Thank you Bruce!
Rashmi
On 3/4/14 12:43 PM, "Bruce Fischl" wrote:
>Hi Rashmi
>
>the regions are disjoint, so if you want all temporal lobe you need to
>add
>them together.
>
>cheers
>Bruce
>
>On Tue, 4 Mar 2014, Rashmi Singh wrote:
>
>> Thank yo
ve
>
>cheers
>Bruce
>On
>Tue, 4 Mar 2014, Rashmi Singh wrote:
>
>> Is there any way to get the volume for the temporal horn using
>>FreeSurfer.
>> Thanks,
>> Rashmi
>>
>>
>
>
>The information in this e-mail is intended only for the p
Is there any way to get the volume for the temporal horn using FreeSurfer.
Thanks,
Rashmi
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The information in this e-mail is intended
Hello,
How can I generate volume for temporal horn, temporal white matter and temporal
gray matter.
Thanks
Rashmi
Sent from my iPhone
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Hi FreeSurfer experts,
How do I get the volume measurements of just the temporal white matter and
gray matter.
Thanks,
Rashmi
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Th
Hello FreeSurfer experts,
I have a question regarding group analysis and running of recon all group
wise.
For example I have group A, B, and C with several subjects in each group, if
want want to compare their cortical and subcortical measurements group wise,
how do I run the recon all.
Also c
v5.3).
>
>https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
>
>-Louis
>
>On Thu, 7 Nov 2013, Rashmi Singh wrote:
>
>> FreeSurfer experts,
>> May you please educate me how the supra tentorial volume (STV)
>>measured by
>> FreeSurfer and which date does i
FreeSurfer experts,
May you please educate me how the supra tentorial volume (STV) measured by
FreeSurfer and which date does it take as input file to calculate this variable.
Thanks,
Rashmi
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htt
Hello,
This morning I tried to get the segmentation measurement in table formate, but
I got the following error message
asegstats2table --subjects AB197.T0b AB232.T0a AD721.T0 --skip --meas volume
--tablefile asegstats1.txt
Error message :SUBJECTS_DIR : /opt/freesurfer/subjects
Parsing the .sta
Hello FreeSurfer experts,
I am trying to run recon all on my data set, but I got following error message.
Please help me understand the message and suggest solution.
Thanks,
Rashmi
#@# Skull Stripping Tue Oct 22 13:57:00 CDT 2013
/home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/ANAL2013/Co
Hello FreeSurfer experts
I was looking into the aseg.stat files following reconall runs and found that
intracranial volume measurements were really small for some subjects, while
other measures were comparable ( example below)
May you suggest the reason for that.
Cortex voll
use this option.
Rashmi
___
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, September 13, 2013 9:09 AM
To: Rashmi Singh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] recon all question
what do you want to do
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, September 13, 2013 8:46 AM
To: Rashmi Singh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] recon all question
1. I don't think I know anyone who has done this, and we haven't asses
, September 12, 2013 5:27 PM
To: Rashmi Singh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon all question
Hi Rashmi
putting them in the orig folder with those numbers will get recon-all to
do motion correction and averaging.
cheers
Bruce
On Thu, 12 Sep 2013, Rashmi Singh wrote
Hello Freesurfer experts,
I am doing volumetrics study. During the scan we get 2-3 mprage per scan for a
subject.
While running the FreeSurfer, if I want to use the three mprages for that
subject as an input file, may I just keep the three mgz files (001.mgz, 002
.mgz and 003.mgz) in the
Hello FreeSurfer experts,
I am doing volumetrics study. During the scan we get 2-3 mprage per scan for
a subject.
While running the FreeSurfer, if I want to use the three mprages for that
subject as an input file, may I just keep the three mgz files (001.mgz,
002.mgz and 003.mgz) in the orig
cking the better mprage (i.e. less motion) and
>analyzing it at each timepoint
>
>cheers
>Bruce
>
>
>
>
>On Thu, 14 Mar 2013, Rashmi Singh wrote:
>
>> Thank you Bruce.
>> So what should I do.
>> Shall I just take one of the mprage values or is it a good
>
>of course they are different - there is noise in the scans and motion and
>other sources of corruption! The amount of difference will depend on the
>structure and the quality of the data.
>
>cheers
>Bruce
>On Thu, 14 Mar 2013, Rashmi Singh
>wrote:
>
>> Hello exp
Hello experts,
I am doing volumetric studies where I am comparing the subcortical
structures volumes among different experimental groups.
I usually do two mprages on one subject in a single scan at two time-points. I
run recon all on both mprages for a single subjects. To my surprise the volu
Hi Melonee,
Please record my off Campus work hrs this morning at OU.
IN 9:30 AM and out 1:10 PM.
I have logged into LIBR when I entered so that should be in records.
Let me know if you may have any question.
Thanks,
Rashmi
On 2/11/13 8:39 AM, "freesurfer-requ...@nmr.mgh.harvard.edu"
wrote:
>Se
;getting rid of all the dura without removing any problem is exceedingly
>difficult (if not impossible). Usually we live with some remaining dura
>as it doesn't affect the surface placement much.
>
>cheers
>Bruce
>On Tue, 2 Oct 2012, Rashmi
>Singh wrote:
>
>> H
Hello experts,
I am getting skull strip issues with FreeSurfer recon-all runs in every data.
I ran recon-all on my T1-data and noticed that the skullstrip is not so good.
Almost in every subjects there were dura included, so I tried the suggestion
of using the flags -skullstrip and -Clean–bm an
u still having trouble? You are definitely still on the list.
>
>> I see. Nick and/or help: can you investigate?
>>
>> thanks
>> Bruce
>>
>>
>> On Thu, 27 Sep 2012, Rashmi Singh wrote:
>>
>>> Reply,
>>> Yes I started posting since l
d time-of-day.
>
>cheers
>Bruce
>
>
>
>On Thu, 1 Mar 2012, Rashmi Singh wrote:
>
>> Hello,
>> I am finding differences in hippocampus voulme of same subject when
>>scanned at different times . Our study requires our subjects to be
>>scanned 3-4 tim
Hello experts,
I have the aparcstat files for corticla thickness. I would want to know is
there any information on how may I group these regions more broadly ex frontal
, temporal lobe areas.
Thanks
Rashmi.
This document may contain information covered under th
Hello,
I am running longitudinal stream processing on mprage scans of some subjects
who have been scanned multiple times using the same sequence with 32 NOVA
channels on GE scanner.
For most subjects the base run exited without error, however for few error was
reported in the runs.
The error wa
copy the list so that others can see the answer
>and so that others can help with the answer.
>thanks!
>doug
>
>On 05/16/2012 11:56 AM, Rashmi Singh wrote:
>>
>> Dough,
>>
>> Yes, the stat files exist with all its content. I can individually
>> import the t
Hello,
I am trying to get the asegmentation information after the recon-all run in
the table form, but I am continuously getting the following error
asegstats2table --subjects AA262.G1 AA267.G2 AA304.G1 --meas volume --tablefile
asegstats.txt
SUBJECTS_DIR : /opt/freesurfer/subjects
Parsing the
Hello,
I ran recon –all on my scans and the output files reported the following error:
SUBJECTS_DIR
/home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer
FREESURFER_HOME /opt/freesurfer
Loading source label.
Invalid argument
ERROR reading
/home/rsingh/storage/labs
Hello,
I converted the aseg. mgz files to nii format and created a hippcampal mask
with 3dcalc.
Using AFNI I opened the hippocampal mask as overlay on the brainmask .nii image
as underlay. For some subjects the hippocampus is not at the correct position.
Please advise.
Thanks,
Rashmi.
__
Hello,
I am finding differences in hippocampus voulme of same subject when scanned
at different times . Our study requires our subjects to be scanned 3-4 times
(T0-T3) within a period of 1 month. We have performed MRI Scanning on all our
subjects with same sequence using 3T GE scanner.
Pleas
Hello.
I am using FreeSurfer to generate subcortical volumes and cortical thickness
for my subjects.
Does FreeSurfer normalizes the subcortical volumes to the whole brain volume
for each subjects.
Let me know.
For among subjects comparison I am assuming that the sub cortical volumes
generat
Hello,
I had this issue raised earlier, but may be it got lost in the pile of
questions you receive everyday.
I am very new to freeSurfer, and may be its me who is dong something wrong so
please advise.
I am getting defects in the volume output of freesurfer with respect to the
pial surfac
Hello,
I am getting defects in the volume output of freesurfer with respect to the
pial surface and whilte-matter surface boundary. I am wanting to measure the
cortical thickness after running recon_all. I was inspecting the pial and white
surface using tkmedit and I noticed (volume data view
While opening tkmedit using terminal I gave following command
% crick:~/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/FreeSurfer> tkmedit
AA471.T0 brainmask.mgz -aux T1.mgz -segmentation aseg.mgz -surfs
$FREESURFER_HOME/FreeSurferColorLUT.txt
The output was
Converting main surface: 100% done.
Conv
Hello,
I ran recon all on my subjects data which went well. Now I would like to use
AFNI-SUMA to view it , how do I go about doing this.
Thanks,
Rashmi.
This document may contain information covered under the Privacy Act, 5 USC
552(a), and/or the Health Insura
Hello,
I was trying to get the cortical thickness in the table format for all of my
subjects on which I had run recon all. I see the stats folder with
rh/lh.aparc.stats files.
My command was:
aparcstats2table --subjects AA471.T1 AA471.T2 AA471.T3 AA474.T0 AA476.T0
AA479.T0 AA483.T0 AA483.T2 AA
easurements for
getting the total cortical surface area?
Looking forward for your response,
Thanks,
Rashmi.
"
On 1/18/12 9:18 AM, "Bruce Fischl"
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
On Wed, 18 Jan 2012, Rashmi Singh wrote:
Hello,
This is Rashmi. I am very new to ne
Hello,
This is Rashmi. I am very new to neurobiology and computing and my very first
project involves measuring cortical thickness from the reconstructed surfaces
generated by FreeSurfer. I have recently started to self teach myself
FreeSurfer, but with a background in immunology and almost no
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