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.
I
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 (fa.sum
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 convert
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
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 wit
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 Tracul
3. Sorry, 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 d
at 20%
or its max value.
a.y
On Sat, 7 Mar 2015, Alshikho, Mohamad J. wrote:
> Hi Anastasia,
> Thank you very much for your answer, kindly I have one more question:
> I wanted to use the path.pd for the corticospinal tract as an ROI in PET
> data. What is the correct method to thrra
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
Freesurfer@
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 recon-
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
: 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
_segstats flags
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 th
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
>
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
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
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.harvar
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 /autofs/cluste
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
Contrast1group.diff.m
Greve
[gr...@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 wor
t 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 ces.nii.gz --wls cesvar.ni
tivity analysis
>
>
> The mri_glmfit command below is for the left hemisphere. so I don't
> 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
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] GLM_ functional connectivity analysis
Can you tar up all the input files and send them to me through our file
drop?
https://gate.nmr.mgh.harvard.edu/filedrop2
doug
On 04/28/2015 11:36 AM, Alshikho, Mohamad J. wrote:
> mri_glmfit --y ces.nii.gz --
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
./my-glm.wls/osgm/cache.th30.pos.sig.o
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 my-glm.wls
, 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
...@nmr.mgh.harvard.edu]
Sent: Thursday, April 30, 2015 5:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glm --wls flag
To the filedrop, url at the end of this email
On 4/30/15 4:58 PM, Alshikho, Mohamad J. wrote:
> Hi Doug,
> To this email address freesurfer@nmr.mgh.harvard.edu
t4g1g2.intercept.mtx
and did not receive an error. Can you try this command?
On 04/30/2015 05:15 PM, Alshikho, Mohamad J. wrote:
> I used the following link https://gate.nmr.mgh.harvard.edu/filedrop2/ to send
> the files and I included your email address
>
I know what is the story.
I am sourcing /usr/local/freesurfer/dev
I tried
/usr/local/freesurfer/stable5_3_0
and it worked
___
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Alshikho, Mohamad J.
Sent
, 2015 6:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glm --wls flag
hmmm, I just tried it in dev and it worked. Type "which mri_glmfit"
while you're in dev and send me the result
On 04/30/2015 06:12 PM, Alshikho, Mohamad J. wrote:
> I know what is t
Hi Doug,
I finished running FSFAST on fmri data set. I corrected the data for multiple
comparison.In order to visualize the results I ran the following command line:
tksurfer fsaverage lh inflated -overlay cache.th30.pos.sig.cluster.nii.gz
-annot cache.th30.pos.sig.ocn.annot -fminmax 1.3 3
I a
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 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 bo
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
htt
etty bizarre but that seems to do the
trick. Did you cut and paste that command from a document? Maybe the web
page?
doug
On 05/05/2015 07:58 PM, Alshikho, Mohamad J. wrote:
> Hi Doug,
>
> I want to do volume based analysis using FSFAST using the FC seed as a task
> regressor
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 t
] 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:
>
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 hostna
t;dwi_snr" in the trac-all.log file to see 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
coil, and the noise 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
>
rvard.edu] On Behalf Of Anastasia 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, Als
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 fl
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 Up
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: Fre
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
Subject: Re: [Freesurfer] Freeview
Weird! The up an
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) l
: 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 in
: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!
From:
frees
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 wm
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
Dear FS experts,
I have PET image "pet.anat.mgz" in subject space. I want to calculate the mean
PET signal for every parcellate and segment in the atlas "wmparc.mgz".
Which one of the following commands is more accurate?
1. mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab
$F
2nd commandline?
On 07/07/2016 05:16 PM, Alshikho, Mohamad J. wrote:
> Thank you very much Doug for your answer.
> Kindly I have one more question:
> Although the registration between my functional data and "wmparc.mgz" is
> perfect. When I run the first command bellow, I get z
2nd commandline?
On 07/07/2016 05:16 PM, Alshikho, Mohamad J. wrote:
> Thank you very much Doug for your answer.
> Kindly I have one more question:
> Although the registration between my functional data and "wmparc.mgz" is
> perfect. When I run the first command bellow, I get z
: [Freesurfer] mri_segstats
I'm at a loss as to why that is the case. Can you send the PET.anat.mgz and
wmparc.mgz to our filedrop?
On 07/18/2016 06:14 PM, Alshikho, Mohamad J. wrote:
> Thank you Doug!
>
> Attached is a report for one of the subjects showing how the
> cerebellum structur
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats
Your suvr is axially sliced whereas the anatomical is corronally sliced.
They must be in exact pixel-for-pixel alignment for mri_segstats to work.
On 07/18/2016 06:27 PM, Alshikho, Mohamad J. wrote:
> Thank you Doug!
>
> Attached is
Thank you Doug,
I used the command fslswapdim
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Alshikho, Mohamad
J.
Sent: Monday, July 18, 2016 6:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re
Dear Freesurfer experts,
I would like to inquire about the tool "dmri_poistats"
https://surfer.nmr.mgh.harvard.edu/fswiki/PoistatsOverview. This tool is
included as a beta release ( in FS5.3 and FS 6.0).
In literature review I found colleagues used the version 1.4 of this tool.
e.g. http://www
bject: Re: [Freesurfer] dmri_poistats
Hi Mohamad - This tool is *way* deprecated. It should not have been included in
beta releases. Thanks for bringing this to our attention.
a.y
On Wed, 24 Aug 2016, Alshikho, Mohamad J. wrote:
>
> Dear Freesurfer experts,
>
> I would like to
Hi Iglesias,
Kindly, we would like to know if there are any methods in Freesurfer that can
help to segment that brain stem nucleus. I mean output the nucleus
automatically as a small masks, so these small masks can be used in other
analyses (e.g. fMRI)
I am thinking of creating masks for these
Dear FS experts,
I ran surface based analysis using PET maps, and the pipeline reported, in FS
list, by multiple colleagues as the following:
* spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
* mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.
?
On 11/04/2016 11:09 AM, Alshikho, Mohamad J. wrote:
> Thank you Doug!
> Kindly in the attached figure are the "projfrac" values for #4 and #5 correct
> for at which level the analysis will be carried out.
>
> -Original Message-
> From: freesurfer-boun..
projfrac = -2 appears to be pointing at the ventricle. It should be 2*thickness
away from the white surface into the white matter
On 11/04/2016 12:11 PM, Alshikho, Mohamad J. wrote:
> Hi Doug,
> I am sorry for sending multiple emails. I wanted to be sure that I understand
> it properly. Kin
, 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
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 Ve
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 a
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 -su
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 gyr
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
> past, this command was a
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
https://su
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 --init-fsl
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 -
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 fs
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 -
t;-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 surface based analysis using FA maps. I am not
>> exactly sure that what I am doing is totally right specia
3/23/16, 7:18 PM, "Alshikho, Mohamad J."
wrote:
>Hi Matt,
>I highly appreciate your input on this!!
>
>Actually my goal is to study the difference in FA values between groups
>within the cortex. I know that diffusivities ( MD, AD and RD) can be
>used to evaluate gra
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, Mohamad J.&qu
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: F
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 Freesurfers,
How can I perform seed based correlation analysis using PET images? In other
words how can I use the same approach of FSFAST, but by including PET images
instead of fmri images, to study the correlation between PET signal within a
seed mask ( e.g precentral gyrus ) and the whole
Hi Max,
I hope this could help
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2015-October/041841.html
Best,
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of BAUTISTA-PERPINYA
Maximilià
Sent: Thursday,
Hi Doug,
I want to analyze rsfMRI data using FS-FAST. Kindly, I have question regarding
the command “ preproc-sess / Freesurfer v6”
In order to begin the analysis, I followed the steps as in FS-FAST wiki. First,
I organized the tree folders for the project as
“study_folder/session_ID/bold/run”.
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FS-FAST (preproc-sess)
What was your preproc-sess command and what folder are you running it from? And
did you use 3-digit, zero-padded strings as your run folder?
On 05/23/2017 09:17 AM, Alshikho, Mohamad J. wrote:
>
> Hi Doug,
>
> I wan
Hi Lanbo,
You need Freesurfer 6 to run this command. The flag --src-label is not part of
FS5.3
Best,
M_
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of lanbo Wang
Sent: Friday, November 3, 2017 11:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Dear Dr Greeve,
Kindly, I'd like t to inquire about the command "mri_gtmpvc" in PET surfer. Can
I use this command to apply partial volume correction on non-PET data (e.g. DTI
or ASL)?
Thanks!
Mohamad
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Dear Dr Greve,
Kindly, I'd like t to inquire about the command "mri_gtmpvc" in PET surfer. Can
I use this command to apply partial volume correction on non-PET data (e.g. DTI
or ASL)?
Thanks!
Mohamad
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Freesurfer@nmr.mgh.harva
Dear FreeSurfer experts,
I have MRS volume of interest (VOI) was placed in the motor cortex during MRS
data acquisition. In order to compute the gray and white matter volume within
the VOI, I synthesized this VOI using "mri_volsynth". Then I registered it to
T1 Freesurfer space using "spmregiste
within VOI
Hi Mohamed
yes, that woud work. Create a label file on the surface from your VOI and give
it to mris_anatomical_stats with the -l flag
cheers
Bruce
On Mon, 2 Jul 2018, Alshikho,
Mohamad J. wrote:
>
> Dear FreeSurfer experts,
>
> I have MRS volume of interest (VOI) was p
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 used
: 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:
>
>
, 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 matt
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 /a
number 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
> unseg
$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 mat
R_HOME/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.
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
>
&g
Hi Fs Experts,
In order to calculate the mean diffusivity MD in my DTI data I did the
following:
1. For the Eigvals.nii (the output of dt_recon) I used the following
command line: fslmaths eigvals -div 3 md.nii
2. mri_vol2vol -mov md.nii --reg register.dat --fstarg -- interp
nea
Greve
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, Alshikh
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.
>
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 in this age
group? Do I need to use the flag -noseg ? (i.e can I use aseg for this range of
age)
Thanks,
Moh
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 fa.anat
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