OK, I will try later. Thanks!
-原始邮件-
发件人:"Douglas N. Greve"
发送时间:2021-03-18 06:03:24 (星期四)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Troubleshooting: Soft Failures
The contrast is pretty low (probably due to the high resol
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