Re: [Freesurfer] Running autorecon2-wm after wm edits makes no difference in final surface

[Huang, Yujing]

Your ‘recon-all -autorecon2-wm -autorecon3’ finished without errors. 
‘unknown-args.txt’ is created to filter out arguments not in recon-config.yaml. 
It doesn’t mean those flags are not recognized.

I don’t know why new surfaces are not created after your editing of wm.mgz. Can 
you re-send your corrections so someone else can help you?

At the meantime, here is the Freesurfer troubleshooting tutorial page. Hope it 
can be helpful - 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fernanda Hansen P. de 
Moraes
Sent: Tuesday, November 21, 2023 7:15 AM
To: Freesurfer support list 
Subject: [Freesurfer] Running autorecon2-wm after wm edits makes no difference 
in final surface


External Email - Use Caution
Dear FreeSurfer experts,

I have been trying to manually correct a wm volume to further fix the wm and 
pial surfaces, but when I ran recon-all -subjid SUBJxxx -autorecon2-wm 
-autorecon3 nothing happened to the surfaces. I found an unknown-args.txt file 
under scripts, and it seems the autorecon2-wm flag is not recognized.
How can I create new surfaces and overcome this issue?

Here attached is the complete recon-all log file from the beginning, including 
all steps attempted. I would be very glad if you could help me overcoming this 
error to include as much subjects as possible in my project.

Best regards,
Fernanda Hansen P. de Moraes

fernandahmor...@gmail.com
Pesquisadora no Instituto de Física da UFRJ | metaBIO (IF-UFRJ)
Doutora em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

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[Freesurfer] Fwd: About Mean LGI value

[笹林大樹]

External Email - Use CautionDear Dr. Greve,I trust this message finds you well. I wanted to follow up on the inquiry I posted to the FreeSurfer mailing list a while back regarding "About Mean LGI value" as below.I understand you are busy, and I appreciate your dedication to the community. If possible, could you revisit my query when time permits?Thank you for your time, and I look forward to hearing from you.

Best,Daiki Sasabayashi転送されたメッセージ:差出人: 笹林大樹 件名: Re: [Freesurfer] About Mean LGI value日付: 2023年11月9日 10:37:38 GMT-5宛先: Freesurfer support list 返信先: Freesurfer support list External Email - Use CautionDear. Dr. Greve,Thank you for your response.I attached both “*h.aparc.pial_lgi.stats” and “*h.aparc.mean_pial_lgi.stats” files.For example, in left hemisphere, mean LGI value is 3.0761 (SegId 1, Seg0001, is it correct as mean LGI value?), while the average of the LGI values is about 3.0327 (the sum of the LGI values of the 34 DK atlas ROIs divided by 34: value calculated here).Are these values acceptable?Daiki Sasabayashi

lh.aparc.pial_lgi.stats
Description: Binary data


lh.aparc.mean_pial_lgi.stats
Description: Binary data


rh.aparc.pial_lgi.stats
Description: Binary data


rh.aparc.mean_pial_lgi.stats
Description: Binary data
2023/11/09 9:33、Douglas N. Greve のメール:

  
  
How different are the values? Those two stats files are created with
different programs, so there could be some small differences. But if
you're seeing large differences, then that is something else. If the
latter, then send both stats files.

On 11/3/2023 9:14 AM, 笹林大樹 wrote:

External
  Email - Use Caution
  
Dear Freesurfer experts,


I have calculated the mean LGI value for each
  hemisphere by referring to previous archives below. 
However, this mean LGI value differs from the
  average of the LGI values listed in *h/aparc.pial_lgi.stats
  (i.e., the sum of the LGI values of the 34 DK atlas ROIs
  divided by 34). 
Are these values originally subject to
  discrepancy?


Best,
  
  
  
  Daiki Sasabayashi
  
  
  

  

  Re: [Freesurfer] Mean
Gyrification indexDougla
 s N.
Greve Wed, 09 Sep 2020 08:26:32
-0700

It is giving you values for two segmentations:
inside the label and outside the label. Use --id 1 to get only
values inside the cortex label
  On 9/9/2020 11:27 AM, vittal korann wrote:

  
External Email - Use Caution

Dear FreeSurfer experts


I am working on the gyrification index of
  schizophrenia patients. I had collated global brain values such as
  thickness, GM, and WM volumes. In addition, I wanted to tabulate
  gyrification values. Using the below link I was able to extract the
  hemispheric mean gyrification values.
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31829.html


But it is giving me 2 rows of output that are
  adding more ambiguity to the existing problem. Below is the command which I used to get mean
  gyrification for the left hemisphere and also the corresponding
  output.
*Command Line: *

mri_segstats --slabel CSRI104 lh
/usr/local/freesurfer//subjects/CSRI104/label/lh.cortex --i
/usr/local/freesurfer//subjects/CSRI104/surf/lh.pial_lgi --sum

lh.aparc.pial_lgi.stats 
*Output: *

# NRows 2
# NTableCols 10
# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
StdDev Min Max Range
  1   0      6879     4687.8  Seg     2.4509     0.2838  
1.8067     2.8873     1.0806
  2   1    128054    84259.7  Seg0001     3.0148     0.6366  

1.9369     4.7611     2.8242 My confusion is that which row I should take
  it as a mean gyrification value for the left hemisphere (seg or
  seg0001)?Please guide me if there is a way to combine
  two hemispheric values and make it as mean gyrification alike mean
  thickness.
With regards
Korann



On Wed, Sep 9, 2020 at 4:51 PM vittal korann
  MailScanner
has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
gmail.com 

[Freesurfer] Large discrepancy in left and right volumes of perirhinal/entorhinal cortices on FreeSurfer 7.1

[Marawi, Tulip]

External Email - Use Caution

Dear FreeSurfer developers,

Our research group used the FreeSurfer's recon-all tool to reconstruct 74 
anatomical images from cognitively healthy older individuals and parcellate the 
cortex based on the Desikan-Killiany atlas.
However, we are running into a consistent issue with the perirhinal volumes on 
the annot stats from BA_exvivo_thresh.stats, where there is a large discrepancy 
between the left and right hemispheres (larger left hemisphere).
Upon visual and numerical investigation, it appears that this could be due to 
mis-labelling the right perirhinal vertices as entorhinal, resulting in an 
unusually small right perirhinal cortex, and unusually large right entorhinal 
cortex.
Could you please clarify why this could be happening, and advise on next steps?
We have used FreeSurfer 7.1 for this analysis.

Sincerely,
Tulip Marawi


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Re: [Freesurfer] How many regions does "aparc.DKTatlas+aseg.mgz" have?

[Huang, Yujing]

Hi Kei,

Here is my calculation:

  198 aparc.a2005s+aseg.mgz
  192 aparc.a2009s+aseg.mgz
  114 aparc+aseg.mgz

I can't find aparc.DKTatlas+aseg.mgz in Freesurfer distribution directory. Is 
it the same as aparc+aseg.mgz?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Kei Nishimaki
Sent: Monday, November 20, 2023 5:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] How many regions does "aparc.DKTatlas+aseg.mgz" have?


External Email - Use Caution
Hello FreeSurfer Developers,

We ran recon-all on a 3D T1-weighted image, by default.
ls *.nii | parallel --jobs 2 recon-all -s {.} -i {} -all -qcache

Our question is very simple.
How many regions does "aparc+aseg.mgz" and "aparc.DKTatlas+aseg.mgz" and 
"aparc.a2009s+aseg.mgz" have in each?

We checked the links below. And we want to renumber the region index from 0 as 
shown in the photo below.
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT

However, the number of regions varies slightly depending on the subjects 
(103~106 in aparc.DKTatlas+aseg.mgz).
Therefore, we want to know the number of regions in three parcellation map.

1) FreeSurfer version: freesurfer-linux-ubuntu20_amd64-7.4.1.tar.gz
2) Linux ~~~ 5.15.0-76-generic #83~20.04.1-Ubuntu SMP Wed Jun 21 20:23:31 UTC 
2023 x86_64 x86_64 x86_64 GNU/Linux

[cid:image001.png@01DA1C68.536FE6F0]

Thanks,
Kei
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[Freesurfer] Errors in recon-all command

[Dunia A Alhamad]

External Email - Use Caution

Hello Freesurfer Developers

I'm attempting to apply preprocess and segment to my data that consist of
24 subjects by recon-all syntax, as described on the FreeSurfer wiki on
macOs software
https://secure-web.cisco.com/1sL0UR9IcjyzN-iiFPRBpUbos_zcdbT2W0RQcJ-3jMPXPBbG7t5-6HgMR60s4YWqde4tZa0XWjtkT0aWl3XybyhjThRfDIZmH8oNIZTQHT3KJDNpBj1DUZ6PKEZrrygdbT1DPTNtfO_zUn04IsLpbI6O57RcgvpVsXEx8ujYU-9-eFN0mWsVDj6gaP-ZccrPky_ruv3wCEiKCyGbSpPLpWXig3WAycCHA4_N_rPef9kRpg4gEFbLVjmjTPA3yx66OOHSaNacYpeFWBHZKyZbf4aKwJBcw2IPYCBLyjn1TOfQIc4V1h7skqAUUfgGHtlo3I_FNzpbevSUMMmOhMJUuzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all

ERROR: cannot find
/Users/duniaalhamad/Desktop/subjects/I83870_MP-RAGE_20071127095752_2/surf/lh.thickness

Darwin dyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct  9
21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64


1) freesurfer version: freesurfer-macOS-darwin_x86_64-7.4.1

2) platform: bash terminal

3) log file


Tue Nov 21 15:50:35 GMT 2023
cd /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3
setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects
/Applications/freesurfer/7.4.1/bin/recon-all -s
I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii
-qcache

subjid I12250_MP-RAGE_20060321115220_3
setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects
FREESURFER_HOME /Applications/freesurfer/7.4.1
Actual FREESURFER_HOME /Applications/freesurfer/7.4.1
build-stamp.txt: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
Darwin dyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct  9
21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8176 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
descriptors  256
memorylocked unlimited
maxproc  1333

PhysMem: 7547M used (1397M wired, 2612M compressor), 77M unused.


program versions used
7.4.1 (freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460)
7.4.1

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info
 ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun
14 2023 00:15:19  BuildStamp:
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad
 Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0
 CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion:
7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun 14 2023 00:15:19
 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User:
duniaalhamad  Machine: dyn145223.shef.ac.uk  Platform: Darwin
 PlatformVersion: 23.1.0  CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label
-all-info  ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT
 BuildTime: Jun 14 2023 00:15:19  BuildStamp:
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad
 Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0
 CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info
 ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun
14 2023 00:15:19  BuildStamp:
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad
 Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0
 CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info
 ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun
14 2023 00:15:19  BuildStamp:
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad
 Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0
 CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info
 ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun
14 2023 00:15:19  BuildStamp:
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad
 Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0
 CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info
 ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun
14 2023 00:15:19  BuildStamp:
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad
 Machine: dyn145223.shef.ac.uk  Platform: Darwin  PlatformVersion: 23.1.0
 CompilerName: Clang  CompilerVersion: 12.0.0
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info
 ProgramVersion: 7.4.1  TimeStamp: 2023/11/21-15:50:36-GMT  BuildTime: Jun
14 2023 00:15:19  BuildStamp:
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460  User: duniaalhamad
 Machine: dyn145223.shef.ac.uk  Platform:

Re: [Freesurfer] How many regions does "aparc.DKTatlas+aseg.mgz" have?

[Kei Nishimaki]

External Email - Use Caution

Hi, Yujing

Thank you for reply.
It is likely that the version of freesurfer is different.
The latest version (7.4.1) output results based on three atlases.
https://secure-web.cisco.com/16kyFKZBTTmJxzWlCpHckTWKfW7NeWPN9nduq80zrB4veUgSnqf_Yxf0V4hYrnX-id0bCIWJ9Wu0QjhaC8hGFsvw5fF7iKqEES2iLMyOuqfEuZ-rCPST4Q2uOFdH4SHYh9FXjbp07AstFZ_m_bljkfF7Sw-5BNFgi6ZMtRPb1vXwm1_ADDTJg59U4PKul_eb1xIhJJKpj9VYPCyOQ39gtP_aWXimwq3FgleENUQFx354be1rUU5sVizr9GuCBxDGaaKVW7wGycCcxIwTSjBdBnJAORnbTvvTP_QKN5-83GSW9IGPf9DyxK2vphprk2JiT/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FCorticalParcellation

Thanks,
Kei


差出人: freesurfer-boun...@nmr.mgh.harvard.edu 
 が Huang, Yujing 
 の代理で送信
送信日?: 2023年11月21日 10:52
宛先: Freesurfer support list 
件名: Re: [Freesurfer] How many regions does "aparc.DKTatlas+aseg.mgz" have?


  External Email - Use Caution



Hi Kei,



Here is my calculation:



  198 aparc.a2005s+aseg.mgz

  192 aparc.a2009s+aseg.mgz

  114 aparc+aseg.mgz



I can’t find aparc.DKTatlas+aseg.mgz in Freesurfer distribution directory. Is 
it the same as aparc+aseg.mgz?



Best,



Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Kei Nishimaki
Sent: Monday, November 20, 2023 5:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] How many regions does "aparc.DKTatlas+aseg.mgz" have?



External Email - Use Caution

Hello FreeSurfer Developers,



We ran recon-all on a 3D T1-weighted image, by default.

ls *.nii | parallel -?jobs 2 recon-all -s {.} -i {} -all -qcache



Our question is very simple.

How many regions does "aparc+aseg.mgz" and "aparc.DKTatlas+aseg.mgz" and 
"aparc.a2009s+aseg.mgz" have in each?



We checked the links below. And we want to renumber the region index from 0 as 
shown in the photo below.

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/132WvSeoaXEyy8CpFxjt9yVSLNRqcdk9XlE2pYSq33zz-bhyMysIClm-j16YORa2NekqiwQAGu-1-E5zUjkrIxWYDd3omIDUlJuSYMA7ZD6mgF10J_O1yJIvsptQldRmqgHpbZrw3MqeY5JWaASlT8VJ_Ej3O1000u3sxSisUgcb8S9PVHh9pq9hTMLZ5ulbGl0xtRa0VQ5DYVHlVA7A5k47TY60nkKToKMzFF2AvOOqhGwfnjwxw2y1H65_KeTxzb-0b1JiYyFv86F42t8Ve75tG2Hu9mlfTPhqEGwdtBZNKP3yRnYpOxXQgJmDElUXI/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FAnatomicalROI%2FFreeSurferColorLUT



However, the number of regions varies slightly depending on the subjects 
(103~106 in aparc.DKTatlas+aseg.mgz).

Therefore, we want to know the number of regions in three parcellation map.



1) FreeSurfer version: freesurfer-linux-ubuntu20_amd64-7.4.1.tar.gz

2) Linux ~~~ 5.15.0-76-generic #83~20.04.1-Ubuntu SMP Wed Jun 21 20:23:31 UTC 
2023 x86_64 x86_64 x86_64 GNU/Linux



[cid:image001.png@01DA1C68.536FE6F0]



Thanks,

Kei
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Re: [Freesurfer] Transformation of volume images

[P Pieperhoff]

External Email - Use Caution

Hi Yujing,
thank you for your help! But I think, this is only the affine registration?
Is it possible that I can use the same transformation, by which e.g.
aseg.mgz-atlas is transformed into the native space of a given subject?
The volume-dataset of the subcortical regions matches quite well with the
subcortical structure of each subject, but I think that this can't be
achieved by an affine transformation only.

Best regards,
Peter




On Fri, Nov 17, 2023 at 3:57 PM Huang, Yujing 
wrote:

> Hi Peter,
>
>
>
> Here is an example to convert from native space to MNI305 (fsaverage) in
> https://secure-web.cisco.com/1ReBfmWJausgcUfY96AjUCIcfqx5PX2Bs775KpxZcv9gOmTBSGzKXWFDQm3aeoDGEum66aG9yEs1oHr1_wTN6i2SvYPOCQ1sz_ZLdti5OCmdKssoz0DU5uDEd4yWNwuPoJ34VTWQlJZehHnFjRZJugcyy1Q4IkVV-FVasIrShFvpSVKNr0hcH_DWpycse2cFHlkv-BlqGkzcj-zeNCZi2giLNTyaz2EJ5KmUau7JMUjqg0vGLIFRRWlaaw_qSJtoHzr6tnk7-SPAyrntbI8Dli8oYsM2nGRZlRx-bFJnLCtgOx-ga_lgPFABOV8jAk6FvlqoxP0Kz6QHY5z6TSfb3yA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_vol2vol
>
>
>
>   mri_vol2vol --mov orig.mgz
>
>  --targ $FREESURFER_HOME/average/mni305.cor.mgz
>
>  --xfm transforms/talairach.xfm
>
>  --o orig-in-mni305.mgz
>
>
>
> In your case, I think you also need ‘—interp nearest’ to convert
> segmentation.
>
>
>
> To convert from fsaverage to native space of a subject, can you try the
> following? I used bert as an example.
>
>  mri_vol2vol
>
>--mov bert/mri/orig.mgz
>
>--targ fsaverage/mri/aseg.mgz
>
>--xfm transforms/talairach.xfm
>
>--inv
>
>--o aseg-from-mni305.mgz
>
>--interp nearest
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *P Pieperhoff
> *Sent:* Thursday, November 16, 2023 12:07 PM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Transformation of volume images
>
>
>
> *External Email - Use Caution*
>
> Dear developers,
>
>
>
> please, may I ask you how I can transform volume images (containing
> discrete region labels) from the fsaverage space into the space of a given
> subject, and vice-versa?
>
>
>
> I tried the following command:
>
> mri_vol2vol --interp nearest --mov fsaverage/mri/aseg.mgz  --o
> test_mask.mgz--s test001  --targ test001/mri/orig.mg
> 
>
>
>
> or
>
> mri_vol2vol   --interp nearest --mov fsaverage/mri/aseg.mgz  --o
> test_mask.mgz--targ  test001/mri/T1.mgz  --lta
>  test001/mri/transforms/talairach.lta --m3z talairach.m3z
> --s test001
>
>
>
> but there was always a large mismatch between the transformed images and
> the target image.
>
>
>
> Best regards,
>
> Peter
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Re: [Freesurfer] recon-all error

[Huang, Yujing]

NaNs are in your original input image. They are replaced with 0 in the output 
mri/orig/001.mgz.

Doug mentioned “Sometimes SPM will put NaNs in the image to indicate a mask.”. 
Is that your case?

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Carlos Alcocer
Sent: Tuesday, November 21, 2023 10:59 AM
To: Freesurfer support list 
Subject: [Freesurfer] recon-all error


External Email - Use Caution
Reposting due to issue with email bouncing. I am receiving following error on 
my subjects. Recon-all still continues after error and finishes "without error" 
I have attached the recon-all log as well.

 mri_convert /path/to/inputt1.nii  /path/to/mri/orig/001.mgz

mri_convert /path/to/anat_t1.nii /path/to/mri/orig/001.mgz
reading from /path/to/anat_t1.nii...
NaN found at voxel (0, 0, 244, 0)
error: No such file or directory
error: WARNING: 319676 NaNs found in volume /path/to/anat_t1.nii...

Thank you,

Carlos


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Re: [Freesurfer] Boundary based registration on partial FoV to MNI space

[Douglas N. Greve]

Is MRS_201_MT_tfl_stripped.mgz  correctly oriented when you view it in 
freeview? Also, bbr is meant to be used for within subject registration. 
For something like registering to the mni152, try mri_coreg and specify 
--dof 12



On 11/20/2023 10:00 AM, Spapens, Jeltje (NP) wrote:


External Email - Use Caution

Hello Freesurfer developers.

I tried the boundary-based registration of a partial FoV to a MNI 
space template with the following two step code:


bbregister --s MRS_201_recon_all --mov 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_201/MRS_201_MT_tfl_stripped.mgz 
--reg MRS_201_NM2mp2rage.dat --t2 --init-header


mri_vol2vol--mov/Users/robspapens/Desktop/Thesis/Subjects/MRS_201/MRS_201_MT_tfl_stripped.mgz 
--targ/Users/robspapens/Desktop/Thesis/Subjects/MNI_upsamp.nii 
--o/Users/robspapens/Desktop/Thesis/Subjects/MRS_201/MRS_201_MT_tfl_regt1.nii.gz 
--reg MRS_201_NM2mp2rage.dat --cubic


When I open the scan in Freeview or FSLeyes the orientation is not 
correct. The Horizontal plane is labeled as the Coronal plane and the 
sagittal plane is rotated 90 degrees.


I tried: fslreorient2std input_file.nii.gz output_file.nii.gz, but 
this gave the same result. I also tried it on 3 scans and all give the 
same wrong orientation after the BBR.


How can I best register the scan with small FoV to the MNI space template?

With kind regards,

Jeltje Spapens


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Re: [Freesurfer] Doubts about GLM contrasts

[Douglas N. Greve]

yes, it is the same contrast

On 11/20/2023 3:30 PM, Laura Willers de Souza wrote:


External Email - Use Caution

Great, thanks so much!
But I am having difficulty understanding how to construct the contrast 
to answer the following question "Is the interaction between group 
(CU/CI) and cortisol significant regressing out the effect of sex, 
age, APOE_carrier, abeta and ptau?" It seems like the contrast would 
be the same as before.. Can you help me with this?



Thanks again!

*Laura Willers de Souza *

PhD Student in Pharmacology and Therapeutics

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil



-

Douglas N. Greve 
 
Wed, 15 Nov 2023 06:54:36 -0800 



Yes, that looks right (assuming that cortisol is your first variable)
 On 11/7/2023 3:49 PM, Laura Willers de Souza wrote:
External Email - Use Caution Hello FreeSurfer Developers, 
Following the FSGD examples on the website, I built the following test:

Question: Is there an association between cortisol and cortical
thickness regressing out the effect of sex, age, APOE4_carrier (1=1 or
2 alleles, 0=no alleles), abeta, ptau, diagnosis (CU and CI)?
Regressors: 2 factors (sex, diagnosis) with 2 levels each, 5
covariates (age, APOE4_carrier (1=1 or 2 alleles, 0=no alleles),
abeta, ptau, cortisol) >> 24 regressors
Contrast: 0 0 0 0 0.5 -0.5 0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
FSGD: GroupDescriptorFile 1 Title CSF_semgrupos Class MaleCU Class 
MaleCI Class FemaleCU Class FemaleCI Variables Cortisol Age ABETA ptau 
APOE4_carrier Input 098_S_4003_I224603 MaleCI 11 81.3 741.5 22.83 1 
Does this feel right to you?

I am having difficulty understanding how to construct the contrast to
answer the following question "Is the interaction between group
(CU/CI) and cortisol significant regressing out the effect of sex,
age, APOE_carrier, abeta and ptau?" It seems like the contrast would
be the same as before.. Can you guys help me with this?
Thanks in advance! *Laura Willers de Souza * PhD Student in 
Pharmacology and Therapeutics Zimmer Lab - Federal University of Rio 
Grande do Sul - Porto Alegre/RS - Brazil



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Re: [Freesurfer] Large discrepancy in left and right volumes of perirhinal/entorhinal cortices on FreeSurfer 7.1

[Douglas N. Greve]

Do you see the same thing in the source BA data (in fsaverage)?

On 11/21/2023 10:22 AM, Marawi, Tulip wrote:


External Email - Use Caution

Dear FreeSurfer developers,

Our research group used the FreeSurfer’s recon-all tool to reconstruct 
74 anatomical images from cognitively healthy older individuals and 
parcellate the cortex based on the Desikan-Killiany atlas.


However, we are running into a consistent issue with the perirhinal 
volumes on the annot stats from BA_exvivo_thresh.stats, where there is 
a large discrepancy between the left and right hemispheres (larger 
left hemisphere).


Upon visual and numerical investigation, it appears that this could be 
due to mis-labelling the right perirhinal vertices as entorhinal, 
resulting in an unusually small right perirhinal cortex, and unusually 
large right entorhinal cortex.


Could you please clarify why this could be happening, and advise on 
next steps?


We have used FreeSurfer 7.1 for this analysis.

Sincerely,

Tulip Marawi

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Re: [Freesurfer] How many regions does "aparc.DKTatlas+aseg.mgz" have?

[Huang, Yujing]

I see now that recon-all produces
aparc.DKTatlas+aseg.mgz
aparc.a2009s+aseg.mgz
aparc+aseg.mgz

Just to clarify, my calculation is based on fsaverage/mri/aparc*.mgz

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Kei Nishimaki
Sent: Tuesday, November 21, 2023 11:02 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How many regions does "aparc.DKTatlas+aseg.mgz" have?


External Email - Use Caution
Hi, Yujing

Thank you for reply.
It is likely that the version of freesurfer is different.
The latest version (7.4.1) output results based on three atlases.
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation

Thanks,
Kei


差出人: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 が Huang, Yujing mailto:yhuan...@mgh.harvard.edu>> 
の代理で送信
送信日?: 2023年11月21日 10:52
宛先: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
件名: Re: [Freesurfer] How many regions does "aparc.DKTatlas+aseg.mgz" have?


  External Email - Use Caution





Hi Kei,



Here is my calculation:



  198 aparc.a2005s+aseg.mgz

  192 aparc.a2009s+aseg.mgz

  114 aparc+aseg.mgz



I can’t find aparc.DKTatlas+aseg.mgz in Freesurfer distribution directory. Is 
it the same as aparc+aseg.mgz?



Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Kei Nishimaki
Sent: Monday, November 20, 2023 5:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] How many regions does "aparc.DKTatlas+aseg.mgz" have?



External Email - Use Caution

Hello FreeSurfer Developers,



We ran recon-all on a 3D T1-weighted image, by default.

ls *.nii | parallel -?jobs 2 recon-all -s {.} -i {} -all -qcache



Our question is very simple.

How many regions does "aparc+aseg.mgz" and "aparc.DKTatlas+aseg.mgz" and 
"aparc.a2009s+aseg.mgz" have in each?



We checked the links below. And we want to renumber the region index from 0 as 
shown in the photo below.

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT



However, the number of regions varies slightly depending on the subjects 
(103~106 in aparc.DKTatlas+aseg.mgz).

Therefore, we want to know the number of regions in three parcellation map.



1) FreeSurfer version: freesurfer-linux-ubuntu20_amd64-7.4.1.tar.gz

2) Linux ~~~ 5.15.0-76-generic #83~20.04.1-Ubuntu SMP Wed Jun 21 20:23:31 UTC 
2023 x86_64 x86_64 x86_64 GNU/Linux



[cid:image001.png@01DA1C77.40089080]



Thanks,

Kei
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Re: [Freesurfer] Distance Measurement After recon-all

[John Anderson]

External Email - Use Caution

Dear Freesurfer Experts,
I would like to inquire if there is a FreeSurfer command that allows me to
measure the distance (in voxels or mm) between a lesion mask (output of
samseg) and the closest voxels in the ribbon after applying "recon-all" to
T1 images. If there is no such command, I am considering measuring the
center of the lesion mask and calculating the distance between this center
and every voxel in the closest parcel in the ribbon, then selecting the
shortest distance. i'm not sure if this is the correct approach so I
appreciate your suggestions.
Thank you
John

On Mon, Nov 20, 2023 at 7:13 AM John Anderson  wrote:

> Dear FreeSurfer experts, I would like to know if there is a command in
> FreeSurfer that can help me measure the distance (in voxels or mm) between
> a lesion mask and the closest voxels in the ribbon after applying recon-all
> to T1 images. Thanks for your advice
>
> John
>
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Re: [Freesurfer] Errors in recon-all command

[Huang, Yujing]

Assuming

  1.  NIFTI files for your subjects are 1.nii, 2.nii, …, 300.nii
  2.  To name the subjects as sub1, sub2, …, sub300

In bash shell, you can do the batch submission as following at prompt:
for i in {1..300}; \
do \
echo “recon-all -all -s sub${i} -i ${i}.nii” \
recon-all -all -s sub${i} -i ${i}.nii \
done

Adjust recon-all command line options for any additional flags, and change the 
subject IDs for something more descriptive.

It is a good idea to submit one first to get familiar with Freesurfer recon-all 
output directory structure before doing the batch submission.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Dunia A Alhamad
Sent: Tuesday, November 21, 2023 12:35 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Errors in recon-all command


External Email - Use Caution
Could explain more, as I am not very expert in freesurfer
For e.g I had 300 subject and their NIFTI files are named by their number 
(1.nii)
How to make a script to launch, do you mean in a txt file ?

Thank you

On Tue, Nov 21, 2023 at 5:29 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:
you can write a script to launch them, eg
foreach subject (your-list-of-subjects)
  recon-all -s $subject -all ...
end


On 11/21/2023 12:04 PM, Dunia A Alhamad wrote:

External Email - Use Caution
But this will take long time because I had another group with 300 patients


On Tue, Nov 21, 2023 at 5:03 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
Each subject needs to be processed separately. You will need submit 24 
recon-all.

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Dunia A Alhamad
Sent: Tuesday, November 21, 2023 12:00 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Errors in recon-all command


External Email - Use Caution
What if I had 24 subjects. Should I specify the name for each one in the line ?

Dunia

On Tue, Nov 21, 2023 at 4:52 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
This is your recon-all submitted

“/Applications/freesurfer/7.4.1/bin/recon-all -s 
I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache”

Add ‘-all’ to the line.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Dunia A Alhamad
Sent: Tuesday, November 21, 2023 11:50 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Errors in recon-all command


External Email - Use Caution
Could you please explain more ho to specify all in recon-all command ?

Dunia

On Tue, Nov 21, 2023 at 4:48 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
It looks like you don’t have data processed. Specify ‘-all’ on recon-all on 
command line.

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Dunia A Alhamad
Sent: Tuesday, November 21, 2023 10:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Errors in recon-all command


External Email - Use Caution
Hello Freesurfer Developers

I'm attempting to apply preprocess and segment to my data that consist of 24 
subjects by recon-all syntax, as described on the FreeSurfer wiki on macOs 
software
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all


ERROR: cannot find 
/Users/duniaalhamad/Desktop/subjects/I83870_MP-RAGE_20071127095752_2/surf/lh.thickness

Darwin 
dyn145223.shef.ac.uk
 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct  9 21:28:31 PDT 2023; 
root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64



1) freesurfer version: freesurfer-macOS-darwin_x86_64-7.4.1

2) platform: bash terminal

3) log file

Tue Nov 21 15:50:35 GMT 2023
cd /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAG

[Freesurfer] recon-all error - MRISlabel2Mask()

[Mark Wagshul]

External Email - Use Caution

Dear Freesurfer experts,

Hi. Hoping someone can give me some guidance in how to proceed with this error 
in recon-all (at the moment, was running autorecon-wm, but not sure that's 
relevant). Just pasting the last few commands which were successfully run, can 
send the whole recon-all.log file if needed. Nothing obvious in terms of the T1 
or T2 images. Thanks!

#===
mri_surf2surf --s sub-XXX --hemi rh --sval-xyz woT2.pial.rawavg --surfreg 
woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz 
--tval woT2.pial.rawavg.conf
Reading header for orig.mgz
Source registration surface changed to woT2.pial.rawavg
Target registration surface changed to woT2.pial.rawavg

7.3.2

setenv SUBJECTS_DIR 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w
cd 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
mri_surf2surf --s sub-XXX --hemi rh --sval-xyz woT2.pial.rawavg --surfreg 
woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz 
--tval woT2.pial.rawavg.conf

sysname  Linux
hostname cpu-771.cluster.local
machine  x86_64
user mwagshul
srcsubject = sub-XXX
srcval = (null)
srctype=
trgsubject = sub-XXX
trgval = woT2.pial.rawavg.conf
trgtype=
srcsurfreg = woT2.pial.rawavg
trgsurfreg = woT2.pial.rawavg
srchemi= rh
trghemi= rh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf/rh.woT2.pial.rawavg
Loading source data
Reading surface file 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf/rh.woT2.pial.rawavg
Applying linear registration transform
1.0   0.0   0.0  -0.4;
0.0   1.0   0.0   0.0;
0.0   0.0   1.0   0.3;
0.0   0.0   0.0   1.0;
INFO: trgsubject = srcsubject
Saving target data
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf
 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
Tue Nov 21 17:49:18 EST 2023

#===
bbregister --s sub-XXX --mov orig/T2raw.mgz --lta transforms/T2raw.auto.lta 
--init-coreg --t2 --surf white.preaparc --proj-abs 1.5 --threads 1
tmp transforms/tmp.bbregister.3166191
Log file is transforms/T2raw.auto.log
Tue Nov 21 17:49:18 EST 2023

setenv SUBJECTS_DIR 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w
cd 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
/public/apps/freesurfer/7.3.2/bin/bbregister --s sub-XXX --mov orig/T2raw.mgz 
--lta transforms/T2raw.auto.lta --init-coreg --t2 --surf white.preaparc 
--proj-abs 1.5 --threads 1

bbregister 7.3.2
Linux cpu-771.cluster.local 4.18.0-477.13.1.el8_8.x86_64 #1 SMP Thu May 18 
10:27:05 EDT 2023 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /public/apps/freesurfer/7.3.2
mri_convert orig/T2raw.mgz transforms/tmp.bbregister.3166191/template.nii
mri_convert orig/T2raw.mgz transforms/tmp.bbregister.3166191/template.nii
reading from orig/T2raw.mgz...
TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to transforms/tmp.bbregister.3166191/template.nii...
mri_coreg --s sub-XXX --mov transforms/tmp.bbregister.3166191/template.nii 
--regdat transforms/tmp.bbregister.3166191/reg.init.dat --reg 
transforms/tmp.bbregister.3166191/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 
--ftol .0001 --linmintol .01

$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $
cwd 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
cmdline mri_coreg --s sub-XXX --mov 
transforms/tmp.bbregister.3166191/template.nii --regdat 
transforms/tmp.bbregister.3166191/reg.init.dat --reg 
transforms/tmp.bbregister.3166191/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 
--ftol .0001 --linmintol .01
sysname  Linux
hostname cpu-771.cluster.local
machine  x86_64
user mwagshul
dof6
nsep1
cras01
ftol0.000100
linmintol0.01
bf   1
bflim30.00
bfnsamp30
SmoothRef 0
SatPct99.99
MovOOB 0
optschema 1
Seed 53
Reading in mov transforms/tmp.bbregister.3166191/template.nii
Reading in ref brainmask.mgz
Reading in and applying refmask aparc+aseg.mgz
Setting cras translation parameters to align volume centers
Creating random numbers for coordinate dithering
Performing intensity dithering
Performing intensity dithering on mov with computed dither
Init matrix params -0.1000  0.1000 -0.9000  0.  0.  0.  1.  
1.  1.  0.  0.  0.
Initial parameters to be opt -0.1000  0.1000 -0.9000  0.