[Freesurfer] Help for pass code to open Freesurfer Virtual Machine image (.7z)

[Yuuichi Oosawa]

External Email - Use Caution

Hello,

I'm a student researching Magnetoencephalography estimation and have been
trying to install Freesurfer on a Windows OS using a Virtual Machine,
following the instructions below:

"You will be prompted for a pass code when the archive is successfully
opened. If you do not have the pass code to open the image, then *send an
email to the Freesurfer help list* to receive it."

I do not have the pass code to open it and therefore I'm emailing the
freesurfer help list, please advise.

Thank you for your help in advance!

Yuuichi Oosawa

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E-Mail: oosawa-yuuichi...@g.ecc.u-tokyo.ac.jp
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[Freesurfer] Parcellation issue

[Addison, Reuben]

I want to use a different template apart from the MNI for my parcellation 
(Yeo_JNeurophysiol11_FreeSurfer.zip). Below are the instructions given in the 
readme. My question is – do I need to run this code before Recon-all or after

In terminal (ASSUMING shell is bash),
   a) "cd" to unzipped folder containing this README file, fsaverage, 
fsaverage6, fsaverage5
   b) export SUBJECTS_DIR=`pwd`
   c) tksurfer fsaverage5 lh inflated -annotation 
fsaverage5/label/lh.Yeo2011_7Networks_N1000.annot



Reuben A.
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Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

[Trolle, Carl]

Sorry, been trying to get this right for some time before getting back to you, 
but not sure that I have. I'm attaching screenshots of the ?h.sphere.reg for 
the original, processed and the fsaverage-subjects with the 
destrieux-annotation. To me, it looks slightly worse after the mris_register 
command. Not sure that I've managed correctly with the mrisp_paint
(mrisp_paint $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif 
surf/?h.sphere.reg ?h.sulc_test) but attaching a screenshot from there as well.

Would be happy to know what I could alter to get it more accurate!

Kind regards,

Carl
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Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

[Fischl, Bruce]

Yes, definitely something wrong. For the paint you want to specify which frame 
in the tiff with #3 I believe (so 
$FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#3).  We 
store information in 3-frame sets, with means,  variances and dofs in that 
order for each of inflated, sulc and curv. So what you are showing is the 
inflated curvature whereas what you probably want is the sulc. Something also 
wrong with the registration though. Can you bounce that command line?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trolle, Carl
Sent: Tuesday, August 9, 2022 12:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Shift in cortical parcellation, issues with 
previously suggested solution

Sorry, been trying to get this right for some time before getting back to you, 
but not sure that I have. I'm attaching screenshots of the ?h.sphere.reg for 
the original, processed and the fsaverage-subjects with the 
destrieux-annotation. To me, it looks slightly worse after the mris_register 
command. Not sure that I've managed correctly with the mrisp_paint
(mrisp_paint $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif 
surf/?h.sphere.reg ?h.sulc_test) but attaching a screenshot from there as well.

Would be happy to know what I could alter to get it more accurate!

Kind regards,

Carl
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[Freesurfer] Thalamus Parcellation - HCP data

[Asa Borzabadi Farahani]

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Hi,

I hope this email finds you all well.

I have a basic question about the right way of using ThalamicSegmentation 
method ( implemented by Iglesias et al. 2018). I plan to use this 
subject-specific atlas on the data processed via the HCP pipeline.

In this regard, after doing the PreFreeSurfer and Freesurfer bash files 
introduced by the HCP team, I use the subject-specific folder created by 
FreeSurfer and run the SegmentThalamicNuclei on the data of the subject.

The point is that, HCP pipeline ultimately converts all timeseries into CIFTI 
format ( subcortical areas in 2mm template), hence the mgz file created by the 
SegmentThalamicNuclei bash file, should be converted into the CIFTI to be 
useful when defining ROIs. So, I am using the following commands to get the 
subject-specific thalamic labels in the CIFTI space.

Could anyone having more experience confirm if it is a reasonable way or help 
if there exists a more accurate option?

Regards,
Asa Farahani

mri_convert -rt nearest -rl /029/T1w/T1w_acpc_dc_restore.nii.gz   
/029/mri/ThalamicNuclei.v13.T1.mgz ThalamicNuclei029.v13.T1.nii.gz

applywarp --rel --interp=nn -i ThalamicNuclei029.v13.T1.nii.gz -r  
/029/MNINonLinear/T1w_restore.nii.gz -w  
/029/MNINonLinear/xfms/acpc_dc2standard -o 
ThalamicNuclei029.v13.T1.native.nii.gz

applywarp --interp=nn -i ThalamicNuclei029.v13.T1.native.nii.gz -r  
/029/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o 
ThalamicNuclei029.v13.T1.Atlas_2mm.nii.gz

wb_command -volume-label-import ThalamicNuclei029.v13.T1.Atlas_2mm.nii.gz 
FreeSurferColorLUT.txt ThalamicNuclei029.v13.T1.Atlas_2mm.nii 
-drop-unused-labels
wb_command -cifti-create-dense-from-template  template..dlable.nii 
T029.dlabel.nii -volume-all ThalamicNuclei029.v13.T1.Atlas_2mm.nii.gz

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Re: [Freesurfer] Thalamus Parcellation - HCP data

[Iglesias Gonzalez, Juan E.]

Dear Asa,

Rather than resampling to 2mm and then applying a linear transform, I would 
first transform and then resample.

Cheers,

Juan Eugenio Iglesias
www.jeiglesias.com


On Aug 9, 2022, at 3:32 PM, Asa Borzabadi Farahani 
mailto:asa.borzabadifarah...@mail.mcgill.ca>>
 wrote:


External Email - Use Caution

Hi,

I hope this email finds you all well.

I have a basic question about the right way of using ThalamicSegmentation 
method ( implemented by Iglesias et al. 2018). I plan to use this 
subject-specific atlas on the data processed via the HCP pipeline.

In this regard, after doing the PreFreeSurfer and Freesurfer bash files 
introduced by the HCP team, I use the subject-specific folder created by 
FreeSurfer and run the SegmentThalamicNuclei on the data of the subject.

The point is that, HCP pipeline ultimately converts all timeseries into CIFTI 
format ( subcortical areas in 2mm template), hence the mgz file created by the 
SegmentThalamicNuclei bash file, should be converted into the CIFTI to be 
useful when defining ROIs. So, I am using the following commands to get the 
subject-specific thalamic labels in the CIFTI space.

Could anyone having more experience confirm if it is a reasonable way or help 
if there exists a more accurate option?

Regards,
Asa Farahani

mri_convert -rt nearest -rl /029/T1w/T1w_acpc_dc_restore.nii.gz   
/029/mri/ThalamicNuclei.v13.T1.mgz ThalamicNuclei029.v13.T1.nii.gz

applywarp --rel --interp=nn -i ThalamicNuclei029.v13.T1.nii.gz -r  
/029/MNINonLinear/T1w_restore.nii.gz -w  
/029/MNINonLinear/xfms/acpc_dc2standard -o 
ThalamicNuclei029.v13.T1.native.nii.gz

applywarp --interp=nn -i ThalamicNuclei029.v13.T1.native.nii.gz -r  
/029/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o 
ThalamicNuclei029.v13.T1.Atlas_2mm.nii.gz

wb_command -volume-label-import ThalamicNuclei029.v13.T1.Atlas_2mm.nii.gz 
FreeSurferColorLUT.txt ThalamicNuclei029.v13.T1.Atlas_2mm.nii 
-drop-unused-labels
wb_command -cifti-create-dense-from-template  template..dlable.nii 
T029.dlabel.nii -volume-all ThalamicNuclei029.v13.T1.Atlas_2mm.nii.gz

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Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

[Trolle, Carl]

I apologize but I'm not familiar with the term bounce; do you want me to re-run 
the mrisp_paint-command but with specifying the optional #3 parameter for the 
 argument? The sphere and the inflated surface look more 
similar but still seem to differ from the fsaverage that way.

Kind regards,

Carl



From: Trolle, Carl 
Sent: 09 August 2022 12:37
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Shift in cortical parcellation, issues with 
previously suggested solution

Sorry, been trying to get this right for some time before getting back to you, 
but not sure that I have. I'm attaching screenshots of the ?h.sphere.reg for 
the original, processed and the fsaverage-subjects with the 
destrieux-annotation. To me, it looks slightly worse after the mris_register 
command. Not sure that I've managed correctly with the mrisp_paint
(mrisp_paint $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif 
surf/?h.sphere.reg ?h.sulc_test) but attaching a screenshot from there as well.

Would be happy to know what I could alter to get it more accurate!

Kind regards,

Carl
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Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

[Fischl, Bruce]

You should paint the template onto the sphere that is registered (i.e. 
sphere.reg), at which point it should look similar to the individual subject's 
sulc pattern.

And by "bounce" I just meant send it to me
Cheers,
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trolle, Carl
Sent: Tuesday, August 9, 2022 6:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Shift in cortical parcellation, issues with 
previously suggested solution

I apologize but I'm not familiar with the term bounce; do you want me to re-run 
the mrisp_paint-command but with specifying the optional #3 parameter for the 
 argument? The sphere and the inflated surface look more 
similar but still seem to differ from the fsaverage that way.

Kind regards,

Carl



From: Trolle, Carl mailto:ctro...@partners.org>>
Sent: 09 August 2022 12:37
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Shift in cortical parcellation, issues with 
previously suggested solution

Sorry, been trying to get this right for some time before getting back to you, 
but not sure that I have. I'm attaching screenshots of the ?h.sphere.reg for 
the original, processed and the fsaverage-subjects with the 
destrieux-annotation. To me, it looks slightly worse after the mris_register 
command. Not sure that I've managed correctly with the mrisp_paint
(mrisp_paint $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif 
surf/?h.sphere.reg ?h.sulc_test) but attaching a screenshot from there as well.

Would be happy to know what I could alter to get it more accurate!

Kind regards,

Carl
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Re: [Freesurfer] MP2RAGE sequence recon-all

[Douglas N. Greve]

If you are going to pass it the UNI, then you will probably need to mask 
out the stuff outside of the head. One way to do this is to run samseg 
on the INV1 or INV2 (INV1 probably better), the run
mri_mask uni.mgz seg.mgz uni.masked.mgz
Then pass uni.masked.mgz to recon-all

On 8/2/2022 8:39 AM, Renew Andrade wrote:
>  External Email - Use Caution
>
> Dear community:
>
> I need to run recon-all on some subjects with a MP2RAGE sequence. Can I do 
> with any flag or directly -i “mp2rage”.
>
> Best,
> Rene Andrade.
>
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Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

[Douglas N. Greve]

There was something a little strange about the cases that were failing 
-- there were very bright values at the back of the head and around the 
nose. This probably messes up the normalization in the unet. I ran it 
with --percentile 99.9 (this eliminates the extreme voxels) and the 
results looked ok after that.



On 7/28/2022 8:58 PM, Miriam Taza wrote:

Nothing strange about them.
They’re T1w scans 1x1x1mm3

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Thursday, July 28, 2022 1:25 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left 
basal forebrain
Have you looked at the input volume to see if there is anything 
strange about them? What kind of scans are you passing to it? What is 
the resolution?


On 7/25/2022 9:03 PM, Miriam Taza wrote:


External Email - Use Caution

Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were 
not picked up after running ScLimbic. These are healthy adults and 
their scans look good. Also, I noticed often when this occurs NAcc is 
also 0 or other regions.
I am concerned if there is a systematic issue with left volumes 
ending up smaller than they should relative to right.


Thanks,
Miriam

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Re: [Freesurfer] Using averaged T1-images to calculate cortical thickness

[Douglas N. Greve]

If I understand correctly, you have one site that acquires two scans, 
one sag and one axial, and you want to register them together and 
compute the average, then feed the average to recon-all? Do they have 
the same isotropic resolution? I'd guess that this would create a 
systematic artifact.


On 8/3/2022 3:17 PM, Trolle, Carl wrote:


Hello dear FreeSurfer team,

We are undertaking a multicenter study analyzing cortical thickness of 
controls and persons with a neurological condition. Unfortunately, 
there are issues with motion artifacts and image quality. To counter 
this, we’ve created averaged T1-images by combining one axial and one 
sagittal image in SPM for one of the study sites. Also, we are using 
recon-all with the optional T2- and T2-pial flags. Our impression is 
that the image quality has improved with the averaged images as 
compared to the non-averaged ones.


Do you have any thoughts on this method or if combining images this 
way might cause issues when trying to calculate and compare cortical 
thicknesses? The averaged T1-images are only created for one of the 
study-sites and we plan on using study site as a covariate in our 
model. Will be happy to post images or logs if those may be helpful


Kind regards,

Carl

FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551

Platform: CentOS Stream 8


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Re: [Freesurfer] adding volume to aparc aseg

[Douglas N. Greve]

Try mergeseg. Run with --help to get more info

On 8/3/2022 3:41 PM, Benjamin Deck wrote:


External Email - Use Caution


Hi there,

I have extracted an ROI mask for the subthalamic nucleus from MNI 
space and registered this with the subject's native space orig.mgz


I would like to append this to the subject's automated segmentation 
from aparc+aseg.mgz. So I can use this segmentation as an atlas file 
for some later analyses.


How should I go about doing this?

Thanks,
Ben


--
*Benjamin L. Deck*
/Doctoral Student/
/Applied Cognitive and Brain Sciences/
/Department of Psychological and Brain Sciences/
/Drexel University/

 
	Virus-free. *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* www.avast.com 
 




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Re: [Freesurfer] Sclimbic segmentation fault error?

[Douglas N. Greve]

not sure. Try running
mri_sclimbic_seg --i GP0050/mri/orig.mgz --o junk.mgz


On 8/4/2022 4:20 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


External Email - Use Caution

Hi all,

I am receiving this error when trying to run sclimbic module. It's not 
being very descriptive about what the error is so I was wondering if 
you all can help debug. My SUBJECTS_DIR is correct


mri_sclimbic_seg --s GP0050
/usr/local/freesurfer/dev7/python/scripts/mri_sclimbic_seg --s GP0050
Excluding seg [853]
Using CPU
Using 1 thread(s)
Loaded lookup table /usr/local/freesurfer/dev7/models/sclimbic.ctab
Loaded population stats 
/usr/local/freesurfer/dev7/models/sclimbic.volstats.csv

nb_labels 14
Segmentation fault

 i am using freesurfer-linux-centos7_x86_64-dev-20220802-56c77e1

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
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Re: [Freesurfer] PET-segmentattion

[Douglas N. Greve]

Can you send the terminal output and the petsuv.segstats.dat? How have 
you verified that the registration is correct? What version of FS are 
you running?


On 8/5/2022 4:44 PM, Bouchra Guelib wrote:


External Email - Use Caution

I want to segment registered PET to T1 MRI to 45 subcortical regions 
as the regions in aseg.stats of MRI.
I used  mri_segstats --seg MRI-floder/mri/aparc+aseg.mgz --reg 
Pet2T1.register.dof12.lta  --sum petsuv.segstats.dat --i PET-SPM.mgh 
 --ctab-default

into petsuv.segstats.dat, I found only 40 regions, not as aseg.stats
what should I change in my commend?

--
*GUELIB Bouchra: *Ph.D. student
*Lire *Laboratory
University: Constantine 2-Abdelhamid Mehri- *Algeria *
Alternative email: guelibbouc...@gmail.com**





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