Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

[WONG Wan Wa]

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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:

External Email - Use Caution

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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Re: [Freesurfer] Mac OS Monterrey and XQuartz 2.8.2

[fsbuild]

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I would try downloading an installing the latest version of Xquartz which is 
2.8.5 
from,https://secure-web.cisco.com/1QbY1_LKpOs8rxg9YmC2vjno1Z4v2i9V4XhLfDJzwmqCqCNtKYV5iKJ97aqCHBWhugUhe9IammuJUWqdIs7TNqvfslqQ7-iNicm1kKFw4SdTFJkeKTstQV2uZgF4LkFiKVqH_sXmfx4-EyPNQaC-IQhbg6vzxSrPPX9tOITRWcrJAOMPi1YGa5Dl09v7xbqRK9OUZ9YQ44l5cfCBcqoEVYtS3E_ktAaWhBM4NFOXOZuv9n-8Q3grR9r0qor3mFFQR4iL_agscdQM2Ia1iey1d6gjN6-c2SbHRikXbWdVZIp0yC3bWj7QD_htWCal6UddDd-B1CQUGn8Fct_OewW2hRA/https%3A%2F%2Fwww.xquartz.org%2F
Works fine with Monterey (at least on an Intel Mac).
- R.


On Mar 21, 2024, at 19:05, Hugo Sandoval  
wrote:External Email - Use 
CautionHi, i am trying to 
install freesurfer using Mac OS Monterrey and XQuartz 2.8.2.  I get 
an error message.  Is it not 
compatible?___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Mac OS Monterrey and XQuartz 2.8.2

[Hugo Sandoval]

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Hi, i am trying to install freesurfer using Mac OS Monterrey and XQuartz
2.8.2.  I get an error message.  Is it not compatible?
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Re: [Freesurfer] Using orig.mgz or T1.mgz as input to recon-all

[Jeong Yeon Kang]

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Hello,

Thank you for your response. I am not trying to preserve previous recon-all
outputs, because the only outputs I have from the previous run are the
orig.mgz and T1.mgz files.

Can I use your commands above, except with the orig.mgz file, not the
00x.mgz file?

If not, which options would you suggest that would get me closest to the
output I would have gotten if I did have the raw T1s?

Thank you,
Melody

On Thu, Mar 21, 2024 at 4:51 AM Huang, Yujing 
wrote:

> Are you trying to preserve previous recon-all output and re-run using
> different version of Freesurfer?
>
>
>
> If not, ‘recon-all -all -s ’ will re-run recon-all from the
> beginning.
>
>
>
> You can find the original input to recon-all in mri/orig/00x.mgz. You can
> also construct new subject directory structure by copying mri/orig/00x.mgz,
> and run ‘recon-all -all -s ’.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Jeong Yeon Kang
> *Sent:* Wednesday, March 20, 2024 6:20 PM
> *To:* Freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] Using orig.mgz or T1.mgz as input to recon-all
>
>
>
> *External Email - Use Caution*
>
> Hello FreeSurfer Developers,
>
>
>
> I am attempting to run recon-all on a group of subjects. We no longer have
> the raw T1s. Instead, we have their orig.mgz and T1.mgz files from a
> previous run of freesurfer. We wish to rerun recon-all using their orig.mgz
> or T1.mgz as inputs, using FreeSurfer5.3. What would be the best way to go
> about this?
>
>
>
> 1. I ran recon-all normally, with orig.mgz as the input file. It ran to
> completion, but some files are missing from subdirectories. I am not sure
> if the outputs are correct, and comparable to other datasets that have
> freesurfer outputs that used raw T1s.
>
>
>
> 2. I converted orig.mgz to orig.nii.gz using mri_convert, and used
> orig.nii.gz as input to recon-all. This also ran to completion. However,
> because I cannot compare this output to any "true" output, I am unsure if
> the outputs are correct, and is the same as using a raw T1 as input.
>
>
>
> 3. I considered manually starting the recon process from T1.mgz
> (organizing subdirectories manually, inserting T1.mgz and orig.mgz into
> /mri, and starting autorecon2. I am unsure if this is best, as I am missing
> nu.mgz, which is an input file in the first step of autorecon2.
>
>
>
> Please let me know what you think, and which method you think would be
> closest to using the raw T1s. I've searched the list and it seems that no
> one has attempted a similar task. Thank you.
>
>
>
> Sincerely,
>
> Melody
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Re: [Freesurfer] nu_correct: Command not found error

[Dong, Yilei]

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Hi Yujing,

My recon-all just ended at that point. It didn't make it through the entire 
processing stream. Should I rerun the entire process or make any additional 
adjustments when I submit my script again?

Sincerely,
Yilei

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

Sent: Thursday, March 21, 2024 6:11 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] nu_correct: Command not found error


It looks like Freesurfer can’t find minc toolkit binaries on your system.



Did your recon-all finish fine? I think FS 7.2 recon-all is configured to use 
ANTS N4BiasFieldCorrection for nu correct by default.



This is from your log:

“mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 
--proto-iters 1000 --distance 50”



Best,



Yujing





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Dong, Yilei
Sent: Wednesday, March 20, 2024 2:01 PM
To: Freesurfer support list 
Subject: [Freesurfer] nu_correct: Command not found error



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Hi Freesurfer support,



Recently, I submitted a script to run recon-all on 100 mri images on UCSD's 
computing cluster, called EXPANSE. I get an error file that says "nu_correct: 
Command not found. FREESURFER: Undefined variable." The sample error file and 
the output file I have attached for one of the subjects are 
recon-all-slurm.29376886.exp-5-44.err & recon-all-slurm.29376886.exp-5-44.out 
respectively. The script I used to submit the job via slurm is called 
recon-all-slurm.sb.



I googled the error and found that someone else who had a similar situation did 
not source their Freesurfer environment correctly. Would this be the same thing 
for us as well? The main thing for us is Freesurfer/7.2.0 already has been 
available as a module for us on EXPANSE.



Sincerely,

Yilei
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Re: [Freesurfer] if: Expression Syntax - preproc-sess

[Stefano Delli Pizzi]

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My command line is
fcseed-sess -s 156484 -cfg wm.config. 
I do not understand where I'm making an error or if a change is needed.
Thanks
Stefano

> Il giorno 21 mar 2024, alle ore 14:35, Douglas N. Greve 
>  ha scritto:
> 
> -funcstem f.even

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Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

[Douglas N. Greve]

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:


External Email - Use Caution

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:


External Email - Use Caution

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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Re: [Freesurfer] What do the stats files tell us?

[Douglas N. Greve]

See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI

On 3/18/2024 4:38 PM, Vivek Kandasamy wrote:


External Email - Use Caution

Hello,

So I ran FreeSurfer to get numeric data from MRI images and got these 
files under the stats page.


Screenshot 2024-03-18 144107.png

Do you know what each file tells us about our MRI images such as 
the lh.aparc.DKTatlas.mapped, lh.BA_exvivo.stats, lh.BA_exvivo.thresh, 
lh.curv, lh.w-g.pct, and wmparc.DKTatlas.mapped files?


Thanks,

Vivek Kandasamy

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Re: [Freesurfer] if: Expression Syntax - preproc-sess

[Douglas N. Greve]

What is your fcseed-config command line? If the input is not fmcpr, then 
you have to set the input when you config, eg, -funcstem f.even


On 3/19/2024 11:37 AM, Stefano Delli Pizzi wrote:


External Email - Use Caution

Thank you Doug.
The preproc-sess command line runs fine.
An error occurs on:
fcseed-sess -s ID -cfg wm.config -overwrite
ERROR: could not determine file for rs-fMRI_AROMA/ID/rest/001/fmcpr

Best regards
Stefano

Il giorno 19 mar 2024, alle ore 15:54, Douglas N. Greve 
 ha scritto:


Hi Stefano, I think I found and fixed the problem. Can you try these?

On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote:


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Hi Doug,

The raw functional file is firstly passed with motion correction 
(i.e., mc-sess -s ID -fsd rest -per-run) and AROMA filtering.

Next, I have renamed the ICA filtered file as f.nii.gz.
Then, I run:

preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305 
-fsd rest -per-run -sliceorder even -force


There are issues with labels since excluding motion correction 
doesn't produce key files necessary for concatenating the files.
The preprocessing script is searching for the fmcpr.nii.gz file, 
which cannot be found because it is not created using the -nomc option.


When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and 
rerun preproc, the operation is done and the 
fmcpr.odd.sm0.fsaverage.lh is created.


However, when I run the next steps (fcseed-sess -s ID -cfg wm.config 
-overwrite), a second error occurs (reported below) because the 
script searches for fmcpr, which cannot be produced since I used -mc.


ERROR: could not determine file for 
/Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr 
This error seems to be related to the script searching for the fmcpr 
file, which isn't available due to the use of -mc.


Thank you.

Best regards,


Stefano




Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi 
 ha scritto:


Hi Doug have you any news
Thank you very much!
Stefano

Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi 
 ha scritto:


Thank you.
I’m attaching the file.
Stefano


Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve 
 ha scritto:


can you send me this file 
/Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess



On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote:


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It seems to me that I've done what you suggest. Attached is a 
new outputs.

Thanks
Stefano

Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve 
 ha scritto:


Are you sure that you are using the new version that I gave 
you? It looks like the previous version. Also, it does not look 
like the entire terminal output.


On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote:


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The entire terminal output is attached.
Thanks!

Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve 
 ha scritto:


entire terminal output




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Re: [Freesurfer] nu_correct: Command not found error

[Huang, Yujing]

It looks like Freesurfer can't find minc toolkit binaries on your system.

Did your recon-all finish fine? I think FS 7.2 recon-all is configured to use 
ANTS N4BiasFieldCorrection for nu correct by default.

This is from your log:
"mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 
--proto-iters 1000 --distance 50"

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Dong, Yilei
Sent: Wednesday, March 20, 2024 2:01 PM
To: Freesurfer support list 
Subject: [Freesurfer] nu_correct: Command not found error


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Hi Freesurfer support,


Recently, I submitted a script to run recon-all on 100 mri images on UCSD's 
computing cluster, called EXPANSE. I get an error file that says "nu_correct: 
Command not found. FREESURFER: Undefined variable." The sample error file and 
the output file I have attached for one of the subjects are 
recon-all-slurm.29376886.exp-5-44.err & recon-all-slurm.29376886.exp-5-44.out 
respectively. The script I used to submit the job via slurm is called 
recon-all-slurm.sb.



I googled the error and found that someone else who had a similar situation did 
not source their Freesurfer environment correctly. Would this be the same thing 
for us as well? The main thing for us is Freesurfer/7.2.0 already has been 
available as a module for us on EXPANSE.



Sincerely,

Yilei
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Re: [Freesurfer] Using orig.mgz or T1.mgz as input to recon-all

[Huang, Yujing]

Are you trying to preserve previous recon-all output and re-run using different 
version of Freesurfer?

If not, ‘recon-all -all -s ’ will re-run recon-all from the beginning.

You can find the original input to recon-all in mri/orig/00x.mgz. You can also 
construct new subject directory structure by copying mri/orig/00x.mgz, and run 
‘recon-all -all -s ’.

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jeong Yeon Kang
Sent: Wednesday, March 20, 2024 6:20 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Using orig.mgz or T1.mgz as input to recon-all


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Hello FreeSurfer Developers,

I am attempting to run recon-all on a group of subjects. We no longer have the 
raw T1s. Instead, we have their orig.mgz and T1.mgz files from a previous run 
of freesurfer. We wish to rerun recon-all using their orig.mgz or T1.mgz as 
inputs, using FreeSurfer5.3. What would be the best way to go about this?

1. I ran recon-all normally, with orig.mgz as the input file. It ran to 
completion, but some files are missing from subdirectories. I am not sure if 
the outputs are correct, and comparable to other datasets that have freesurfer 
outputs that used raw T1s.

2. I converted orig.mgz to orig.nii.gz using mri_convert, and used orig.nii.gz 
as input to recon-all. This also ran to completion. However, because I cannot 
compare this output to any "true" output, I am unsure if the outputs are 
correct, and is the same as using a raw T1 as input.

3. I considered manually starting the recon process from T1.mgz (organizing 
subdirectories manually, inserting T1.mgz and orig.mgz into /mri, and starting 
autorecon2. I am unsure if this is best, as I am missing nu.mgz, which is an 
input file in the first step of autorecon2.

Please let me know what you think, and which method you think would be closest 
to using the raw T1s. I've searched the list and it seems that no one has 
attempted a similar task. Thank you.

Sincerely,
Melody
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