[Freesurfer] parallel recon-all using T1,T2 images

2023-04-27 Thread Toshiharu Kamishikiryo 
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Hello Freesurfer experts

I am trying to recon-all using T2 images as well to improve pial
surfaces. Does anyone know how to use GNU Parallel in bash to run the
following commands in parallel?

recon-all -subject subjectname -i /path/to/T1w.nii -T2 /path/to/T2w.nii
-T2pial -all -qcache

Thanks in advance.

Regards
Kamishikiryo
Research Student
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Re: [Freesurfer] parallel recon-all using T1,T2 images

2023-04-27 Thread Michael Mc Laughlin 
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That is a single command. How can you run a single command in parallel?

You can add the -parallel flag to get freesurfer to run recon-all in
parallel threads.


On Thu, Apr 27, 2023 at 8:16 AM Toshiharu Kamishikiryo 
wrote:

> External Email - Use Caution
>
> Hello Freesurfer experts
>
> I am trying to recon-all using T2 images as well to improve pial
> surfaces. Does anyone know how to use GNU Parallel in bash to run the
> following commands in parallel?
>
> recon-all -subject subjectname -i /path/to/T1w.nii -T2 /path/to/T2w.nii
> -T2pial -all -qcache
>
> Thanks in advance.
>
> Regards
> Kamishikiryo
> Research Student
>
>
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Re: [Freesurfer] contrast-FSGD question

2023-04-27 Thread Federico Uquillas 
External Email - Use Caution

Bumping this up. Thanks so much!

Best,

Fred

> On Apr 24, 2023, at 8:52 PM, Fred d'Oleire Uquillas  
> wrote:
> 
> 
> Dear Fs support,
> 
> If I have the following FSGD with 4 classes and 3 variables, and I'd like to 
> run an interaction of ROIa x ROIb controlling for the third covariate (eTIV), 
> would I use the following contrast?
> 
> [0 0 0 0 0.25 -0.25 -0.25 0.25 0.25 -0.25 -0.25 0.25 0 0 0 0]
> 
> For the interaction of ROIa x ROIb x class + eTIV.
> 
> Thank you so much in advance for your help!
> 
> All the best,
> 
> Fred
> 
> 
> 
> 

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Re: [Freesurfer] EasyReg for group-average template?

2023-04-27 Thread AmirHussein Abdolalizadeh 
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Hi Eugenio,

Thanks for your reply. Just to check if I've understood correctly, these
can be the steps by using mri_easyreg:

*Linear (with --affine-only):*

   1. Register all the subjects to the MNI (subj_to_MNI_lin_1)
   2. Average the subj_to_MNI_lin_1s to reach a new template (MNI_mod_lin_1)
   3. Register subj_to_MNI_lin_1s to MNI_mod_lin_1 and
   achieve subj_to_MNI_lin_2 and MNI_mod_lin_2 (and repeat it 5-6 times)

*NonLinear:*

   1. Register subj_to_MNI_lin_5s to MNI_mod_lin_5 nonlinearly to achieve
   subj_to_MNI_nlin_1 and MNI_modified_nlin_1.
   2. Repeat the steps similarly 5 times.

Correct? I also have another question: Should I do the linear-nonlinear in
an interleaved manner or first linear registrations iterations and then
non-linear?

Best,
Amir
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[Freesurfer] Fwd: questions about mri_normalize

2023-04-27 Thread John Anderson 
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Dear experts,
I have been using the mri_normalize in FSv7.3.2 to standardize the
intensity of FLAIR images , and I've observed that increasing the sigma
parameter up to 25 is effective in improving the quality of the normalized
images for noisy datasets.
mri_normalize -sigma 25 -g 1 FLAIR_skullstripped.nii
FLAIR_skullstripped_norm.mgz

However, I have questions about the n argument, which is set to 2 by
default. For noisy images, white matter intensity after normalization is
around 140-150. When using n=10, I noticed that the white matter intensity
decreased from 140-150 to around 110-120, resulting in better quality
normalized images.
1) I'm wondering if there is a cut-off value for the number of iterations,
or if a higher number of iterations always yields better results.
2) Also, if the intensity of the white matter after normalization is not
around 110, but instead around 140 or 150, does that indicate that the
normalization was not effective and that we need to increase the number of
iterations?

Thank you for your assistance.
John
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Re: [Freesurfer] parallel recon-all using T1,T2 images

2023-04-27 Thread Toshiharu Kamishikiryo 
External Email - Use Caution

Thanks for pointing that out, sir.

2023年4月27日(木) 16:15 Toshiharu Kamishikiryo :

> Hello Freesurfer experts
>
> I am trying to recon-all using T2 images as well to improve pial
> surfaces. Does anyone know how to use GNU Parallel in bash to run the
> following commands in parallel?
>
> recon-all -subject subjectname -i /path/to/T1w.nii -T2 /path/to/T2w.nii
> -T2pial -all -qcache
>
> Thanks in advance.
>
> Regards
> Kamishikiryo
> Research Student
>
>
>
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[Freesurfer] visualization, heatmap

2023-04-27 Thread Eszter Boros 
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Dear Freesurfer team,

I noticed that some studies/publications add figures with heatmaps to
visualize the significant cortical results (after correction), others do
not.

We tried to use the heat map (from yellow/red to dark blue/light blue) to
visualize the group differences using Freeview but after correcting for
multiple corrections (after mri_glm we used Monte Carlo simulation), we are
not sure how to do that. Only the sig.mgh file can be visualized that way,
right?
Or that was available in tksurfer but not in Freeview?
https://secure-web.cisco.com/1iHssxc0c4EPn_NgIsbQnxACsBkIj4sWVm7WSdle6CMXnC7lziJSf72Xf0R0IQauJlgtrgyaABlxaS8KDVSXkTd5xQsND4UTiBueGmAHyufIrqNQDVv17DNoJ_0UHnaa2jCwMGJPyX1Tn-fr5thwqqd5HMZyk99wg0OvtSPdExbjQ6u0qaJmWhBqvaBALcICzFBBCBUlufadC-K_k_5kWmJaDIgspU3XEbpRSujR5g56KBsMuHCfCv63jpZBH1o3tYkVucx0ewfoDyfpKJQzFeqYjZhJbqZNOWYFEtm4f0ic-CJLmUayTPdukI-bHx8hDoidjwKYewiaz7q4vJnP1RQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FVisualization

Is tksurfer still available? We use Freesurfer 7.1.1.

Thank you for your help in advance!

Eszter
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Re: [Freesurfer] FSFAST: wrong brain mask in preproc

2023-04-27 Thread Elmira Hassanzadeh 
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Thank you for clarifying.

Elmira

On Wed, Apr 26, 2023 at 6:44 PM Douglas N. Greve 
wrote:

> External Email - Use Caution
>
> Yes, this is the expected behavior, ie, it should cover only subcortical
> GM regions. It is expected that cortical regions will be handled with the
> surface based analysis. You can recombine the results at the end with
> vlrmerge.
>
> On 4/26/2023 12:22 PM, Elmira Hassanzadeh wrote:
>
> External Email - Use Caution
> Hi everyone,
>
> We preprocessed resting-state data with preproc-sess. In the output, I
> noticed although *fmcpr.nii* covers the whole brain,*
> fmcpr.sm6.mni305.2mm.nii* is only covering brain stem+cerebellum
> (screenshots attached).
>
> Any clue what went wrong? This is an example of the command we ran for one
> of our subjects(R19):
>
> *preproc-sess -surface R19 lhrh -s R19 -fwhm 6 -fsd rest -mni305 -per-run*
>
> Thanks,
> Elmira
>
>
>
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Re: [Freesurfer] visualization, heatmap

2023-04-27 Thread Federico Uquillas 
External Email - Use CautionHey Eszter,Have you tried loading in the “sig.masked.mgh” file that’s in your contrast results folder? It should show only the significant cluster after multiple comparisons correction with the original colorbar gradient inside.Best,FredOn Apr 27, 2023, at 11:00 AM, Eszter Boros  wrote:External Email - Use CautionDear Freesurfer team, I noticed that some studies/publications add figures with heatmaps to visualize the significant cortical results (after correction), others do not.We tried to use the heat map (from yellow/red to dark blue/light blue) to visualize the group differences using Freeview but after correcting for multiple corrections (after mri_glm we used Monte Carlo simulation), we are not sure how to do that. Only the sig.mgh file can be visualized that way, right?Or that was available in tksurfer but not in Freeview?MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/VisualizationIs tksurfer still available? We use Freesurfer 7.1.1.Thank you for your help in advance!Eszter
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