subject:"\[Freesurfer\] mri

Re: [Freesurfer] mri_segstats --avgwf output question

2023-08-11 Thread Douglas N. Greve

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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:


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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


The results from my statistical analysis in the case of left 
hemisphere thickness shows 4 clusters that are significant in total, 
but the clusterAverages.txt contains a total of 5 mean thickness 
values per subject. This extra value is also reflected in other 
analyses in my dataset (for other hemisphere and for thickness, area 
and volume).


Is the extra value listed per subject a global mean of some sort? If 
so, is it the first column of values or the last?


Thank you,
Lara

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[Freesurfer] mri_segstats --avgwf output question

2023-08-10 Thread Lara Foland-Ross

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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

The results from my statistical analysis in the case of left hemisphere 
thickness shows 4 clusters that are significant in total, but the 
clusterAverages.txt contains a total of 5 mean thickness values per subject. 
This extra value is also reflected in other analyses in my dataset (for other 
hemisphere and for thickness, area and volume).

Is the extra value listed per subject a global mean of some sort? If so, is it 
the first column of values or the last?

Thank you,
Lara
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Re: [Freesurfer] mri_segstats --sbTIVin

2023-08-07 Thread Douglas N. Greve

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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:


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Dear Freesurfer developer.
According to the explanation in the *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
https://secure-web.cisco.com/1IqPogMjpBtw8frwqWnhb_ZJPG-R7cC1JDTgjrWqRbMGYrWBaYcuyonlnFwSw7eku9S4Vur02AnPYkwtVDFyosxFYhuxkxnqx8x_Jok9xzaQ9DPzz25OCX-f6yrabacvmdX6Ez0U9E66B5t5ChLHADkdXhU8VzaWdYA9EOHNcuNJxVC0qtU1TWlQoanVartraPfKptrukczRXRfNUBVmyjPU0vFqw08EXaTNLEevjvbzco-M-LxmseP7ZJflH1zezYTWaP9AurmdrSsVDerG6Mg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FsbTIV 
, 
it seems that the TIV volume of SAMSEG pipeline could be added to the 
aseg.stats with the option of mri_segstats --sbTIVin  ...
But, I can not find "--sbTIVin" option in the mri_segstats command of 
FreeSurfer 7.4.1 or the recent developer version.

How can I add sbTIV to aseg.stats?

Sincerely yours

Woo-Suk, Tae

--


Woo-Suk, Tae  Ph.D.  Research Professor
Brain Convergence Research Center, Medical Research Center
Anam Hospital, Korea University Medical Center, Seoul, Korea
mobile: 82-10-9120-4629
office: 82-2-920-6831
email: ws...@korea.ac.kr, woosuk@gmail.com,
wo os...@gmail.com



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[Freesurfer] mri_segstats --sbTIVin

2023-08-06 Thread Woo-Suk Tae

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Dear Freesurfer developer.
According to the explanation in the
https://secure-web.cisco.com/1coHbpSG3RMsDJ9eWWcn4zb_ld9qaPCVetqOo5rL5vuLfQQSISVGpVYl8aGgrzcAEShM1ov3Y1kaR3TI9f0riiixXrDWduFbq9YZu7vap8N9ooLrsMvKWnmIS21q5izT5EkhCL70i1Sw_90CUN-1TrF_pR-59FpT3F4Q9wFq-PqMEJ2eu_XExuWxU7lg6O-l_bycvdyEMCDXqh5RGJYHjh0n922PUlRzDFxpXB8bor7XeJEHKpJ7iaaxXxDJo4GuVe1z20CKD41HuVyeQ0zBLLXc6lE6yAoVBRTqJi6XtSiPdd685ICogk8xAkAqtfalRQljoFIba-du8mUaEixFIPA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FsbTIV,
 it seems that the TIV
volume of SAMSEG pipeline could be added to the aseg.stats with the option
of mri_segstats --sbTIVin  ...
But, I can not find "--sbTIVin" option in the mri_segstats command of
FreeSurfer 7.4.1 or the recent developer version.
How can I add sbTIV to aseg.stats?

Sincerely yours

Woo-Suk, Tae

-- 


Woo-Suk, Tae  Ph.D.  Research Professor
Brain Convergence Research Center, Medical Research Center
Anam Hospital, Korea University Medical Center, Seoul, Korea
mobile: 82-10-9120-4629
office: 82-2-920-6831
email: ws...@korea.ac.kr, woosuk@gmail.com,
  wo os...@gmail.com

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Re: [Freesurfer] mri_segstats dimension mistach

2023-07-20 Thread Douglas N. Greve

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It should not be that pixelated. My guess is that slicer is doing some 
kind of smart interpolation to make it look better. One way around it 
would be to map your input to the conformed space and run mri_segstats 
on that


On 7/6/2023 3:57 PM, Fahad Hannan wrote:


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Hi,

Just to follow up, is there a way to retain the segmentation quality? 
It becomes pixelated when returning to native space. Is there a method 
similar to how I can load the wmparc.mgz + my volume into 3DSlicer and 
they overlap perfectly despite the wmparc being in freesurfer space. 
I'm trying to find a better way to get segmentation based stats 
without the use of 3Dslicer which can be tedious. I've attached images 
showing the difference.


Regards,
Fahad

*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


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Hi Fahad,

Here is the wiki page about how to Convert from FreeSurfer Space Back 
to Native Anatomical Space  - *MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to be* 
https://secure-web.cisco.com/1PaHYdg_MxPaxqo4NGZ5ytczPBujdEVOKdh7sTk2xwvmj416d5EenaE48YGuIjT5DA_YGzI1lE_v7XHoA4OIpuxxIyOA4ZjXYKXwGYa2PL8EhjtxRrqAUt4ToduQxTuMFnQau4Dv7-p1ltPOf7eDMrLz7UIWf5Zqz2Y7eryRIfeF7L2itYS_92UaWuMbeCBTGSFEG2y7QHzkf0qPZGhPzjoCRoHp_jCuVfQogSJzYuMM2Fgx29A-7IgM0t7pslbkTr6zwc05-v0nfHQcRg3r43A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat 
<https://secure-web.cisco.com/1SH-F86njclC8pQKcB6nkwsqK8lnEDnPON_A24-6CmCwRHC_v0s6AwvY_foOYGXPrbz_PgXgmdPkQnHYy_AMudJENZoBcBNcrqdJGYd-N6ZKQjjSH-gzCI5Dq5ZHU2wFNKxRh944qf6UZNgqhb4s_XDC669KdGDt4GGk_mpnPRMKrIRyGvLfJb8vKw02AHSq1SM528T730feGzUsjm9FM5CgiF3QW5mg-UlGeOlPUDGd9xvS0cKt60Wny7zkFNwJMyH553-KKUKzzeyOvA09Wnw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat>


Best,

Yujing

*From:* freesurfer-boun...@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 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/mri/wmparc.mgz --sum 
$SUBJECTS_DIR/P6V1/stats/T2lobestest.stats --id 3201 4201 3203 4203 
3204 4204 3205 4205 3206 4206 3207 4207 --in T2_Map.nii.gz 
--in-intensity-name norm --in-intensity-units MR --etiv --subject P6V1 
--surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt"


I get a dimension mismatch error:

ERROR: dimension mismatch between input volume and seg

  input 112 112 80

  seg   256 256 256

Seems like during the recon-all process, freesurfer changed the 
dimensions of the segmentation file to 256 256 256. Is there a way I 
can resample the segmentation file to the input files dimensions, I 
know I can resample the input to the norm.mgz file but I do not want 
to tamper with the input file.


Thanks,

Fahad


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Re: [Freesurfer] mri_segstats dimension mistach

2023-07-06 Thread Fahad Hannan

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That worked, thank you so much!

Regards,

Fahad

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

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Hi Fahad,



Here is the wiki page about how to Convert from FreeSurfer Space Back to Native 
Anatomical Space  -  MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1ra2U8cDomVFQCO-1Aat6B6-AjtuLqzp5FeIV0ef8j4TJy4jL5YVqk0ZY85q9VvQDjTt7JlbClqTkflt4zTQ4sqfTYqGRXuNdiCGhMnf5d67sEtbQk0YI6f7UvWZJu6UCuW1IXSUYcBDEVhL02QNX1vzQWPXde2i0UAneFHWY0vBcouq8FIVZYxqvbEkbJ4v30ojDYiYpTnmFfhGcpCpr7FzDbbLGEvclrtC-LSQ3WE35x99pDRZl4BNiJhyRkKJyvLE7Wsd2eoH8yY92UteJy2ABFzFlR6vfHOchiwVZOvnDT-bb4MeVCw0cHGsGqKvRnMD4wKABsFD843JK2iLEOA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat<https://secure-web.cisco.com/1SH-F86njclC8pQKcB6nkwsqK8lnEDnPON_A24-6CmCwRHC_v0s6AwvY_foOYGXPrbz_PgXgmdPkQnHYy_AMudJENZoBcBNcrqdJGYd-N6ZKQjjSH-gzCI5Dq5ZHU2wFNKxRh944qf6UZNgqhb4s_XDC669KdGDt4GGk_mpnPRMKrIRyGvLfJb8vKw02AHSq1SM528T730feGzUsjm9FM5CgiF3QW5mg-UlGeOlPUDGd9xvS0cKt60Wny7zkFNwJMyH553-KKUKzzeyOvA09Wnw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat>



Best,



Yujing



From: freesurfer-boun...@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 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/mri/wmparc.mgz --sum 
$SUBJECTS_DIR/P6V1/stats/T2lobestest.stats --id 3201 4201 3203 4203 3204 4204 
3205 4205 3206 4206 3207 4207 --in T2_Map.nii.gz --in-intensity-name norm 
--in-intensity-units MR --etiv --subject P6V1 --surf-wm-vol --ctab 
$FREESURFER_HOME/FreeSurferColorLUT.txt"



I get a dimension mismatch error:



ERROR: dimension mismatch between input volume and seg

  input 112 112 80

  seg   256 256 256



Seems like during the recon-all process, freesurfer changed the dimensions of 
the segmentation file to 256 256 256. Is there a way I can resample the 
segmentation file to the input files dimensions, I know I can resample the 
input to the norm.mgz file but I do not want to tamper with the input file.



Thanks,

Fahad
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Re: [Freesurfer] mri_segstats dimension mistach

2023-07-05 Thread Huang, Yujing

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Hi Fahad,

Here is the wiki page about how to Convert from FreeSurfer Space Back to Native 
Anatomical Space  -  
https://secure-web.cisco.com/1SH-F86njclC8pQKcB6nkwsqK8lnEDnPON_A24-6CmCwRHC_v0s6AwvY_foOYGXPrbz_PgXgmdPkQnHYy_AMudJENZoBcBNcrqdJGYd-N6ZKQjjSH-gzCI5Dq5ZHU2wFNKxRh944qf6UZNgqhb4s_XDC669KdGDt4GGk_mpnPRMKrIRyGvLfJb8vKw02AHSq1SM528T730feGzUsjm9FM5CgiF3QW5mg-UlGeOlPUDGd9xvS0cKt60Wny7zkFNwJMyH553-KKUKzzeyOvA09Wnw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat

Best,

Yujing

From: freesurfer-boun...@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 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/mri/wmparc.mgz --sum 
$SUBJECTS_DIR/P6V1/stats/T2lobestest.stats --id 3201 4201 3203 4203 3204 4204 
3205 4205 3206 4206 3207 4207 --in T2_Map.nii.gz --in-intensity-name norm 
--in-intensity-units MR --etiv --subject P6V1 --surf-wm-vol --ctab 
$FREESURFER_HOME/FreeSurferColorLUT.txt"

I get a dimension mismatch error:

ERROR: dimension mismatch between input volume and seg
  input 112 112 80
  seg   256 256 256

Seems like during the recon-all process, freesurfer changed the dimensions of 
the segmentation file to 256 256 256. Is there a way I can resample the 
segmentation file to the input files dimensions, I know I can resample the 
input to the norm.mgz file but I do not want to tamper with the input file.

Thanks,
Fahad
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[Freesurfer] mri_segstats dimension mistach

2023-07-03 Thread Fahad Hannan

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/mri/wmparc.mgz --sum 
$SUBJECTS_DIR/P6V1/stats/T2lobestest.stats --id 3201 4201 3203 4203 3204 4204 
3205 4205 3206 4206 3207 4207 --in T2_Map.nii.gz --in-intensity-name norm 
--in-intensity-units MR --etiv --subject P6V1 --surf-wm-vol --ctab 
$FREESURFER_HOME/FreeSurferColorLUT.txt"

I get a dimension mismatch error:

ERROR: dimension mismatch between input volume and seg
  input 112 112 80
  seg   256 256 256

Seems like during the recon-all process, freesurfer changed the dimensions of 
the segmentation file to 256 256 256. Is there a way I can resample the 
segmentation file to the input files dimensions, I know I can resample the 
input to the norm.mgz file but I do not want to tamper with the input file.

Thanks,
Fahad
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Re: [Freesurfer] mri_segstats

2023-03-13 Thread Douglas N. Greve

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:


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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). thanks for any suggestions.


Thank you, John

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[Freesurfer] mri_segstats

2023-03-07 Thread John Anderson

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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). thanks for any suggestions.

Thank you, John
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Re: [Freesurfer] mri_segstats question: --avgwf for cross hemisphere ROI

2023-01-23 Thread Douglas N. Greve

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 waveforms (weighted by the number of vertices in each)

doug


On 1/16/2023 4:30 PM, Bram Diamond wrote:


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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 hemispheres. In essence, I would like to treat 
these contralateral labels as a single label.


Is there a way to use freesurfer binaries (e.g., mri_segstats) with, 
lh.func.mgz, rh.fun.mgz, lh.ROI.label, and rh.ROI.label to write a 
text file with a single average waveform column?


Thanks! I hope all is well in Boston!

Cheers,
Bram

Bram R. Diamond, BSc
Clinical Neuropsychology Doctoral Student
Northwestern University Feinberg School of Medicine
Mesulam Center for Cognitive Neurology & Alzheimer’s Disease
300 E. Superior Street | Tarry 8 | Chicago, IL 60611
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* www.brain.northwestern.edu 




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[Freesurfer] mri_segstats question: --avgwf for cross hemisphere ROI

2023-01-16 Thread Bram Diamond

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 hemispheres. In essence, I would like to treat these
contralateral labels as a single label.

Is there a way to use freesurfer binaries (e.g., mri_segstats) with,
lh.func.mgz, rh.fun.mgz, lh.ROI.label, and rh.ROI.label to write a text
file with a single average waveform column?

Thanks! I hope all is well in Boston!

Cheers,
Bram

Bram R. Diamond, BSc
Clinical Neuropsychology Doctoral Student
Northwestern University Feinberg School of Medicine
Mesulam Center for Cognitive Neurology & Alzheimer’s Disease
300 E. Superior Street | Tarry 8 | Chicago, IL 60611
http://secure-web.cisco.com/1rd9CGB1epEqWboZc37JDhl3-uOBS_KFp5wmeeP-n7zZWCMwlDuTlV1o551fqjOqYzccPbm5c2DzzARujomLrHcIqfB79clc5P6e6LiEy3vST3uj-eGX7Aexz1uQatXJJIYh8vcM7aQZ3W0pTMsr6qLUuUR4gDjKsqvrzSEhaQlARJ2f7JApYv9ndO8OauqODIvKlbRic_BD0itpGeWIm6OCHaBAbgvrnwaUbH_Q47_V8AdPoG2qe6Oh1YFHD4GENNjNx_8Q7ZbkvP7L_RqcN9iiNbWLd7xFC-9TiIOkBzPGWFXS35xlsjVx9ZZVcSMUCvus_m8cFGWF3qM56C4WMtA/http%3A%2F%2Fwww.brain.northwestern.edu

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