Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

[Marina Fernández]

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Hi Andrei,

I was referring to .bashrc file located in these directories:
/root/.bashrc
/home/'your_user'/.bashrc
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Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

[Marina Fernández]

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Hi Andrei and Freesurfer experts,

We had the same problem in the past and we noticed there was an extra line
in the .bashrc file of Ubuntu:
export FS_DISABLE_LANG="true"
Deleting this line solves the problem.

The .bashrc file should contain only the following FS lines:
#Freesurfer:
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

Make sure you do this for home and root .bashrc files.

Hope this helps.

Best wishes,
Marina
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[Freesurfer] Remove border vertices

[Marina Fernández]

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Dear experts,

I would like to project a parcellation (annot file) onto the cortical
surface removing or hiding the border vertices of the different labels of
the parcellation. I thought that I can do that scripting but first I would
need to know which vertices are border vertices. Or is there a simpler way
to do it?

Thank you very much in advance.
Bets regards,
Marina
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Re: [Freesurfer] PetSurfer - MG coregister

[Marina Fernández]

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Dear Rahul,

I just used the wiki of the Freesurfer functions, the information is very
complete. If you want to use Freesurfer, you can start by doing the
cortical reconstruction process for each subject (
https://secure-web.cisco.com/1Lj_XzmtE_iAYreTtmjwq2Q0VTCaZWdcX4QFapQPQO_Y7jt5UUJInKYqrNhnXGwnk1sLb7wJq2Wh3qysFyE7A2vatYoHcPHMZHo7GYENuDlLem9W0-2BYIamTvvCFMLLdCUnxLU_G7Cxt88FHc7rc9SBSXeNFKxnmcE92mDpGq17kkG7e5z1xxHMzZ3qqP3i3PsGWTuJ6iXrcCjxYWeUhyFKY-4sYocBxCbnGhmtklucq_krPXq_4UJxnqM4r9GRbforAUguSKj5gWmdJM1j2aenoUDAnZ8cJD7FDo8lzUrrdw-V0NiaO0QpgQu0IuT31aquJZ0ozRGVWMjncSaL6_g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all)
 and then prepare the
maps to do the analysis that interests you. In the case of PET analysis,
you can follow the steps explained on the PetSurfer wiki (
https://secure-web.cisco.com/1SUsUq0XwDtpjwx2dSpE1KOdwDPRl2MG5fyhegdBeDHaK3Kus53Dl6TsyWNEAmQYkn3zf_z62wLaf9lukg3fVOx19cKVvlp-3v3YJWc3n5olJg5s58sSDWVl30wlU6zsBXAQTPs5T4sbeal0Emw9SBV5Rm6WNIfFZ6YRqbQISso9Qaa-CZMD4fKaiP6VNNEYJyAT5OMcGS3C7yfEz9pqobDPA9nbmXH4hTxnURBQjj7_w4ViNBDGceVs6u7qpGUUI7-BBcn1ilRhAM33-kZF3Wmf3EslOFVPXhw8BZD5CPBoHh2Koriy242CdL90U-fp3-SVsHmj4TLz6889vBVOaVQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer).
 If you have any
particular questions about feature options, you can search this list if
other users have asked before. In case the question is not resolved, you
can ask it here so that the experts can answer you.

I hope it helps.

Cheers,

Marina.
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[Freesurfer] PetSurfer - MG coregister

[Marina Fernández]

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Dear experts,

I am trying to do PVC on FBB-PET images using the following commands:

"
mri_coreg --s s_001 --mov s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta

mri_gtmpvc --i s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta --psf 6
--seg gtmseg.mgz --rescale 174 --default-seg-merge  --auto-mask  --mgx .1
--o s_001_pet_fbb
"

The problem is that when overlaying the mgx.ctxgm.nii.gz file with the
T1.mgz of the corresponding subject, they don't match, since the resulting
MG-image is in the space of the original PET (without PVC) instead of in
the space of the freesurfer subject.

How can I make the MG image be in the freesurfer's subject space? Where is
the error?
Thank you very much in advance.

Best regards,
Marina
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[Freesurfer] NoPVC PET

[Marina Fernández]

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Dear experts,

I would like to get a noPVC PET volume scaled by the intensity of the pons,
then project it and apply standard surface-based analysis. On the PetSurfer
website it says:

**

If you do not want to perform PVC, you can just run

mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --seg  gtmseg.mgz
 --default-seg-merge  --auto-mask 1.01 --no-tfe --o gtmpvc.output

 **

If I do this, I cannot find any output in the folder which I can project on
the surface corresponding to the non-PVC PET volume referenced to the pons.

The idea is to have comparable PET-PVC vs. PET-noPVC data scaled to the
pons in both cases. In order to do this, should I divide (externally to the
mri_gtmpvc function) each voxel of the PET image by the average of the
pons?


Thank you very much in advance.

Best regards,

Marina
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[Freesurfer] resample anatomical mask

[Marina Fernández]

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Dear experts,

I would like to downsample the GM mask, which is at 1mm isotropic voxel
size (freesurfer subject space), at 3mm isotropic. What is the most
efficient way to do it with freesurfer?

Thank you in advance.
Marina
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[Freesurfer] SNR

[Marina Fernández]

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Dear experts,

I would like to calculate the SNR by dividing the mean intensity of the
signal of interest by the SD of the noise. To do this, I would like to
create a small circular ROI and place it within the region of interest and
a larger circular ROI and place it within the 'background' region that is
parcelled to each subject in apas+head.mgz (ID=130).

Do you know what functions I can use to create these ROIs and place them
within the regions I want?  Do you know a better method to calculate the
SNR?

Thank you in advance.

Best regards,
Marina
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[Freesurfer] vertex ID in the contralateral hemisphere

[Marina Fernández]

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Dear experts,

I would like to know the corresponding vertex in the contralateral
hemisphere of a given vertex. Do you have a function that allows me to know
it?

Thank you very much in advance.

Best regards,
Marina
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[Freesurfer] Tissue fraction effects correction

[Marina Fernández]

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Dear FS experts,

We are planning to correct for tissue fraction effects on T1w/T2w ratio
images using PETsurfer, setting the point spread function estimate to
zero. My questions are:

1. Does it make sense to correct for tissue fraction effects on T1w/T2w
ratio images even when T1w and T2w images were acquired using the same
matrix size with identical voxel resolution (i.e., 1mm3)?

2. If that makes sense, which PVC method would work best for correcting
tissue fraction effects (i.e., SGTM, MG, RBV) on structural MRI scans?

Many thanks in advance.

Best,
Marina
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[Freesurfer] parallel make_average_subject

[Marina Fernández]

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Dear experts,

I would like to create an average subject from a very large population. I
am going to compute it on a computer with a lot of threads and I would like
to know if it is possible to parallelize the make_average_subject function
to try to shorten the computation time. I have tried to add the -openmp
flag but I get the error that the flag is unrecognized.
How can I solve this?

Thank you in advance.

Best regards,
Marina
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[Freesurfer] Building a model

[Marina Fernández]

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Dear experts,

We run the following analysis in Freesurfer:

*Group* (2 levels) x *X1* (continuous IV) x *X2 *(continuous IV) +
*Sex *(categorical
covariate) + *Age* (continuous covariate)

We exported the vertex with the maximum statistic after applying FWE
correction to replicate the analysis in R. We want to make sure about the
structure of the model to later do a Bayesian analysis using the same
structure.

We got significant results for most of our analyses but not for all of
them, likely because we are not doing exactly the same thing.

We have fitted several models in R, but the one that gave the closest
results was the following:

model  <-  lm (vertex ~ NewFactor (4 levels: Group*Sex) + X1X2 (resulting
from X1*X2) * Group + Age*NewFactor, data=mydata)

How should we introduce the interaction term in order to make the models
fitted by Freesurfer and R comparable?

Thanks a lot in advance,

Marina
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[Freesurfer] results visualization

[Marina Fernández]

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Dear experts,

Do you know what are the steps to follow to visualize a surface-map of
freesurfer results in Caret?

Thank you very much in advance.
Best regards,
Marina
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Re: [Freesurfer] bias field correction and intensity normalization

[Marina Fernández]

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Hi Matt,


We always really appreciate your help and advice.

Thank you very much for your answer, now we understand much better why
it is correct not to apply this correction.

Best,
Marina
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[Freesurfer] bias field correction and intensity normalization

[Marina Fernández]

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Dear experts,

I would like to create myelin maps calculating the T1w/T2w ratio. Should
I apply bias field correction and intensity normalization (i.e., "nu
correction" in the Freesurfer pipeline) to T1w and T2w images separately
before calculating the T1w/T2 ratio?

I applied nu correction to T1w images and worked fine but results were
weird when nu correction was applied applied to T2w images. I am not
sure if nu correction must only be applied to T1w images for this
purpose, or if I have to modify some parameters to apply nu correction
to T2w images.

Thank you in advance for your help.

Best,
Marina
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[Freesurfer] T2 T1 registration with mri_robust_register

[Marina Fernández]

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Dear experts,

I would like to co-register T2 to T1 robustly, both images have a
resolution of 0.65mm3.

Firstly, I tried bbregister with the '--init-rr' flag, but this function
doesn't allow to keep the native voxel resolution (i.e., 0.65mm3),
changing it to 1 mm.  As I wanted to maintain the native voxel
resolution , I tried the mri_robust_register function (corresponding to
the '--init-rr' flag) as explained in the help associated with this
function, but this process took thirteen hours:

EXAMPLE 4. Robust cross modal registration:

mri_robust_register --mov movT2.mgz --dst dstT1.mgz --satit --iscale

--mapmov T2_to_T1.mgz --lta T2_to_T1.lta --cost ROBENT --entradius 2

--entcorrection --weights T2_to_T1_weights.mgz

I also tried the standard cross modal registration. The process didn't
take as long, but the result was not as accurate as bbregister.

EXAMPLE 5. Standard cross modal registration:

mri_robust_register --mov movT2.mgz --dst dstT1.mgz --mapmov T2_to_

T1.mgz --lta T2_to_T1.lta --cost NMI

Could you suggest me how to accurately register T2 to T1 images
maintaining the native voxel resolution in a shorter time?

Thank you very much in advance.

Best,
Marina
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[Freesurfer] nu correction

[Marina Fernández]

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Dear experts,

I would like to create myelin maps calculating the T1w/T2w ratio. Should
I apply bias field correction and intensity normalization (i.e., "nu
correction" in the Freesurfer pipeline) to T1w and T2w images separately
before calculating the T1w/T2 ratio?

I applied nu correction to T1w images and worked fine but results were
weird when nu correction was applied applied to T2w images. I am not
sure if nu correction must only be applied to T1w images for this
purpose, or if I have to modify some parameters to apply nu correction
to T2w images.

Thank you in advance for your help.

Best,
Marina
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Re: [Freesurfer] PVC to calculate myelin maps

[Marina Fernández]

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Thank you very much for your response Doug.

What PVC method is most recommended to use to calculate the T1 / T2 ratio
(RBV or MG)?
And what value of PSF should we specify to calculate this ratio? To my
knowledge, this is an acquisition related parameter and if I set it to 0 I
will turn off PVC.


Best wishes,
Marina.


%%

Douglas N. Greve
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Yes, you can use PETsurfer. I would apply it to the ratio


On 5/28/2021 10:25 AM, Marina Fernández wrote:

External Email - Use Caution

Dear experts,


I want to calculate myelin maps using the ratio of T1w and T2w MRI images.
I saw that the correction of partial volume effects can be used to create
the maps (Shafee, Buckner & Fischl, 2015)*.

Can I use the PVC functions of PetSurfer for this purpose? And in case I
can:

Should I apply PVC only on T1? Or also in T2?


Which T1 should I use? The original T1 or the T1 with corrections (for example,
the nu.mgz file that is corrected for variations in intensity)?

Any other advice for calculating myelin maps would be welcome.

Thank you in advance,

Marina


*Link:


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[Freesurfer] myelin maps

[Marina Fernández]

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Dear experts,



I want to calculate myelin maps using the ratio of T1w and T2w MRI images.
I would like to perform a correction of partial volume effects to create
the maps (Shafee, Buckner & Fischl, 2015)*, instead of creating the maps
using HCP Pipelines.



Can I use the PVC functions of PetSurfer for this purpose? And in case I
can:



Should I apply PVC only on T1? Or also in T2?



Which T1 should I use? The original T1 or the T1 with corrections (for
example, the nu.mgz file that is corrected for variations in intensity)?



Thank you in advance,



Marina



* Link:

https://secure-web.cisco.com/1uklY3paR4n5Apdl5Hfz0cV9XIEUybKcHiz2RGaJAVrIhn4Pr30hkvyaC1AEe6qQWUpZbtz6wEj4c9-kZjvH1rYXOsvvgQY4Z6RMSrXdmwMdwF6oH3e1ORxB-9ufa1E33VgyJs1uQ8t7T9tEI7BFDCR5ZcqmUPrjKQJW36awUkwXh9OUrXoffGTMSXtPMb_w92IzVb3sJvB9pGWOZ-qFC87fc_MO1RcmjYim0Uqw4nxbQy2V9cjs_sennoz55gQNUko6A_A0ZHeZD-zaWbVmfrg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4262571%2F%23R48
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[Freesurfer] PVC to calculate myelin maps

[Marina Fernández]

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Hi Matt,

Thank you very much for the quick answer.

We have our data analyzed with another pipeline that also uses Freesurfer
functions. For this reason we prefer to calculate myelin maps outside of
the HCP Pipelines.

Do you think the way of calculating the maps that I explained in the
previous question is evenly valid?

Best wishes,
Marina




%


Glasser, Matthew
<https://secure-web.cisco.com/1EkIb4RUBbvp4aaCzTKvZqXi5mpWtbK6dEiwb2GFTBe5yhOUyifO_hV_E7W1QbzRQK0FwD5cE3KcRI74D3Ovox656ePedxamjtVAEW4AgL4A-7CpFTGP6z5Tq41NoOZ1ojD9zFUJk5ThErtAOajuSKZWvKvti9tqMIHF1q6hCwGlKHevaGmbXlNhh9Qy7R3bO5NIgNuF-fVDEzMvEnu0zjfgN_OsOBclQQKnAUOgbQN0YXzNIZrmOblbk3L2t_TpeCz4wAM71ypty2rwIPsMJYA/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Glasser%252C%2BMatthew%2522>
Fri, 28 May 2021 07:34:15 -0700
<https://secure-web.cisco.com/1ljnBFwkQWFVBlnoXgh6utmDhvf7eskDl5mAoznGoGHO9FTeVRUYQtO-bfot3HqDYDehtfxbJhabnlcLwYGpH0dXP12Y55bVR65aMaKLBI2m5e3DpuIaGvkf3ceK3XJu0-ejvTaS0490ojIjr2iIxgGPOUX8HzFmINOe0OqACHWQa_U11JZn92WpectdOwu7kUNnLEJ1EEOKgypAFQnxBzkuHv-Esidv8bS9Fwbh--pHmipQ4dKxzOK4XeRnn2fte3bTthJQyxPdc-hxBj4-oqg/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20210528>

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I would use the HCP Pipelines for this.

Matt.



%%%%%%%

Marina Fernández
<https://secure-web.cisco.com/1jnEmX8pyslFDNAKq1ESVKhaVYgavR5DWrZDCQVw6EIjIeRPu8VsMW2BmjjGD5q-TEhUnOvxdrLSTT5-Y6k0YXgDL7svI9z3nYXjvFbLZ7RTupBSGPm81_9ITZGgKJJOgPJdln72nUn8_i_M0BwX5vAQJhvU59P4tJ425dDyWnDLjXoT8Isqf8qqqez-ioXBS40q0Uny8MDDL0kBndUynxMfDLd8eLFxK2zhH_m6k3AE0fJN7n9AYbodo3QU0dDBjU5tlYbAcURsJL_uHxBtJ5Q/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Marina%2BFern%25C3%25A1ndez%2522>
 Fri, 28 May 2021 07:26:19 -0700
<https://secure-web.cisco.com/1ljnBFwkQWFVBlnoXgh6utmDhvf7eskDl5mAoznGoGHO9FTeVRUYQtO-bfot3HqDYDehtfxbJhabnlcLwYGpH0dXP12Y55bVR65aMaKLBI2m5e3DpuIaGvkf3ceK3XJu0-ejvTaS0490ojIjr2iIxgGPOUX8HzFmINOe0OqACHWQa_U11JZn92WpectdOwu7kUNnLEJ1EEOKgypAFQnxBzkuHv-Esidv8bS9Fwbh--pHmipQ4dKxzOK4XeRnn2fte3bTthJQyxPdc-hxBj4-oqg/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20210528>

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Dear experts,

I want to calculate myelin maps using the ratio of T1w and T2w MRI images.
I saw that the correction of partial volume effects can be used to create
the maps (Shafee, Buckner & Fischl, 2015)*.

Can I use the PVC functions of PetSurfer for this purpose? And in case I
can:

Should I apply PVC only on T1? Or also in T2?

Which T1 should I use? The original T1 or the T1 with corrections (for
example, the nu.mgz file that is corrected for variations in intensity)?

Any other advice for calculating myelin maps would be welcome.

Thank you in advance,

Marina


*Link:
https://secure-web.cisco.com/1JlAz9aQioBCdg379E7idALB4EltLyOBrORvLMLOKKAfsOZ5T86whDDL8Q-4ZOYG7rMgwoBYIyC4d5BsThH9nR2UT-_82NU3WKyCZrii6txF4QxCWh-K6Hy6aC2vsOwRupJhTnA_Menjtq1hXOSwjndsWxN3BBnw625eBs0OgB8t1ZM0uY7sLR_VuAuMcsvNsQQ9qofNHMaLp6aidYJh3yhta2kwGeWzCXmtyE1XOS-Z2uiDZa5gqmp9A0egHtAOC68aEN1v8l0S-ikEhif20Qg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4262571%2F%23R48
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[Freesurfer] PVC to calculate myelin maps

[Marina Fernández]

External Email - Use Caution

Dear experts,

I want to calculate myelin maps using the ratio of T1w and T2w MRI images.
I saw that the correction of partial volume effects can be used to create
the maps (Shafee, Buckner & Fischl, 2015)*.

Can I use the PVC functions of PetSurfer for this purpose? And in case I
can:

Should I apply PVC only on T1? Or also in T2?

Which T1 should I use? The original T1 or the T1 with corrections (for
example, the nu.mgz file that is corrected for variations in intensity)?

Any other advice for calculating myelin maps would be welcome.

Thank you in advance,

Marina


*Link:

https://secure-web.cisco.com/1JlAz9aQioBCdg379E7idALB4EltLyOBrORvLMLOKKAfsOZ5T86whDDL8Q-4ZOYG7rMgwoBYIyC4d5BsThH9nR2UT-_82NU3WKyCZrii6txF4QxCWh-K6Hy6aC2vsOwRupJhTnA_Menjtq1hXOSwjndsWxN3BBnw625eBs0OgB8t1ZM0uY7sLR_VuAuMcsvNsQQ9qofNHMaLp6aidYJh3yhta2kwGeWzCXmtyE1XOS-Z2uiDZa5gqmp9A0egHtAOC68aEN1v8l0S-ikEhif20Qg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4262571%2F%23R48
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[Freesurfer] fspalm output

[Marina Fernández]

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Dear experts,

I used the function fspalm to run permutations with the following options:
fspalm --glmdir /my_glmdir/ --cft 1.3 --name palm --iters 1 --cwp .05
--onetail

Checking the palmcofig.txt file that is generated as output, I realized
that even if the "–logp" flag wasn't specified in the function, this flag
is always applied with fspalm, and therefore the p-values of the
*dpv_tstat_uncp.mgz file are saved as -log10(p). Consequently, if I want to
threshold with p, I must first convert these values to p-values using 10^(-
p) and then use p<0.05.

In contrast, when I load the files *dpv _tstat_fwep.mgz and
*clustere_tstat_fwep.mgz, the results don't appear to be -log10(p), and
then these files wouldn't need to be transformed with 10^(- p) to use a
threshold of p<0.05.

What is the use of this flag in fspalm and why does it only affect the
uncorrected p values?

Thank you in advance.
Marina
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[Freesurfer] beta coefficients

[Marina Fernández]

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Dear experts,



In addition to t and p-value, I would like to report the beta coefficient
of the fixed effects in the following regression equation for the vertex
showing the max statistic within the cluster that survived multiple
comparison correction:



y = β0 + β1*sex + β2*age + β3*(sex+age) + e



I know that beta.mgh contains the beta estimates corresponding to the
intercepts of male and female and the slopes of age for each sex. However,
what I need is the beta corresponding to the intercept (β0), and the beta
for the slope of sex (β1), age (β2) and sex*age interaction (β3). I also

need the residual variance of the model (e), but rvar.mgh contains 4
values, 2 for the intercepts and another two for the slopes. I would really
appreciate if you could help me to obtain this information.



Thanks a lot in advance



Marina
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[Freesurfer] report results

[Marina Fernández]

External Email - Use Caution

Dear experts,


In addition to t and p-value, I would like to report the beta
coefficient of the fixed effects in the following regression equation
for the vertex showing the max statistic within the cluster that
survived multiple comparison correction:

y = β0 + β1*sex + β2*age + β3*(sex+age) + e

I know that beta.mgh contains the beta estimates corresponding to the
intercepts of male and female and the slopes of age for each sex.
However, what I need is the beta corresponding to the intercept (β0),
and the beta for the slope of sex (β1), age (β2) and sex*age
interaction (β3). I also
need the residual variance of the model (e), but rvar.mgh contains 4
values, 2 for the intercepts and another two for the slopes. I would
really appreciate if you could help me to obtain this information.

Thanks a lot in advance

Marina
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[Freesurfer] beta coefficient of the fixed effects

[Marina Fernández]

External Email - Use Caution

Dear Doug,



In addition to t and p-value, I would like to report the beta coefficient
of the fixed effects in the following regression equation for the vertex
showing the max statistic within the cluster that survived multiple
comparison correction:



y = β0 + β1*sex + β2*age + β3*(sex+age) + e



I know that beta.mgh contains the beta estimates corresponding to the
intercepts of male and female and the slopes of age for each sex. However,
what I need is the beta corresponding to the intercept (β0), and the beta
for the slope of sex (β1), age (β2) and sex*age interaction (β3). I also
need the residual variance of the model (e), but rvar.mgh contains 4
values, 2 for the intercepts and another two for the slopes. I would really
appreciate if you could help me to obtain this information.



Thanks a lot in advance

Marina
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[Freesurfer] fspalm contrasts {Disarmed}

[Marina Fernández]

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Dear experts,



To correct multiple comparisons on the surface I'm using fspalm. I know
that this command internally transforms the design contrast and desing
matrix from the Freesurfer format to the fsl format so that FSL-PALM
understands the input.

When the freesurfer contrasts include only one line, I can run permutations
with fspalm without errors. The problem arises when the contrast has two
lines (e.g., when including a three-level factor like in the example
"Contrast 4: group.effect.mtx" from the link
https://secure-web.cisco.com/1zRPseSPjbEGgbMXbZRKYmGKkEKOP342L-FeUKM_km6ilBsfbfQJ_8-GKG0ysjrbni7SSqZSiRJEwGoNdTaDT7odDRtL4P8fXeJYKwJhPkQkrvUtYk6NsdQmQbrH5peBojO-GhYGC4fJBL8oiTjdRUnWElMzVNTDVVzcpeyhF4J-oNKoDjCnw7KeXyN6LJukL1rX7L9IjS4gmANZHEgbA8LyjIyhGxboT3lU_JSnWQGXoN93TpE-Th6Kv5ZIGHRensM51F7oceekuHSwqwMzpsQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdf3G0V;
 or when including a
two-way interaction between a dichotomic factor and two covariates of
interest). You can see below the error. How can I solve this problem?



Thank you in advance.

Marina



**ERROR:**

Loading surface 1/1:
/usr/local/freesurfer/subjects/amyloid74_thickness_average/surf/lh.white

Reading input 1/1:
/usr/local/freesurfer/subjects/amyloid74_thickness_stats/smoothing/gaussians/lh.fsgd_subj_gauss003.mgh

Reading design matrix and contrasts.

Error using palm_vestread (line 56)

File not in the correct format: design.con



Error in palm_miscread (line 110)

[X.data,X.extra.PPH] = palm_vestread(X.filename);

Error in palm_takeargs (line 2111)

tmp = palm_miscread(opts.t{t},[],[],opts.precision);

Error in palm_core (line 33)

[opts,plm] = palm_takeargs(varargin{:});

Error in palm (line 81)

palm_core(varargin{:});
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[Freesurfer] fspalm error : --sig2p-max unknown

[Marina Fernández]

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Dear experts,

When I was running permutations with fspalm an error appeared because it
couldn't find the --sig2p-max option when using mri_surfcluster
internally.  You can find below the terminal output.

How can I fix this error?

Thank you in advance
Marina.

 *Terminal output:
...

>> >> palm processing complete - running the surface cluster analysis...

/usr/local/freesurfer/subjects/merchi182_thickness_stats/stats/thickness/permutation/lctx/across/across_age_cov_none_0.05/pos/lh.fsgd_subj_gauss003/palm

mri_surfcluster --in fsp_clustere_tstat_fwep.mgz --thmin 1.301030 --subject
merchi182_thickness_average --hemi lh --annot aparc --sum
contrast.clustertable.summary --no-fixmni --surf white --ocn
contrast.ocn.mgz --oannot ./contrast.ocn.annot --sig2p-max

ERROR: Option --sig2p-max unknown

error: mri_surfcluster failed

fspalm --glmdir
/usr/local/freesurfer/subjects/merchi182_thickness_stats//stats/thickness/permutation/lctx/across//across_age_cov_none_0.05/pos//lh.fsgd_subj_gauss003
--cft 1.301 --name palm --iters 100 --cwp .05 --onetail: Signal 127

ans =

   255
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[Freesurfer] Multiple regression analysis

[Marina Fernández]

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Dear all,

I am doing a multiple regression analysis with 3 covariates of interest. I
know that for testing two-way and three-way interactions I must create new
variables by multiplying the covariates of interest. As Freesurfer
transforms continuous variables to z score before applying statistic, is it
correct to transform to z score the result of the previous multiplication?
I am asking this because the result of multiplying two z transformed
variables would be different.

Thanks a lot in advance.

Marina
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[Freesurfer] PET image format

[Marina Fernández]

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Dear experts!

I am using PetSurfer and I have a PET dataset that is in ecat format (.v).
I would like to convert the images to nifti format to start processing the
data.
What function can I use to convert the images?
How can I check that the left-right orientation doesn't flip?

Thank you in advance!
Marina.
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[Freesurfer] Display results with tksurfer

[Marina Fernández]

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Thanks for the reply Doug,

We used the tksurfer command lines because they were run in matlab after
performing some analysis to obtain the figures of the results. With the
scripts, these figures are automatically saved for later review. We would
like to know if what you propose with freeview is appropriate for this and
if we can modify the scale of min-max significant t values with the
freeview options (I copy the previous message below).

Thank you so much for your attention.

Best regards,
Marina

---

Douglas N. Greve
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+N.+Greve%22>
 Mon, 19 Oct 2020 07:50:56 -0700
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20201019>
Not sure, we don't use tksurfer that much anymore. Have you tried freeview?
You can run freeview with tksurferfv and the same tksurfer arguments (makes
it easier)

On 10/13/2020 5:03 AM, Marina Fernández wrote:

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Dear Freesurfer experts,


I would like to modify the values of the colorbar scale to display results
in the inflated surface with tksurfer, in such a way that displayed values
in the colorbar range from the minimum t- value detected to the maximum t
value detected. I have tried to use the -fminmax flag, but the colorbar
scale shows values from 0 to the maximum t value. Is it possible to limit
values of the colorbar scale to min-max significant t values?

On the other hand, is it possible to invert the colors of the colorbar scale
(e.g., red for higher t values and yellow for lower t values)?

Thank you in advance.

Best regards,
Marina

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[Freesurfer] display results with tksurfer

[Marina Fernández]

External Email - Use Caution

Dear Freesurfer experts,

I would like to modify the values of the colorbar scale to display results
in the inflated surface with tksurfer, in such a way that displayed values
in the colorbar range from the minimum t- value detected to the maximum t
value detected. I have tried to use the -fminmax flag, but the colorbar
scale shows values from 0 to the maximum t value. Is it possible to limit
values of the colorbar scale to min-max significant t values?

On the other hand, is it possible to invert the colors of the colorbar
scale (e.g., red for higher t values and yellow for lower t values)?

Thank you in advance.

Best regards,
Marina
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Re: [Freesurfer] lobe annotation and stats file

[Marina Fernández]

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Hi Doug,

I used the command that you sent me but I have the same error message
(ERROR: stating file /usr/local/freesurfer/...).

Do you know other options?

Thank you in advance.
Marina


-


Douglas N. Greve
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+N.+Greve%22>
 Tue, 08 Sep 2020 08:14:19 -0700
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20200908>

Try something like this


mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.lobe.stats
-b -a ../label/lh.lobe.annot fsm010 lh white

On 9/8/2020 7:58 AM, Marina Fernández wrote:

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Dear experts,


I would like to get a .stats file this the volume and thickness of lobe
annotation, so I am following the steps indicated in this link
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation.

Specifically, I used these commands:

mri_annotation2label --subject s_001 --hemi lh --lobesStrict lobe.annot

cd /usr/local/freesurfer/subjects/; mris_anatomical_stats -a
s_001/label/lh.lobe.annot
-f s_001/stats/lh.lobe.stats -b s_001 lh

The output file that I get (lh.lobe.stats) seems normal and contains the
measurements that I need (volume and thickness). The problem is that the
terminal output contains this error message: ERROR: stating file
/usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot

(below you can find the full terminal output)


What I have to do to obtain the lh.lobe.stats file (with the same or similar
stucture) without the error message?

Best regards,
Marina


  % /TERMINAL OUTPUT / % /

subject = s_001
annotation = aparc
hemi = rh
surface   = white

Reading surface
 /usr/local/freesurfer/subjects/s_001/surf/rh.white

Loading annotations from
/usr/local/freesurfer/subjects/s_001/label/rh.aparc.annot

reading colortable from annotation file...

colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

Seg base 2000
MRISmergeAnnotations: parcCount=11, newparcname=frontal
mri_annotation2 supposed to be reproducible but seed not set
MRISmergeAnnotations: parcCount=9, newparcname=temporal
MRISmergeAnnotations: parcCount=5, newparcname=parietal
MRISmergeAnnotations: parcCount=4, newparcname=occipital
MRISmergeAnnotations: parcCount=4, newparcname=cingulate
computing statistics for each annotation in s_001/label/rh.lobe.annot.
reading volume /usr/local/freesurfer/subjects/s_001/mri/wm.mgz...

reading input surface /usr/local/freesurfer/subjects/s_001/surf/rh.white...

Using TH3 vertex volume calc
Total face volume 176610
Total vertex volume 173305 (mask=0)

reading input pial surface
/usr/local/freesurfer/subjects/s_001/surf/rh.pial... reading input white
surface /usr/local/freesurfer/subjects/s_001/surf/rh.white...

reading colortable from annotation file...
colortable with 8 entries read (originally none)

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name


ERROR: stating file
/usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot

atlas_icv (eTIV) = 1198953 mm^3(det: 1.624839 )
37262  24668  63218  2.363 0.474 0.124 0.029  41443.8  frontal
 3602   2412   6370  2.374 0.615 0.137 0.027 54 3.8  cingulate

12917   8443  18251  2.024 0.428 0.134 0.030  17115.6
 occipital 19235  12890  36112  2.488 0.535 0.119 0.028  211
 21.0  temporal 26568  17417  41499  2.204 0.466 0.119 0.024  287
 25.6  parietal

 2510   1617   4741  3.018 0.820 0.126 0.036 28 3.9  insula/

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[Freesurfer] lobe annotation and stats file

[Marina Fernández]

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Dear experts,

I would like to get a .stats file this the volume and thickness of lobe
annotation, so I am following the steps indicated in this link
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation.
Specifically, I used these commands:

mri_annotation2label --subject s_001 --hemi lh --lobesStrict lobe.annot
cd /usr/local/freesurfer/subjects/; mris_anatomical_stats -a
s_001/label/lh.lobe.annot -f s_001/stats/lh.lobe.stats -b s_001 lh

The output file that I get (lh.lobe.stats) seems normal and contains the
measurements that I need (volume and thickness). The problem is that the
terminal output contains this error message:
ERROR: stating file
/usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot
(below you can find the full terminal output)

What I have to do to obtain the lh.lobe.stats file (with the same or
similar stucture) without the error message?

Best regards,
Marina


  % *TERMINAL OUTPUT * %















































*subject = s_001annotation = aparchemi = rhsurface   = whiteReading surface
 /usr/local/freesurfer/subjects/s_001/surf/rh.whiteLoading annotations from
/usr/local/freesurfer/subjects/s_001/label/rh.aparc.annotreading colortable
from annotation file...colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)Seg
base 2000MRISmergeAnnotations: parcCount=11,
newparcname=frontalmri_annotation2 supposed to be reproducible but seed not
setMRISmergeAnnotations: parcCount=9,
newparcname=temporalMRISmergeAnnotations: parcCount=5,
newparcname=parietalMRISmergeAnnotations: parcCount=4,
newparcname=occipitalMRISmergeAnnotations: parcCount=4,
newparcname=cingulatecomputing statistics for each annotation in
s_001/label/rh.lobe.annot.reading volume
/usr/local/freesurfer/subjects/s_001/mri/wm.mgz...reading input surface
/usr/local/freesurfer/subjects/s_001/surf/rh.white...Using TH3 vertex
volume calcTotal face volume 176610Total vertex volume 173305
(mask=0)reading input pial surface
/usr/local/freesurfer/subjects/s_001/surf/rh.pial...reading input white
surface /usr/local/freesurfer/subjects/s_001/surf/rh.white...reading
colortable from annotation file...colortable with 8 entries read
(originally none)table columns are:number of verticestotal surface
area (mm^2)total gray matter volume (mm^3)average cortical
thickness +- standard deviation (mm)integrated rectified mean
curvatureintegrated rectified Gaussian curvaturefolding index
intrinsic curvature indexstructure nameERROR: stating file
/usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annotatlas_icv
(eTIV) = 1198953 mm^3(det: 1.624839 )37262  24668  63218  2.363 0.474
  0.124 0.029  41443.8  frontal 3602   2412   6370  2.374 0.615
0.137 0.027   54 3.8  cingulate12917   8443  18251  2.024
0.428 0.134 0.030  17115.6  occipital19235  12890  36112
 2.488 0.535 0.119 0.028  21121.0  temporal26568  17417
 41499  2.204 0.466 0.119 0.024  28725.6  parietal 2510
1617   4741  3.018 0.820 0.126 0.036   28 3.9  insula*
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Re: [Freesurfer] G_subcallosal region is missing

[Marina Fernández]

External Email - Use Caution

Hi Doug,

I sent you the images attached to the email and also through FTP File
Exchange.

Thank you for your attention.
Best regards,

Marina




> 
>   Douglas N. Greve
> I'm still not understanding what is happening. Can you send three pics of
> the inflated surface of same location, one with cortex.label, one with
> aparc.annot, and one with aparc.a2009s.annot? Also, please remember to
> include previous emails so that I have context, thanks



>
> On 9/3/2020 9:55 AM, Marina Fernández wrote:

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Sorry for the misunderstanding Doug . I have checked the lh.aparc.annot on
the surface and there is no G_subcallosal label in these subjects. In that
region are the G_and_S_cingul-Ant label / S_pericallosal labels. On the
other hand,  the surface appears normal.

What do you recommend us to do?

Thank you in advance.
Marina.


Douglas N. Greve
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+N.+Greve%22>
 Wed, 02 Sep 2020 10:31:13 -0700
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20200902>
Sorry, I meant to look on the surface and see if the label is there and what
the lh.aparc.annot looks like there

On 9/2/2020 11:05 AM, Marina Fernández wrote:

External Email - Use Caution

Hi Doug,


When I load the volume aparc.a2009s+aseg.mgz in a subject without the
G_subcallosal
region in the lh.aparc.a2009s.stats file, I can see that in the other
hemisphere (right in this case) there is G_subcallosal while in the left
hemisphere this contralateral region is filled by the lh_S_suborbital
region. So, it's covered by another label.

What should we do?

Best wishes,
Marina





Douglas N. Greve <
https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+N.+Greve%22
> Wed, 02 Sep 2020 07:23:58 -0700 <
https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20200902
>

Does the cortex label cover it? What does the aparc look like in that area?

On 9/2/2020 6:09 AM, Marina Fernández wrote:

External Email - Use Caution Dear experts,

I have noticed that some subjects don't show the G_subcallosal
region in the *h.aparc.a2009s.stats file. Do you know why is this
happening? Is there a way to fix it?

Thank you in advance. Best regards, Marina
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Re: [Freesurfer] G_subcallosal region is missing

[Marina Fernández]

External Email - Use Caution

Sorry for the misunderstanding Doug . I have checked the lh.aparc.annot on
the surface and there is no G_subcallosal label in these subjects. In that
region are the G_and_S_cingul-Ant label / S_pericallosal labels. On the
other hand,  the surface appears normal.
What do you recommend us to do?

Thank you in advance.
Marina.
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Re: [Freesurfer] G_subcallosal region is missing

[Marina Fernández]

External Email - Use Caution

Hi Doug,

When I load the volume aparc.a2009s+aseg.mgz in a subject without
the G_subcallosal region in the lh.aparc.a2009s.stats file, I can see that
in the other hemisphere (right in this case) there is G_subcallosal while
in the left hemisphere this contralateral region is filled by
the lh_S_suborbital region. So, it's covered by another label.
What should we do?

Best wishes,
Marina




Douglas N. Greve
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+N.+Greve%22>
 Wed, 02 Sep 2020 07:23:58 -0700
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20200902>

Does the cortex label cover it? What does the aparc look like in that area?


On 9/2/2020 6:09 AM, Marina Fernández wrote:

External Email - Use Caution

Dear experts,


I have noticed that some subjects don't show the G_subcallosal region in
the *h.aparc.a2009s.stats file. Do you know why is this happening? Is there
a way to fix it?

Thank you in advance.
Best regards,
Marina

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[Freesurfer] G_subcallosal region is missing

[Marina Fernández]

External Email - Use Caution

Dear experts,

I have noticed that some subjects don't show the G_subcallosal region in
the *h.aparc.a2009s.stats file. Do you know why is this happening? Is there
a way to fix it?

Thank you in advance.
Best regards,
Marina
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[Freesurfer] total vertices does not match between results and labels

[Marina Fernández]

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Dear experts,

I am using the mri_surfcluster function to cluster the surface results:

mri_surfcluster --subject fbb_average --mask mask.mgh --hemi lh --olab
label --in sig_results_tvalues.mgh --thmin 0.001

When I count vertices different than 0 in the results file that I give as
input (which contains only the significant vertex t values) I get a value
(for example, total= 6237 vertices).
The problem is that when I add the vertices of the output labels, the total
number of vertices is less (for example: total=6152 vertices).

Why does the number of total vertices not match?
Is the function I use correct?

Thank you very much in advance.
Marina
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Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

[Marina Fernández]

External Email - Use Caution

Hi Bruce,

The talairach transform is reasonable and the aseg segment the cc correctly.

I run with freesurfer dev version the same command (recon all
-autorecon-2wm -subjid post_006) and now I have more information about what
could be the problem. The output of the terminal (that you can see below)
says that there is a vertex in the curv file of each hemisphere that has
one vertex number that it  is not expected. When I open the curv file in
tksurfer there is a 0 in these positions.

Maybe this output can be useful to help me solve the problem.
What do you think I should do? Thanks in advance!


mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10
rh.inflated

setting seed for random number generator to 1234
normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
128 vertices thresholded to be in k1 ~ [-0.27 0.70], k2 ~ [-0.10 0.11]
total integrated curvature = 0.637*4pi (8.002) --> 0 handles
ICI = 1.5, FI = 8.0, variation=142.940
106 vertices thresholded to be in [-0.03 0.02]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at
99.90% level
curvature mean = 0.000, std = 0.001
125 vertices thresholded to be in [-0.16 0.23]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std =
0.023
done.
@#@FSTIME  2020:05:28:10:21:34 mris_curvature N 12 e 52.03 S 0.20 U 51.78 P
99% M 334852 F 0 R 89611 W 0 c 174 w 1 I 0 O 1888 L 2.00 2.00 1.76
@#@FSLOADPOST 2020:05:28:10:22:26 mris_curvature N 12 2.00 2.00 1.77

#-
#@# Curvature Stats lh Thu May 28 10:22:26 CEST 2020
/usr/local/freesurfer/subjects/post_006/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats
-F smoothwm post_006 lh curv sulc

 Toggling save flag on curvature files   [
ok ]
 Outputting results using filestem   [
../stats/lh.curv.stats ]
 Toggling save flag on curvature files   [
ok ]
   Setting surface [
post_006/lh.smoothwm ]
Reading surface...   [
ok ]
   Setting texture [
curv ]
Reading texture...error: No such file or
directory
error: MRISreadNewCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/post_006/surf/lh.curv

***WARNING!***
Some error has occurred while reading 'lh.curv'.
This might be due a vertex incompatibility
between the surface 'lh.smoothwm' and curv 'lh.curv'.

You might be able to correct this by re-running
'mris_make_surfaces' on this dataset.

Skipping this (and any remaining) curvature files.
Any measurements / calcuations that depend on the
curvature file will be skipped.
*

  Calculating Discrete Principal Curvatures...
  Determining geometric order for vno faces... [] [
ok ]
  Determining KH curvatures... [] [
ok ]
Determining k1k2 curvatures... [] [
ok ]
   deltaViolations  [
208 ]

WARN:S lookup   min:  -0.238596
WARN:S explicit min:  0.00 vertex = 1525
@#@FSTIME  2020:05:28:10:22:26 mris_curvature_stats N 11 e 2.95 S 0.14 U
2.79 P 99% M 170736 F 6 R 48708 W 0 c 56 w 7 I 1104 O 7584 L 2.00 2.00 1.77
@#@FSLOADPOST 2020:05:28:10:22:29 mris_curvature_stats N 11 2.00 2.00 1.77

#-
#@# Curvature Stats rh Thu May 28 10:22:29 CEST 2020
/usr/local/freesurfer/subjects/post_006/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats
-F smoothwm post_006 rh curv sulc

 Toggling save flag on curvature files   [
ok ]
 Outputting results using filestem   [
../stats/rh.curv.stats ]
 Toggling save flag on curvature files   [
ok ]
   Setting surface [
post_006/rh.smoothwm ]
Reading surface...   [
ok ]
   Setting texture [
curv ]
Reading texture...error: No such file or
directory
error: MRISreadNewCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/post_006/surf/rh.curv

***WARNING!***
Some error has occurred while reading 'rh.curv'.
This might be due a vertex incompatibility
between the surface 'rh.smoothwm' and curv 'rh.curv'.

You might be able to correct this by re-running
'mris_make_surfaces' on this dataset.

Skipping this (and any remaining) curvature files.
Any measurements / calcuations that depend on the
curvature file will be skipped.
*

  

Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

[Marina Fernández]

External Email - Use Caution

Hi Bruce,

Yes, everything seems normal in the input files of mri_fill. We review it
slice by slice in freeview.

Do you know what could have happened?

Best regards,
Marina



--


> Hi Marina



> have you looked at the inputs to mri_fill? Does the aseg.auto_noCCseg.mgz and
> the wm.mgz look ok?
> Bruce
>
> On Wed, 27 May 2020, Marina Fernández wrote:
> External Email - Use Caution Dear Freesurfer experts, When
> I run "recon-all -autorecon2-wm -subjid post_006" I get the following
> error: ... #
> #@# Fill Tue May 26 16:13:33 CEST 2020
> /usr/local/freesurfer/subjects/post_006/mri  mri_fill -a
> ../scripts/ponscc.cut.log -xform transforms/talairach.lta
> -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting
> plane coordinates to ../scripts/ponscc.cut.log...
> INFO: Using transforms/talairach.lta and its offset for Talairach volume
> ...
> using segmentation aseg.auto_noCCseg.mgz...
> reading input volume...done.
> searching for cutting planes...voxel to talairach voxel transform
>  1.03994   0.01456   0.07738  -16.87541;
> -0.02607   1.18971   0.24142  -16.40842;
> -0.06544  -0.23822   1.03825   18.09422;
>  0.0   0.0   0.0   1.0;
> reading colortable from MGH file...
> colortable with 14176 entries read (originally
> /usr/local/freesurfer/FreeSurferColorLUT.txt)
> voxel to talairach voxel transform
>  1.03994   0.01456   0.07738  -16.87541;
> -0.02607   1.18971   0.24142  -16.40842;
> -0.06544  -0.23822   1.03825   18.09422;
>  0.0   0.0   0.0   1.0;
> reading segmented volume aseg.auto_noCCseg.mgz...
> mri_fill: could not find any points where lh and rh wm  are nbrs
> No such file or directory
> Linux sleep2014 4.13.0-45-generic #50~16.04.1-Ubuntu SMP Wed May 30
> 11:18:27
> UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s post_006 exited with
> ERRORS at Tue May 26 16:13:41 CEST 2020 To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I have seen in
> other questions that this error may be due to the CC and the
> aseg files, and it is interesting because when I load aseg.auto.mgz or
> aseg.auto_noCCseg.mgz files in Freeview, the following message in Freeview
> terminal is shown in red:
> "colortable with 14176 entries read (originally
> /usr/local/freesurfer/FreesurferColorLUT.txt)", when I think they should be
> 1475 entries. I'm using freesurfer v6.0. Could you help me to solve this
> problem?
> Thank you in advance! Marina.
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[Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

[Marina Fernández]

External Email - Use Caution

Dear Freesurfer experts,

When I run "recon-all -autorecon2-wm -subjid post_006" I get the following
error:

...

#
#@# Fill Tue May 26 16:13:33 CEST 2020
/usr/local/freesurfer/subjects/post_006/mri

 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta
-segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
 1.03994   0.01456   0.07738  -16.87541;
-0.02607   1.18971   0.24142  -16.40842;
-0.06544  -0.23822   1.03825   18.09422;
 0.0   0.0   0.0   1.0;
reading colortable from MGH file...
colortable with 14176 entries read (originally
/usr/local/freesurfer/FreeSurferColorLUT.txt)
voxel to talairach voxel transform
 1.03994   0.01456   0.07738  -16.87541;
-0.02607   1.18971   0.24142  -16.40842;
-0.06544  -0.23822   1.03825   18.09422;
 0.0   0.0   0.0   1.0;
reading segmented volume aseg.auto_noCCseg.mgz...
mri_fill: could not find any points where lh and rh wm  are nbrs
No such file or directory
Linux sleep2014 4.13.0-45-generic #50~16.04.1-Ubuntu SMP Wed May 30
11:18:27 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s post_006 exited with ERRORS at Tue May 26 16:13:41 CEST 2020

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting




I have seen in other questions that this error may be due to the CC and the
aseg files, and it is interesting because when I load aseg.auto.mgz or
aseg.auto_noCCseg.mgz files in Freeview, the following message in Freeview
terminal is shown in red:
"colortable with 14176 entries read (originally
/usr/local/freesurfer/FreesurferColorLUT.txt)", when I think they should be
1475 entries.

I'm using freesurfer v6.0.

Could you help me to solve this problem?
Thank you in advance!

Marina.
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Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

[Marina Fernández]

External Email - Use Caution

 Thank you, Doug.

That makes sense.
Do you think in this case it is a good option to add the flag --illcond to
run this analysis without getting an error? or is it better not to use the
variable apoe in these statistical analyzes?
What do you recommend us?

Best wishes,
Marina.
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Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

[Marina Fernández]

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Hi Douglas,

I email you the fsgd file and I have also sent it through FTP.

Thank you for your attention.

Best regards,
Marina.
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[Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

[Marina Fernández]

External Email - Use Caution

Dear Freesurfer experts,

I get the error that you can find at the end of this message when I am
running mri_glmfit.

Whenever I run an analysis in which the experimental design has more than
12 columns, I get the same error, whereas if the experimental design has
less than 12 columns, the analysis is successful.

I also send you the fsgd.txt file (through FTP File Exchange). In this file
you can see that there are four groups that have been created by the
combination of two discrete variables (sex and apoe-type).

How can I solve this problem?

Thank you in advance.



ERROR MESSAGE:
(...)

Saving design matrix to
/usr/local/freesurfer/subjects/amy_frapsaliva_stats/stats/cortex/cortex_caseageeducfrap/pruebax_frapsalgroup_NEG/lh.fsgd_subj_gauss001/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1e+08
Design matrix --
 0.0   1.0   0.0   0.0   0.0   0.83619   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.79984
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700   0.0
0.0   0.0  -0.73337   0.0   0.0   0.0  -0.84287
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.74935   0.0
0.0   0.0   0.91963   0.0   0.0   0.0  -0.82284
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.45403   0.0   0.0
0.0  -0.32012   0.0   0.0   0.0   0.17882   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.57318   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.33908
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0   1.71704
0.0   0.0   0.0   0.09313   0.0   0.0   0.0
 -0.02652   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.66002   0.0   0.0   0.0  -0.11350   0.0   0.0
0.0   0.46929;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.48385   0.0   0.0   0.0  -0.94000   0.0   0.0
0.0   1.23055;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.83619   0.0   0.0   0.0  -2.38637   0.0   0.0
0.0  -0.90297;
 0.0   1.0   0.0   0.0   0.0  -0.04466   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.28399
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.48385   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.86996
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
1.18853   0.0   0.0   0.0   0.91963   0.0   0.0
0.0   0.18883;
 0.0   1.0   0.0   0.0   0.0  -2.15871   0.0
0.0   0.0  -0.94000   0.0   0.0   0.0   1.53105
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.98254   0.0   0.0
0.0   0.50638   0.0   0.0   0.0   0.73974   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -1.45403   0.0
0.0   0.0   0.50638   0.0   0.0   0.0   0.23391
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.13151   0.0
0.0   0.0   0.91963   0.0   0.0   0.0  -0.91298
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
 -1.63020   0.0   0.0   0.0   0.09313   0.0   0.0
0.0   0.78982;
 0.0   1.0   0.0   0.0   0.0   0.66002   0.0
0.0   0.0  -1.55987   0.0   0.0   0.0  -0.15173
0.0   0.0;
 1.0   0.0   0.0   0.0   1.54087   0.0   0.0
0.0  -0.32012   0.0   0.0   0.0   1.28564   0.0
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0   0.30768
0.0   0.0   0.0  -0.94000   0.0   0.0   0.0
 -0.76775   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
1.71704   0.0   0.0   0.0   0.50638   0.0   0.0
0.0   1.41085;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.48385   0.0   0.0   0.0  -0.52675   0.0   0.0
0.0   0.73974;
 1.0   0.0   0.0   0.0  -0.92552   0.0   0.0
0.0   1.53950   0.0   0.0   0.0  -0.76274   0.0
0.0   0.0;
 1.0   0.0   0.0   0.0   0.66002   0.0   0.0
0.0   0.91963   0.0   0.0   0.0  -0.50731   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700   0.0
0.0   0.0  -0.94000   0.0   0.0   0.0  -0.93803
0.0   0.0;
 1.0   0.0   0.0   0.0  -0.04466   0.0   0.0
0.0   0.29975   0.0   0.0   0.0  -1.07325   0.0
0.0   0.0;
 0.0   1.0   

[Freesurfer] mri_glmfit error

[Marina Fernández]

External Email - Use Caution

 Dear Freesurfer experts,

I get the error that you can find at the end of this message when I am
running mri_glmfit.

Whenever I run an analysis in which the experimental design has more than
12 columns, I get the same error, whereas if the experimental design has
less than 12 columns, the analysis is successful.

I also send you the fsgd.txt file (through FTP File Exchange). In this file
you can see that there are four groups that have been created by the
combination of two discrete variables (sex and apoe-type).

How can I solve this problem?

Thank you in advance.



ERROR MESSAGE:
(...)

Saving design matrix to
/usr/local/freesurfer/subjects/amy_frapsaliva_stats/stats/cortex/cortex_caseageeducfrap/pruebax_frapsalgroup_NEG/lh.fsgd_subj_gauss001/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1e+08
Design matrix --
 0.0   1.0   0.0   0.0   0.0   0.83619   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.79984
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700   0.0
0.0   0.0  -0.73337   0.0   0.0   0.0  -0.84287
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.74935   0.0
0.0   0.0   0.91963   0.0   0.0   0.0  -0.82284
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.45403   0.0   0.0
0.0  -0.32012   0.0   0.0   0.0   0.17882   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.57318   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.33908
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0   1.71704
0.0   0.0   0.0   0.09313   0.0   0.0   0.0
 -0.02652   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.66002   0.0   0.0   0.0  -0.11350   0.0   0.0
0.0   0.46929;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.48385   0.0   0.0   0.0  -0.94000   0.0   0.0
0.0   1.23055;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.83619   0.0   0.0   0.0  -2.38637   0.0   0.0
0.0  -0.90297;
 0.0   1.0   0.0   0.0   0.0  -0.04466   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.28399
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.48385   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.86996
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
1.18853   0.0   0.0   0.0   0.91963   0.0   0.0
0.0   0.18883;
 0.0   1.0   0.0   0.0   0.0  -2.15871   0.0
0.0   0.0  -0.94000   0.0   0.0   0.0   1.53105
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.98254   0.0   0.0
0.0   0.50638   0.0   0.0   0.0   0.73974   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -1.45403   0.0
0.0   0.0   0.50638   0.0   0.0   0.0   0.23391
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.13151   0.0
0.0   0.0   0.91963   0.0   0.0   0.0  -0.91298
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
 -1.63020   0.0   0.0   0.0   0.09313   0.0   0.0
0.0   0.78982;
 0.0   1.0   0.0   0.0   0.0   0.66002   0.0
0.0   0.0  -1.55987   0.0   0.0   0.0  -0.15173
0.0   0.0;
 1.0   0.0   0.0   0.0   1.54087   0.0   0.0
0.0  -0.32012   0.0   0.0   0.0   1.28564   0.0
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0   0.30768
0.0   0.0   0.0  -0.94000   0.0   0.0   0.0
 -0.76775   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
1.71704   0.0   0.0   0.0   0.50638   0.0   0.0
0.0   1.41085;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.48385   0.0   0.0   0.0  -0.52675   0.0   0.0
0.0   0.73974;
 1.0   0.0   0.0   0.0  -0.92552   0.0   0.0
0.0   1.53950   0.0   0.0   0.0  -0.76274   0.0
0.0   0.0;
 1.0   0.0   0.0   0.0   0.66002   0.0   0.0
0.0   0.91963   0.0   0.0   0.0  -0.50731   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700   0.0
0.0   0.0  -0.94000   0.0   0.0   0.0  -0.93803
0.0   0.0;
 1.0   0.0   0.0   0.0  -0.04466   0.0   0.0
0.0   0.29975   0.0   0.0   0.0  -1.07325   0.0
0.0   0.0;
 0.0   1.0   

Re: [Freesurfer] convert MNI152 coordinates into vertex index

[Marina Fernández]

External Email - Use Caution

Thank you for the information, Bruce and Thomas!

Thomas, I think this utility is perfect! I tried it with fsaverage subject
without problems.
 Do you think I can use this function to calculate the vertex of the
fsaverage5 (instead of the fsaverage)?

Really, thank you very much, this help is very useful for us!
Best regards,
Marina
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Re: [Freesurfer] convert MNI152 coordinates into vertex index

[Marina Fernández]

External Email - Use Caution

Hi Bruce,

Thank you very much for the information. It is very useful. I'm taking a
look at both possibilities.

Regarding the second option you gave me:

you can just run through the list of vertices and find the one that is
> closest to your MNI coord



What file should I use to find the coordinates correspondence? Should I use
[l/r].pial? Or maybe  [l/r].orig?

Do you think it is a good idea to load that file in matlab and look for the
closest coordinates there, and see what vertex index those coordinates
correspond to?

Thank you in advance.

Best wishes,
Marina
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[Freesurfer] convert MNI152 coordinates into vertex index

[Marina Fernández]

External Email - Use Caution

Dear Freesurfer experts,

I would like to convert the x, y, z MNI152 coordinates into the vertex
index of the fsaverage5.

I would like to do it with a function that can give me the vertex index as
output, because I would like to use this information in a matlab script
that continues with more calculations.

Is there any function that can give me the vertex index (which corresponds
to certain coordinates) as output?

Thank you very much for your attention.

Best wishes,
Marina
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[Freesurfer] convert gii to mgh/nii.gz (freesurfer surface)

[Marina Fernández]

External Email - Use Caution

Hi experts,

How can I convert a surface in .gii format to a surface in .mgh or nii.gz
format?

I tried with mris_convert but it doesn't work.


Best regards,
Marina
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[Freesurfer] vertex number to MNI coordinates

[Marina Fernández]

External Email - Use Caution

Dear Freesurfer experts,

I hope you can help me with the following questions:

1. What is the best way to know the MNI coordinates to which a vertex of a
surface corresponds?

2. I have projected the surfaces of the subjects onto the average subject
from this dataset.
Can I know the MNI coordinates corresponding to a vertex of the average
subject of my dataset?
Or do I need to project it onto the fsaverage to know the correspondence to
de MNI space?

3. I know that the average surface is constructed by computing the MNI305
coordinate at each vertex,
But how can I obtain the MNI152 coordinates (instead of MNI305) to which a
vertex corresponds? (if it is possible).


Thank you very much in advance.

Best regards,
Marina
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Re: [Freesurfer] sphere.reg file

[Marina Fernández]

External Email - Use Caution

These are the previous emails:



1 » » » » » » » » » » » »



Dear freesurfer experts,


I run the following commands to perform analysis with projected
surfaces on my average subject:


make_average_subject --out my_avg_subject --fsgd  fsgd.txt


surfreg --s s_001 --t  my_avg_subject --o my_avg_subject.sphere.reg


mris_preproc --fsgd nfsgd.txt --target my_avg_subject --meas thickness
--srcfmt curv --hemi [l/r]h --out  [l/r]h.fsgd.mgh


Theoretically, the mri_preproc function will automatically use the
my_avg_subject.sphere.reg file because I specify my_avg_subject as the
target subject. The problem is that in the output that comes out in
the terminal while this function is running, it is specified that the
file [l/r]h.sphere.reg is selected instead of
[l/r]h.my_avg_subject.sphere.reg.


Additionally, I did a test specifying the flag "--surfreg
my_avg_subject.sphere.reg" in mris_preproc and the values of the
output surface are different from the output that I have when I don't
specify the flag --surfreg in mris_preproc (so, If I don't specify it,
I think that definitely the function doesn't automatically use the
file generated in surfreg, I think the default sphere.reg is used).


What should I do? Is it better to specify the “--surfreg
my_avg_subject.sphere.reg” flag in the mris_preproc function?


Thanks in advance.
Best regards,
Marina.




2 » » » » » » » » » » » »


what version of freesurfer are you running?



3 » » » » » » » » » » » »


We are using Freesurfer v6.0



4 » » » » » » » » » » » »


can you include the previous emails?






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Re: [Freesurfer] sphere.reg file

[Marina Fernández]

External Email - Use Caution

We are using Freesurfer v6.0
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[Freesurfer] sphere.reg file

[Marina Fernández]

External Email - Use Caution

Dear freesurfer experts,


I run the following commands to perform analysis with projected
surfaces on my average subject:


make_average_subject --out my_avg_subject --fsgd  fsgd.txt


surfreg --s s_001 --t  my_avg_subject --o my_avg_subject.sphere.reg


mris_preproc --fsgd nfsgd.txt --target my_avg_subject --meas thickness
--srcfmt curv --hemi [l/r]h --out  [l/r]h.fsgd.mgh


Theoretically, the mri_preproc function will automatically use the
my_avg_subject.sphere.reg file because I specify my_avg_subject as the
target subject. The problem is that in the output that comes out in
the terminal while this function is running, it is specified that the
file [l/r]h.sphere.reg is selected instead of
[l/r]h.my_avg_subject.sphere.reg.


Additionally, I did a test specifying the flag "--surfreg
my_avg_subject.sphere.reg" in mris_preproc and the values of the
output surface are different from the output that I have when I don't
specify the flag --surfreg in mris_preproc (so, If I don't specify it,
I think that definitely the function doesn't automatically use the
file generated in surfreg, I think the default sphere.reg is used).


What should I do? Is it better to specify the “--surfreg
my_avg_subject.sphere.reg” flag in the mris_preproc function?


Thanks in advance.

Best regards,

Marina.
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[Freesurfer] Segmentation problem

[Marina Fernández]

External Email - Use Caution

Dear Freesurfeer experts,


After running the recon-all, a part of the temporal lobe of one subject was
removed.

I used the watershed algorithm to be less agressive in the skull stripping
step:

recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001

And the problem was solved in the brainmask.mgz volume because I can see
the temporal lobe completely, but the surfaces are still displaced. In
order to correct the surfaces I used the white matter edit tool but there
is no change after correcting WM and running the recon-all -autorecon2-wm
-autorecon3. I also used control points and but the following error was
shown in the terminal when I run the recon-all -autorecon2-cp -autorecon3:

recon-all -s sub_001 existed with errors

I detected that there are very high values in the white matter of this part
of the temporal lobe (even 132), maybe it has something to do. What can I
do to solve the problem with this subject?


Thank you very much in advance.

Best regards,

Marina.
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[Freesurfer] skull stripping problem

[Marina Fernández]

External Email - Use Caution

Dear Freesurfeer experts,

After running the recon-all, a part of the temporal lobe of one subject was
removed.

I used the watershed algorithm to be less agressive in the skull stripping
step:

recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001

And the problem was solved in the brainmask.mgz volume because I can see
the temporal lobe completely, but the surfaces are still displaced. In
order to correct the surfaces I used the white matter edit tool but there
is no change after correcting WM and running the recon-all -autorecon2-wm
-autorecon3. I also used control points and but the following error was
shown in the terminal when I run the recon-all -autorecon2-cp -autorecon3:

recon-all -s sub_001 existed with errors

I detected that there are very high values in the white matter of this part
of the temporal lobe (even 132), maybe it has something to do. What can I
do to solve the problem with this subject?


Thank you very much in advance.

Best regards,

Marina.
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Re: [Freesurfer] surfreg function

[Marina Fernández]

External Email - Use Caution

Hi Doug,

Thank you for your replay.

I understood that if I did not specify "--surfreg
my_avg_subject.sphere.reg"  mri_preproc was going to use the original file (
sphere.reg), because in the help of mri_preproc it mentions this:

--surfreg SurfReg : default is sphere.reg

With this in mind,  do you think it would not  be necessary to specify it
in mris_preproc?

What is the difference between sphere.reg and  my_avg_subject.sphere.reg?

Best wishes,
Marina
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[Freesurfer] nopvc.nii.gz

[Marina Fernández]

External Email - Use Caution

Dear Freesurfer experts,

I have compared the PVC uptake values of gtm.stats with the values of
gtm.nii.gz (that I loaded with the function load_nii in matlab). I realized
that the values in matlab are transposed, i. e., the first value in
gtm.stats is the same that the last value in gtm.nii.gz and the same with
the rest of the values.

I couldn't find a way to check if the values are also in a transposed order
in nopvc.nii.gz if I load it with load_nii in matlab. Could you tell me a
method to verify it or confirm me that?

Thanks again!
Marina.
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[Freesurfer] surfreg function

[Marina Fernández]

External Email - Use Caution

Hi experts,
I am running the following command to create de average subjecto with
Freesurfer v6.0:
 make_average_subject --out my_avg_subject --fsgd  fsgd.txt
Then, I want to do surface analysis with the thickness of each subject
projected onto my_avg_subject. I would like to know if it is correct
to run these commands  before that statistical analysis:
 surfreg --s s_001 --t  my_avg_subject --o
my_avg_subject.sphere.reg
 mris_preproc --fsgd nfsgd.txt --target my_avg_subject
--surfreg my_avg_subject.sphere.reg --meas thickness --srcfmt curv
--hemi [l/r]h --out  [l/r]h.fsgd.mgh
Finally, I would use "[l/r]h.fsgd.mgh" file to do the thickness
surface analysis.
Is it correct? Should I run surfreg and use the output in
mris_preproc?What is the advantage?
Thank you very much!Marina-
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Re: [Freesurfer] Volume to 5th order icosahedron tesselation Surface (with PET images)

[Marina Fernández]

External Email - Use Caution

Hi Doug,

We thought it would be better to use 5th order icosahedron tesselation for
PET because the resolution of the volume is lower: If, for thickness
analysis, we carry the structural volumes with a resolution of 1x1x1 to
ico7 on the surface, with PET-volumes or connectivity maps (resolution of
2x2x2 or 3x3x3) we thought it would be more appropriate to use ico5 on the
surface because in the surface transformation the interpolation of the data
is lower.
In addition the number of statistical comparisons is greatly reduced.


Regards,
Marina.

Marina.

>


Hi experts,

This is a question related to PetSurfer steps.

I would like to know if it is correct to sample the mgx volume onto the
surface of the average subject of my dataset (created with 5th order
icosahedron tesselation) instead of the fsaverage (created with 7th order
icosahedron tesselation) or if there is any problem in the next steps
following this procedure.
We would like to do that because the volume PET resolution is more
proportional to this number of vertex (10242). Do you think it is correct?

Best wishes,
Marina.


>

You could do it, but  I would just use fsaverage. I don't understand
what the relationship would be between the number of vertices on the
surface and the number of voxels in the PET volume or the rational for
using the 5th order ico
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[Freesurfer] Volume to 5th order icosahedron tesselation Surface (with PET images)

[Marina Fernández]

External Email - Use Caution

Hi experts,

This is a question related to PetSurfer steps.

I would like to know if it is correct to sample the mgx volume onto the
surface of the average subject of my dataset (created with 5th order
icosahedron tesselation) instead of the fsaverage (created with 7th order
icosahedron tesselation) or if there is any problem in the next steps
following this procedure.
We would like to do that because the volume PET resolution is more
proportional to this number of vertex (10242). Do you think it is correct?

Best wishes,
Marina.
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Re: [Freesurfer] Problem with registration (PetSurfer)

[Marina Fernández]

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Doug, the full terminal output from the terminal after running tkregisterfv was:


freeview -transform-volume -viewport cor -v
/usr/local/freesurfer/subjects/s_001/mri/orig.mgz:visible=0:name=orig.mgz(targ)
/home/sleep2014/0_Analisis_Marina/PET/s_001_PET.nii:name=s_001_PET.nii(mov):reg=/home/sleep2014/0_Analisis_Marina/PET/s_001.reg.lta
--surface
/usr/local/freesurfer/subjects/s_001/surf/lh.white:edgecolor=yellow
--surface
/usr/local/freesurfer/subjects/s_001/surf/rh.white:edgecolor=yellow

Warning: Transformation can only apply to volumes for now. If your data
includes ROI/Surface/Way Points, please do not use this feature yet.
MatrixAsciiReadFrom: could not scanf parms

Source temporarily unavailable

LTAchangeType: src geometry must be valid

Source temporarily unavailable
terminate called after throwing an instance of 'int'
Abort


Thanks for your attention.
Marina.
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Re: [Freesurfer] Problem with registration (PetSurfer)

[Marina Fernández]

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The error was shown after running tkregisterfv.



Marina.
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[Freesurfer] Problem with registration (PetSurfer)

[Marina Fernández]

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Dear experts,
I am following  PetSurfer steps
(https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer).
Something was wrong using mri_coreg function  because when  I checked
the registration with tkregisterfv this error was shown in the
terminal:

*Warning: Transformation can only apply to volumes for now. If your data
includes ROI/Surface/Way Points, please do not use this feature yet.*

*MatrixAsciiReadFrom: could not scanf parms*

*Source temporarily unavailable*

*LTAchangeType: src geometry must be valid*


Can you help me?
*I use these commands:*

dcm2niix s_001_PET_dicom (to convert dicom PET files to nii)gtmseg --s
s_001mri_coreg --s s_001 --mov s_001_PET.nii --reg
s_001.reg.ltatkregisterfv --mov s_001_PET.nii --reg s_001.reg.lta
–surfs
And it happens with all the subjects.
Thank you in advance.Best regards,Marina.
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Re: [Freesurfer] Oval shape in average subject inflated

[Marina Fernández]

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It works! Thank you very much Bruce!
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Re: [Freesurfer] Oval shape in average subject inflated

[Marina Fernández]

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Is there something wrong?

> Dear Freesurfer team,
>
> I created the FS average subject of the same dataset with 5th and 6th
order icosahedron tesselation using the following commands:
> make_average_subject --fsgd fsgd.txt --ico 5 --out avg_subject_ico5
> make_average_subject --fsgd fsgd.txt --ico 6 --out avg_subject_ico6
>
> When I load the inflated surface of the avg_subject_ico5 with tksurfer ,
it has a oval shape while > when I load the avg_subject_ico6 it seems to be
a normal shape.
> Please, see attached image.
>
> Thank you in advance.
 >
> Best wishes,
> Marina.
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Re: [Freesurfer] average subject with 5th order icosahedron tesselation

[Marina Fernández]

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That's it! Thank you Doug!

Best wishes,
Marina.
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[Freesurfer] average subject with 5th order icosahedron tesselation

[Marina Fernández]

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Dear Freesurfer experts,

Now, I would like to downsample the average subject of a dataset (that is a
7th order icosahedron tesselation) to have surfaces with 10242 vertices (5th
order icosahedron tesselation).

How can I do that?

Thank you in advance.

Best regards,
Marina.
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Re: [Freesurfer] Projection on fsaverage5

[Marina Fernández]

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Hi Doug,


Thank you for your advice. I checked the results using ico 5 and
fsaverage5 and it seems to have  exactly the same values, but we are
going to use --trgsubject fsaverage5, as you told me.


On the other hand if we use EPI that it is coregistered to the T1 of
Freesurfer there is no problem with the projection on fsaverage5.

Thank you very much!


Cheers,

Marina
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[Freesurfer] Projection on fsaverage5

[Marina Fernández]

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Hi Bruce,

Thanks for the quick response.

I found that the problem was the input. If I use the EPI that it is
coregistered to the T1 of Freesurfer instead of the EPI that it is also
normalized to the MNI space, it works and I can project the surface (that I
created with the command that I sent you) on fsaverage 5.

Could you confirm that the command has no errors?

mri_vol2surf --mov EPI.nii --reg register.dat --hemi [l/r]h --projfrac
0.5 --interp trilinear --trgsubject ico --icoorder 5 --o
EPI_surface.mgh


Best wishes,
Marina
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[Freesurfer] Projection on fsaverage5

[Marina Fernández]

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Dear Freesurfer experts,

I would like to convert the individual preprocessed EPI volume (that it is
normalized to MNI152 space and without smoothing) to surface and project it
on fsaverage5.  I used the following command:
mri_vol2surf --mov EPI.nii --reg register.dat --hemi [l/r]h --projfrac 0.5
--interp trilinear --trgsubject ico --icoorder 5 --o EPI_surface.mgh

Is it correct? Then, I tried to project the surface in fsaverage5 and it
seems to be rotated (it doesn't match).
What should I do to project it correctly?

Thank you in advance.
Best regards,
Marina.
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[Freesurfer] Fill holes in BOLD surface

[Marina Fernández]

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Hi Freesurfer experts,

I have projected 4D-preprocessed BOLD data to Freesurfer cortical surfaces.
Resulting individual surfaces have many holes (see attached image) that I
would like to fill with nearest neighbors values around each hole (avoiding
the medial wall). Could you indicate me how to do this?

Thank you in advance.

Marina
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Re: [Freesurfer] Conversion fMRI volumes to surface

[Marina Fernández]

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Thanks Doug.

I created the surface with the command line that I sent you (mri_vol2surf
...) and then, I run that command that you sent me (tkregisterfv...) but I
have the following error when freeview is trying to load the file: 'Failed
to load  MRI  /.../4d_inputBOLD.nii'.

I discard that the problem is not with the EPI file because when I load
only the 4d_inputBOLD.nii there is no problem. I guess that the problem is
the register.dat.

What do you think I should do?

Best regards,
Marina.
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[Freesurfer] Transform LIA orientation to RAS

[Marina Fernández]

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Dear Freesurfer experts,

How can I transform an EPI-surface with LIA orientation to RAS orientation?

Thank you in advance.

Best regards,
Marina.
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Re: [Freesurfer] Conversion fMRI volumes to surface

[Marina Fernández]

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Thank you Doug/Bruce.

We would like to project our AFNI preprocessed EPI scans (T1-registration,
motion correction, linear regression, but unsmoothed) to Freesurfer
cortical surfaces in order to obtain one file containing 250 (number of
dynamics) EPI-cortical surfaces in the native space. For this, we are using
the following command:

mri_vol2surf --mov '4d_inputBOLD.nii' --reg 'register.dat' --hemi '[l/r]h'
--projfrac 0.5 --interp nearest --o 'output.nii'

Is that correct?

As our EPI scans were previously registered with AFNI to T1 (that it is in
FS space), I guess that bbregister is not required, right?

Thank you in advance.

Best wishes,

Marina.
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[Freesurfer] Conversion fMRI volumes to surface

[Marina Fernández]

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Dear experts,

I’ve done the fMRI preprocessing and now I would like to convert each file
(that contains 250 volumes) to surface.

Is it correct to use the function mri_vol2surf? Should I use any specific
flag because they are 4D files? What is the best way to transform the
volumes to surface?

Thank you in advance.



Best regards,

Marina.
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[Freesurfer] Problem with the segmentation of subregions

[Marina Fernández]

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Hi experts,

We are doing the segmentation of the subfields of the hippocampal and
amygdala subfields, brainstem subestructures and thalamic nuclei. When we
used segmentHA_T1.sh and segmentThalamicNuclei.sh, 'Command not found'
appears.

On the other hand, we used segmentBS.sh and we got the following message:
'Software requires 4 arguments:
segmentSFnewT1.sh matlabRuntimeDirectory FShomeDirectory subjectName
subjectDir'.
But, when we typed 'segmentSFnewT1.sh'  we got  'Command not found' again.


Note:  We have FS v6.0 and the runtime Matlab 2014b.

Best wishes,
Marina
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[Freesurfer] (no subject)

[Marina Fernández]

External Email - Use Caution

Hi experts,

We are doing the segmentation of the subfields of the hippocampal and
amygdala subfields, brainstem subestructures and thalamic nuclei. When we
used segmentHA_T1.sh and segmentThalamicNuclei.sh, 'Command not found'
appears.

On the other hand, we used segmentBS.sh and we got the following message:
'Software requires 4 arguments:
segmentSFnewT1.sh matlabRuntimeDirectory FShomeDirectory subjectName
subjectDir'.
But, when we typed 'segmentSFnewT1.sh'  we got  'Command not found' again.


Note:  We have FS v6.0 and the runtime Matlab 2014b.

best wishes,
Marina
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Re: [Freesurfer] ERROR gtmseg

[Marina Fernández]

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Dear Douglas,

Did you get the subjects? I hope I loaded them correctly.

Best regards,
Marina.
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Re: [Freesurfer] ERROR gtmseg

[Marina Fernández]

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Dear Douglas,

I put the subjects yesterday. They are: qsm_04_yr3 (it is the first subject
with problems and we have another copy that is solved) and mci13_hsp (it is
the new subject with problems).

Thank you very much for your attention.
Marina.
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Re: [Freesurfer] ERROR gtmseg

[Marina Fernández]

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Dear Douglas,



Thank you very much for the help. We could solve the problem with that
subject but now we have a similar problem with another subject. In the
previous case, we have only one problematic voxel in the skull, but now the
label 75 (it shouldn't exist either) is taking a lot of voxels in the
ventricles and the caudate. So, I think that we should use other solution
to fix it.



I know that this issue is weird. We use gtmseg command with more or less
500 subjects and we only have this type of problem with two subjects.



Best regards,

Marina.



 > Probably the easiest thing is just to edit that voxel  to be one of the
neighboring

 > segments. First, load the aseg and find that voxel. See which segment(s)
are around

 > that voxel and get the segmentation id. Then run
 > mri_binarize --replaceonly 229 YourNewSegID --i aparc+aseg.mgz --o

 > aparc+aseg.mgz

 >  then re-run gtmseg
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Re: [Freesurfer] ERROR gtmseg

[Marina Fernández]

External Email - Use Caution

Dear Douglas,

Thank you very much for the help. We could solve the problem with that
subject but now we have a similar problem with another subject. In the
previous case, we have only one problematic voxel in the skull, but now the
label 75 (it shouldn't exist either) is taking a lot of voxels in the
ventricles and the caudate. So, I think that we should use other solution
to fix it.

I know that this issue is weird. We use gtmseg command with more or less
500 subjects and we only have this type of problem with two subjects.

Best regards,
Marina.

 > Probably the easiest thing is just to edit that voxel  to be one of the
neighboring
 > segments. First, load the aseg and find that voxel. See which segment(s)
are around
 > that voxel and get the segmentation id. Then run
 > mri_binarize --replaceonly 229 YourNewSegID --i aparc+aseg.mgz --o
 > aparc+aseg.mgz
 >  then re-run gtmseg
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Re: [Freesurfer] ERROR gtmseg

[Marina Fernández]

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I run the command that you told me (mri_binarize --i aseg.presurf.mgz
--match 229 --o bin229.mgz) and I get a mask with one voxel.

How can I do to solve it?

Thank you.

Marina.

El lun., 7 oct. 2019 a las 23:19, Greve, Douglas N.,Ph.D. (<
dgr...@mgh.harvard.edu>) escribió:

> We'll have to figure out where those 229s are coming from. Try this
> mri_binarize --i aseg.presurf.mgz --match 229 --o bin229.mgz
> It should print out whether there were any voxels that matched. If so, you
> can load bin229.mgz with the norm.mgz and the aseg.presurf.mgz and see
> where they are. If there are not any, then do the same thing with
> aparc+aseg.mgz
>
> On 10/7/2019 4:54 PM, Marina Fernández wrote:
>
> External Email - Use Caution
> Dear Douglas,
>
> Sorry! This is the previous information:
>
>
> > Dear Douglas,
> >
> > Thank you for the replay.
> >
> > I think so, I can't find the code 229 in any subject.
> >
> > I can't see anything strange in the aparc+aseg.mgz. The cerebral voxels
> have the normal > > segmentation and labels. Could it be a problem with the
> extracerebral voxels?
> >
> > Best regards,
> > Marina.
>
>
>  > That is kind of weird. It says it has found a segmentation with number
> > 229, but we don't have that code in our system. Can you find the 229
> voxels
> > in the aparc+aseg.mgz?
>
>
>
> > Dear experts,
> >
> > The following error occurs with one subject when I am running gtmseg
> > command:
> >
> > Computing colortable
> > ERROR: cannot find match for subcortical segid 229
> > ERROR: mri_gtmseg -s qsm_04_year3 --usf 2 --o gtmseg.mgz --apas
> > apas+head.mgz --no-subseg-wm --no-keep-cc --no-keep-hypo
> > gtmseg existed with errors
> > ans=1
> >
> > Do you know what happened with this subject? What can I do to solve it?
> >
> > Thank you very much in advance.
> > Marina.
>
>
> The information in this e-mail is intended only for the person to whom it
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> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] ERROR gtmseg

[Marina Fernández]

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Dear Douglas,

Sorry! This is the previous information:


> Dear Douglas,
>
> Thank you for the replay.
>
> I think so, I can't find the code 229 in any subject.
>
> I can't see anything strange in the aparc+aseg.mgz. The cerebral voxels
have the normal > > segmentation and labels. Could it be a problem with the
extracerebral voxels?
>
> Best regards,
> Marina.


 > That is kind of weird. It says it has found a segmentation with number
> 229, but we don't have that code in our system. Can you find the 229
voxels
> in the aparc+aseg.mgz?



> Dear experts,
>
> The following error occurs with one subject when I am running gtmseg
> command:
>
> Computing colortable
> ERROR: cannot find match for subcortical segid 229
> ERROR: mri_gtmseg -s qsm_04_year3 --usf 2 --o gtmseg.mgz --apas
> apas+head.mgz --no-subseg-wm --no-keep-cc --no-keep-hypo
> gtmseg existed with errors
> ans=1
>
> Do you know what happened with this subject? What can I do to solve it?
>
> Thank you very much in advance.
> Marina.
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Re: [Freesurfer] ERROR gtmseg

[Marina Fernández]

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Dear Douglas,

Thank you for the replay.

I think so, I can't find the code 229 in any subject.

I can't see anything strange in the aparc+aseg.mgz. The cerebral voxels
have the normal segmentation and labels. Could it be a problem with the
extracerebral voxels?

Best regards,
Marina.
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[Freesurfer] ERROR gtmseg

[Marina Fernández]

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Dear experts,

The following error occurs with one subject when I am running gtmseg
command:

*Computing colortable*
*ERROR: cannot find match for subcortical segid 229*
*ERROR: mri_gtmseg -s qsm_04_year3 --usf 2 --o gtmseg.mgz --apas
apas+head.mgz --no-subseg-wm --no-keep-cc --no-keep-hypo*
*gtmseg existed with errors*
*ans=1*

Do you know what happened with this subject? What can I do to solve it?

Thank you very much in advance.
Marina.
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[Freesurfer] Create no-skull brain with gray matter mask

[Marina Fernández]

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Dear experts,

I need to get a no-skull brain. The automated no-skull brain has many
errors and I was thinking that I could create it taking into account the
gray matter mask (we segment manually, so the mask is accurate) in such a
way that everything outside the gray matter mask is eliminated and
everything inside is maintained.

Do you know how can I create it?

Any idea will be welcome. Thank you very much.

Best regards,

Marina.
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[Freesurfer] CSF MASK

[Marina Fernández]

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Dear Freesurfer experts,

Is there any way to obtain a CSF mask in Freesurfer similar to that
obtained with the SPM segmentation (see attached)?

Thank you in advance.

Best regards,
Marina.
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[Freesurfer] CSF MASK

[Marina Fernández]

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Dear Freesurfer experts,

Is there any way to obtain a CSF mask in Freesurfer similar to that
obtained with the SPM segmentation (see attached)?

Thank you in advance.

Best regards,
Marina.
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[Freesurfer] CSF mask

[Marina Fernández]

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Dear Freesurfer experts,

Is there any way to obtain a CSF mask in Freesurfer similar to that
obtained with the SPM segmentation (see attached)?

Thank you in advance.

Best regards,
Marina.
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[Freesurfer] Maximum vertex value

[Marina Fernández]

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Dear Freesurfer Team,

How can I get the maximum vertex value for each subject in a particular
cluster?

Thank you very much.

Marina.
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