Re: [Freesurfer] mri_volsynth fails but exits with 0 exit status

[Douglas N. Greve]

Done

On 3/29/2024 3:31 PM, Aaron Tanenbaum wrote:


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I am currently running FreeSurfer 7.4.  I wrote a script using the 
program mri_volsynth.  I noticed for the first time the program was 
trying to write files where it did not have write permissions. It 
outputted a few error messages but gave a 0 exit status. It would be 
nice to have it exit with a nonzero exit status.


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Re: [Freesurfer] Extracting significant regions - Longitudinal two stage model

[Douglas N. Greve]

what do you mean "extract" the cluster? Do you want mean thickness for 
each cluster? Or the mean contrast? Of all the voxels in a cluster? For 
the first two, you can use something like

mri_segstats --seg clusterseg.mgz --i contrast.mgz --sum summary.txt


On 3/26/2024 9:47 AM, Liliana Wu wrote:


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Hi,

I ran a longitudinal two stage model analysis in 83 participants 
comparing two groups. After applying cluster correction, I am seeing 
several significant regions, and I was wondering if there is a way to 
extract each significant cluster from each participant.


I appreciate any help!

Thank you,

Liliana


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Re: [Freesurfer] autorecon1 issue

[Douglas N. Greve]

What are the errors that you are facing? Can you provide more detail?

On 3/26/2024 9:12 AM, Saifullah Tumrani wrote:


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I am using freesurfer to preprocess my t1w 3d Mris using autorecon1 
which includes first 5 preprocessing techniques till skullstripping it 
worked well for 4 different datasets including ixi one from open neuro 
SRBPS but when i am using it for another dataset which has alsmost 
same configuration it’s talairach transformation fails for some 
samples and brain matter is removed in the final brainmask.mgz file 
moreover i applied autorecon-all for this dataset and even the process 
stopped for some showing error talaraich failed and for some samples 
the whole pipeline was executed without any error but in manual 
inspection i found brain matter removed by freesurfer kindly help me 
solving this problem. I later found bad skull stripping fix at this 
link FsTutorial/SkullStripFix_freeview - Free Surfer Wiki 
 using 
some commands but i am facing errors using these command recon-all 
-skullstrip -wsthresh -clean-bm -no-wsgcaatlas -subjid skullstrip1_before


kindly look into this if you have also experience same issues or have 
any insight on this. A response will be appriciated.


Thanks


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Re: [Freesurfer] Part brain is missing

[Douglas N. Greve]

Is that an MP2RAGE? The background may be messing things up. You can try 
masking it, eg,
mri_synthstrip --i yourimage.mgz --o stripped.mgz
Then pass stripped.mgz to recon-all

On 3/25/2024 6:33 AM, Chen Yang wrote:
>  External Email - Use Caution
>
> Dear FreeSurfer Developers,
>
> I am trying to do the processing for structural MRI data. I found that part 
> of brain is missing in one data (see Fig.1). Then I tried to change the 
> watershed parameter, but it didnt work at all (no matter which number I use), 
> the brainmask looks the same as before. So I did the manual editing, cloned 
> voxel from T1.mgz to brainmask.mgz. Then I run the -autorecon-pial, but it 
> froze in this step - fix topology. I checked 'wm.mgz', it contained a lot 
> skull and a lot of WM are missing (see Fig.2).
>
> I also tried to manually edit the brainmask.mgz and wm.mgz, then run 
> '-autorecon-wm' but it also froze in -fix topology. I put other might 
> relevant information in the end.
>
> I've searched in the mail archive but didn't find similar errors. I am not 
> sure if I did anything wrong. Does anyone have any thoughts on how to 
> trouble-shoot this problem? Also, Ive attached the recon-all.log in case it's 
> of any use.
>
> Thanks in advance!
>
> Best regards,
> Chen
>
>
> Other might relevant Information:
> 1) Coil element is wrong. 'HE2,4;NE2'.
> 2) I got an error message when I wad doing the recon-all first time: 
> watershed error: indices out of bounds. Then I added the command line 
> 'mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz 
> $mir/nu.mgz' based on this page 
> .
> Then I got another error message in recon-all: mri_em_register: could not 
> open brainmask.mgz so I added some cp to nu.mgz. It worked but the part of 
> brain is missing, as I mentioned in the beginning (Fig.1).
>
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
> 2) Platform: Linux 5.10.0-28-amd64
> 3) uname -a: Linux ramones 5.10.0-28 -amd64 #1 SMP Debian 5.10.209-2 
> (2024-01-31) x86_64 GNU/Linux
> 4) recon-all.log: see attached
>
>
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Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

[Douglas N. Greve]

That 2mm for the gaussian is just the post-processing filter and does 
not represent the full amount of partial volume effect. What kind of 
scanner is it?


On 3/22/2024 12:42 AM, WONG Wan Wa wrote:


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Hi Douglas,

Thanks for your clarification. This is my first time to run PetSurfer. 
We did want to normalize by cerebellar grey matter, and I will add the 
"--rescale 8 47". I just copied "6" from the example command. I know 
"6" should be the FWHM of the point-spread function (PSF) of the 
scanner as measured in image space. I did ask the technician at the 
PET centre, and he replied that the reconstruction method was "OP-OSEM 
8i21s" and the filter was "XYZ gaussian 2.00". Can I use "2" for psf 
in the command?


Thanks,
Angel


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


*Sent:* Thursday, March 21, 2024 9:44 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied 
to PET data with single frame?
Yes, though that will normalize by the pons. If you want to normalize 
by something else, you will need to specify it with --rescale. Eg, if  
you want to normalize by ceberbellar gray matter, add

--rescale 8 47
Where did you get "6" from for the psf?

On 3/20/2024 10:57 PM, WONG Wan Wa wrote:


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Hi Douglas,

Thanks for your reply. We used different tracers for diagnosis of AD 
or other neurodegenerative diseases, including PIB, FDG, Flutemetamol 
and TAU. If an SUV analysis is used, is it done by mri_gtmpvc? Is 
there any subsequent analysis needed?


This is my mri_gtmpvc command:

mri_gtmpvc \
  --i

$SUBJECTS_DIR/sub-QM001/pet/sub-QM001_ses-001_trc-C11PIB_rec-05MINS_run-001_pet.nii.gz
\
  --reg

$SUBJECTS_DIR/sub-QM001/pet/sub-QM001_ses-001_trc-C11PIB_rec-05MINS_run-001_pet.reg.lta
\
  --psf 6 \
  --seg $SUBJECTS_DIR/sub-QM001/mri/gtmseg.mgz \
  --default-seg-merge  \
  --auto-mask 1 .01 \
  --mgx .01 \
  --o $SUBJECTS_DIR/sub-QM001/pet/gtmpvc.output


Is this command okay?

Thanks,
Angel


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

*Sent:* Wednesday, March 20, 2024 11:27 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 
*Subject:* Re: [Freesurfer] PetSurfer: Can kinetic modeling be 
applied to PET data with single frame?
you cannot apply kinetic modeling to one frame. What is you ligand? 
For a one frame acquisition, you usually use an SUV analysis.


On 3/20/2024 12:03 AM, WONG Wan Wa wrote:


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Hi experts,

As stated in the subject, can kinetic modeling be applied to PET 
data with only one frame? Or we just stop at ROI analysis without 
kinetic modeling?


Best,
Angel


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The information in this e-

Re: [Freesurfer] Fw: Discrepancy between mris_preproc and mri_surf2surf results when mapping individual's measures to fsaverage space

[Douglas N. Greve]

oops, should have read your 2nd email. Yes, jacobian is the reason

On 3/20/2024 5:34 AM, tyzh...@ibp.ac.cn wrote:


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Dear FreeSurfer Experts,


Sorry, I think I've found the answer. It's because Jacobian correction 
was performed for mris_preproc, right?



Tongyu Zhang



-原始邮件-
*发件人:*tyzh...@ibp.ac.cn
*发送时间:*2024-03-20 16:31:23 (星期三)
*收件人:* freesurfer@nmr.mgh.harvard.edu
*抄送:*
*主题:* Discrepancy between mris_preproc and mri_surf2surf results
when mapping individual's measures to fsaverage space

Dear FreeSurfer Experts,

I'm currently working on mapping cortical morphometric
measurements from each individual in the HCP dataset to the
fsaverage space.

I have noticed that both the mris_preproc and mri_surf2surf
commands can achieve this function. However, I found that the
vertex-level measurements for cortical thickness, sulcal depth,
and curvatures are consistent between these two commands, but the
results for surface area and gray matter volume are totally different.

I am puzzled by this inconsistency and speculate that perhaps
these two commands are calculated on different surfaces? I don't
understand why the two commands get different results since the
inputs are the same.

My command are as follows: (Different surface area values will be
obtained in lh.area.fsaverage.mgh and lh.area.fsaverage.gii files)

mris_preproc --s  id  --meas  area --target fsaverage --hemi lh
–out /Results/CorticalFeatures/id/lh.area.fsaverage.mgh

mri_surf2surf --srcsubject id --trgsubject fsaverage --hemi lh
--sval /HCP/id/surf/lh.area --tval
/Results/CorticalFeatures/id/lh.area.fsaverage.gii

Thank you so much!

Tongyu Zhang


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Re: [Freesurfer] Discrepancy between mris_preproc and mri_surf2surf results when mapping individual's measures to fsaverage space

[Douglas N. Greve]

When working with area, you need to turn on jacobian correction. 
mris_preproc will do this automatically, but you have to add --jac to 
mri_surf2surf explicitly


On 3/20/2024 4:31 AM, tyzh...@ibp.ac.cn wrote:


External Email - Use Caution

Dear FreeSurfer Experts,

I'm currently working on mapping cortical morphometric measurements 
from each individual in the HCP dataset to the fsaverage space.


I have noticed that both the mris_preproc and mri_surf2surf commands 
can achieve this function. However, I found that the vertex-level 
measurements for cortical thickness, sulcal depth, and curvatures are 
consistent between these two commands, but the results for surface 
area and gray matter volume are totally different.


I am puzzled by this inconsistency and speculate that perhaps these 
two commands are calculated on different surfaces? I don't understand 
why the two commands get different results since the inputs are the same.


My command are as follows: (Different surface area values will be 
obtained in lh.area.fsaverage.mgh and lh.area.fsaverage.gii files)


mris_preproc --s  id  --meas  area --target fsaverage --hemi lh –out 
/Results/CorticalFeatures/id/lh.area.fsaverage.mgh


mri_surf2surf --srcsubject id --trgsubject fsaverage --hemi lh --sval 
/HCP/id/surf/lh.area --tval 
/Results/CorticalFeatures/id/lh.area.fsaverage.gii


Thank you so much!

Tongyu Zhang


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Re: [Freesurfer] aparc & wm underestimation

[Douglas N. Greve]

Oh, I see you are using 7.1.1. You can upgrade to 7.4.1. This will not 
change the basic recon-all output and you'll have access to those new 
features.


On 3/16/2024 4:21 PM, Stanica, Maria wrote:


External Email - Use Caution

We checked and the ?h.orig surface looks right. We tried the -expert 
options file that you suggested anyway, but it exited with errors 
unfortunately and didn’t work. Is there anything else we can try?


Thanks again for your help!

Best,

Maria

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


*Date: *Wednesday, March 6, 2024 at 9:20 AM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] aparc & wm underestimation

This is difficult to debug remotely. The first thing to look at is the 
?h.orig surface. Does that look more-or-less right? If not, then it 
means that the wm.mgz is wrong. If it does not look right, it means 
that the surface placement algorithm is pushing the surface into 
subcortical gray. One way to overcome this is to create a 
brain.finalsurfs.manedit.mgz by copying the brain.finalsurfs.mgz, then 
edit the brain.finalsurfs.manedit.mgz to set those areas where the 
surface is off to 255. Then create an expert options file with

WhitePreAparc --rip-bg-no-annot --restore-255  --outvol mrisps.wpa.mgz
PlaceWhiteSurf --restore-255 --outvol mrisps.white.mgz
T1PialSurf --restore-255 --outvol mrisps.pial.mgz
And pass that to recon-all with the -expert option

On 3/5/2024 7:10 PM, Stanica, Maria wrote:

*External Email - Use Caution *

Yes, the problem is that the white surface on the left side of the
image is extending too far into subcortical gray matter. We did
delete the control points and ran some white matter edits, but the
image I sent you is after we applied those edits (it was even
worse before). I don’t see any other wm edits we can make to the
image. It didn’t resolve our issue enough to make the image usable
for our analyses, so I wanted to see if there was anything else we
could do to resolve the problem.

Thank you!

*From: *freesurfer-boun...@nmr.mgh.harvard.edu

 on behalf of
Douglas N. Greve 

*Date: *Tuesday, March 5, 2024 at 9:11 AM
*To: *freesurfer@nmr.mgh.harvard.edu


*Subject: *Re: [Freesurfer] aparc & wm underestimation

Just to make sure I understand, the problem is that the white
surface on the left side of the image is extending too far into
subcortical gray matter, right? This can be difficult to fix, but
the right fix is to edit the wm.mgz. Make sure to delete your
control points as that is not the right fix. Also, remember that
the surfaces in this area may always be inaccurate if you can see
where the boundary is.

On 3/3/2024 6:09 PM, Stanica, Maria wrote:

*External Email - Use Caution *

This is after the most recent round of edits for one of the
subjects.

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu 

Pronouns: she/her/hers

Image

*From: *freesurfer-boun...@nmr.mgh.harvard.edu

 on behalf of
Douglas N. Greve 

*Date: *Sunday, March 3, 2024 at 3:38 PM
*To: *freesurfer@nmr.mgh.harvard.edu


*Subject: *Re: [Freesurfer] aparc & wm underestimation

Can you send pictures of the slices showing the problem?

On 3/3/2024 3:18 PM, Stanica, Maria wrote:

*External Email - Use Caution *

Hello FS developers,

I ran my subjects through skullstripping and recon-all.
Everything processed correctly (and exited without
errors), except 4 images which have an underestimation in
coronal subcortical region. The underestimation is
significant and goes on for about 10-12 slices (for one
image it was 153-162, for another it was 150-164).

After searching the list, we attempted control points,
which ended up not working (I don’t believe this was the
right method to correct the error). Then we tried white
matter edits, and one of the images was resolved, but the
other 3 did not get better. Is there anything else we
could do to try to resolve the issue? I can provide any
other information needed. Any help would be appreciated!

 1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
 2. Operating System: Red Hat Enterprise Linux 7
 

[Freesurfer] mri_volsynth fails but exits with 0 exit status

[Aaron Tanenbaum]

External Email - Use Caution

I am currently running FreeSurfer 7.4.  I wrote a script using the program
mri_volsynth.  I noticed for the first time the program was trying to write
files where it did not have write permissions. It outputted a few error
messages but gave a 0 exit status. It would be nice to have it exit with a
nonzero exit status.
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