External Email - Use Caution
Hi Freesurfer team,
I want to calculate the average PET intensity values per lobe. I want to
use the lobar annotations as outlined here in 'lobe mapping':
https://secure-web.cisco.com/1Opn2TyIP5_MF5tP6PRtaju8QtoITdCtzrmIlxZvYGO1bUWJFDMXcyGSrhgGeBk9csj3
External Email - Use Caution
It is going to list the cluster=0 value as the first value. cluster=0
are all the voxels not in a cluster. If you want to exclude this, just
add --excludeid 0
On 8/10/2023 7:58 PM, Lara Foland-Ross wrote:
External Email - Use Caution
Hi th
External Email - Use Caution
Hi there,
I'm running mri_segstats on a collection of clusters resulting from a
statistical analysis. My command line usage is as follows:
mri_segstats --i lh.fwhm10.thickness.mgh --avgwf clusterAverages.txt
--seg cache.th13abs.sig.ocn.mgh
Th
External Email - Use Caution
Hmm, it does not look like that option was ever added (ie, that wiki
page is incorrect).
On 8/6/2023 8:13 AM, Woo-Suk Tae wrote:
External Email - Use Caution
Dear Freesurfer developer.
According to the explanation in the *MailScanner has de
External Email - Use Caution
Dear Freesurfer developer.
According to the explanation in the
https://secure-web.cisco.com/1coHbpSG3RMsDJ9eWWcn4zb_ld9qaPCVetqOo5rL5vuLfQQSISVGpVYl8aGgrzcAEShM1ov3Y1kaR3TI9f0riiixXrDWduFbq9YZu7vap8N9ooLrsMvKWnmIS21q5izT5EkhCL70i1Sw_90CUN-1TrF_pR-59FpT3
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Huang, Yujing
*Sent:* Wednesday, July 5, 2023 9:53 AM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] mri_segstats dimension mistach
You don't often get email from yhuan...@mgh.harvard.edu. Learn why
th
nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_segstats dimension mistach
External Email - Use Caution
Hello,
I'm trying to run the mri_segstats on different input volume. The input volume
has the same dimensions as the original volume used to perform recon-all.
However, when try
...@nmr.mgh.harvard.edu
On Behalf Of Fahad Hannan
Sent: Monday, July 3, 2023 3:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_segstats dimension mistach
External Email - Use Caution
Hello,
I'm trying to run the mri_segstats on different input volume. The input volume
has the
External Email - Use Caution
Hello,
I'm trying to run the mri_segstats on different input volume. The input volume
has the same dimensions as the original volume used to perform recon-all.
However, when trying to use the following command:
"mri_segstats --seg $SUBJECTS_DIR/P6V1
You can pass it a --mul SCALE option to multiply the output by any
scaling factor
On 3/7/2023 1:16 PM, John Anderson wrote:
External Email - Use Caution
Dear Freesurfer community,
Please forgive me for the basic nature of my question.
I was wondering whether there is an argument that
External Email - Use Caution
Dear Freesurfer community,
Please forgive me for the basic nature of my question.
I was wondering whether there is an argument that can be included in
mri_segstats to display the results in cubic centimeters (cm^3) instead of
cubic millimeters (mm^3). t
Hi Bram, there is not a way to do it with a single command. You could
use the aparc+aseg, merge the two hemi labels into one, then run
mri_segstats. If you want to stick with pure surface-based analysis,
then you'd have to run mri_segstats twice, then just compute a weighted
mean of the two wa
External Email - Use Caution
Hello FreeSurfer Team,
I've made a New Year's resolution to stop bothering Andrew Hoopes and
instead send my questions to the FreeSurfer Mailing List.
I would like to calculate a single average waveform for two surface labels
on contralateral hemisphe
half Of Brooklyn Wright
Sent: Wednesday, January 4, 2023 9:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_segstats error:
External Email - Use Caution
Hello Freesurfer Developers,
I am currently trying to perform reconstructions on 1mm^3 T1 data and am
finding this error
External Email - Use Caution
Hello Freesurfer Developers,
I am currently trying to perform reconstructions on 1mm^3 T1 data and am
finding this error towards the end of the processing;
\n mri brainvol _stats cor. 15 \n
Segmentation fault
Darwin UW-C02L2083DNMP 18.7.0 Darwin K
Try adding --empty
On 4/12/2021 4:58 PM, miracle ozzoude wrote:
External Email - Use Caution
Hello Experts,
I am using mri_segstats with the --ctab flag to extract dti and suvr
values from a white matter hyperintensities parcellation. Running
mri_segstats on the image and parcellati
External Email - Use Caution
Hello Experts,
I am using mri_segstats with the --ctab flag to extract dti and suvr values
from a white matter hyperintensities parcellation. Running mri_segstats on
the image and parcellation with --ctab only reports on non-empty
segmentations. I want
External Email - Use Caution
The WM was cropped out by applying a grey-matter mask in SPM, and I am trying
to extract non-zero voxels with mri_segstats.
Best,
Renxi
> On Nov 29, 2020, at 11:23 AM, Greve, Douglas N.,Ph.D.
> wrote:
>
> I don't understand why WM was cropped out.
what is your command line?
On 11/29/2020 2:55 PM, RENXI LI wrote:
> External Email - Use Caution
>
> The WM was cropped out by applying a grey-matter mask in SPM, and I am trying
> to extract non-zero voxels with mri_segstats.
>
> Best,
> Renxi
>
>> On Nov 29, 2020, at 11:23 AM, Greve, D
I don't understand why WM was cropped out. What command were you trying
to use?
On 11/18/2020 2:39 AM, RENXI LI wrote:
> External Email - Use Caution
>
> Hi Freesurfer experts:
>
> I am trying to extract the mean-time series from the functional image using
> mri_segstats. However, the c
External Email - Use Caution
Hi Freesurfer experts:
I am trying to extract the mean-time series from the functional image using
mri_segstats. However, the cerebral white matter signals were cropped out in my
functional images, and the regions that I am trying to extract signal f
Great. thanks Doug!
Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
On Sep 4, 2020, at 1:07 PM, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
I'm not entirely su
I'm not entirely sure what those steps are trying to do. Extract out
signal from voxels in thalamus that have a positive sig? You can do that
with one call to mri_segstats. This page has an example:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview
On 9/4/20
Dear Freesurferers
Hi
I am trying to extract the BOLD signal values from a functional subcortical
area. I did the below steps to make the functional thalamus ROI and then used
the mri_segstats to extract the BOLD signal from it.
I would like to know 1-if my approach is correct? 2- should I use
An ROI does not have a GM probabability, so I'm not sure what to say.
Perhaps he/she wants the average amount of GM in the ROI relative to the
size of the ROI? You can get this with mri_compute_volume_fractions.
This will produce maps of the GM fraction in each voxel (separating
cortical and su
External Email - Use Caution
Hi Freesurfer Team,
I have used mri_segstats to get ythe mean PET uptake across all the
parcellations in the WMPARC space. These values were calculated in the native
PET space (following the DTI tutorial). A reviewer asked what is the grey
matter pro
From: Nasiriavanaki, Zahra
Sent: Thursday, April 11, 2019 4:52:49 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_segstats
Thank you so very much.
Yes, the values look normal now.
Mona
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf
arvard.edu
> on behalf of Greve, Douglas
> N.,Ph.D.
> *Sent:* Thursday, April 11, 2019 4:19:00 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] mri_segstats
> The value of what is too high?
>
>
> On 4/11/19 4:07 PM, Nasiriavanaki, Zahra wrote:
&g
vard.edu
> on behalf of Greve, Douglas
> N.,Ph.D.
> *Sent:* Thursday, April 11, 2019 4:19:00 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] mri_segstats
> The value of what is too high?
>
>
> On 4/11/19 4:07 PM, Nasiriavanaki, Zahra wrote:
&g
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
Sent: Thursday, April 11, 2019 4:19:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats
The value of what is too high?
On 4/11/19 4:07 PM, Nasiriavanaki, Zahra
The value of what is too high?
On 4/11/19 4:07 PM, Nasiriavanaki, Zahra wrote:
>
> Hi
>
>
> I have not got the answer to my question yet, and I appreciate if you
> could please let me know what you think about it.
>
>
> Thanks
>
> Mona
>
> ---
Hi
I have not got the answer to my question yet, and I appreciate if you could
please let me know what you think about it.
Thanks
Mona
From: Nasiriavanaki, Zahra
Sent: Tuesday, April 9, 2019 5:55:58 PM
To: Freesurfer support list
Subject: mri_segstats
Dear
Dear Freesurferers
I was trying to do a connectivity analysis using subnuclei of Amygdala.
I had an Amygdala segmentation file (reg.lh.HBT.mgz for letf Amygdala) and I
tried to use that in mri_segstats to extract the timeseries and then use it as
a seed in my analysis. However when I looked at
Hi Daniel
left and right hippocampus have different indices (17 and 53)
cheers
Bruce
On Wed, 6 Mar
2019, Daniel Callow wrote:
External Email - Use Caution
Never mind. I see that I can use those to id #'s to call from
FreeSurferColorLUT.txt.
I assume that those Id's are co
External Email - Use Caution
Never mind. I see that I can use those to id #'s to call
from FreeSurferColorLUT.txt.
I assume that those Id's are consistent for both left and right hippocampus.
Thanks for the help!
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
E
External Email - Use Caution
Hi Doug,
Thank you for your reply!
Unfortunately when I run the same code as before but by calling to
/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt
instead of /Applications/freesurfer/FreeSurferColorLUT.txt and using the
a
look in $FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt
The first number should be the one you are looking for.
On 3/6/19 12:26 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am trying to extract stats from the hippocampal subfield volumes
> t
External Email - Use Caution
Hello,
I am trying to extract stats from the hippocampal subfield volumes that I
have warped to diffusion space.
mri_vol2vol --mov
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lowb.nii.gz --targ
/Volumes/DANIEL/dti_freesurf/diffusion_recons/$
which ROIs are different?
On 2/22/19 5:39 PM, Winkelbeiner, Stephanie A wrote:
>
> External Email - Use Caution
>
> Hi Freesurfers,
>
> I’m trying to read out GM and WM values from parcels (ROIs) but get a
> different amount of ROIs for GM and WM.
>
> I use the following commands (embedde
External Email - Use Caution
Hi Freesurfers,
I'm trying to read out GM and WM values from parcels (ROIs) but get a different
amount of ROIs for GM and WM.
I use the following commands (embedded in a loop),
for GM
mris_anatomical_stats -mgz \
-cortex label/lh.cortex.l
There is not a way to get more decimals but you can apply a scaling
factor with --mul, eg, --mul 1000 will multiply the output by 1000
On 12/19/2018 04:01 PM, Winkelbeiner, Stephanie A wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer,
>
> Is there a way to print out more decimals
External Email - Use Caution
Hi Freesurfer,
Is there a way to print out more decimals with mri_segstats?
The mean diffusivity values are very small and with only four decimals not
really distinguishable from each other.
Thanks for your help!
Stephanie
The information contain
External Email - Use Caution
Hi Freesurfers,
Is there an option to write out more decimals when using the mri_segstats
command?
I'm extracting mean diffusivity values and would need at least 5 decimals to
make sense of them.
Thanks for your help!
Cheers
Stephanie
The informa
External Email - Use Caution
Hi freesurfer experts,
I'm trying to extract mean FA values (dti_FA.nii.gz) using a segmentation
volume (parc2502dwi.nii.gz) and the corresponding color table with:
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
#
and does that file exist in /tmp? Is there space in /tmp?
On 02/28/2018 01:33 PM, Yash Patel wrote:
> Yes, I made sure I had permission to write into /tmp.
>
> On Wed, Feb 28, 2018 at 12:23 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> do you have write permission to /t
Thanks for the advice. I did have permission to write into /tmp; however
the HPC wouldn't allow it through the mri_segstats command line.
The issue was resolved by making a directory in the tmp manually, and then
mri_segstats works normally.
Thanks,
Yash
On Wed, Feb 28, 2018 at 1:33 PM, Yash Pate
Yes, I made sure I had permission to write into /tmp.
On Wed, Feb 28, 2018 at 12:23 PM, Douglas N Greve wrote:
> do you have write permission to /tmp ?
>
>
> On 02/27/2018 03:25 PM, Yash Patel wrote:
> > Hello FreeSurfer experts,
> >
> > I am attempting to run "mri_segstats --annot [subjectid] l
do you have write permission to /tmp ?
On 02/27/2018 03:25 PM, Yash Patel wrote:
> Hello FreeSurfer experts,
>
> I am attempting to run "mri_segstats --annot [subjectid] lh aparc
> --sum [outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035"
>
> Whenever I try, I receive the following e
Hello FreeSurfer experts,
I am attempting to run "mri_segstats --annot [subjectid] lh aparc --sum
[outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035"
Whenever I try, I receive the following error (in error.log file);
CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15
Also, unless something is wrong with your processing or time point
naming, you should get different volumes also for each time point in the
longitudinal stream. Manually open the aseg.stats and check to determine
if the problem is in way you processed the longitudinal data or when
creating the
Sorry, I'm not sure what you are trying to do. Can you send command lines?
On 5/9/17 6:42 AM, Ferdi van de Kamp wrote:
Hi all,
My question is twofold
using an user specified ROI in MNI512-space I ask Freesurfer to create
tables for both cross-sectionally& longitudinally processed data.
M
Hi all,
My question is twofold
using an user specified ROI in MNI512-space I ask Freesurfer to create
tables for both cross-sectionally& longitudinally processed data.
Mri_segstats performed over both cross-sectional data folders and
longitudinal data folders
However, when inspecting the data,
Dear Dr. Greve,
Thank you for the response.
I will definitely try those.
Best regards,
Chih-Yang Hsu
On Tue, Mar 7, 2017 at 9:34 AM, Douglas Greve
wrote:
> There are no more moments you can get from it. You're best bet is to load
> the thickness (read_curv.m) and aparc (read_annotation) maps
There are no more moments you can get from it. You're best bet is to
load the thickness (read_curv.m) and aparc (read_annotation) maps into
matlab and then do what you want with them.
On 3/7/17 9:14 AM, Chih-Yang Hsu wrote:
Hi, I am using Freesurfer to estimate cortical thickness.
Is there an
Dear Dr. Fischl,
Thank you for the fast response.
We would like to obtain the entire distribution of the cortical thickness
so we can calculate more statistical, such as the first and third quartile.
I tried read_cuv.m and it works perfect.
Thank you again.
Best regards,
Chih-Yang Hsu
On Tue,
not sure exactly what you mean, but you can use read_curv.m to load the
entire spatial map of thickness into matlab for each subject. If you tell
us what you want to do we can give you more detailed advice
cheers
Bruce
On Tue, 7 Mar
2017, Chih-Yang Hsu wrote:
> Hi, I am using Freesurfer to est
Hi, I am using Freesurfer to estimate cortical thickness.
Is there any way to get all the details of the thickness distribution?
I used mri_segstats but it only provided mean and standard deviation.
Thank you.
___
Freesurfer mailing list
Freesurfer@nmr.m
That is everything that has a segmentation number = 0. You can exclude
it with, --excludeid 0
On 02/24/2017 10:08 AM, John Anderson wrote:
> Dear Freesurfer experts,
> I have used the following commandline to generate the final statistics
> in my analysis:
> mri_segstats --seg aseg.mgz --ctab-
Dear Freesurfer experts,
I have used the following commandline to generate the final statistics in my
analysis:
mri_segstats --seg aseg.mgz --ctab-default --i suvr.nii --mask mask.nii --sum
stats.dat
The final output of this command is (attached). Depedning on the anatomical
location of the ma
You can add --mul 1000 to multiply everything by 1000
On 10/11/16 4:47 PM, Chung, Yoonho wrote:
Hi!
I ran mri_segstats as instructed in the wiki to extract ADC values
from adc.nii. And as you can see below in my output, I think the
decimal digits are truncated and missing the following dec
Hi!
I ran mri_segstats as instructed in the wiki to extract ADC values from
adc.nii. And as you can see below in my output, I think the decimal digits are
truncated and missing the following decimal values. Is there an option or other
way to get around this problem and extract ADC values from
mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Monday, July 18, 2016 6:56 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_segstats
>
> Your suvr is axially sliced whereas the anatomical is corronally slic
: [Freesurfer] mri_segstats
Thank you Doug,
Kindly how can I make the suvr and the anatomical images in the same slice?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, July 18, 2016 6:56 PM
To
@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
n...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Monday, July 18, 2016 5:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_segstats
>
> What do you mean you got 0s only for the cblum segs? Did all other segs have
> non-zeros, but clbum have 0s
: [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
On Behalf Of Douglas N Greve
> Sent: Monday, July 18, 2016 5:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_segstats
>
> What do you mean you got 0s only for the cblum segs? Did all other segs have
> non-zeros, but clbum have 0s? And did you get non-0s in the 2nd comm
freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, July 18, 2016 5:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats
What do you mean you got 0s only for the cblum segs? Did all other segs have
non-zeros, but clbum have 0s? And did you get non-0s in the
freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, July 18, 2016 5:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats
What do you mean you got 0s only for the cblum segs? Did all other segs have
non-zeros, but clbum have 0s? And did you get non-0s in the
lated to a missing flags in my "mri_segstats" command line?
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Thursday, July 7, 2016 12:17 PM
> To
The first one
On 07/06/2016 08:22 PM, Alshikho, Mohamad J. wrote:
>
> 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 ac
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
...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, April 13, 2015 4:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats flags
Only the structures in the color table (--ctab) are reported; the 1st
ctab
__
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, April 13, 2015 4:29 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re:
ic white matter?
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, April 13, 2015 4:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri
_
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, April 13, 2015 4:16 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_s
: 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
...@nmr.mgh.harvard.edu]
> Sent: Monday, April 13, 2015 3:22 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_segstats flags
>
> Try this one
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats
>
> This is for linux. If that is not your
...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, April 13, 2015 3:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats flags
Try this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats
This is for linux. If that is
Try this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats
This is for linux. 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 comman
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-
There is not a flag to control the printing format. However, you can
multiply the values by a constant (--mul flag). Eg, you can multiply all
values by 100 or divide by 100.
doug
On 1/30/15 11:42 AM, Alshikho, Mohamad J. wrote:
> Dear FS Experts,
> In order to generate the statistics using mri_
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
Thanks Doug,
That is what I needed to know!
Brad
On Jun 26, 2014, at 11:13 AM, Douglas N Greve wrote:
>
> It is helpful to have a command line, but I think I can figure it out
> from what you have written. The first row is everything outside your
> seg. The second is everything inside your
It is helpful to have a command line, but I think I can figure it out
from what you have written. The first row is everything outside your
seg. The second is everything inside your seg.
doug
On 06/25/2014 05:54 PM, Martins, Brad wrote:
> Hi everyone,
>
> I’m new to Freesurfer and I have a que
Hi everyone,
I’m new to Freesurfer and I have a question about the output of mri_segstats. I
have created an ROI in which I am measuring cortical thickness. When I run
mri_segstats I get a table with 2 rows of segmentation values. What are the 2
rows? The SegId of the two rows are 0 and 1 but I
On 6/9/14 7:10 PM, sha...@nmr.mgh.harvard.edu wrote:
> Hi,
> I have two questions about mri_segstats. I want to measure the surface
> area of a functionally-defined ROI. I used the mri_segstats as below
> and I want to be sure that it is correct. Please note that ROIs were
> defined in the
Hi,
I have two questions about mri_segstats. I want to measure the surface
area of a functionally-defined ROI. I used the mri_segstats as below
and I want to be sure that it is correct. Please note that ROIs were
defined in the native space.
mri_segstats --i $SUBJECTS_DIR/SBJ1/surf/rh.area -
>
> On 04/24/2014 09:40 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> Thanks again for your help. I had two questions that came up from doing
>> some preliminary analysis with the mri_segstats:
>>
>> 1) When running the mri_segstats command with --seg
>> aparc+aseg_nocortex.mgz (which is
On 04/24/2014 09:40 AM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> Thanks again for your help. I had two questions that came up from doing
> some preliminary analysis with the mri_segstats:
>
> 1) When running the mri_segstats command with --seg
> aparc+aseg_nocortex.mgz (which is the resul
Hi Doug,
Thanks again for your help. I had two questions that came up from doing
some preliminary analysis with the mri_segstats:
1) When running the mri_segstats command with --seg
aparc+aseg_nocortex.mgz (which is the result of the matlab code you
provided below) and with --seg wmparc.mgz, even
That is great,
Thanks a lot, Doug!
>
> You can just do it in matlab, somethhing like
>
> a = MRIread('aparc+aseg.mgz');
> ind = find(a.vol > 999);
> a.vol(ind) = 0;
> MRIwrite(a,'nocortex.mgz')
>
>
>
> On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> I'm sorry, what I m
You can just do it in matlab, somethhing like
a = MRIread('aparc+aseg.mgz');
ind = find(a.vol > 999);
a.vol(ind) = 0;
MRIwrite(a,'nocortex.mgz')
On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> I'm sorry, what I meant to ask in the previous question is whether there
>
Hi Doug,
I'm sorry, what I meant to ask in the previous question is whether there
is a way to come up with a segmentation volume for the mri_segstats
command that is exactly like aseg.mgz but that does not include the
cortex. The reason I'm asking is because by using the aseg.mgz volume in
the --s
If you want the volume of cortex, you should definitely not use
aseg.mgz. aparc+aseg is better, but the best is to use the surface-based
measure found in aseg.stats
doug
On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> Thanks again for your reply. One last question: Th
Hi Doug,
Thanks again for your reply. One last question: The aseg.mgz file includes
the cortex as well. If I want to extract the cortex from the aseg.mgz
file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and
subtract them, and then use the result in the mri_segstats command, or is
On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> Thanks for the quick reply! In addition:
>
> 1) The average intensity measure in the above example does not include the
> intensity of the skull, just everything inside, right?
It includes all the structures that are segmented i
Hi Doug,
Thanks for the quick reply! In addition:
1) The average intensity measure in the above example does not include the
intensity of the skull, just everything inside, right?
2) Just to be clear on the purpose of including the segmentations in the
command line: The segmentations only specify
On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS community,
>
> I had some questions regarding the mri_segstats command:
>
> 1) In the excludeid flag, are the ids the ones shown in the
> FreeSurferColorLUT.txt?
Yes
> 2) In case I would like to measure the mean intensity of the orig f
Hi FS community,
I had some questions regarding the mri_segstats command:
1) In the excludeid flag, are the ids the ones shown in the
FreeSurferColorLUT.txt?
2) In case I would like to measure the mean intensity of the orig file as
outlined in the second example in
https://surfer.nmr.mgh.harvard.
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