] mri_gtmpvc RBV - cannot find file from a
custom subject directory
That is the way I would have suggested. Does it run to completion when you use
the softlink? Reorganizing the folder structure it likely to break a lot of
things. On 7/11/2024 10: 02 AM, Sneha Pandya wrote: External Email - Use
External Email - Use Caution
Dear team,
I am running mri_gtmpvc using RBV correction, however when I do so I get an
error message saying it cannot find $SUBJECTS_DIR/$subject_id/mri/orig.mgz
needed for RBV.
Our Freesurfer outputs are nested as
output volume where the resolution is high enough to resolve the tissue types
into different volumes (rbv).
On 6/11/2024 11:11 AM, Sneha Pandya wrote:
External Email - Use Caution
Dear team,
I am using mri_gtmpvc to obtain PVC’ed regional data which we will use as an
input TAC to perform
External Email - Use Caution
Dear team,
I am using mri_gtmpvc to obtain PVC'ed regional data which we will use as an
input TAC to perform kinetic analysis.
In addition, we are also doing static SUVR analysis (sum of frames from 60-90
mins) in which I am scaling input PET data
External Email - Use Caution
Dear team,
I am using mc-afni2 to perform motion correction on dynamic PET images (ref:
petsurfer wiki page). I am planning to use an average of un-censored frames as
a template to do so. What should the threshold be to estimate these set of
External Email - Use Caution
The Division of Medical Nuclear Physics in the Department of Radiology at Weill
Cornell Medicine is seeking a full-time Medical Imaging Analyst to support its
active research program in PET and Nuclear Medicine.
Interested individuals must have at
th subfields {Disarmed}
Actually, I don't think there is an example. You can run samseg without it
running samseg2recon, but once you specify --s, it will run samseg2recon
On 6/8/2020 11:22 AM, Sneha Pandya wrote:
External Email - Use Caution
Ahh perfect, thank you Doug
Can you share an examp
surfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields {Disarmed}
Oh, sorry, that way of running recon-all will run samseg2recon. Sorry, I lost
track of what you are asking
On 6/8/2020 10:45 AM, Sneha Pandya wrote:
External
rd.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields {Disarmed}
On 6/5/2020 4:47 PM, Sneha Pandya wrote:
External Email - Use Caution
Thank you Doug.
it is not run by default
* When I ran “samseg2recon –s subject” after running sa
rvard.edu>
Sent: Friday, June 5, 2020 4:05 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields {Disarmed}
On 6/5/2020 3:54 PM, Sneha Pandya wrote:
External Email - Use Caution
Dear Dough,
I
that folder
On 5/5/2020 10:45 AM, Sneha Pandya wrote:
External Email - Use Caution
Dear experts,
I want to revisit if anyone has ran subfield analysis just by running samseg?
If it is possible is it as reliable as from running regular routine with “-all”
recon-all flag?
Thank you,
Sneha
OrE=B8aRiWly3gmmmg0vnY6wn5kmlR0tHteUEB2hOkzaoCE=3enydUNbkb3fHf4FjYUaK6STd9w98j288fmleKlGijs=>
From:
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Sneha Pandya
<mailto:snp2...@med.cornell.edu>
Reply-To: Freesurfer support list
<mailto:freesurfer@nmr.mgh.harvard.edu>
Da
lT9-RXrryqt9KZX2qu2s=AEsux002jQ5JzIPYIcsXKAuQmrt-1dubP8ZVldIiOrE=nvkbJLwGOMiMASjTHtMkLyhmC8Acu6t2DmhnDK56BfY=Jzs0r2z0IWEF_kMnRWpLOUDfJdqkszjHdQCQKVvAnfs=>
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Sneha Pandya
mailto:snp2...@med.cornell.edu>>
Reply-To:
External Email - Use Caution
Dear experts,
I want to revisit if anyone has ran subfield analysis just by running samseg?
If it is possible is it as reliable as from running regular routine with "-all"
recon-all flag?
Thank you,
Sneha
From: Sneha Pandya
Sent: Thurs
External Email - Use Caution
Dear experts,
Is it possible to run subfield analysis (hippcampal subfields, amygdalar,
thalamic nuclei, and brainstem structures) when we only run samseg on our
dataset?
Thank you,
Sneha
___
Freesurfer
, or is it because I
am saving pairwise difference maps in a completely different folder?
Thanks,
Sneha
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sneha Pandya
<snp2...@med.cornell.edu>
Sent: Thursda
ime. I think mri_concat can do pairwise differences. And
you would have to setup the GLM on your own with mri_glmfit or create a qdec
table where you only have one entry per subject.
Best, Martin
On 10. Aug 2017, at 17:02, Sneha Pandya
<snp2...@med.cornell.edu<mailto:snp2...@med.cornell.edu&
Hi Bruce and Martin,
Wanted to follow up and see if you'll got a chance to look at the error and if
I could try out something?
Thanks,
Sneha
From: Sneha Pandya
Sent: Tuesday, August 8, 2017 11:29:23 AM
To: Freesurfer support list
Subject: Re: [Freesurfer
support list
Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case
thanks Sneha
you'll probably need to wait until tomorrow for Martin to read his email :)
cheers
Bruce
On Mon, 7 Aug 2017, Sneha Pandya wrote:
>
> Hi Bruce,
>
>
> Sure, please see highlighted below pa
eha
can you include the output as text instead of an image?
thanks
Bruce
On Mon, 7 Aug 2017,
Sneha Pandya wrote:
>
> Hi Bruce,
>
>
> Please find attached recon-all.log file and I used following command to run
> the base:
>
>
> recon-all -base ped1_base -tp ped1_0 -tp ped1_1 -
Dear team,
I have completed cross-sectional pipeline on my pediatric case with a baseline
and 4 follow up time points between 4-7 years of age. However, I was not able
to run longitudinal pipeline on it as the base template creation failed with
some topological errors. I assume this failure
re including the "-clean-FLAIR" flag in your autorecon3 command will
> do the job.
>
>
> best,
>
> Andrew
>
> --------
> *From:* Sneha Pandya <snp2...@med.cornell.edu>
> *Sent:* Tuesday,
Perfect, shall go ahead with bbr-init-spm and will try running it with
"-clean-FLAIR" flag.
Thanks again!
Sneha
From: Hoopes, Andrew <ahoo...@mgh.harvard.edu>
Sent: Tuesday, January 24, 2017 2:15:31 PM
To: Sneha Pandya; Freesurfer support
with bbr-init-spm and
FLAIRpial flags, but it did not overwrite FLAIR.prenorm.mgz and FLAIR.mgz
volumes.
Thanks,
Sneha
From: Hoopes, Andrew <ahoo...@mgh.harvard.edu>
Sent: Tuesday, January 24, 2017 12:20:03 PM
To: Freesurfer support list; Sneha Pandya
Subje
Hi Bruce,
Any luck with what went wrong?
Thanks,
Sneha
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sneha Pandya
<snp2...@med.cornell.edu>
Sent: Wednesday, January 18, 2017 2:43:01 PM
To
rfer support list
Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
oh, something else went wrong, it's not a memory issue.If you upload the
subject we will take a look
Bruce
On Wed, 18 Jan 2017, Sneha Pandya wrote:
>
> Sure, please find it attached.
>
t-header
Hi Sneha
how much RAM do you have in your machine? And what is the resolution of
your data?
cheers
Bruce
On Wed, 18 Jan 2017, Sneha Pandya wrote:
>
> Hi all,
>
>
> I have successfully ran recon-all on my subjects with multiple T1s. We want
> to use flair to refine pial su
Hi all,
I have successfully ran recon-all on my subjects with multiple T1s. We want to
use flair to refine pial surfaces as for all the subjects pial surfaces are
messy and will demand lots of control point edits.
After successfully running entire recon-all stream I am running following
nd certainly those results are way
worse than what we typically find. From the little bit of data it looks
like the motion corruption is pretty bad. Is that the case?
If you upload a representative subject we will take a look
cheers
Bruce
On Thu, 17 Nov 2016, Sneha Pandya wrote:
>
> Hi team,
behalf of Douglas Greve
<gr...@nmr.mgh.harvard.edu>
Sent: Friday, October 28, 2016 12:07:13 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tmp directory not created {Disarmed}
you can make it with mkdir tmp
On 10/28/16 11:41 AM, Sneha Pandya wrote:
Hi
Douglas
,
Ideally, when
ay, October 28, 2016 11:27:25 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tmp directory not created
which tmp folder?
On 10/26/16 11:26 AM, Sneha Pandya wrote:
Hi all,
I am running recon-all stream for ~200 subjects and after successful run of
them I observed that for some of the pat
Hi all,
I am running recon-all stream for ~200 subjects and after successful run of
them I observed that for some of the patients recon-all ran successfully
without error but it did not create "tmp" sub-folder. Can anyone please advice
when recon-all stream does not create "tmp" folder and do
Dear all,
I am new to FS QA tool and would like to understand interpretation of results
from QA tool as indicated by Matthieu below. Any guidance or directions will be
of great help as I need to QC ~400 subjects and think this tool can come in
handy.
1) Which problems to identify by looking
le not found' messages). Anyway.
This is 5.1 and very old. I would recommend to check the IO disk space thing
above and rerun these cases.
Best, Martin
On 04/01/2016 11:36 AM, Sneha Pandya wrote:
Dear experts,
We are running longitudinal pipeline for bunch of our MS subjects. Longitudinal
reco
Dear experts,
I usually setup batch jobs for my studies and use '-mail' option that emails me
completion of recon-all with or without errors. Is there a way or any other
option that I can use alongside '-mail' to give me custom status message than
the usual one which says "recon-all -s XYZ
Dear freesurfer experts,
I want to concatenate *.xfm transformation from bbregister with *.mat from
flirt. For that I need to convert .xfm to .mat. Any idea how can that be done?
Thanks,
Sneha
___
Freesurfer mailing list
...@nmr.mgh.harvard.edu] on behalf of Sneha Pandya
[snp2...@med.cornell.edu]
Sent: Tuesday, January 27, 2015 12:03 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Which command to use if pial extends to cerebellum
Hi Team,
I have few of my images in which pial surface extends to the cerebellum
Oct 2014, Sneha Pandya wrote:
Thanks again, yes that's what it looks like, but I just have one concern, if
I have to manually edit dura and wm in all the slices and in most of the
subjects, will it still give me reliable cortical thickness measure?
Thanks,
Sneha
2014, Sneha Pandya wrote:
Dear all,
I am running recon-all on few SPGR T1s and few MPRAGE T1s. However most of
my dataset, may it be SPGR or MPRAGE has some artifacts and poor wm/gm
contrast. Have attached a screen shot of bad pial and wm error (going beyond
dura). Even gcut did not do a good
is your best bet (sorry)
Bruce
On Fri, 10 Oct 2014, Sneha Pandya wrote:
Hi Bruce,
Yes, there is a lot of dura. Unfortunately we do not have either flair or
T2 as a reference to remove dura. I tried running gcut to cut off dura,
it still won't help and I still had to manually edit whole volume
Hi all,
Sorry for the follow up but hope someone can clarify following doubts.
Thanks,
Sneha
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sneha Pandya
[snp2...@med.cornell.edu]
Sent: Tuesday, October 07
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