Hi Fs Experts,
I am working on FA ROI analysis for my subjects, I did the following:
1. Mri_vol2vol -mov fa.nii -reg register.dat -fstarg -interp nearest -o
fa.anat.mgh
2. Mri_segstat wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt
-I fa.anat.mgh -sum fa.stats
Then I
: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Thursday, June 26, 2014 5:03 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aparc+aseg OR wmparc
yes
On 06/26/2014 04:49 PM, Alshikho, Mohamad J. wrote:
Hi Fs
, Alshikho, Mohamad J. wrote:
Thank you Doug,
Kindly I have one more question..
What is the best way to deal with unsegmented white matter in wmparc.mgz and
is there any other atlases that can give me better results regarding this
huge structure of unsegmented white matter?
Mohamad
-Original
Hi Fs Experts,
In order to calculate the right hemispheric white matter mean fractional
anisotropy (FA), I did the following:
1. I used rh.dwhite.ribon.mgz as input in mri_binaraize to create a
binary mask (I did convert mgz to nii and vice versa)
2. I used mri_segstats --seg
to be something very large, and all WM will be
assigned to a gyrus
On 06/26/2014 06:00 PM, Alshikho, Mohamad J. wrote:
I thought that I will find more details about this unsegmented white matter
in aparc+aseg; Actually my problem here is how can I deal with this huge
unsegmented white matter
$subject --hemi $hemi --lobesStrict lobes
to create a lobes surface annotation (or customize it to make your own), then
you could run mri_aparc2aseg to create a new wmpar with the lobes annotation.
On 06/27/2014 02:35 PM, Alshikho, Mohamad J. wrote:
Can I classify this unsegmented white matter
/FreeSurferColorLUT.txt --i fa.anat.mgh --sum fa.stats
And just look at segmentation 41 (RH WM)
Or you could add --segid 41
and only RH WM will appear in the table
I would also add --seg-erode 2 to reduce the amount of partial voluming with GM
doug
On 06/27/2014 02:28 PM, Alshikho, Mohamad J. wrote:
Hi
FA
you get out whatever you put in
On 06/27/2014 03:32 PM, Alshikho, Mohamad J. wrote:
One more Question...
If I used --seg-erode 1 then I will have the mean diffusivity (MD)
as an output of mri_segstats
Is that right?
Thanks,
Mohamad
-Original Message-
From: freesurfer-boun
Sent: Tuesday, July 01, 2014 10:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Mean diffusuvuty MD
I don't know about the first step but 2 and 3 look ok. But why are you using
the aseg? It will just give you the lh and rh cerebral WM
On 06/30/2014 03:11 PM, Alshikho, Mohamad
diffusivity is the same as the apparent diffusion coef (ADC); there
should be an adc volume in the output of dt_recon doug
On 07/01/2014 12:38 PM, Alshikho, Mohamad J. wrote:
Thanks Doug,
Actually I want to calculate the MD just for the right and left hemispheric
white matter.
The output
Hi Fs Expert,
I have a group of kids subjects (4-15) year old. I want to do cortical
reconstruction process using Freesurfer. My question is:
is still correct to use the command line recon-all -all -subjid in this age
group? Do I need to use the flag -noseg ? (i.e can I use aseg for this range
Hi Fs Experts,
In order to calculate the global white matter fractional anisotropy FA I used
(wm.mgz ) the output of recon-all as a mask in the following command line
mri_segstats --seg $SUBJECTS_DIR/015601/mri/wmparc.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --mask wm.mgz --i
Hi Dear Fs Experts
I will post my question again, hopefully I can find an answer :)
In order to calculate the global white matter fractional anisotropy FA I used
(wm.mgz ) the output of recon-all as a mask in the following command line
mri_segstats --seg $SUBJECTS_DIR/015601/mri/wmparc.mgz
Hi Dear Fs Experts,
I am looking for an atlas segmented all white matter without to leave any
unsegmented white matter like in WMPARC
I highly appreciate your help and support
Thanks
Mohamad
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Hi Fs expers,
What is the best way in Freesurfer to create a mask for the cerebellum white
matter from the output of T1 segmentation?
Thanks
mohamad
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
on the aseg.mgz.
cheers
Bruce
On
Mon, 28 Jul 2014, Alshikho, Mohamad J. wrote:
Hi Fs expers, What is the best way in Freesurfer to create a mask for the
cerebellum white matter from the output of T1 segmentation?
Thanks
mohamad
___
Freesurfer
{Disarmed}
With mri_binarize you can give it multiple match options to merge
different segments
On 07/28/2014 11:50 AM, Alshikho, Mohamad J. wrote:
Hi Bruce,
Thank you very much for your quick answer,
The output of those command lines are left and right cerebellum white matter.
How can I create
Dear Fs Experts,
What is the difference between (wm.mgz and wm.seg.mgz)_ in the output of
recon-all? i.e is wm.mgz means the whole white matter (right_left hemispheres
and brain stem except the cerebellum)
Thanks
Mohamad
___
Freesurfer mailing list
really well (so well that the MJ ported it to FSL!)
cheers
Bruce
On Tue, 29
Jul 2014, Alshikho, Mohamad J. wrote:
Thanks, Actually I tried to create a mask for the cerebellum using
mri_binarize --i aseg.mgz --o cerebellum.mgz --match 7 46 . Then I re
positioned this mask in the same direction
Hi,
I have a question about the flag -wm in mri_binarize:
The following segments IDs 8 2 41 82 251 252 253 254 255 are included in this
flag (based on the summary of this command line when I run it). Kindly what is
the segment ID (Right-non-WM-hypointensities) means? and why the
are hypointense voxels (in T1 images) in
the right hemisphere in regions that are not normally white matter
(like the middle of the putamen).
I'll leave your other questions for Doug
cheers
Bruce
On Wed, 30 Jul 2014, Alshikho, Mohamad J. wrote:
Hi,
I have a question about the flag -wm
Dear FS Experts,
I am beginner in FS and I need you precious advice...
In order to compare the volume of the right and left hemispheric white matter
in my dataset (29 controls 23 patients). I did recon_all for my T1 data then I
used the volume of the Left and right cerebral white matter which
in a subsequent invocation of recon-all with the -T2pial
flag
cheers
Bruce
On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote:
Hi FS Experts,
The T1 and T2 images in my data set are as the attached images. Kindly do
you recommend that I do segmentation for the white matter using recon-all on
my T1 or T2
Hi ,
The command unpacksdcmdir is only used to unpack Siemens DICOM files, How can
I unpack the non Siemens DICOMs?
Thanks,
Moahmad
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi ,
The command unpacksdcmdir is only used to unpack Siemens DICOM files, How can
I unpack the non Siemens DICOMs?
Thanks,
Moahmad
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
, Mohamad J. wrote:
Hi ,
The command unpacksdcmdir is only used to unpack Siemens DICOM files,
How can I unpack the non Siemens DICOMs?
Thanks,
Moahmad
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman
...@nmr.mgh.harvard.edu]
Sent: Monday, October 20, 2014 3:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] unpacksdcmdir
did you try dcmunpack?
On 10/20/2014 03:30 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
But in freeSurfer wiki
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData
suggestions please?.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Alshikho, Mohamad J.
Sent: Monday, October 20, 2014 3:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] unpacksdcmdir
Sorry I did
use
it to avoid dura in a subsequent invocation of recon-all with the -T2pial
flag
cheers
Bruce
On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote:
Hi FS Experts,
The T1 and T2 images in my data set are as the attached images. Kindly do
you recommend that I do segmentation for the white
Hi Bruce,
I wanted to calculate the right and left hemispheric white matter volume using
a mask.
Is there any difference between lh.dwhite.mgz , rh.dwhite.mgz (the outputs of
mris_volmmask after binarize them) and the right and left hemispheric white
matter masks from aseg.mgz atlas (the output
, October 31, 2014 10:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] White matter volume
The aseg is not surface-based and will not be as accurate
doug
On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote:
Hi Bruce,
I wanted to calculate the right and left hemispheric white
-volume correction that we typically
compute when we estimate volumes in the stats files.
cheers
Bruce
On Fri, 31 Oct 2014,
Alshikho, Mohamad J. wrote:
Thanks Doug,
In order to improve my understanding for the analysis that I am working on
and in the process of my learning I am tring
] White matter volume
yes. Partial volume correction helps both accuracy and repeatability. You
can certainly use our (partial-volume) corrected WM volumes and the FA
from FSL if you want
cheers
Bruce
On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote:
Hi Bruce,
Actually I am totally confused
Hi Anastasia,
One of Tracula's output is the pathstats.overal.txt and in this file we have
a list of numbers. Kindly what is the difference between the metrics average
and the metrics average center also which one do you recommend to do statistic?
Thanks,
Mohamad
Hi Anastasia,
I started recently using Tracula to do tractography for my DTI data. I did the
analysis exactly as mentioned in wiki. The problem is that when I am repeating
the third step (trac-all -path -c ) for the same subjects to generate the
statistics; Tracula is updating all the
Dear Bruce,
My questions is just to learn and to improve my understanding.
The commands recon-all and dt-recon are routinely generating the statistics at
the end of there running and we can check the results in aseg.stats (the
output of recon-all) and fa.stats (the output of dt-recon for FA).
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] White matter volume
On 11/06/2014 12:53 AM, Alshikho, Mohamad J. wrote:
Dear Bruce,
My questions is just to learn and to improve my understanding.
The commands recon-all and dt-recon are routinely generating the
statistics at the end
Hi Doug and Bruce,
I posted this question before and I hope that you can help me to find an answer
for this issue!
I started recently using Tracula to do tractography for my DTI data. I did the
analysis exactly as mentioned in wiki and every thing ran smoothly. The problem
started when I was
Hi Freesurfers,
I want to calculate the FA in a VOI 8 mm3 in the left and right prefrontal
white matter areas. My plan is to derive a mask for that area from aseg.mgz
then I will register this mask to the FA map to calculate the FA value. Is it
possible to derive like this mask from aseg.mgz
for this.
cheers
Bruce
cheers
Bruce
On Fri, 14 Nov
2014, Alshikho, Mohamad J. wrote:
Hi Freesurfers, I want to calculate the FA in a VOI 8 mm3 in the left and
right
prefrontal white matter areas. My plan is to derive a mask for that area
from
aseg.mgz then I will register this mask
think so, but I defer to Doug
Bruce
On Fri, 14 Nov 2014, Alshikho, Mohamad J.
wrote:
Doug an Bruce thanks a lot!!
I will do the following as I understood from your orientations and kindly
correct me if I am wrong:
first of all I will resample my FA map into the anatomical space
average measures are the most reliable, as they are less
affected by the tails of the distribution.
a.y
On Wed, 5 Nov 2014, Alshikho, Mohamad J. wrote:
Hi Anastasia,
I started recently using Tracula to do tractography for my DTI data. I did
the analysis exactly as mentioned
in wiki
Dear FS Experts,
In order to generate the statistics using mri_segstats I ran the following
command line:
mri_segstats --seg${in}/${i}/mri/aparc+aseg.mgz --ctab-default --i
${insa}/${i}/fa.anat.nii --mask ${insa}/${i}//svs.anat.nii --sum
${insa}/${i}/fa.summary.dat
In the final report
metrics inside a single voxel
Hi Mohamed, that looks great, very clear. We'll have to engage your services to
write some of our wiki pages :)
doug
On 2/2/15 1:05 PM, Alshikho, Mohamad J. wrote:
Sorry for the mistake:
I wanted to correlate the DTI metrics inside this single voxel
Dear Doug and Bruce,
I have a single voxel spectroscopic data (SVS) and a (DTI) data for the same
subjects. I wanted to correlate the DTI metrics inside this single voxel with
the DTI metrics inside the voxel.
In order to do that I used the following steps:
1. I used mri_convert to
Sorry for the mistake:
I wanted to correlate the DTI metrics inside this single voxel with the
concentration of the metabolites (the output of LCMODEL) inside the voxel.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Alshikho, Mohamad
Dear FS Experts,
In this paper
http://jmbe.bme.ncku.edu.tw/index.php/bme/article/viewFile/1558/939 the authors
explained the effects of b-Value and Echo Time on Magnetic Resonance Diffusion
Tensor Imaging but they didn't say what is the recommended range for the echo
time that we should use.
Hi Anastasia,
Kindly I have the following questions and I highly appreciate if you answered
me:
1. I would like to ask how Tracula do calculate the weighted metrics and
weighted volumes. Is there any command line that Tracula use in order to do
this process?
2. After running
, tracula doesn't do exploratory tractography.
Best,
a.y
On Tue, 17 Feb 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
Kindly I have the following questions and I highly appreciate if you answered
me:
1. I would like to ask how Tracula do calculate the weighted metrics and
weighted
Hi Anastasia,
dwi_snr.txt is an output of the preprocessing step in TRACULA. Kindly how
TRACULA is calculating the SNR for every direction in DTI data? Is there any
command line that can do it?
Thanks,
Mohamad
___
Freesurfer mailing list
. If that is not your system, tell me what your system is
doug
On 04/13/2015 02:22 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
Kindly I have the following questions regarding the command mri_segstats:
·I wanted to use the flag --seg-erode 2 in the command mri_segstats
but I am receiving an error message
Hi Doug,
Kindly I have the following questions regarding the command mri_segstats:
* I wanted to use the flag --seg-erode 2 in the command mri_segstats
but I am receiving an error message that this flag is not available ( I am
using FreeSurfer 5.3.0 ).
* When the command
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats flags
Are you sure you're using the new version?
what do you get if you type
which mri_segstats
On 04/13/2015 03:41 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
My system is Linux Centos 7
I tried to run it and I got
maybe zeke can help you sort it out
On 04/13/2015 04:24 PM, Alshikho, Mohamad J. wrote:
I got
/usr/local/freesurfer/stable5_1_0/bin/mri_segstats
and this is really weird because I thought that I am using FS 5.0.3.
I am sourcing routinely the following script before I start FS
#!/bin/tcsh
does not have those strcutures. In the 2nd, does
On 04/13/2015 04:41 PM, Alshikho, Mohamad J. wrote:
Thank you Doug,
Kindly one more question regarding mri_segstats:
The following two mri_segstats command lines:
mri_segstats --seg ${out1}/${i}/mri/aseg.mgz --sum
${out1}/${i}/stats/aseg.stats
Hi FS experts,
In order to start FS I am sourcing the following script routinely:
#!/bin/tcsh
setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0
setenv USE_STABLE5_3_0
setenv LD_LIBRARY_PATH /usr/lib64/GLoverride:/usr/lib/GLoverride
setenv FSENV_KEEP_PROMPT
setenv SUBJECTS_DIR
Hi Anastasia,
I am trying to run the command trac-all with the flag -stat as mentioned in
wiki (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics)
but I am receiving and ERROR message that this flag unrecognized. Any
suggestions please.
Mohamad
(this
will overwrite the old versions). This should provide the -stat flaf.
Best,
Lee
On Wed, 22 Apr 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
I am trying to run the command trac-all with the flag -stat as
mentioned in wiki
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial
run it again on the left hemi but get an error. Can
you post just the command that you ran that gave the error as well as the
terminal output for that command?
On 4/27/15 4:17 PM, Alshikho, Mohamad J. wrote:
I ran only one command line :
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --fsgd
Hi Doug,
After running FSFAST tool and correcting the results for multiple comparisons.
I want t visualize the results using the command line (AS IN WIWKI):
tksurfer fsaverage lh inflated -overlay
my-glm.wls/osgm/cache.th30.pos.sig.cluster.nii.gz -annot
...@nmr.mgh.harvard.edu]
Sent: Monday, April 27, 2015 4:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] GLM_ functional connectivity analysis
can you send the two command lines you ran?
On 04/27/2015 02:53 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
I am working on a GLM for functional
Hi Doug,
I finished recently running FSFAST on fmri data set.
I want to run group GLM for the following analysis:
OSGM, FSGD( no covariates)
For OSGM I ran the following command line like in Wiki:
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surface fsaverage lh
--glmdir
, 2015 4:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glm --wls flag
Can you tar or zip the following files and post them to me on our file
drop (see below): ces.nii.gz cesvar.nii.gz fsgd C1.mtx C2.mtx C3.mtx C4.mtx
doug
On 4/30/15 2:06 PM, Alshikho, Mohamad J. wrote
Hi Doug,
I am working on a GLM for functional connectivity analysis. I made simple FSGD
file for two groups + NO covariates then I ran the following command line on
the right hemisphere and the left hemisphere.
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --fsgd fsgd --C
understand when you later say that you run it again on the left hemi but get
an error. Can you post just the command that you ran that gave the error as
well as the terminal output for that command?
On 4/27/15 4:17 PM, Alshikho, Mohamad J. wrote:
I ran only one command line :
mri_glmfit --y
Hi Doug,
I want to do volume based analysis using FSFAST using the FC seed as a task
regressor. I ran the following command lines:
1. preproc-sess -s ${i} -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd
bold -per-run
2. fcseed-config -segid 1024 -fcname L_Precentralgyrus.dat -fsd
Hi FS Experts,
Kindly, I want to inquire if there is any tool in FreeSurfer that can help to
extract or isolate Free water map from Diffusion Weighted Imaging (DWI) data.
Thanks
Mohamad
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Hi Doug,
I wanted to run FSFAST without using the paradigm file in the analysis using
the following command lines:
1. preproc-sess -s ${i} -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd
bold -per-run
2. fcseed-config -segid 1024 -fcname L_Precentralgyrus.dat -fsd bold -mean
-cfg
Hi Doug,
I want to use the command fcseed-config to configure the segment 1126 (in
aparc+aseg) as a seed to pass it to connectivity analysis. I ran the command
line:
fcseed-config -segid 1126 -fcname L_G_Precentralgyrus.dat -fsd bold -mean -cfg
mean.L_G_Precentralgyrus.config
Then I ran
is for the 2005 atlas, try 11129 (ctx_lh_G_precentral) instead
On 05/11/2015 03:00 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
Here is the output:
cmdline mri_binarize --i aparc.a2009s+aseg.mgz --binval 1 --o
L_G_Precentralgyrus.mgz --match 1126 sysname Linux hostname glia
machine x86_64
] Fcseed-sess
Use aparc.a2009s+aseg.mgz
On 05/11/2015 02:01 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
I want to use the command fcseed-config to configure the segment 1126 (in
aparc+aseg) as a seed to pass it to connectivity analysis. I ran the command
line:
fcseed-config -segid 1126 -fcname
Hi Doug,
If I check the file aseg.stats ( the output of the command line recon-all
-subjid -all ) I don't see in the table (in the file aseg.stats ) any
volumes regarding right and left hemispheric white matter.
The mri_segstats in aseg.stats was reported as the following:
mri_segstats
is the variation around the mean. The more the noise, the
more the variation.
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
But in our command line
fslstats -t dwi.nii.gz -k White-Matter++.flt.nii.gz -m -s | awk
'{print $1/$2}' dwi_snr.txt
the flag -m is the mean intensity
the
command line that produces this file.
a.y
On Mon, 30 Mar 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
“dwi_snr.txt” is an output of the preprocessing step in TRACULA.
Kindly how TRACULA is calculating the SNR for every direction in DTI data? Is
there any command line that can do
there is not going to be representative of the
noise inside the head coil.
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
Hi Anastasi,
Thank you very much for your support.
Actually I did. I checked trac-all.log and I found the following command
line:
fslstats -t dwi.nii.gz -k White-Matter
Yendiki
Sent: Friday, May 22, 2015 3:15 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
The mean is the signal, the standard deviation is the noise.
http://en.wikipedia.org/wiki/Signal-to-noise_ratio#Alternative_definition
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
Hi
Page up / down is moving the current slice up and down but it not flipping
between the slices ?!
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Eugenio Iglesias
Sent: Wednesday, August 19, 2015 12:21 PM
To:
Hi Freesurfers,
I can't change the current slice in freeview using the Up or Down key as
described in the Freesurfer wiki. Instead the Up/Down key are moving the
current slice up or down and not changing the current slice. Is there any
shortcut that can change the current slice instead of the
Got it!
Thanks Iglesias
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Eugenio Iglesias
Sent: Wednesday, August 19, 2015 12:38 PM
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Subject: Re:
need anything else?
On 8/26/15 10:51 AM, Alshikho, Mohamad J. wrote:
I attached the photo.
Actually I didn't realize that this FOV 20 will be consisted of 40 voxels
because when I view the output of the previous command line this will look like
one big volume
: Wednesday, August 26, 2015 10:08 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Create matrix
does mri_volsynth not work for this?
On 8/26/15 9:25 AM, Alshikho, Mohamad J. wrote:
Hi Doug,
I am using the command “mri_volsynth” to create voxel has specific dimensions
and position
Hi Doug,
I am using the command mri_volsynth to create voxel has specific dimensions
and position in the brain.
Kindly, I would like to inquire if there is any tool in Freesurfer that can
help to create volumetric matrix has a number of columns and rows ( and as a
results number of voxels)
dt_recon
On 9/25/15 9:28 AM, Alshikho, Mohamad J. wrote:
Hi Doug and Bruce,
After running the command :
dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals
f.bvecs --s M87102113 --o dti <<< source: Freesurfer wiki>>>
I need to generat
, Alshikho, Mohamad J. wrote:
Hi Doug and Bruce,
After running the command :
dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals
f.bvecs --s M87102113 --o dti <<< source: Freesurfer wiki>>>
I need to generate the final statistics ( FA fo
Hi Doug and Bruce,
After running the command :
dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals
f.bvecs --s M87102113 --o dti <<< source: Freesurfer wiki>>>
I need to generate the final statistics ( FA for every parcellate and segment
in aseg and
Dear Freesurfer experts,
I am working on brain stem segmentation analysis using the new module included
in FS6.
The analysis ran properly for 38/40 subjects. I have an issue with two subjects.
I sent my jobs to the cluster as always using the following command line:
pbsubmit -c " recon-all
Dear Freesurfers,
After segmenting the brain stem using FS6 tools. I used Free view to visualize
the final images. In Free view I opened "orig.mgz", "wmparc.mgz" and
"brainstemSsLabels.v10.mgz" Then I tried to check the segmented structures by
flipping the images.
I noticed an overlap between
Bruce and Juan,
Thanks a lot for your quick answer. I have one more question please:
What are the anatomical definitions that the brain stem module uses in order to
segment the brain stem. If you can point me to a reference that can help me to
understand this point this will be great!!
Thanks
Hi Doug,
I have two groups of subjects and I want to study the difference in cortical
thickness between the groups. I used Qdec to run the analysis and I got
significant difference between the groups in areas support what I am looking
for.
I repeated the analysis as mentioned in Wiki
Hi Doug,
I would like to inquire about the command " mri_binarize". In the past, this
command was able to create a binarized nifti mask from aseg.mgz, wmparc.mgz
etc without the need to convert the output "mgz" files to nifti. In other
words If I want to create a mask for the precentral
doing it both ways?
The output format shouldn't change things - there is no reason you shouldn't be
able to write directly to nifti
cheers
Bruce
On Sat, 12 Mar 2016, Alshikho, Mohamad J. wrote:
>
> Hi Doug,
>
> I would like to inquire about the command “ mri_binarize”. In the
&g
Dear Experts,
I am working on ASL analysis using Freesurfer's tools "rcbf-prep" and
"rcbf-merge"
I can't find the script "rcbf-merge" in Freesurfer 5.3 ( i.e when I call the
command rcbf-merge in terminal, it returns as : command not found)
Any suggestions are highly appreciated!
Best,
Mohamad
Hi Doug,
I would like to run surface based analysis using FA maps. I am not exactly sure
that what I am doing is totally right specially step 2 . I used the following
commands:
1. I registered the FA maps to T1 using the command: bbregister --s bert
--mov dtifit_FA.nii --bold
you want to sample in the WM?
>Doing that is a little tricky, but you can use something like --projabs
>-1 to sample 1mm *away* from the ribbon into the WM.
>
>On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:
>>
>> Dear FS experts,
>>
>> I would like to run surfa
eurobiologically in the grey matter?
Matt.
On 3/23/16, 7:18 PM, "Alshikho, Mohamad J."
<freesurfer-boun...@nmr.mgh.harvard.edu on behalf of malshi...@mgh.harvard.edu>
wrote:
>Hi Matt,
>I highly appreciate your input on this!!
>
>Actually my goal is to study the difference in FA
a number of things:
1) Decrease the strength of radial diffusion
2) Increase the strength of tangential diffusion
3) Decrease the strength of both radial and tangential diffusion
Are you looking for a measure that shows tissue damage?
Matt.
On 3/23/16, 7:55 PM, "Alshikho, Moha
Dear FS experts,
I ran cortical thickness analysis as previously explained in Wiki :
Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
1. My data is previously cached so I ran the command : mris_preproc
--fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage
Are you sure that all your DTI images have the same acquisition parameters?!!
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Elijah Mak
[fk...@medschl.cam.ac.uk]
Sent: Thursday, March 24, 2016 7:33 PM
To:
Dear FS experts,
I ran cortical thickness analysis as previously explained in Wiki :
Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
My data is previously cached so I ran the command : mris_preproc --fsgd
gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target
Dear FS experts,
I would like to run surface based analysis using FA maps. I am not exactly sure
that what I am doing is totally right specially step 2 . I used the following
commands:
1. I registered the FA maps to T1 using the command: bbregister --s bert
--mov dtifit_FA.nii --bold
1 - 100 of 121 matches
Mail list logo
