Re: [Freesurfer] ma_ca_register is not called anymore in version 7.3.2

2022-12-07 Thread Kilian M Pohl 
External Email - Use Caution

sorry listed wrong command line - after autrecon1 I run the following 
command

/usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd 
LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 
-autorecon2 -autorecon3 -no-isrunning -s 
LAB_S01541_standard_20180307_4541_03072018 -no-fix-with-ga -rng-seed 1234

which is the one failing bc it cannot find transforms/talairach.m3z

#--
#@# SubCort Seg Tue Dec  6 17:58:54 UTC 2022

  mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz 
transforms/talairach.m3z 
/usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca 
aseg.auto_noCCseg.mgz

sysname  Linux
hostname 3c46017221f4
machine  x86_64

setenv SUBJECTS_DIR 
/data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7
cd 
/data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz 
transforms/talairach.m3z 
/usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca 
aseg.auto_noCCseg.mgz

relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
     -renormalize
     -renormalize_mean 0.500
     -regularize 0.500

== Number of threads available to for OpenMP = 4 ==
reading 1 input volumes
reading classifier array from 
/usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca
reading input volume from norm.mgz
average std[0] = 7.2
reading transform from transforms/talairach.m3z
ERROR: cannot find or read transforms/talairach.m3z
error: No such file or directory
error: transforms/talairach.m3z: could not open transform

Best,

Kilian
On 12/7/2022 10:37 AM, Huang, Yujing wrote:
> Hi Kilian,
>
> I'm wondering what were your initial recon-all commands for FS 5.3 and FS 
> 7.1.1 because I'm not sure '-autorecon1' is making mri_ca_register call by 
> default.
>
> But It looks like you can use '-careg' to turn on mri_ca_register call.
>
> Here is a description of recon-all steps:
> https://secure-web.cisco.com/1htG9ZyeR94R_NHNY2O3znkDPMKCM94AkH1H0RTut4TvM_XNOMp0b5IpfWMN7VaDVEGT1aTGDBGyyZvW4Nj5L3Jb4Tp90UiTrCAvyd27dxmIE_XROTE0gqoE38RdR4TKP6LuV7mtS1Z-CIqEVQbcWi8yu-PKAb0IwpB8IfntCbMCcVlRSbMfJHKa1FDowaKA1unNg3oUyPiX8AYXRQHKTyuIt5xsfA7-sPU3N4BRDSQSOJ-FH0oNHnApsKUytFLrwfuhXgCiF_erN1CzrSjUDJxHgWmdO50hq99m225g7BQmmhC7eWJbORDT4zpF-8osy/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all
>
> Best,
>
> Yujing
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Kilian M Pohl
> Sent: Wednesday, December 7, 2022 12:53 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] ma_ca_register is not called anymore in version 7.3.2
>
>  External Email - Use Caution
>
> Hi ,
>
> I have used the following call starting at Freesurfer 5.3
>
> /usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd
> LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7
> -autorecon1 -noskullstrip -no-isrunning -s
> LAB_S01541_standard_20180307_4541_03072018 -rng-seed 1234
>
> It is still working with Freesurfer 7.1.1 but we now tried updating to
> 7.3 and it is failing (on the same case). Looking at the recon-all.log it 
> seem that ma_ca_register is not called anymore so that I get the following 
> error message
>
> ERROR: cannot find or read transforms/talairach.m3z
>
> (see attached recon-all .log)
>
> Do I have to add flags ?  I need to run with -noskullstrip
>
> Best,
>
> Kilian
>
>
>
> --
> Kilian M. Pohl, Ph.D.
>
> Associate Professor
> Department of Psychiatry & Behavioral Sciences Stanford University
>
> 401 Quarry Road
> Stanford, CA 94305-5717
>
> https://secure-web.cisco.com/18F69KCiyMWMSCouFYLrT3r9PgA1L7oUNzDa59-gQWUTsShFpsrS5hQaNO0pEiGsaHKqzn0e7h779L6bRMyMzCb5lAaJ0fwqBPOW8lLemFVir4TX77sLrDhxEwmH-_K67k8Wcj5yqqwssCRe30iCQlZMOzk85FBTQjdmczVPEVeGst3kfkscpPmkXiXo-cwSGKJXv1R11Ewgyiwc5CjQCPFAqtUjQeb7euLkZkt3-C8o6obbJ0vMPi_LRo-acT8JTG3md3jIZp5SKjkGKtcMoXGHrFwNJDMhft67lw3HEeOS622OvlwvJ-uB9Pag7DGyNwYPOk96CddmcVnHow7dIvw/https%3A%2F%2Fweb.stanford.edu%2F%7Ekpohl
>
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[Freesurfer] 7.3.2-patch issues - thalamic segmentation

2022-12-07 Thread Katie Rose Jobson 
External Email - Use Caution

Hi FS experts,

I am attempting to implement the patch on version 7.3.2 for issues with 
thalamic segmentation. I followed the instructions found here: 
https://secure-web.cisco.com/1JULaWPox6hiL5oNotdoE4us3D1hhs0HqpeHRUYFRvLuHPjNtpIrfTSk2Oor44j2FBUk_pFk20EpHFiM3R1FVkDnc65JJPCI2jaG74UkvfjSzqwjWygwvquVzF3AUampB5BRXbiKSY7Eq72Qbr3mY5H5t3RtHvfghMkNSXw1ggCZ3hzozbWLX2XVfU6Y5rB9JzogJtWSki-SikTk1LjM-Zp5AqdAc4RDMLOPK5MST93Dqz207lgJp4Isj6YZIOqM1Fms1_LkZdkfuWRZVT-8jSSycyBTF13XHfqQC3TqOL541UgCoyh-f4b9wH1mNOwjdTyfJIP8epMLDFkafQf_-Ow/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2-patch%2Freadme.txt
 and placed the scripts in their designated directories. However, I received 
the same error as before. The output indicates that the core.py script is 
located in the '$FREESURFER/python/packages/freesurfer/subregions/' directory, 
as opposed to the directory I was instructed to put the core.py script in 
('$FREESURFER/python/packages/gems/subregions/').

Should I replace the core.py script within 
'$FREESURFER/python/packages/freesurfer/subregions/'? Or is there another 
course of action that I can do that may solve this issue?

Here is the exact error, if that is at all helpful:
Step 2: aligning atlas to reference segmentation
Traceback (most recent call last):
  File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions", line 
99, in 
subregions.run_cross_sectional(args.structure, parameters)
  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py", 
line 52, in run_cross_sectional
model.align_atlas_to_seg()
  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py", 
line 240, in align_atlas_to_seg
mask = mask.resize(1, interp='nearest')
TypeError: resize() got an unexpected keyword argument 'interp'

Thank you in advance for your help!

Best Wishes,
Katie
--
Katie Jobson, M.S. | Personal 
Website
Ph.D. Student | Cognitive Neuroscience 
Lab
Department of Psychology and Neuroscience | Temple University

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Re: [Freesurfer] Regarding MRI Understanding.

2022-12-07 Thread Wighton, Paul 
Andy's brain book and neurostars are other great resources

https://andysbrainbook.readthedocs.io/en/latest/index.html
https://neurostars.org/

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of FELICITY SIMPSON 

Sent: Tuesday, December 6, 2022 10:19 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Regarding MRI Understanding.


External Email - Use Caution

Hi all,

I am in a similar boat to Rahul and would like to teach myself more about 
neuroimaging, specifically, for my PhD I would like to determine a brain age 
gap (possibly using HCP/UKbiobank to train my model etc).
A colleague has recommended using datacamp to learn machine learning and coding 
in python. I was wondering whether there were any other resources that may be 
useful?

Kind regards,
Felicity


On Wed, Dec 7, 2022 at 7:33 AM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Rahul,

There is are a lot of resources on the "Teach Youself FreeSurfer" page
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/TeachYourselfFreeSurfer

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Rahul Sharma 
mailto:sharmarahul.26...@gmail.com>>
Sent: Tuesday, December 6, 2022 1:02 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Regarding MRI Understanding.


External Email - Use Caution

Hello everyone, I am very new to this neuroimaging and belongs to technical 
background. Could anyone provide me any source or material for understanding 
MRI scans and the neuroimaging tools such as Freesurfer or FSL. Eagerly waiting 
for your reply.
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Re: [Freesurfer] Request for Assistance

2022-12-07 Thread Huang, Yujing 
Hi Eric,

Here are some online Freesurfer tutorials TeachYourselfFreeSurfer - Free Surfer 
Wiki 
(harvard.edu)

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of MANSON ERIC NAAB
Sent: Friday, December 2, 2022 6:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Request for Assistance


External Email - Use Caution
Dear Sir/Madam,
I am Eric Naab, a Ph.D. student at the University of Ghana, and currently doing 
my research at the University of Ghana MRI Medical Center. The title of my 
research is "Optimization of Pulse Sequence Protocols for Magnetic Resonance 
Imaging of the Brain". I am working with a 1.5T MRI Philips scanner and I 
intend to use the FreeSufer software for the first time.

I would be very glad if you could provide me with the specific recommended 
protocol for imaging and any other assistance that could help me with my 
research.

Thank you

Counting on your usual cooperation.
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[Freesurfer] Converting Volumes from Old Format to Current FreeSurfer Format

2022-12-07 Thread Ngo, Nathan Xi 
Hello,

I have several flash volumes that I am able to open using stable5 but not with 
the current version of freesurfer. Is there a way to convert these volumes into 
the current freesurfer format?

Best,
Nathan

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Re: [Freesurfer] ma_ca_register is not called anymore in version 7.3.2

2022-12-07 Thread Huang, Yujing 
Hi Kilian,

I'm wondering what were your initial recon-all commands for FS 5.3 and FS 7.1.1 
because I'm not sure '-autorecon1' is making mri_ca_register call by default.

But It looks like you can use '-careg' to turn on mri_ca_register call.

Here is a description of recon-all steps:
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

Best,

Yujing

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Kilian M Pohl
Sent: Wednesday, December 7, 2022 12:53 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ma_ca_register is not called anymore in version 7.3.2

External Email - Use Caution

Hi ,

I have used the following call starting at Freesurfer 5.3

/usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd
LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7
-autorecon1 -noskullstrip -no-isrunning -s
LAB_S01541_standard_20180307_4541_03072018 -rng-seed 1234

It is still working with Freesurfer 7.1.1 but we now tried updating to
7.3 and it is failing (on the same case). Looking at the recon-all.log it seem 
that ma_ca_register is not called anymore so that I get the following error 
message

ERROR: cannot find or read transforms/talairach.m3z

(see attached recon-all .log)

Do I have to add flags ?  I need to run with -noskullstrip

Best,

Kilian



--
Kilian M. Pohl, Ph.D.

Associate Professor
Department of Psychiatry & Behavioral Sciences Stanford University

401 Quarry Road
Stanford, CA 94305-5717

https://secure-web.cisco.com/18F69KCiyMWMSCouFYLrT3r9PgA1L7oUNzDa59-gQWUTsShFpsrS5hQaNO0pEiGsaHKqzn0e7h779L6bRMyMzCb5lAaJ0fwqBPOW8lLemFVir4TX77sLrDhxEwmH-_K67k8Wcj5yqqwssCRe30iCQlZMOzk85FBTQjdmczVPEVeGst3kfkscpPmkXiXo-cwSGKJXv1R11Ewgyiwc5CjQCPFAqtUjQeb7euLkZkt3-C8o6obbJ0vMPi_LRo-acT8JTG3md3jIZp5SKjkGKtcMoXGHrFwNJDMhft67lw3HEeOS622OvlwvJ-uB9Pag7DGyNwYPOk96CddmcVnHow7dIvw/https%3A%2F%2Fweb.stanford.edu%2F%7Ekpohl

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Re: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error

2022-12-07 Thread Andrew Beaudin 
   External Email - Use Caution


Hi Yujing,
 No problem at all.  I really appreciate yours, and now Martin's, help with this issue.  If you would like to 
start with dicoms, please let me know.


Again, thank you both for your help.

Andrew


*Andrew Beaudin, PhD* | Research Associate
University of Calgary | Cumming School of Medicine
Department of Clinical Neurosciences
HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1
Phone: (403) 210-6273


--
*From:* Huang, Yujing [mailto:yhuan...@mgh.harvard.edu]
*Sent:* Wednesday, December 7, 2022 at 10:27
*To:* Andrew Beaudin , Freesurfer support list 

*Cc:* Reuter, Martin,Ph.D. 
*Subject:* [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error


[△EXTERNAL]



Hi Andrew,

Sorry for the late response. I’m able to reproduce your error.

I have included Martin to the communication. He is the author of the program. He is going to take a look at 
your data.


Best,

Yujing

*From:*Andrew Beaudin 
*Sent:* Friday, November 25, 2022 3:25 PM
*To:* Huang, Yujing ; Freesurfer support list 

*Subject:* RE: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean 
Error

*External Email - Use Caution *

Hi Huang,

  Thank you very much for your help with this.  Apologies for the delay.

  You should be able to retrieve sample images from the following link (expires on Dec. 2).  I have also 
included a brief word document at the link that includes some details of the nifti images.


https://secure-web.cisco.com/1u-XjnB7jp5aUY3P1eL9t3mjpEr4XAP3TY2U7XxL4Sk87YBdOSl_IQZ5JxeKcPMFrkH1D-DL51W3gJTpja96AmSeeT6NQ-dEWQRnDoseAfuoXPdol4fUEj456GfCfg6j6TtlrWRZoceOKpLjcxVFnsacYsf16cLSN-f6q0Sbbc0InWMXztU4Wy6y0t1g_7ySgm0Nc6-uXHG8pXVATn179wXImzhZu1it0pGrkoYjI0g6eUpUKXmb5AwPI0oaQZUaiMUxvvZMEIDGHEmGBTYBoZBfCSn_YRcLlNDAPu9m1IlJo22qTgCbu8sgHPQszXhUWwLqcZSrhBQP4hmRgdIJumtNtYVbbc8YuFjLZXax3WT0/https%3A%2F%2Fuofc-my.sharepoint.com%2F%3Af%3A%2Fg%2Fpersonal%2Fabeaudin_ucalgary_ca%2FEmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ 



The command call I am using is:

mri_robust_template --mov 2001A_T1o_brain.nii.gz 2001B_T1o_brain.nii.mgz --lta 2001A2template.lta 
2001B2template.lta --average 1 --template 2001_template.nii.gz --satit


  However, while troubleshooting I have also tried the following with no 
success:


1) using the --iscale flag - same MyMatrix::RotationMean Error (see below for 
log)

2) using --inittp 0 - results in a 'Segmentation fault'
3) using --average 0 - same MyMatrix::RotationMean Error
4) using Freesurfer v7.2 - same MyMatrix::RotationMean Error

5) running mri_robust_template call on Catalina and Big Sur systems with FS v6.0 - same 
MyMatrix::RotationMean Error.


Again, thank you for the help….and please let me know if your need any additional information or anything 
clarified.


Andrew


*Andrew Beaudin, PhD* | Postdoctoral Scholar
University of Calgary | Cumming School of Medicine
Department of Clinical Neurosciences
HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1
Phone: (403) 210-6273

*From:*Huang, Yujing 
*Sent:* November 22, 2022 7:32 AM
*To:* Freesurfer support list 
*Cc:* Andrew Beaudin 
*Subject:* RE: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean 
Error

[△EXTERNAL]

Hi Andrew,

Can you send us some data to debug? The link has expired. Also, the command line that you are having trouble 
with.


Thanks.

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu  *On Behalf Of *Andrew 
Beaudin

*Sent:* Wednesday, June 29, 2022 10:45 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error

*External Email - Use Caution *

Hello Freesurfer Community,
  I am trying to use mri_robust_template (with its default 6 DOF registration) outside of the Freesurfer 
longitudinal pipeline to generate within-participant T1 templates from 2 time points.  Unfortunately, I am 
coming up against a 'MyMatrix::RotationMean input(s) not rotation' error on images acquired on our GE 3T 
Discovery 750 system, but not our colleagues' Seimens 3T Prisma images.  I have pasted the output from the 
--debug flag below (and attached as text file - line 188 is the MyMatrix message).   If helpful, images can 
be download from the following link: *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
h

[Freesurfer] missing values, aseg

2022-12-07 Thread Eszter Boros 
External Email - Use Caution

Dear FreeSurfer Team,

I am writing because I was extracting the aseg values using Freesurfer
7.1.1 and much to my surprise, these values were 'empty', or zero:

5th-Ventricle WM-hypointensities
Left-WM-hypointensities
Right-WM-hypointensities
non-WM-hypointensities
Left-non-WM-hypointensities
Right-non-WM-hypointensities

What could be the reason behind this? How can I get these values?

I used the following command:
asegstats2table --subjects subject1 subject2 (... etc) --common-segs --meas
volume --stats=aseg.stats --table=aseg.volume.txt

Thank you for your help in advance! And let me know if you need any more
information.

All the best,
Eszter Boros
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Re: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error

2022-12-07 Thread Huang, Yujing 
Hi Andrew,

Sorry for the late response. I’m able to reproduce your error.

I have included Martin to the communication. He is the author of the program. 
He is going to take a look at your data.

Best,

Yujing



From: Andrew Beaudin 
Sent: Friday, November 25, 2022 3:25 PM
To: Huang, Yujing ; Freesurfer support list 

Subject: RE: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean 
Error


External Email - Use Caution
Hi Huang,
  Thank you very much for your help with this.  Apologies for the delay.

  You should be able to retrieve sample images from the following link (expires 
on Dec. 2).  I have also included a brief word document at the link that 
includes some details of the nifti images.

https://uofc-my.sharepoint.com/:f:/g/personal/abeaudin_ucalgary_ca/EmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ


The command call I am using is:

mri_robust_template --mov 2001A_T1o_brain.nii.gz 2001B_T1o_brain.nii.mgz --lta 
2001A2template.lta 2001B2template.lta --average 1 --template 
2001_template.nii.gz --satit

  However, while troubleshooting I have also tried the following with no 
success:

1) using the --iscale flag - same MyMatrix::RotationMean Error (see below for 
log)
2) using --inittp 0 - results in a 'Segmentation fault'
3) using --average 0 - same MyMatrix::RotationMean Error
4) using Freesurfer v7.2 - same MyMatrix::RotationMean Error
5) running mri_robust_template call on Catalina and Big Sur systems with FS 
v6.0 - same MyMatrix::RotationMean Error.


Again, thank you for the help….and please let me know if your need any 
additional information or anything clarified.

Andrew

Andrew Beaudin, PhD | Postdoctoral Scholar
University of Calgary | Cumming School of Medicine
Department of Clinical Neurosciences
HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1
Phone: (403) 210-6273

From: Huang, Yujing mailto:yhuan...@mgh.harvard.edu>>
Sent: November 22, 2022 7:32 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Andrew Beaudin mailto:abeau...@ucalgary.ca>>
Subject: RE: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean 
Error

[△EXTERNAL]

Hi Andrew,

Can you send us some data to debug? The link has expired. Also, the command 
line that you are having trouble with.

Thanks.

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Andrew Beaudin
Sent: Wednesday, June 29, 2022 10:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error


External Email - Use Caution
Hello Freesurfer Community,
  I am trying to use mri_robust_template (with its default 6 DOF registration) 
outside of the Freesurfer longitudinal pipeline to generate within-participant 
T1 templates from 2 time points.  Unfortunately, I am coming up against a 
'MyMatrix::RotationMean input(s) not rotation' error on images acquired on our 
GE 3T Discovery 750 system, but not our colleagues' Seimens 3T Prisma images.  
I have pasted the output from the --debug flag below (and attached as text file 
- line 188 is the MyMatrix message).   If helpful, images can be download from 
the following link: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://uofc-my.sharepoint.com/:f:/g/personal/abeaudin_ucalgary_ca/EmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ?e=lcovfR

Briefly:
   - the images are skull-stripped niftis and I am running Freesurfer 6.0 
(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) on a WSL2 Ubuntu 
18.04 installation.
   - the call is: mri_robust_template --mov 2001A_T1o_brain.nii.gz 
2001B_T1o_brain.nii.mgz --lta 2001A2template.lta 2001B2template.lta --average 1 
--template 2001_template.nii.gz --satit

   -  I have tried the following with no succ

Re: [Freesurfer] Fusion of PET and T1 weighted

2022-12-07 Thread Amar Shukla 
External Email - Use Caution

Dear Sir,

I have got the .dat files from the mri_segstats command.How to convert the
those multiple dat files into one excel or csv file.

regards
Amar Shukla

On Mon, 17 Oct 2022 at 2:56 AM, Douglas N. Greve 
wrote:

> yes, but how are you combining them? And what features after you do?
>
> On 10/16/2022 10:18 AM, Amar Shukla wrote:
>
> External Email - Use Caution
> Dear Sir,
>
>
> Fusion means combining the two modalities  that is T1 and Pet. Then
> extracting features from combined image. This is what I am thinking Sir.
>
> regards
> amar Shukla
>
>
>
> On Thu, 13 Oct 2022 at 11:19 AM, Amar Shukla 
> wrote:
>
>> Dear Freesurfer Community.
>>
>> I want to do image fusion (PET+T1) = T' weighted image. Then I want to go
>> for the feature extraction from this T1 modality which I will get from the
>> fusion.So how i can go for this.
>>
>> Questions are:
>>
>> 1) Do I have to use PET Surfer for this? Does Pet Surfer support the
>> fusion of the two different modality.
>> 2) I am in the perception that I want  PET+ T = T' , or does it justify
>> the multimodality approach for the detection of disease.
>> 3) If i extract features from the different modality and then i combine
>> it. Can we say that this is the multimodality approach of Image Fusion.
>>
>> Please advise me and provide the approach or the tool which will help me
>> for the multimodality.
>>
>>
>>
>>
>> --
>> With Regards,
>> Amar Shukla
>> Assistant Professor,
>> M tech AI ANN(2014-2016),
>> Centre Of Information Technology,
>> UPES
>> Contact :+91 897 977 8016
>>
> --
> With Regards,
> Amar Shukla
> Assistant Professor,
> M tech AI ANN(2014-2016),
> Centre Of Information Technology,
> UPES
> Contact :+91 897 977 8016
>
> ___
> Freesurfer mailing 
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> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
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> https://secure-web.cisco.com/1_8V3KHWYJSHOozsJwx_PlagbDgiCtoPnrXM7dUP5ceGJhEqesRQ9WlGS51FT9OvJigLpmNSxaV_-lW4Eqlh7lHX3LUpu2gGd2xKP_Z3jG9r42u4aZ0ZlHjJ-o187JsazBTW7W7pm5JVyVYOoh1dRBtwjJXp7oR4Ljvu9YJj2R5WTuOrYLd_-CjzWnH1jN1-sZvB1F7YUYW0Xp0OuLiyI9fXhiNt3qE0e5Y6tZwrma22C4A1QMFaafIMzOLIPvevcNw9wV4O32BQzMQ26YGHQQks0DS3YQsHF4ZOT_ZhUGYmx5dXe9lNdhMS22s9pfVfz_D3B1MKtnQsGHaRFw2cTrA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>
-- 
With Regards,
Amar Shukla
Assistant Professor,
M tech AI ANN(2014-2016),
Centre Of Information Technology,
UPES
Contact :+91 897 977 8016
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[Freesurfer] password request for file FS_7_2_0_Ubuntu_18_04_06.ova.7z

2022-12-07 Thread Daniele Ranieri 
External Email - Use Caution

Hello FreeSurfer,

I downloaded VM from the official website: FS_7_2_0_ubuntu_18_04_06.ova.7z

but I need the password to successfully open the compressed package.

I hope that is the right place for this request.


Thank you for your time.
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