Hello,
Just a quick question regarding the computed intracranial volume. I have
ran Freesurfer version 5.1 and I have been using the intracranial volume
from the aseg.stats file to correct for head size. I just want to ensure
this is where I get the intracranial volume from.
Thank you in advance
list
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Hi Tamara
have you visualized the multiple time points of a subject whose ventricular
volume is decreasing? How big a decrease are you seeing?
cheers
Bruce
On Tue, 5
Sep 2017, Tamara Tavares wrote:
> Hello,
Hello,
I used the default longitudinal stream to calculate ventricular volumes
over time. When I examined the difference score (longitudinal-baseline) I
noticed that for some participants ventricular volumes *decreased*. The
same site, scanner and scanning protocol was used for both baseline and
l
Hello,
I have made edits to aseg files in the longitudinal outputs
(participantID.long.participantID-temp). I am beginning the reconstruction
phase and as suggested by a response to an earlier post I am running:
recon-all -long tpN1 template ID -autorecon2-noaseg -autorecon3, where tpN1
is cross-s
Hi All,
I was hoping someone can help me with two naive questions I have:
I have read on the Freesufer wiki that you should smooth surface data
before analyzing. Should I smooth the data only after I have ran recon-all
and have made edits? Also, should volumetric data be smoothed or is this
limit
09:51 AM, Douglas Greve wrote:
>
>The data does not necessarily need to be smoothed, but people
usually do because it improves stats. But I thought you were doing
an ROI analysis based on the first question
>
> On 6/6/17 11:50 AM, Tamara Tavares wrote:
>> Hello,
>>
Hi Douglas,
The message stream indicates you replied to my email but I don't see your
response in the email thread. I am not sure what happened. Can you please
reply again?
Thank you,
Tamara
On 6/6/17 11:50 AM, Tamara Tavares wrote:
> Hello,
>
> I have ran my data through the def
Hello,
I have ran my data through the default recon-all processing stream and am
planning on analyzing ventricular volume and cortical thickness. I was
wondering whether I need to use the Qdec to complete the ventricular volume
and cortical thickness analysis, or can I export the data (txt files f
Hello,
I am currently checking and editing the aseg outputs in my longitudinal
data. I was wondering whether Freesurfer offers a report indicating the
edits I have made to aseg output.
Thank you,
Tamara
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Hello,
After I make edits to my aseg output in the longitudinal stream, do I just
run the following command to recreate the final volumes:
recon-long -autorecon2-noaseg -subjid
I assume the -subjid is the name of the edited time point and is
the name of the recreated volumes?
Thank you,
Tamar
Hello,
I have two questions which I was hoping to get some help with.
(1) I was wondering whether there was a intensity threshold for grey matter
and CSF. I know that Freesurfer scales the intensity so white matter has an
intensity of 110 (as can be seen at the bottom of Freeviewer when I open
th
Hello,
After I make edits to my aseg output in the longitudinal stream, do I just
run the following command to recreate the final volumes:
recon-long -autorecon2-noaseg -subjid
I assume the -subjid is the name of the edited time point and is
the name of the recreated volumes?
Thank you,
Tamar
Hello,
After I make edits to my aseg output in the longitudinal stream, do I just
run the following command to recreate the final volumes:
recon-long -autorecon2-noaseg -subjid
I assume the -subjid is the name of the edited time point and is
the name of the recreated volumes?
Thank you,
Tamar
nds some scaling (approx 1% in each axis direction, so a total of
3%). This can happen in individual cases, but if it is consistent I would
be worried.
Best, Martin
> On 11 Jan 2017, at 21:21, Tamara Tavares wrote:
>
> Hi Dr. Reuter.
>
> Thank you again for your help.
Hello,
I was wondering whether it is possible to view the atlases that are used to
construct the cortical surface ROIs in a visualization program?
Thank you in advance for your help.
Best,
Tamara
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Hi Dr. Reuter.
Thank you again for your help.
I ran the following command: "mri_robust_register --mov rawavg_1.mgz --dst
rawavg_2.mgz --lta v1to2.lta --affine --satit" on the two rawavg.mgz
images; one from each time point from the cross-sectional outputs. I have
attached the information from the
Hi Dr. Reuter,
Thank you for the clarification.
The differences I am seeing are also in the T1.mgz file in the longitudinal
run folder. I assume it is okay to use the T1.mgz from the longitudinal
outputs as the original image as I can easily compare the same slice across
different time points?
A
Thank you for your reply Dr. Reuter.
I have about 3 scans in which the acquisition parameters are slightly
different between time 1 and time 2 which probably contributes to these
differences. Do you recommend that I do not use these scans?
For my other scans, sometimes the differences in intensit
Hello,
I am in the process of checking the alignment of my participant's baseline
and followup scans to the template scan using the norm.mgz files. I notice
that sometimes the image appears brighter in the first scan vs. the second
follow up scan. Is this problematic? I don't see any clear distort
Hello,
I have a participant who has very large ventricles and as a result, there
are substantial errors in the aseg output. Looking at the mailing list, I
see that the newest version of Freesurfer is suppose to be better at
handling large ventricles; however, I want to be consistent with the
Frees
Thank you for the clarification Martin
I have a follow-up question. When I load the base to make sure it doesn't
look blurry, should I check the norm.mgz or brainmask.mgz? Online says
norm.mgz but I just want to make sure. Also, would the "blurriness" be
obvious?
Similarly, when I open the base
Thank you for the clarification Martin
I have a follow-up question. When I load the base to make sure it doesn't
look blurry, should I check the norm.mgz or brainmask.mgz? Online says
norm.mgz but I just want to make sure.
Similarly, when I open the base and the longitudinal runs to see whether
Hello,
I am wondering where I find the protocol used to segment the ventricles for
Freesurfer version 5.1. Looking at the citations in Fischl et al 2002, I
have found some information regarding the segmentation of the surfaces and
some subcortical areas but not the ventricles. I was hoping to comp
Hello,
I am interested in looking at ventricular changes over time and thus, have
ran the longitudinal stream on my participants scans. As suggested online,
I am checking the ventricular segmentation in the longitudinal outputs and
am planning on making any edits to the longitudinal stream if the
Hello,
I have a question regarding the outputs to the longitudinal processing
stream.
I ran my two participant's scans through the Cross, then created a Base and
two longitudinal runs. I am primarily interested in looking at ventricular
change over time. Other than the aseg output overlaid on the
Hello Experts,
I have a question regarding the outputs to the longitudinal processing
stream.
I ran my two participant's scans through the Cross, then created a Base and
two longitudinal runs. I am primarily interested in looking at ventricular
change over time. Other than the aseg output overlai
wrote:
>
> I don't understand what the problem is. Can you elaborate?
>
>
> On 9/27/16 12:13 PM, Tamara Tavares wrote:
> The differences have been found in the outputs from the aseg
> file. Particularly, I am interested in the ventricles and the
>
The differences have been found in the outputs from the aseg file.
Particularly, I am interested in the ventricles and the intracranial
volumes. I have loaded both anatomicals in FreeView and toggled between
them and have found no differences visually.
I have attached the files (Via Google Drive s
Thank you Bruce!
Theoretically, I should get the same results if I pass my nii file through
the recon-all command if I converted my dicom/IMA file into a nii using
Slicer4 or the mri convert command? I did this and I got different volumes.
Thank you,
Tamara
___
Hi All,
I have been using the following command line to convert my dcm/IMA files
into a nii files.
mri_convert -it dicom x.dcm .nii (where are the name of my
files)
I realized now that I did not specify the output file type (-ot nii) before
the file name. Is this a big concern or a
That seemed to work, thank you!
Tamara
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The information in this e-mail is intended only for the person to whom it is
addressed. If yo
Hello,
I am trying to extract the volumes from the aseg file of multiple subjects
using the command:
asegstats2table --subjects C9F03_1 C9F03_2 C9F07_1 --meas volume
--tablefile aseg_stats_test.txt
I keep getting the following error:
SUBJECTS_DIR : home/bmiadmin/Tamara/FreeSurfer_GENFI/analysis
the surface outputs are used the calculate the
structure's volumes? I am fairly new to Freesurfer so I am trying to get a
good understanding of it.
Thank you in advance,
Tamara
---
Tamara Tavares, HBSc <http://H.B.Sc>
PhD Candidate
Brain and Mind Institute, Department of Neuroscience
T
Thank you again Bruce.
Since I am primarily interested in ventricular volume, do you think it is
necessary to check the the brainmask.mgz for bright or dark spots
indicating an intensity normalization error? As well, what about a skull
strip error such as removal of brain tissue? I have noticed th
Hi All,
I was hoping to get some help with understanding the surface and aseg
volumes. I have some patient's scans and I am interested in examining the
ventricular volume but may look at other areas later on. I understand from
earlier threads that it is important to check the surface volumes (pial
Hello!
I was hoping someone can provide me with some clarification on an issue I
have been having with the FOV size.
I have a database of scans which I am running through recon-all
cross-sectionally. The majority of the scans have an FOV of 256x256x208;
however, when I run them through recon-all
Hello All,
I am planning to run the longitudinal stream on my data set and I have a
few questions:
1) When I run the data cross sectionally using "recon-all -all" should I
specify all my subject's T1 volumes (using the -file1.nii -1file2.nii) or
can I run each of my subject's T1 volumes individua
Hello All,
I am planning to run the longitudinal stream on my data set and I have a
few questions:
1) When I run the data cross sectionally using "recon-all -all" should I
specify all my subject's T1 volumes (using the -file1.nii -1file2.nii) or
can I run each of my subject's T1 volumes individua
Hello All,
I am currently using Freesurfer version 5.1 and when I run the recon-all
command I get the following warning message: Use of ?PATTERN? without
explicit operator is deprecated at
/usr/local/freesurfer/mni/bin/sharpen_volume line 153. Recon-all continues
to run and finishes completely wit
uctures.
>
> -Zeke
>
>
>
> On 05/12/2016 10:20 AM, Tamara Tavares wrote:
>
>> Hello All,
>>
>> I was hoping someone would be able to shed some light on an issue I have
>> been having concerning the volumetric data calculated by FreeSurfer
>> (version 5
Hello All,
I was hoping someone would be able to shed some light on an issue I have
been having concerning the volumetric data calculated by FreeSurfer
(version 5.3) using the asegstats output file. For information purposes, I am
currently using the following command line: recon-all –I [path] –s –
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