Re: [Freesurfer] Problem with brainstem overlap after BBR

[Spapens, Jeltje (NP)]

External Email - Use Caution

Hello Freesurfer Developers,

I have never received an answer to my problem, maybe it was lost in the e-mails.

Kind regards,

Jeltje Spapens

From: "Spapens, Jeltje (NP)" 
Date: Wednesday, 8 November 2023 at 13.55
To: "Freesurfer@nmr.mgh.harvard.edu" 
Subject: Problem with brainstem overlap after BBR

Hello Freesurfer Developers,

I have performed a boundary-based registration followed by a mri_vol2vol on a 
Neuromelanin sensitive MRI scan (partial FoV) with a T1 structural scan. I used 
this code:

Boundary-based registration in Freesurfer

Set the environment in the terminal.

bbregister --s MRS_203_recon_all --mov 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_stripped.mgz 
--reg MRS_203_NM2mp2rage.dat --T1 --init-fsl
mri_vol2vol --mov 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_stripped.mgz 
--targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_upsamp.nii --o 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_regt1.nii.gz 
--reg MRS_203_NM2mp2rage.dat –cubic

I performed the analysis on two participants, but the brainstem does not 
overlap very nicely. I attached the screenshots of Freeview of the two 
participants with the T1 scan and the NM scan after the BBR. Our analysis 
focuses on the Substantia Nigra.
I also attached the full script that we use including the pre analysis.
Do you have a tip how to improve the BBR to reach better overlap.

Kind regards,

Jeltje Spapens



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Re: [Freesurfer] [EXTERN] Re: Issue with PALS_B12_Brodmann.annot Labels in FreeSurfer

[Xinjie Chen]

External Email - Use Caution

Hi Yujing,


Thanks for the response.


We addressed the issues by modifying the labels of the vertices that represent 
specific areas. To do this, we employed the 'write_annotation' function in FS 
(MATLAB-based).
Anyway, It's worth noting that the PALS_B12 annotation files in FreeSurfer may 
require further refinement.

Best,
Xinjie

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Tuesday, November 14, 2023 4:46:42 PM
To: Freesurfer support list
Subject: [EXTERN] Re: [Freesurfer] Issue with PALS_B12_Brodmann.annot Labels in 
FreeSurfer

Sorry, I take my suggestion back. Annotation values are saved in .annot file, 
not the label id. Different colortable won’t work.

Yujing

From: Huang, Yujing
Sent: Tuesday, November 14, 2023 9:24 AM
To: Freesurfer support list 
Subject: RE: Issue with PALS_B12_Brodmann.annot Labels in FreeSurfer

Hi Xinjie,

?h.PALS_B12.labels.gii in fsaverage/label/ seem to have duplicated color 
schemes assigned to the labels you mentioned.  I’m assuming 
?h.PALS_B12_Brodmann.annot is generated from the GIFTI 
https://secure-web.cisco.com/1T831HwdcEs9uXAG2x-7aldFZHZ4KU-2yr3C9R4WJCtuy80BemyJiH_Fq24Lc2X34QD-LDO-M6U3VN7W0sXPaym6KOncuFpxdlUX5Eqhbbe8MsPcfeayVbs54dR9NlFaJ31W7E-IhU38z5TH2-v2IeTQJksF1hsvrSuyoS2UI46fzT8jinhfP7Xf4Ri1uuOMNEVL1JlZoWZiuwZTvpLb5-sIvHnjmRlGaGOsSVGgUBdugCx5jqyJ0lmXj1pA7_RTWy_tyHGFHukcPX7YUMydMCI_K5RIpTKl5Afv8cuhT1abHMQljLYi9eMoiZq4bBWQH0geKKl6MjTLb9dJErEcW6g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPALS_B12

Maybe a different colortable will help the visualization?

Best,

Yujing


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Xinjie Chen
Sent: Tuesday, November 14, 2023 6:59 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Issue with PALS_B12_Brodmann.annot Labels in FreeSurfer


External Email - Use Caution

Dear FreeSurfer Team,


I am writing to report a significant issue I have encountered while using the 
PALS_B12_Brodmann.annot files in FreeSurfer. I have noticed a critical error 
concerning labeling certain Brodmann areas.

Specifically, in the left hemisphere, labels such as Brodmann area 33, 
CON_deeper_than_WS_t_2', and ASP deeper' appear to share the same label ID. 
Similarly, in the right hemisphere, the label for Brodmann area 3 seems to be 
merged with Brodmann area 33. This overlap of labels and the lack of unique IDs 
for distinct Brodmann areas like Brodmann 3 and Brodmann 33 are causing 
significant confusion and potential errors in analysis. For instance, this 
issue complicates tasks such as calculating variables for individual Brodmann 
areas, leading to inaccurate results.

I am keenly interested in any solutions or methods you could suggest for 
resolving this problem. Thank you in advance for your assistance and I am 
looking forward to a resolution.

Best regards,
Xinjie


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[Freesurfer] Question about lesions output of samseg

[reza razmara]

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Hi freesurfer team

I use samseg for lesion segmentation. In the result of .stats i see the
lesions volume. But when i extract lesions seprately as a new file we know
that it uses the label 99 for extraction. But when i calculate the volume
of this extracted lesions which i created it seprately. The volume of these
two results are not the same.
The volume of extracted lesions seprately is higher than what samseg
automatically calculated in .stats file.
Why is this happened? Why the volumes are not the same. And how can i
calculate the lesions volume from extracted file that i created which is a
flair that i masked with label 99? How can i recalculate the lesions volume
from just exracted lesions filr without using samseg?

Thanks a lot for your help
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Re: [Freesurfer] Problem with brainstem overlap after BBR

[Douglas N. Greve]

I answered it yesterday. Check your inbox

On 11/16/2023 4:08 AM, Spapens, Jeltje (NP) wrote:


External Email - Use Caution

Hello Freesurfer Developers,

I have never received an answer to my problem, maybe it was lost in 
the e-mails.


Kind regards,

Jeltje Spapens

*From: *"Spapens, Jeltje (NP)" 
*Date: *Wednesday, 8 November 2023 at 13.55
*To: *"Freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Problem with brainstem overlap after BBR

Hello Freesurfer Developers,

I have performed a boundary-based registration followed by a 
mri_vol2vol on a Neuromelanin sensitive MRI scan (partial FoV) with a 
T1 structural scan. I used this code:


*/__/*

*/_Boundary-based registration in Freesurfer_/*

/Set the environment in the terminal./

bbregister --s MRS_203_recon_all --mov 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_stripped.mgz 
--reg MRS_203_NM2mp2rage.dat --T1 --init-fsl


mri_vol2vol--mov 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_stripped.mgz--targ 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_upsamp.nii 
--o 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_regt1.nii.gz 
--reg MRS_203_NM2mp2rage.dat –cubic


I performed the analysis on two participants, but the brainstem does 
not overlap very nicely. I attached the screenshots of Freeview of the 
two participants with the T1 scan and the NM scan after the BBR. Our 
analysis focuses on the Substantia Nigra.


I also attached the full script that we use including the pre analysis.

Do you have a tip how to improve the BBR to reach better overlap.

Kind regards,

Jeltje Spapens


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Re: [Freesurfer] Question about lesions output of samseg

[Douglas N. Greve]

Internally, samseg uses partial volume to compute a more accurate 
volume. They should still be very close though.


On 11/16/2023 6:46 AM, reza razmara wrote:


External Email - Use Caution

Hi freesurfer team

I use samseg for lesion segmentation. In the result of .stats i see 
the lesions volume. But when i extract lesions seprately as a new file 
we know that it uses the label 99 for extraction. But when i calculate 
the volume of this extracted lesions which i created it seprately. The 
volume of these two results are not the same.
The volume of extracted lesions seprately is higher than what samseg 
automatically calculated in .stats file.
Why is this happened? Why the volumes are not the same. And how can i 
calculate the lesions volume from extracted file that i created which 
is a flair that i masked with label 99? How can i recalculate the 
lesions volume from just exracted lesions filr without using samseg?


Thanks a lot for your help

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Re: [Freesurfer] Question about lesions output of samseg

[reza razmara]

External Email - Use Caution

Thanks

The volume of lesions in label 99 in seg.mgz result is 745 mm^3.

The samseg output for lesions in samseg.stats is 633 mm^3.
Is it ok?

On Thu, Nov 16, 2023, 5:57 PM Douglas N. Greve 
wrote:

> Internally, samseg uses partial volume to compute a more accurate volume.
> They should still be very close though.
>
> On 11/16/2023 6:46 AM, reza razmara wrote:
>
> External Email - Use Caution
> Hi freesurfer team
>
> I use samseg for lesion segmentation. In the result of .stats i see the
> lesions volume. But when i extract lesions seprately as a new file we know
> that it uses the label 99 for extraction. But when i calculate the volume
> of this extracted lesions which i created it seprately. The volume of these
> two results are not the same.
> The volume of extracted lesions seprately is higher than what samseg
> automatically calculated in .stats file.
> Why is this happened? Why the volumes are not the same. And how can i
> calculate the lesions volume from extracted file that i created which is a
> flair that i masked with label 99? How can i recalculate the lesions volume
> from just exracted lesions filr without using samseg?
>
> Thanks a lot for your help
>
> ___
> Freesurfer mailing 
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>
>
> ___
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> Brigham Compliance HelpLine at
> https://secure-web.cisco.com/1F2NxclipTs9ebvlCQMzVboE5w-Td04Btx-V-1gnvOu3GS5Y9Y0D3yWRl8yXX8t7XlQ3jW5JuYVd0J2umagW3SRRpMYBM9Tuo9Km__M-_PNH1CnmuRAb4eHkY4s43_n6etLQ6DSBeBlNvpxoSCAiyko1slPFoQjQmsy9VEhDoxMrgKIFTAHrjuQB2crHH6KJmaqvR7jrslnIkjpw9An7ECNNnNMoFIz6_ArTMfD-wHZlKD_jyPJpHZP6E5LW7JeV_i4haH-3e5fyJyY-ebMTVcbR9q8XTzQ2PbypDtvIMkiro4RYAaH5r-Zju2Gy6EaB5CcYXYJiLy8xzyTcuRjZSgQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
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Re: [Freesurfer] Problem with brainstem overlap after BBR

[Spapens, Jeltje (NP)]

External Email - Use Caution

I have found the answer, thank you very much!

From:  on behalf of "Douglas N. Greve" 

Reply to: Freesurfer support list 
Date: Thursday, 16 November 2023 at 15.27
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Problem with brainstem overlap after BBR

I answered it yesterday. Check your inbox
On 11/16/2023 4:08 AM, Spapens, Jeltje (NP) wrote:

External Email - Use Caution
Hello Freesurfer Developers,

I have never received an answer to my problem, maybe it was lost in the e-mails.

Kind regards,

Jeltje Spapens

From: "Spapens, Jeltje (NP)" 

Date: Wednesday, 8 November 2023 at 13.55
To: "Freesurfer@nmr.mgh.harvard.edu" 

Subject: Problem with brainstem overlap after BBR

Hello Freesurfer Developers,

I have performed a boundary-based registration followed by a mri_vol2vol on a 
Neuromelanin sensitive MRI scan (partial FoV) with a T1 structural scan. I used 
this code:

Boundary-based registration in Freesurfer

Set the environment in the terminal.

bbregister --s MRS_203_recon_all --mov 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_stripped.mgz 
--reg MRS_203_NM2mp2rage.dat --T1 --init-fsl
mri_vol2vol --mov 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_stripped.mgz 
--targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_upsamp.nii --o 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_regt1.nii.gz 
--reg MRS_203_NM2mp2rage.dat –cubic

I performed the analysis on two participants, but the brainstem does not 
overlap very nicely. I attached the screenshots of Freeview of the two 
participants with the T1 scan and the NM scan after the BBR. Our analysis 
focuses on the Substantia Nigra.
I also attached the full script that we use including the pre analysis.
Do you have a tip how to improve the BBR to reach better overlap.

Kind regards,

Jeltje Spapens






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Re: [Freesurfer] "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"

[Ludmila Midrigan]

External Email - Use Caution

Dear Douglas, thank you for the reply.
I am attaching it here. I usually create it  (using BASH)  as such: <<  echo
“1 -1” > File_Name.mtxand have never had issues, however I have not
used "[ ] " on my contrasts before...
Thank you so so much for your willingness to help and your time!


On Wed, Nov 15, 2023 at 6:47 PM Douglas N. Greve 
wrote:

> Can you send
> /data/Ghana_MRI_Data_lmid/StructT1/subjDir_FS_GHANA/Contrasts/GM_FM_ONE_minus_ZERO.mtx
> ?
> How did you create this file? A lot of word processors will add special
> characters that can cause a read failure.
>
> On 11/9/2023 12:33 PM, Ludmila Midrigan wrote:
>
> External Email - Use Caution
> Hi Douglas,
> Thank you for your reply.
> Yes, find attached the fsgd file, the contrast is [1 1 1 -1 -1 -1 0 0 0
> 0]/3
> As well as the code I am running and the whole output from the terminal.
>
> Thank you so much for your help!
>
> On Thu, Nov 9, 2023 at 6:35 AM Douglas N. Greve 
> wrote:
>
>> Can you send the command line, all the terminal output, and your fsgd
>> file?
>>
>> On 11/3/2023 11:51 AM, Ludmila Midrigan wrote:
>>
>> External Email - Use Caution
>> Hi dear FS experts,
>> I am having issues with ( I am assuming) the design matrix for my GM
>> analysis.
>> I am getting the error:
>>
>> "error: MatrixReadTxT: could not scan value [1][1]
>> ERROR: loading C Path_to_contrast"
>>
>> I am only interested in a difference for Group ONE - Group ZERO;
>> I am trying to run a DOSS ( with three groups and 4 nuisance covariates)
>> my contrast is :
>> [1 1 1 -1 -1 -1 0 0 0 0]/3
>>
>> I have standardized all variables.
>> Attached is the FSGD.xlxs file ( that I did transform into a .fsgd file)
>> Please let me know what I'm doing wrong.
>> Thank you so much!
>>
>>
>> *milly mc *
>>
>>
>> *"Life is a foreign language; all mispronounce it."  *
>> *Christopher Morley*
>>
>> ___
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[Freesurfer] Question about lesions output

[reza razmara]

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Hi freesurfer
I did an experiment about lesions about the output of samseg. And the
results are as follows:

The volume of lesions in label 99 in seg.mgz result is 745 mm^3.

The samseg output for lesions in samseg.stats is 633 mm^3.

Is it ok? Why are they different?

Thanks for your help
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[Freesurfer] Transformation of volume images

[P Pieperhoff]

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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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[Freesurfer] recon-all error

[Carlos Alcocer]

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Hi,

For some of my subjects I get the following error at the beginning of
recon-all:

 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...

However, recon-all will keep running and then later finish without error.
What exactly is going on? This is only happens on some subjects.

Thank you,

Carlos
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[Freesurfer] Downloading OVA

[Tellis, Wyatt]

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Hi,

I'd like to download the OVA to run in VirtualBox, but the wiki article 
(https://secure-web.cisco.com/14mYPNciAyjJLQ-z9NWag-roFmGKjbtQeqtDD8X-3yq9rTtadYABr3UpoxrMaCW8_BlwK9x8AQAudWlmm4uTqGUFujduli9konMGekbhvRUXxRUAA28ydMp9cQdfV4mN7wgg8E3xwXOZo4WKFS_tNc5Qd7ymGnmDcm2qVx5hirOLmS3akz_r7yAYI6CHW8rFYnH25ePolCS5l6L7fJuD61dce2Tu3MEC06vGPYlciGcovzShPOgcjnPD9OwMbqa7DrsOnFQWPCKZvxfCF-PXeZHvMMPDLAnIyNzXSm-N1v8o1dr6vbddJfU4Lt59Bl_r3tYLOL04m9VeGF2B0zJBadg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67),
 says its being updated:

As of 09/11/2023 he (sic) VM image is currently being updated and the link to 
it will be restored when the update is complete.


Is there an estimate for when the new OVA will be released?

Thanks,

Wyatt
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