Re: [Freesurfer] Permission denied error from -localGI

[Douglas N. Greve]

Can you just try it with 7.2? We had some problems at one point with 
temporary files in lGI that were fixed with 7.2


On 4/27/2022 9:36 AM, Billah, Tashrif wrote:

Sorry about missing your earlier question--our FreeSurfer is 7.1.0

We still need your help with this issue.

Thank you,
Tashrif



     Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700

===


What version of FS are you running?

On 3/20/2022 8:47 PM, Billah, Tashrif wrote:

    It does not exist and cannot be created in a shared cluster.
Is there a way to define a different folder for
/scratch/tp24093955057547375.load_mgh.m.mgh?



    ===
    Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800

    Do you have permission to /scratch? Does it exist?

    ===
    Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800

    Hi all,

    We are trying to run recon-all with -localGI but running into an 
unknown

    permission denied error:

    $ recon-all -s sub-1001 -localGI

    ```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
     exit
    =


    < M A T L A B (R) >
    Copyright 1984-2017 The MathWorks, Inc.
    R2017a (9.2.0.556344) 64-bit (glnxa64)
    March 27, 2017


    >> reading filled volume...
    /bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission 
denied



    ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh 
for reading


    ERROR: loading
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
     as MGH
    Struct contents reference from a non-struct array object.


    Error in make_outer_surface (line 25)
    volume=vol.vol;

    >>
    ERROR: make_outer_surface did not create output file
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


    recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 
2022


    ```

    Our MATLAB environment is properly setup and we regularly run other
    FreeSurfer-MATLAB commands. So I do not think that is causing the 
issue.


    Best,
    Tashrif

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Beta values (resubmitting)

[Douglas N. Greve]

oh, yes, that is correct for DOSS

On 4/26/2022 3:38 PM, Laura Willers de Souza wrote:


External Email - Use Caution

Ok.
In this case I used the DOSS model (I tested the interaction before 
and it was not significant). So wouldn't the two groups have the same 
slope?

But the beta values extraction file has only 3 lines (image below).


To extract the beta values I used this command:
mri_segstats --seg 
lh.CU_CI_CSF_doss.glmdir/cortisol.diff/perm.th20.neg.sig.ocn.mgh --i 
lh.CU_CI_CSF_doss.glmdir/beta.mgh --excludeid 0 --avgwf 
lh.CU_CI_CSF.cortisol.beta.clusters.dat


Thank you so much,
Laura.


*De:* Douglas N. Greve 
*Enviado:* terça-feira, 26 de abril de 2022 15:01
*Para:* Laura Willers de Souza 
*Cc:* freesurfer@nmr.mgh.harvard.edu 
*Assunto:* Re: [Freesurfer] Beta values (resubmitting)
3rd line for the slope of CU, 4th line for the slope of CI

On 4/25/2022 4:03 PM, Laura Willers de Souza wrote:


External Email - Use Caution

Thanks so much!

I would also like to confirm that I am interpreting the beta values 
correctly for a second model.


Model 2: Two Groups, One Covariate

Contrasts (DOSS): difference between the group intercepts; covariate 
effect.


The fsgd file looks like this:

GroupDescriptorFile 1

Title CU_CI_CSF
MeasurementName thickness
Class CU
Class CI
Variables cortisolCSF
Input 011_S_0003_S9128 CI 2.397895273
Input 022_S_0004_S9233 CI 2.772588722
Input 011_S_0005_S9137 CU 3.044522438
Input 011_S_0008_S9196 CU 2.397895273
Input 011_S_0010_S8800 CI 2.151762203

... (n=300)


The file with the beta values contains 3 lines (image below).

  * The first line would be the beta value for the intercept of the
1st group; the second line for the intercept of the 2nd group;
and the third line for the slope of the covariate?
  o Thus the glm equation for the 1st cluster would be:
  o 1st group  cortical thickness = 2.64 - 0.12X + n
  o 2nd group --- cortical thickness = 2.54 – 0.12X + n

Am I interpreting correctly?

Thank you very much for all the help!
*Laura Willers de Souza *

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil




The information in this e-mail is intended only for the person to whom 
it is addressed.  If you believe this e-mail was sent to you in error 
and the e-mail contains patient information, please contact the Mass 
General Brigham Compliance HelpLine at 
https://www.massgeneralbrigham.org/complianceline 
<https://secure-web.cisco.com/1HECg2TtyynrqtUVDjlhNbLxCHvklSBvD73oUyYtH8qcRQ_iEq5gYPwF209ksvTxnH5NqVOW61pbHnwM1hDdwldCxNscWQ64xBzQSRiG8euXkcK4LiWXF-Le06A27SXJJigyUnfnU4Q2cQMbNwc2JE3QQiH2a40IqOEv0yGjtYYDUpwFG0-NzsEVxZ9sPTuW0tp9-Tk8BxOOrGqUNekAinQasdgxe3JXpVekS0rRp5cZqBquyHgBIuKmfoi8yZyM2YoLIMOaic0r5Paf30_Ji-MdzeYBkroKOqstCJeD0U5OBVWaYh0wRuhQLq23DAnz2/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> 
.



Please note that this e-mail is not secure (encrypted).  If you do not 
wish to continue communication over unencrypted e-mail, please notify 
the sender of this message immediately. Continuing to send or respond 
to e-mail after receiving this message means you understand and accept 
this risk and wish to continue to communicate over unencrypted e-mail.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Resampling of surface-based bivariate data

[Douglas N. Greve]

No, there is not (at least that I know of). Bruce might have something 
along these lines.

On 4/26/2022 3:32 PM, Burke Rosen wrote:
>  External Email - Use Caution
>
> Is there a way to resample a vertex-by-vertex matrix of data from one subject 
> to another or to ico? For example, I have calculated the Euclidean distance 
> matrix for all the vertices of lh.white for my subjects and wish to find the 
> average distance matrix. Another example might be functional connectivity 
> values.
>
> If the data were univariate (i.e. vectors not matrices), I could save my 
> measure as a .w file for each subject and use mri_surf2surf to morph each 
> vector to ico and then average across the resulting ico vectors. One idea is 
> to use make_average_subject to morph each subject’s surface to ico and then 
> calculate bivariate measures on these surfaces. This might be ok for the 
> functional connectivity case. However, this morphing distorts the absolute 
> size of the surface, so the Euclidean distance matrix would be untenably 
> distorted.
>
> In other words, is there an extension of mri_surf2surf (or maybe 
> mris_convert) that operates on v(i,j) measures rather than v(i) measures?
>
> Thank you,
>
> -Burke
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

[Douglas N. Greve]

yes, in the gtm.stats file. See 
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer for docs



On 4/26/2022 3:29 PM, Zhener Zhang wrote:


External Email - Use Caution

Thank you, Douglas!
Is it possible to extract the number of voxels in each segment [of the 
FreeSurfer DK atlas]?
We are hoping to ‘reverse’ the spatial averaging process to get the 
sum of expression level in each ROI.


Thanks,
ZZ
On Apr 25, 2022, 11:34 -0700, Zhener Zhang , wrote:

Hi Douglas,

Thanks! We ran the following for one of our subjects:

mri_gtmpvc --i sz013_BPnd.nii --reg sz013_BPnd.reg.lta --seg
~/sz013/mri/gtmseg.mgz --default-seg-merge --no-tfe --no-rescale
--o ~/sz013/gtmpvc.output


Thanks,
ZZ
On Apr 24, 2022, 13:45 -0700, Zhener Zhang , wrote:

Hi Douglas,

Thank you for the reply!

The mri_gtmpvc outputs were expected and there was no reason for us 
to suspect that something was wrong. I was just curious as to the 
general process behind PETSurfer’s ROI-wise value calculation. Was 
each ROI-wise output generated by averaging across all voxels of an ROI?


Thanks!
Zhener Zhang


On Apr 20, 2022, 09:50 -0700, Zhener Zhang , wrote:

Hello,

I have a question regarding the way ROI-wise values are calculated 
using PETSurfer.


We ran the PETSurfer pipeline with PVC=0 and noticed that a 
relatively small ROI like Putamen has one of the highest values of 
regional distribution of a PET tracer.


Is it the case that the PETSurfer ROI-wise value outputs were 
averaged, or normalized by each ROI’s volume? And what measure was 
divided, GM volume, number of voxels, or something else?


Thank you in advance!

Best regards,
Zhener



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Beta values (resubmitting)

[Douglas N. Greve]

3rd line for the slope of CU, 4th line for the slope of CI

On 4/25/2022 4:03 PM, Laura Willers de Souza wrote:


External Email - Use Caution

Thanks so much!

I would also like to confirm that I am interpreting the beta values 
correctly for a second model.


Model 2: Two Groups, One Covariate

Contrasts (DOSS): difference between the group intercepts; covariate 
effect.


The fsgd file looks like this:

GroupDescriptorFile 1

Title CU_CI_CSF
MeasurementName thickness
Class CU
Class CI
Variables cortisolCSF
Input 011_S_0003_S9128 CI 2.397895273
Input 022_S_0004_S9233 CI 2.772588722
Input 011_S_0005_S9137 CU 3.044522438
Input 011_S_0008_S9196 CU 2.397895273
Input 011_S_0010_S8800 CI 2.151762203

... (n=300)


The file with the beta values contains 3 lines (image below).

  * The first line would be the beta value for the intercept of the
1st group; the second line for the intercept of the 2nd group; and
the third line for the slope of the covariate?
  o Thus the glm equation for the 1st cluster would be:
  o 1st group  cortical thickness = 2.64 - 0.12X + n
  o 2nd group --- cortical thickness = 2.54 – 0.12X + n

Am I interpreting correctly?

Thank you very much for all the help!
*Laura Willers de Souza *

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

[Douglas N. Greve]

In that case, it mapping the seg into the pet space (see aux/seg.nii.gz) 
and just averaging over the voxels in each segment.


On 4/25/2022 2:34 PM, Zhener Zhang wrote:


External Email - Use Caution

Hi Douglas,

Thanks! We ran the following for one of our subjects:

mri_gtmpvc --i sz013_BPnd.nii --reg sz013_BPnd.reg.lta --seg
~/sz013/mri/gtmseg.mgz --default-seg-merge --no-tfe --no-rescale
--o ~/sz013/gtmpvc.output


Thanks,
ZZ
On Apr 24, 2022, 13:45 -0700, Zhener Zhang , wrote:

Hi Douglas,

Thank you for the reply!

The mri_gtmpvc outputs were expected and there was no reason for us 
to suspect that something was wrong. I was just curious as to the 
general process behind PETSurfer’s ROI-wise value calculation. Was 
each ROI-wise output generated by averaging across all voxels of an ROI?


Thanks!
Zhener Zhang


On Apr 20, 2022, 09:50 -0700, Zhener Zhang , wrote:

Hello,

I have a question regarding the way ROI-wise values are calculated 
using PETSurfer.


We ran the PETSurfer pipeline with PVC=0 and noticed that a 
relatively small ROI like Putamen has one of the highest values of 
regional distribution of a PET tracer.


Is it the case that the PETSurfer ROI-wise value outputs were 
averaged, or normalized by each ROI’s volume? And what measure was 
divided, GM volume, number of voxels, or something else?


Thank you in advance!

Best regards,
Zhener



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

[Douglas N. Greve]

There are several ways it might work depending upon how you ran it. This 
is why I was asking for your command line.


On 4/24/2022 4:46 PM, Zhener Zhang wrote:


External Email - Use Caution

Hi Douglas,

Thank you for the reply!

The mri_gtmpvc outputs were expected and there was no reason for us to 
suspect that something was wrong. I was just curious as to the general 
process behind PETSurfer’s ROI-wise value calculation. Was each 
ROI-wise output generated by averaging across all voxels of an ROI?


Thanks!
Zhener Zhang


On Apr 20, 2022, 09:50 -0700, Zhener Zhang , wrote:

Hello,

I have a question regarding the way ROI-wise values are calculated 
using PETSurfer.


We ran the PETSurfer pipeline with PVC=0 and noticed that a 
relatively small ROI like Putamen has one of the highest values of 
regional distribution of a PET tracer.


Is it the case that the PETSurfer ROI-wise value outputs were 
averaged, or normalized by each ROI’s volume? And what measure was 
divided, GM volume, number of voxels, or something else?


Thank you in advance!

Best regards,
Zhener



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] ERROR: Talairach failed!

[Douglas N. Greve]

Try adding --no-surfs

On 4/22/2022 11:38 AM, Fritze, Stefan wrote:


External Email - Use Caution

Thanks for your reply! The command is:

tkregisterfv --s participant_name  --fstal
ERROR: cannot find participant_name/surf/lh.white

Best
Stefan


*Von:* freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. 
Greve 

*Gesendet:* Donnerstag, 21. April 2022 20:03:32
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* Re: [Freesurfer] ERROR: Talairach failed!
Can you provide the tkregisterfv command line and the terminal output?

On 4/21/2022 3:37 AM, Fritze, Stefan wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to computerecon-all -all -subjid XXX -qcache -3T, which works 
fine with most of my study participants, but for some of them I receive 
Talairach error (s. error message below):
  
I've searched the list and similar errors have been reported and there is a webpage dealing with this type of error (*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview  <https://secure-web.cisco.com/12PSM0kyIYIR5OmViKurKErWOjGNautv6OLjOZ2Xfwd9-oX2biUAK1AqD22LlXvKLAl5W6fybm9dLhz4luX4Eqiz2b0aS2ToqMmXx0qSLpx275tpw3qoUg_7fUXcZCCEp2RQpUERty8Yo6YaF6_Jtpqn5lyc7YK5ococ-pt2nmnkO-uvv0v7cCCl4i9XyLH9APKbI9tXzGzLhWXK9wDz13HbNxSYe3TtS7uSmGatyz5D7NUKn7BHK3a1blPd021yAJDL2u8jwgb1was-7uvCOhIhp1H6mAi-skh_cw0ETN2FlQZNqlcgOcQhZ5ZedSvE-tFtEYfcOTySxW1Mz8AXduQ/https%3A%2F%2Fsmex-ctp.trendmicro.com%3A443%2Fwis%2Fclicktime%2Fv1%2Fquery%3Furl%3Dhttps%253a%252f%252fsecure%252dweb.cisco.com%252f1RvZhQl7xG9ZOQtDHxIejsIaxH%252dSzi0GVQwXNg3elCyaJxdS%255fia2rbovg7amDfXBOXgvzkzgRGIifK5a14I9S%252dY2wfUx%252dTyK5HpLSKuxchVxsveJhVmkXUABKfpKz3g1xPOw7DH9%255fRarrJdByWjKpp4O7t5mo2Ayi2KsghGio%252dQnbuEbUci21Tl4uEi%252dtGkDN1Hxd143cydV9CFXuRGWf1lB1Qe2YPkOJ4zNkRewkk1i%252dS%252df%255faGd9i%255f5RoGUgkY5lD1%252dh2rod%252d383tXpTQ%252dcZUsk%252dKAGAL0fHL8hh91V%255fVFMqQr%255flBuayIOjsP%255fFdc9aI2n1wlnbmr7zuzQtyDXVTvQ%252fhttps%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Ffswiki%25252FFsTutorial%25252FTalairach%255ffreeview%26umid%3D7ed17774-f51c-4368-becd-51a015929d02%26auth%3D9ed9a254ae8a0a504cee5b89eb68d1de87cd0c46-65a702a50662ca1b466b6e9af5fe2bdc80c230ed>). Yet, tkregisterfv produces also an error, even when I do not set the --surf orig flag (the surf folder of these participants is empty). Running the mritotal utility from the MNI toolset produces the same error. In one participant, the problem was solved when I converted the .nifti file to .mgz and started recon-all from there. But this did not help with the other participants. Including the -notal-check flag allows recon-all to complete, yet I do not know whether the results are trustworthy.

Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive 
attached the recon-all.log in case it's of any use.
1) FreeSurfer version:freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
2) Platform: 54G7T63 Kernel: 5.0.0-32-generic x86_64 bits: 64 compiler: gcc v: 
7.4.0
           Desktop: MATE 1.22.2 wm: marco dm: LightDM Distro: Linux 
Mint 19.3 Tricia

           base: Ubuntu 18.04 bionic
3) recon-all.log: see attached
Best wishes,
Stefan
#@# Talairach Failure Detection Fr 11. Mär 18:44:03 CET 2022


talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
***FAILED*** (p=0.0321, pval=0.0034 < threshold=0.0050)

Command exited with non-zero status 1
@#@FSTIME 2022:03:11:18:44:03 talairach_afd N 4 e 0.00 S 0.00 U 0.00 
P 100% M 6312 F 0 R 247 W 0 c 0 w 1 I 0 O 0 L 83 1 60

@#@FSLOADPOST 2022:03:11:18:44:03 talairach_afd N 4 83 1 60

Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See:

*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

ERROR: Talairach failed!


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mai

Re: [Freesurfer] mri_segment_hypothalamic_subunits error

[Douglas N. Greve]

From Benjamin Billot:
Yep, that’s just an out of memory issue for the GPU. He/she can use the 
cropping flag, or use the cpu flag.


On 4/18/2022 9:58 AM, Chen ZY wrote:


External Email - Use Caution

Dear FreeSurfer Developers,

I'm attempting to use the mri_segment_hypothalamic_subunits tool on 
subjects that have been analyzed with recon-all as described on the 
wiki page


(https://surfer.nmr.mgh.harvard.edu/fswiki/HypothalamicSubunits), but 
I received the following error when I run the 
mri_segment_hypothalamic_subunits


command (mri_segment_hypothalamic_subunits --s):

(tensorflow) brain@neurodebian:/usr/local/apps/freesurfer/subjects$ 
mri_segment_hypothalamic_subunits --s bert


using 1 thread

processing 1/1

*** Error in `/usr/local/apps/freesurfer/python/bin/python3': 
munmap_chunk(): invalid pointer: 0x7fa1707b3400 ***


Aborted

I would be appreciated if you can help me solve this problem.

Thank you very much!

Regrads,

发送自Windows 10 版邮件 
应用



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] ERROR: Talairach failed!

[Douglas N. Greve]

Can you provide the tkregisterfv command line and the terminal output?

On 4/21/2022 3:37 AM, Fritze, Stefan wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to computerecon-all -all -subjid XXX -qcache -3T, which works 
fine with most of my study participants, but for some of them I receive 
Talairach error (s. error message below):
  
I've searched the list and similar errors have been reported and there is a webpage dealing with this type of error (*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview  ). Yet, tkregisterfv produces also an error, even when I do not set the --surf orig flag (the surf folder of these participants is empty). Running the mritotal utility from the MNI toolset produces the same error. In one participant, the problem was solved when I converted the .nifti file to .mgz and started recon-all from there. But this did not help with the other participants. Including the -notal-check flag allows recon-all to complete, yet I do not know whether the results are trustworthy.

Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive 
attached the recon-all.log in case it's of any use.
1) FreeSurfer version:freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
2) Platform: 54G7T63 Kernel: 5.0.0-32-generic x86_64 bits: 64 compiler: gcc v: 
7.4.0
           Desktop: MATE 1.22.2 wm: marco dm: LightDM Distro: Linux 
Mint 19.3 Tricia

           base: Ubuntu 18.04 bionic
3) recon-all.log: see attached
Best wishes,
Stefan
#@# Talairach Failure Detection Fr 11. Mär 18:44:03 CET 2022


talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
***FAILED*** (p=0.0321, pval=0.0034 < threshold=0.0050)

Command exited with non-zero status 1
@#@FSTIME 2022:03:11:18:44:03 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 
100% M 6312 F 0 R 247 W 0 c 0 w 1 I 0 O 0 L 83 1 60

@#@FSLOADPOST 2022:03:11:18:44:03 talairach_afd N 4 83 1 60

Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
ERROR: Talairach failed!


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] differences between Freesurfer 6.0 and 6.0-beta

[Douglas N. Greve]

basically, you should not have been using the beta version since it is a 
beta version. hard to know what the differences were


On 4/20/2022 6:21 PM, Paul Wighton wrote:


External Email - Use Caution

Hi Matt,

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c was compiled 
from this commit of the source code on Jan 18, 2017
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://github.com/freesurfer/freesurfer/commit/2beb96c6099d96508246c14a24136863124566a3 



Judging by the datestring of 
freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015, I'm guessing 
it was compiled from this commit on Oct 14, 2015.
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://github.com/freesurfer/freesurfer/commit/b654364c9bc0365a5063050f118384e7be4d2508 



There are tons of differences between these two releases and I would 
not expect identical results.


-Paul

On Wed, Apr 20, 2022 at 1:51 PM Hoptman, Matthew (NKI) 
 wrote:


External Email - Use Caution

Hi all,

I have access to a system that has both
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c vs.
freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015

Could someone please let me know what the primary differences are
between these versions? They have been used exclusively to get
volumes/thickness/surface area. Should those values be identical?

Thanks,

Matt

Prounouns: He/Him/His

IMPORTANT NOTICE: This e-mail is meant only for the use of the
intended recipient. It may contain confidential information which
is legally privileged or otherwise protected by law. If you
received this e-mail in error or from someone who was not
authorized to send it to you, you are strictly prohibited from
reviewing, using, disseminating, distributing or copying the e-mail.

PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND
DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.




IMPORTANT NOTICE: This e-mail is meant only for the use of the
intended recipient. It may contain confidential information which
is legally privileged or otherwise protected by law. If you
received this e-mail in error or from someone who was not
authorized to send it to you, you are strictly prohibited from
reviewing, using, disseminating, distributing or copying the
e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL
AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your
cooperation.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to
whom it is addressed.  If you believe this e-mail was sent to you
in error and the e-mail contains patient information, please
contact the Mass General Brigham Compliance HelpLine at
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://www.massgeneralbrigham.org/complianceline

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

[Douglas N. Greve]

Can you send your mri_gtmpvc command line?

On 4/20/2022 12:50 PM, Zhener Zhang wrote:


External Email - Use Caution

Hello,

I have a question regarding the way ROI-wise values are calculated 
using PETSurfer.


We ran the PETSurfer pipeline with PVC=0 and noticed that a relatively 
small ROI like Putamen has one of the highest values of regional 
distribution of a PET tracer.


Is it the case that the PETSurfer ROI-wise value outputs were 
averaged, or normalized by each ROI’s volume? And what measure was 
divided, GM volume, number of voxels, or something else?


Thank you in advance!

Best regards,
Zhener


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recontruction of an elephant brain

[Douglas N. Greve]

HI Malav, did you create the subcortical mass? Have you separated the 
hemispheres?


On 4/18/2022 4:48 PM, Malav Shah wrote:


External Email - Use Caution

Hi Dr. Greve,
I send a gentle reminder, in case the previous mail skipped your 
attention.

with regards,
Malav


*From: *"Malav Shah" 
*To: *"Freesurfer support list" 
*Sent: *Tuesday, April 12, 2022 3:08:50 PM
*Subject: *Re: [Freesurfer] recontruction of an elephant brain

Hi Douglas,
thank you so much for your suggestions.
Your understanding of my task is very precise, and I would love to 
move in the direction you recommend. I would appreciate a bit more 
detailed guidance.

Would you have a little bit of time to spare for me in those regards?

Looking foward,
Malav Shah

--------
*From: *"Douglas N. Greve" 
*To: *"freesurfer" 
*Sent: *Saturday, April 9, 2022 10:18:18 PM
*Subject: *Re: [Freesurfer] recontruction of an elephant brain

Lot's of people have adapted FS to non-human brains, just google it. 
For surface analysis, you need to get the "subcortical mass" -- the 
equivalent to the filled.mgz. This is the cerebral white matter + 
subcort gray structures. Once you have that, you might be able to run 
mris_place_surfaces. I'd have to walk you through the options to use 
or not.


On 4/8/2022 6:01 AM, Malav Shah wrote:

External Email - Use Caution

Hi Lilla,

Thank you so much for your feedback.

I completely understand the tool's bias for human brains. As you
said, the elephant brain images are not well understood so far. We
aim to take initial steps in that direction, starting with small
goals like WM-GM seperation, cortical thickness measurements, and
surface visualisation with flattening. Do you think it can be
achieved with FreeSurfer's volume-based analysis pipeline? We
would be more than happy to collaborate on that.

Looking forward to hearing from you :)
Thanks and regards,
Malav Shah



*From: *"Zollei, Lilla,Ph.D." 
<mailto:lzol...@mgh.harvard.edu>
*To: *"freesurfer" 
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Sent: *Wednesday, April 6, 2022 8:29:33 PM
*Subject: *Re: [Freesurfer] recontruction of an elephant brain

Hi Malav,

Freesurfer is guided by an atlas that was built from human adult
brain images. In the past though, we did have collaborators who
have tried some modified versons of the pipeline to work on
non-human data. Here are some pointers:

*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData

<https://secure-web.cisco.com/1149bxkRGOm5AzvVYmA-Bxc160t7HU-wHF-xUFdBZaQ-CBDMhfyoMiEkF7LgJIJ_w2ZHvZc48UMSj3dntsS0oSNQ8vdQc73Jlmd34JnP5adcUaLvPSYD34MknD4RGJCciLXDv6LLLWHftORNu5-I2UJ9s-3vmM0xvwEOg_rP6R_H06ZkjIIqqSlghgO6dQWO2TD0avKyXnSU_eDy0zm0jtaUQQo_9wjJxYXzzbruHepTSyu0mPr2m1plsCrh1oqcnOIO52xQ59mJxjJHGSSG0NSkfLM9x7-WkZswQgb9jyx13SmLAfd8qay-lglviBvnwJnizBfEJwrJyEuIJ53mdzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMonkeyData>
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://hal.archives-ouvertes.fr/hal-01854607/document

<https://secure-web.cisco.com/1hWAtvKnqtTh7X5HFZdRhQKvG5qfkbftxeOlgW8K8ZQVAWK819JdXTeTLKb0ZBsyMLy1VhpeygvLjaYwwxrmYVPViJNnTZZi9lFJE3tW0UOfiyDRYL7LSqSBBf_ZQy7aj0eQky-xkHYta4Qae7thrJY6l-1EknyGByegvwFwKtaWKUyOVnMP4pNqYPVIf_dHiu63tvct2_QXvF24hUJ9sZhtopGTpdD9PDpBB3ZLYnfZ2eE2exZkaEVnyBVavesE8Realx7SY17iZbjmtmZ6kmQtoDEkBoGHiN562LEyksb8hPFBCewiJJYH3lwGBNbpE7Z3s9FRtJyE2hkb4z5uzTQ/https%3A%2F%2Fhal.archives-ouvertes.fr%2Fhal-01854607%2Fdocument>

As far as I know elephant brain images have not yet been
processed. Good luck, Lilla


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

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Malav
Shah  <mailto:malav.s...@bccn-berlin.de>
*Sent:* Wednesday, April 6, 2022 1:10 PM
*To:* freesurfer@nmr.mgh.harvard.edu

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* [Freesurfer] recontruction of an elephant brain

External Email - Use Caution

hi,
I am trying to reconstruct elephant brain MRI. I am wondering if
FreeSurfer can manage this, or does the recon-all command has an
inherent bias for human data.
Does anyone have an experience using FreeSurfer with a non-human
mammal for such purposes?

I have some hopes with this idea, because I am not trying to
achieve parcellation or segm

Re: [Freesurfer] rerunning on 7.2 with edited brainmask using hi-res

[Douglas N. Greve]

Yes, same command

On 4/17/2022 10:24 PM, Alexopoulos, Dimitrios wrote:


External Email - Use Caution

Can someone confirm?

Thx.

Jim

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Alexopoulos, 
Dimitrios

*Sent:* Tuesday, April 12, 2022 3:24 PM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] rerunning on 7.2 with edited brainmask using 
hi-res


** External Email - Caution **

*External Email - Use Caution *

We are running some hi-res 0.8mm3 isotropic data through FS 7.2 using 
the following command.


*recon-all -s subj -all –hires*

**

We are adding back brain which has been removed by the masking process 
by cloning the T1/brainmask images in freeview and adding back voxels.


A revised brainmask.mgz is saved.

Can/should the same command be used to rerun using hi-res data?

Jim

**



The materials in this message are private and may contain Protected 
Healthcare Information or other information of a sensitive nature. If 
you are not the intended recipient, be advised that any unauthorized 
use, disclosure, copying or the taking of any action in reliance on 
the contents of this information is strictly prohibited. If you have 
received this email in error, please immediately notify the sender via 
telephone or return mail.




The materials in this message are private and may contain Protected 
Healthcare Information or other information of a sensitive nature. If 
you are not the intended recipient, be advised that any unauthorized 
use, disclosure, copying or the taking of any action in reliance on 
the contents of this information is strictly prohibited. If you have 
received this email in error, please immediately notify the sender via 
telephone or return mail.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Recon process for skull-stripted data

[Douglas N. Greve]

I'm not sure. You can try just passing the skull stripped as input to 
recon-all. The talairach transform will probably be off, but the rest 
might work


On 4/17/2022 9:09 PM, Muhammed Görünen wrote:


External Email - Use Caution

Hi,

How can I run a recon process if I have just skull stripted data? I 
need surface and annot files. Does the process need the volume files 
produced before the skull-stripting process? Thanks in advance.


Best,

--Muhammed

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Rerunning freesurfer with manual edits and T2 or FLAIR pial refinement

[Douglas N. Greve]

you need to add these flags again

On 4/16/2022 11:49 AM, VINCENT KOPPELMANS wrote:


External Email - Use Caution

I have made manual edits to a subject that was initially run with the 
-FLAIR  and -FLAIRpial input flags. When I want to rerun 
freesurfer to implement these edits should I add these flags again, or 
is it sufficient to run recon-all -all?


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Multiple comparison correction

[Douglas N. Greve]

Do you mean the difference between the d,m,h classes? If so, it would be
1 1 -1 -1 0 0 (rest all 0s)
1 1  0  0 -1 -1 ...
0 0 1 1 -1 -1 ...



On 4/14/2022 9:50 AM, David wrote:


External Email - Use Caution

Hi Freesurfer experts,

    I'm very sorry to bother you, but I am very confused with the
    following questions:

    My experimental design includes two discrete factors:
    with three levels (d,m,h); gender (f, m), and two Nvariables

    So I can get 6 classes: df, dm,mf, mm,hf,hm.

 I want to perform the difference between any of the classes
    leves analysis with regressing out the effect of gender and two
    Nvariables, but I don't know the rules for setting the contrasts for
    the F-test.  The contrast matrix I used is:

    1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
    0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0
    1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
    0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0
    My orders are as follows：
    mris_preproc --fsgd glmteach.fsgd --target fsaverage --hemi lh 
--meas area --out lh_teach.mgh
    mris_preproc --fsgd glmteach.fsgd --target fsaverage --hemi rh 
--meas area --out rh_teach.mgh


    mri_glmdir --y lh_teach.mgh --fsgd glmteach.fsgd --C glmteach.mtx 
--glmdir group.area_sm.lh --fwhm 10 --surface fsaverage lh --eres-save


    mri_glmdir --y rh_teach.mgh --fsgd glmteach.fsgd --C glmteach.mtx 
--glmdir group.area_sm.rh --fwhm 10 --surface fsaverage rh --eres-save


    mri_glmdir-sim --glmdir group.area_sm.lh --2spaces --cwp 0.05 
--perm 100 1.3 abs
    mri_glmdir-sim --glmdir group.area_sm.rh --2spaces --cwp 0.05 
--perm 100 1.3 abs


   But there is no region of interest after running，
   Can I change the correction method or did I use it wrong


    Any help will be very appreciated.

    Best wishes,




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] How to make surfaces below the GM-WM boundary?

[Douglas N. Greve]

Try using mris_expand, eg,
mris_expand lh.white -1 lh.subwhite
will create a surface 1mm into the WM

On 4/14/2022 7:50 AM, Lee Subin Kristine wrote:


External Email - Use Caution

Dear FreeSurfers,

I am interested in sampling values in the superficial white matter 
(SWM) region, which is an area of about 0.5mm below the GM/WM boundary.


To extract values of each vertex in that region, I have successfully 
used the mri_vol2surf function with the projfrac option, such as below:


/mri_vol2surf --src  --out  --out_type mgh 
--hemi lh --projfrac -0.5 --regheader  --surf white 
--interp trilinear/


However, I would also like to get surface type files (like lh.pial, 
lh.white, etc) that I could overlay on Freeview for visualization 
purposes.


I see papers with figures that have a visualization of surfaces below 
the GM/WM boundary, but I am not sure how I can obtain this.


I would really appreciate if anyone could give me any hints or 
suggestions on how I could do the same.


Thanks in advance!

Best regards,

Kristine

Windows용 메일 
에서 
발송된 메일입니다.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] [Freeview] View Flatmap

[Douglas N. Greve]

in freeview, runsomethiing like
freeview -f rh.white:patch=rh.full.flat.patch.3d
The rh.white is just there to give freeview a full surfce to load. You 
will only see your patch


On 4/14/2022 4:30 AM, Morgenroth Elenor wrote:


External Email - Use Caution

Dear Freesurfer Experts,
I have been using
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch 


to create flatmaps of individual subjects. This ran without any errors and I 
have a 'rh.full.flat.patch.3d’ file now.
I can’t figure out how to visualise it to check it (in freeview).
I have also tried to use pycortex to visualise this as I’m eventually aiming to 
plot data onto my flatmap, but that isn’t working either (I get a different 
error (ExpatError) using my flatmap as I get with the example flatmap, but I 
also can’t visualise the example flatmap in freeview).
Thank you for your help!
Ellie

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Beta values (resubmitting)

[Douglas N. Greve]

Yes, first line intercept, 2nd line slope

On 4/12/2022 3:44 PM, Laura Willers de Souza wrote:


External Email - Use Caution

Hey! I'm resending this email because I think it got lost on the list.

Hello FreeSurfer Developers,

I'm extracting beta values​​from some analyzes and I would like toknow 
if I'm extracting and interpreting these values​​correctly.


To extract the beta values ​​I used this command:

mri_segstats 
--seglh.cortisol_CSF.glmdir/cortisol_CSF_slope/perm.th20.neg.sig.ocn.mgh--i 
lh.cortisol_CSF.glmdir/beta.mgh --excludeid 0 
--avgwflh.cortisol_CSF.beta.clusters.dat


The model consists of 1 group and 1 covariate.
I used the contrasts for intercept and slope.
The fsgd file looks like this:
GroupDescriptorFile 1
Title cortisol_CSF
Class Main
Variablescortisol_CSF
Input011_S_0003_S9128Main2.397895273
Input022_S_0004_S9233Main2.772588722
Input011_S_0005_S9137Main3.044522438
Input011_S_0008_S9196Main2.397895273
Input011_S_0010_S8800Main2.151762203
... (n=300)
The beta values ​​extraction file contains 2 lines (image below).

  *  Would the first line be the beta value for the intercept and the
second line for the slope?
  * Thus the glm equation for the 1st cluster would be: cortical
thickness = 2.57 - 0.12X + n
Is this correct?
Thank you very much in advance.
*Laura Willers de Souza *

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] parallel make_average_subject

[Douglas N. Greve]

There is not an easy way to do this. Internally, there is a binary that 
loads all the subjects then creates an average. You need some way to 
create intermediate files, then combine them together, which we don't 
support. Why do you want to create an average subject?


On 4/11/2022 9:54 AM, Marina Fernández wrote:


External Email - Use Caution

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





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] mri_glmfit error

[Douglas N. Greve]

You don't have enough members in the classes to fit the model that you 
have. Eg, class d has 4 members with which you are fitting an offset and 
3 slopes leaving you with 0 degrees of freedom. You need to get more 
subjects or change your model. btw, gender is usually modeled as a 
discrete rather than continuous covariate.


On 4/11/2022 8:06 AM, David wrote:


External Email - Use Caution

Hello FreeSurfer Developers,
my fsgd is this：
GroupDescriptorFile 1
Title post compane
Class d
Class m
Class h

RescaleFlag 1
DemeanFlag 1
Variables gender Age Edu
Input bd1 d 0 15 8
Input bd2 d 1 19 13
Input bd7 d 0 17 11
Input bd8 d 1 19 13
Input bd6 m 1 22 12
Input bd9 m 1 26 7
Input bd10 m 0 53 15
Input bd11 m 1 56 4
Input hc3 h 0 45 7
Input hc4 h 1 18 13
Input hc1 h 0 52 7
Input hc2 h 1 24 10

When I run Three Groups (One Factor/Three Levels), three Covariates,my 
MTX is


1 -1 0 0 0 0 0 0 0 0 0 0
1 0 -1 0 0 0 0 0 0 0 0 0
It’s wrong,What should I do

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08



 ERROR: READ THIS -
--vv-
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
    mri_glmfit --y rh_teach66.mgh --fsgd glmteach66.fsgd --C 
glmteach66.mtx --glmdir group66.area_66sm.rh --fwhm 10 --surface 
fsaverage rh --eres-save
  2. The terminal output of this program (ie, everything it prints to 
the screen)

  3. The FSGD file (glmteach66.fsgd)
  4. The design matrix group66.area_66sm.rh/Xg.dat
Attempting to diagnose further
WARNING: Class d has 4 members. With 3 variables and using DODS, This 
is the bare minimum which may cause problems with the design matrix.
WARNING: Class m has 4 members. With 3 variables and using DODS, This 
is the bare minimum which may cause problems with the design matrix.
WARNING: Class h has 4 members. With 3 variables and using DODS, This 
is the bare minimum which may cause problems with the design matrix.

SumSq: Min=1.491914 (col 10), Max=2.676059 (col 11)
 ... could not determine the cause of the problem
--


ERROR: cannot find residual group66.area_66sm.lh/eres needed with 
--perm-resid

  when running mri_glmfit, make sure to include --eres-save
ERROR: cannot find residual group66.area_66sm.rh/eres needed with 
--perm-resid

  when running mri_glmfit, make sure to include --eres-save
glm66.sh: line 14: --perm-resid: command not found
---





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] mkheadsurf error: mris_smooth and mris_inflate synthesized bizarre output paths

[Douglas N. Greve]

I recently made a lot of changes to mkheadsurf. Can you download the dev 
version and try it?


On 4/5/2022 4:24 PM, Megan Schendel wrote:


External Email - Use Caution

Hello,
I am also trying to use mkheadsurf and getting the same errors 
described in the January topic by user Yong-Jun Lin.
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg71781.html 
<https://secure-web.cisco.com/1gWrCRE26r6WP8WhRpdFnJDHSFKaCpEOt6y_UEivpQG5fGvRy3zcw4ehLwKt3CPDelcJs4tkIsZm2-6KQ30txqRCdiaOdDtzMIxUH5BWv9e_t-2t0cqsvVYZsI2e1Epyh0SDCjg3ljg-zsEt4Ee9uv4y4btxkxt19IuRFs4oyw2jLRPX-YZhr5VglfbcZ-Wdh7TbC2e7DfXrrcmafGiQyyu5ghy74dMbaPG_0QaNOIYG-XRfTQqaqO_YqnqOf66KXdBdLdyHGuP1a9bC3mlLtolhdi2R8VB_smf569LRSGYSQRh-yxBcz6qf760vOIK8S/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg71781.html>

1. The first error message is "subjdir: Undefined variable.".
     I followed the thread and also manually defined subjdir
2. Same problems with
mris_smooth -n 10 -b /..
resulting in error: MRISwriteCurvature: could not open
lh./...
and
 mris_inflate -n 10 -sulc /...
resulting in error: MRISwriteCurvature: could not open /...
Lastly, I followed the response from Douglas N. Greve  <https://secure-web.cisco.com/1ahbUvtJEJ2YIzAb-v2Vq6dQ8vxhI4tzwwkf_H3Yz4GyLGM7YvV79qByQvW-Kpj0lueIrI67DwfRrcgmTtD9jyK7SHOSxPScms3rWbYgKXx0gVxlWTJGfbgLxIY60CqFq6wtKL5NiCf7m5cYmGxLmtdlstJhehCBfwV-jHzPS4K_mz_LPJ_EjGu9y6BNk-BkZgfRLpTeCVISW1GbVmnRhiCVMukqLVSLal_Yf0Thby0a2tXYTYAVNzaYUsOZyZmw76AXWbWVirtp-NbZYkwVamJt8oi8oXcEPsjjCe8ES6cuQ2JcZ4c4DvGm9KH65Uz7Q/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Douglas%2BN.%2BGreve%2522>to try the new mkheadsurf. When I tried that, the subjdir error went 
away, but the output paths errors with the mris_smooth and 
mris_inflate persisted. The end result output files that I need were 
created, however, so I can go on with my work.
But I thought I'd reply to the list and let you know that I'm also 
getting these path errors.

Thanks for any help, Megan
MEG Technician
Pronouns: she/her
The Mind Research Network
1101 Yale Blvd. NE
Albuquerque, New Mexico 87106


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Freesurfer stats output meaning

[Douglas N. Greve]

wow, I've never even looked at the ?h.curv files before. Looks like 
there is a lot of info but only on a global (whole hemi basis). Some of 
the measures are different (eg, min and max curv rather then mean or 
gaussian). I don't know whether these would be helpful in your app.


On 4/5/2022 12:16 PM, Rafael Navarro wrote:


External Email - Use Caution

Hello Freesurfer developers,

I am attempting to build a brain age estimator with FreeSurfer output. 
However, I am having some problems disentangling Freesurfer stats 
output. I will be using only the Desikan-Killiany atlas cortical 
segmentation. I have identified these files as useful:


aseg.stats   -> subcortical segmentation features
lhaparc.stats -> DK cortical segmentation left hemisphere features
rhaparc.stats -> DK cortical segmentation right hemisphere features
lh.w-g.pct.stats -> DK cortical segmentation left hemisphere grey 
matter - white matter contrast features
rh.w-g.pct.stats -> DK cortical segmentation right hemisphere grey 
matter - white matter contrast features
wmparc.stats -> white matter close to DK cortical segmentation areas 
features


However, I checked these two files too:

lh.curv.stats
rh.curv.stats

But I don't have a clear idea of the meaning of the features in those 
files. For what I understand the features are the mean and standard 
deviation of the white matter surface and the pial surface. However, 
these measurements would be redundant if I include the features from 
xhaparc.stats, wouldn't they?


Thanks for your help!

___
---
||  Rafael Navarro González
||  Ph.D. Student
||  ETSI Telecomunicación
||  Universidad de Valladolid
||  Campus Miguel Delibes
||  47011 Valladolid, Spain
||  e-mail: rafael.nava...@uva.es
||  Phone: +34 672 394 294
||_
---

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Medial prefrontal cortex

[Douglas N. Greve]

I don't know. Look at Christophe's paper.

On 4/8/2022 8:46 AM, Patricia Schwery wrote:


External Email - Use Caution

Thank you Douglas for your reply.
Do you know if i can find the medial frontal gyrus in the a2009s? I 
found other-regions that i need for the mPFC but this one i cant find 
in there ( perhaps there is a different name for the medial frontal 
gyrus in the a2009s).


Thank you again in advance for your help.

Best wishes, Patricia

Le lun. 4 avr. 2022 à 03:55, Douglas N. Greve  
a écrit :


Have you looked in the destrieux atlas? It is the a2009s annot.

On 4/1/2022 10:28 AM, Patricia Schwery wrote:


External Email - Use Caution

Hi there,


I would like to know if someone could tell me how i can measure
the medial prefrontal cortex (mPFC) with freesurfer as i see it
is displayed within the superior frontal but i would need only
the mPFC.


I thank you so much for your help.


Patricia


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
<https://secure-web.cisco.com/1USa84O8vJ26SrTeBXy-19mqJlMyIXaYyiGhhGh8Hh45zWuie-6UMzrbH7-KIvpTl8guFgL-7CJwPj_LjtJ-7zWmMrO1uqv289-_s_cqLAYpmYwaZ6rN3pesBAjtI8mQXc5AT-rOZ4I1NhkDiMd3zauBbI83kOD1zzbzIdMgZP_KUPnjUuw6Gaw1HtWc5XEYOFLAaoOC92TAQ9EMR1Ahv8Ge5WAa5yF9ciJ6J6g2ZdG6cNdKXj-KYwF0zIu5zj0WTheSx_0O5j9FLd4a1fQcsFF8xjOAdAcyNobJMHss-IaEy2UFUgKYPGqbSUyclhSky/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

<https://secure-web.cisco.com/1USa84O8vJ26SrTeBXy-19mqJlMyIXaYyiGhhGh8Hh45zWuie-6UMzrbH7-KIvpTl8guFgL-7CJwPj_LjtJ-7zWmMrO1uqv289-_s_cqLAYpmYwaZ6rN3pesBAjtI8mQXc5AT-rOZ4I1NhkDiMd3zauBbI83kOD1zzbzIdMgZP_KUPnjUuw6Gaw1HtWc5XEYOFLAaoOC92TAQ9EMR1Ahv8Ge5WAa5yF9ciJ6J6g2ZdG6cNdKXj-KYwF0zIu5zj0WTheSx_0O5j9FLd4a1fQcsFF8xjOAdAcyNobJMHss-IaEy2UFUgKYPGqbSUyclhSky/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
The information in this e-mail is intended only for the person to
whom it is addressed.  If you believe this e-mail was sent to you
in error and the e-mail contains patient information, please
contact the Mass General Brigham Compliance HelpLine at
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://www.massgeneralbrigham.org/complianceline

<https://secure-web.cisco.com/1yODbqCSeqhQo4rrK4iVcNZJf4nzpFlKlgvqX6-5xlP0Lhx2LINnrhVYZhIMiGc6GIbetfLzRuMuH5fmfM-GqV_saDtBQVmCP9HO8MLxADUTA6AqlCqfp1jYJ3eDl-jvbKBAnx-qLSP-RJ4vWb6_QRLm1c0smLsO6GTsW-KLQDsjb_66ycMhy39Gz1rDiM-0CgkC9xeLeaS0_9F41g0vfDeL6MAnzZoO5-1Nh-X8CmPmdek56CuxHrhR6TUf7aE-h23m0jdlHU3vOug3AcKtyZatsiEvso1ZJUY98lxUJjXcIIwGOrmpuAeT4CmfZv2lF/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
<*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://www.massgeneralbrigham.org/complianceline

<https://secure-web.cisco.com/1yODbqCSeqhQo4rrK4iVcNZJf4nzpFlKlgvqX6-5xlP0Lhx2LINnrhVYZhIMiGc6GIbetfLzRuMuH5fmfM-GqV_saDtBQVmCP9HO8MLxADUTA6AqlCqfp1jYJ3eDl-jvbKBAnx-qLSP-RJ4vWb6_QRLm1c0smLsO6GTsW-KLQDsjb_66ycMhy39Gz1rDiM-0CgkC9xeLeaS0_9F41g0vfDeL6MAnzZoO5-1Nh-X8CmPmdek56CuxHrhR6TUf7aE-h23m0jdlHU3vOug3AcKtyZatsiEvso1ZJUY98lxUJjXcIIwGOrmpuAeT4CmfZv2lF/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>>
.
Please note that this e-mail is not secure (encrypted).  If you do
not wish to continue communication over unencrypted e-mail, please
notify the sender of this message immediately.  Continuing to send
or respond to e-mail after receiving this message means you
understand and accept this risk and wish to continue to
communicate over unencrypted e-mail.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is

Re: [Freesurfer] recontruction of an elephant brain

[Douglas N. Greve]

Lot's of people have adapted FS to non-human brains, just google it. For 
surface analysis, you need to get the "subcortical mass" -- the 
equivalent to the filled.mgz. This is the cerebral white matter + 
subcort gray structures. Once you have that, you might be able to run 
mris_place_surfaces. I'd have to walk you through the options to use or 
not.


On 4/8/2022 6:01 AM, Malav Shah wrote:


External Email - Use Caution

Hi Lilla,

Thank you so much for your feedback.

I completely understand the tool's bias for human brains. As you said, 
the elephant brain images are not well understood so far. We aim to 
take initial steps in that direction, starting with small goals like 
WM-GM seperation, cortical thickness measurements, and surface 
visualisation with flattening. Do you think it can be achieved with 
FreeSurfer's volume-based analysis pipeline? We would be more than 
happy to collaborate on that.


Looking forward to hearing from you :)
Thanks and regards,
Malav Shah



*From: *"Zollei, Lilla,Ph.D." 
*To: *"freesurfer" 
*Sent: *Wednesday, April 6, 2022 8:29:33 PM
*Subject: *Re: [Freesurfer] recontruction of an elephant brain

Hi Malav,

Freesurfer is guided by an atlas that was built from human adult brain 
images. In the past though, we did have collaborators who have tried 
some modified versons of the pipeline to work on non-human data. Here 
are some pointers:


*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData 

*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://hal.archives-ouvertes.fr/hal-01854607/document 



As far as I know elephant brain images have not yet been processed. 
Good luck, Lilla



*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Malav Shah 


*Sent:* Wednesday, April 6, 2022 1:10 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* [Freesurfer] recontruction of an elephant brain

External Email - Use Caution

hi,
I am trying to reconstruct elephant brain MRI. I am wondering if 
FreeSurfer can manage this, or does the recon-all command has an 
inherent bias for human data.
Does anyone have an experience using FreeSurfer with a non-human 
mammal for such purposes?


I have some hopes with this idea, because I am not trying to achieve 
parcellation or segmentation. Rather, we want to separate White matter 
from grey Matter, and then probe into various surface measurements 
across cortical regions. So as per my understanding, all I am 
expecting from FreeSurfer, is WM-GM segregation, and later (if 
possible) cortical surface flattening, and DTI.


All words of advice are welcome.
Thanks :)

Malav Shah
PhD candidate, Michael Brecht Lab,
Humboldt University zu Berlin.
(+49) 163-216-9391

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom 
it is addressed.  If you believe this e-mail was sent to you in error 
and the e-mail contains patient information, please contact the Mass 
General Brigham Compliance HelpLine at 
https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not 
wish to continue communication over unencrypted e-mail, please notify 
the sender of this message immediately.  Continuing to send or respond 
to e-mail after receiving this message means you understand and accept 
this risk and wish to continue to communicate over unencrypted e-mail.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list

Re: [Freesurfer] recon-all error in a specific data

[Douglas N. Greve]

Did you check the transform? It was the automatic failure detection that 
threw the error. This can sometimes happen when the head is at a "funny" 
orientation in the scanner, but at 7T there might be some bias fields 
having an effect. Also, see if it works when you sample it at 1mm (just 
don't use the -hires option to recon-all).


On 4/7/2022 12:17 PM, Lee, Jeungchan wrote:


Hi freesurfer team,

I collected an MPRAGE in Bay2 scanner (0.75 x 0.75 x 0.75 mm 
resolution), and the recon-all procedures with freesurfer version 
6.0.0 and 7.1.1 were both failed. I'm not sure if this is due to the 
participant's large CSF or motion or something else.


I have attached the log files (recon-all.log and talairach.log from 
both versions), which I noticed a warning/error in the recon-all.log :


(version6.0.0) *WARNING*: only one run found. This is OK, but motion 
correction cannot be performed on one run, so I'll copy the run to 
rawavg and continue.


(version6.0.0 and 7.1.1) *ERROR*: talairach_afd: Talairach Transform: 
transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < 
threshold=0.0050)


mritotal -verbose -debug -clobber -modeldir 
/space/lyon/9/pubsw/Linux2/packages/mni/current/bin/../share/mni_autoreg 
-protocol icbm transforms/tmp.talairach.7133/src.mnc 
transforms/talairach.auto.xfm


Can't locate shellwords.pl in @INC (@INC contains: 
/autofs/cluster/pubsw/1/pubsw/Linux2/packages/mni/1.4/bin/../lib/mni_autoreg 
/usr/local/freesurfer/stable6_0_0/mni/share/perl5 
/usr/local/lib64/perl5 /usr/local/share/perl5 
/usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl 
/usr/lib64/perl5 /usr/share/perl5 .) at 
/space/lyon/9/pubsw/Linux2/packages/mni/current/bin/mritotal line 460.


*ERROR*: mritotal failed, see transforms/talairach.log

I have tested the recon-all with another Bay2 data (from different 
project in our group), and it worked perfectly (with version 6.0.0) 
with the same script. Thus, I did not think this is due to my script 
or FS version..


Thanks,

Jeungchan


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] DenoiseImage shifting scan orientation

[Douglas N. Greve]

have you tried asking the ANTS people?

On 4/6/2022 10:05 AM, Nathan Kindred (PGR) wrote:


External Email - Use Caution

Hi,

I have been using DenoiseImage from ANTs during pre-processing 
(DenoiseImage -i T1.nii -o denoised.nii.gz -v), however for some scans 
I am having an issue where this step is changing the scan orientation.


The scans appear shifted so they now no longer match the orientation 
of my T2 scans. Does anyone know why this is happening and how to 
prevent it?


Thank you,

Nathan


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Inverse transform

[Douglas N. Greve]

The rawavg.mgz should be the same dimension as your T1 MPRAGE. Why are 
they not? Look at the dims for the  volume subject/mri/orig/001.mgz


On 4/4/2022 2:25 AM, Aleksandra Szum-Jakubowska wrote:


External Email - Use Caution

Dear Freesurfer Experts,
I conduct the segmentations' examines using Freesurfer recon-all (for 
segmentation hippocampus and ventricles), SAMSEG (for ventricles) and 
using FSL FIRST (for hippocampus). Now I have a problem with compare 
the result (calculating overlap).

For Freesurfer and FIRST I used T1 MRAGE image (dimentions 176x256x256).
For Samseg I used T2 FLAIR images coregistered to T1 MPRAGE 
(dimentions 176x256x256)

I have result from Freesurfer with dimensions 256x256x256
I have results from FSL First and SAMSEG with dimensions 176x256x256.

It is important that all results are concerned other spaces, so I 
cannot calculate overlap using that results and I have to perform 
transformation to the same space.


I tried doing this:
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz 
--regheader aseg.mgz
but my rawavg image has dimensions 176x256x174).
But when I used brain.mgz or T1.mgz image, my results are moved.  I 
have no idea how to perform the properly inverse transformation for 
getting segmentation results in originally T1 MPRAGE space.


Could You give me some advice?

Thanks a lot for your help.

Best regards,
Aleksandra

UMB_MUB

  

Niniejsza wiadomosc oraz jej zalaczniki moga zawierac informacje 
chronione prawem. Jesli Panstwo nie jestescie adresatem tej 
wiadomosci, prosimy poinformowac o tym fakcie nadawce i usunac ja wraz 
z zalacznikami. Kopiowanie i/lub przesylanie dalej informacji 
zawartych w tej wiadomosci przez osoby do tego nieuprawnione jest 
zabronione.


  

The information in this e-mail may be legally privileged. It is 
intended solely for the addressee. Access to this e-mail by anyone 
else is unauthorised. If you are not the intended recipient, any 
disclosure, copying, distribution or any action taken or omitted to be 
taken in reliance on it, is prohibited and may be unlawful.


  

Administratorem Panstwa danych osobowych jest Uniwersytet Medyczny w 
Bialymstoku. Informacja dotyczaca zasad przetwarzania Panstwa danych 
dostepna jest pod adresem: https://www.umb.edu.pl/rodo



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Tkregister2 not opening GUI

[Douglas N. Greve]

autorecon1 will not create the white surface, you'll need to do at least 
autorecon2 or try adding --no-surfs to the tkregisterfv command lien


On 4/4/2022 11:12 AM, Isabelle Deschamps wrote:


External Email - Use Caution

My apologies. I did run autorecon1. I copied the wrong part of the 
script. Should I just run as you suggested -all and do the edits 
after? Freeview should open then, as I will have the required files.


isabelle

foreach i ("S0589" "S0601" "S0650" "S0669" "S0676" "S0682" "S0715" 
"S0727" "S0738")


recon-all -autorecon1 -subjid "$i"_FS

end

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


*Date: *Monday, April 4, 2022 at 10:56
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] Tkregister2 not opening GUI

*CAUTION:* This email originated from outside of Georgian College. Do 
not click links or open attachments unless you recognize the sender 
and know the content is safe.


That recon-all command does not actually do anything. You need to add 
a directive, eg, -all to do everything. You did not run it even as far 
as doing the talairach reg, so you can't check it yet. Why not just 
run everything and to the checks when it is done?


On 4/4/2022 10:11 AM, Isabelle Deschamps wrote:

*External Email - Use Caution *

Good morning,

Just to follow-up, on this thread.

I have permission to read and write. The lh.white does not exist
as I have only ran the

recon-all -i
/Volumes/CopyPaste/fMRI/fMRI/Freesurfer/"$i".anat.nii.gz -subjid
"$i"_FS

I wanted to verify the registration before moving on to the other
stages, and according to the tutorial, this is something that can
be done. Do you recommend that are run the rest of the pipeline
and then go back and verify registration?

Thank you for your help,

isabelle

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

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
*Date: *Sunday, March 27, 2022 at 16:59
*To: *freesurfer@nmr.mgh.harvard.edu

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Tkregister2 not opening GUI

*CAUTION:* This email originated from outside of Georgian College.
Do not click links or open attachments unless you recognize the
sender and know the content is safe.

Does
/Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/surf/lh.white
exist and do you have permission to read it? If yes to both, then
try running it with --debug as the first option, then send all the
terminal output

On 3/21/2022 5:02 PM, Isabelle Deschamps wrote:

*External Email - Use Caution *

I did try tkregisterfv, but I get the following error:

cannot find
/Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/surf/lh.white

[MacBook-Pro-4:~] Isa% tkregisterfv --fstal --s S0010_FS

According to the tutorial, if I leave the –surfs out, the
command should work but it does not.

I also tried running it with the –surf I get the same error.

I have only ran the following commands so far:

foreach i ("S0010" "S0028" "S0039" "S0057" "S0074" "S0081"
"S0096" "S0120" "S0131" "S0139" "S0146" "S0152" "S0163"
"S0168" "S0171" "S0179" "S0205" "S0250" "S0262" "S0263"
"S0272" "S0299" "S0300" "S0313" "S0328" "S0363" "S0372"
"S0375" "S0378" "S0391" "S0409" "S0418" "S0419" "S0432"
"S0442" "S0448" "S0451" "S0471" "S0481" "S0493" "S0504"
"S0509" "S0524" "S0525" "S0528" "S0537" "S0544" "S0557"
"S0589" "S0601" "S0650" "S0669" "S0676" "S0682" "S0715"
    "S0727" "S0738" "S0741" "S0747" "S0762" "S0768" "S0770"
"S0800" "S0809" "S0837" "S0839" "S0861" "S0888" "S0896"
"S0933" "S0949" "S0955" "S0982" "S0988" "S1031" "S1058"
"S1082" "S1088" "S1091" "S1128" "S1133")

recon-all -i
/Volumes/CopyPas

Re: [Freesurfer] Tkregister2 not opening GUI

[Douglas N. Greve]

That recon-all command does not actually do anything. You need to add a 
directive, eg, -all to do everything. You did not run it even as far as 
doing the talairach reg, so you can't check it yet. Why not just run 
everything and to the checks when it is done?


On 4/4/2022 10:11 AM, Isabelle Deschamps wrote:


External Email - Use Caution

Good morning,

Just to follow-up, on this thread.

I have permission to read and write. The lh.white does not exist as I 
have only ran the


recon-all -i /Volumes/CopyPaste/fMRI/fMRI/Freesurfer/"$i".anat.nii.gz 
-subjid "$i"_FS


I wanted to verify the registration before moving on to the other 
stages, and according to the tutorial, this is something that can be 
done. Do you recommend that are run the rest of the pipeline and then 
go back and verify registration?


Thank you for your help,

isabelle

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


*Date: *Sunday, March 27, 2022 at 16:59
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] Tkregister2 not opening GUI

*CAUTION:* This email originated from outside of Georgian College. Do 
not click links or open attachments unless you recognize the sender 
and know the content is safe.


Does /Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/surf/lh.white 
exist and do you have permission to read it? If yes to both, then try 
running it with --debug as the first option, then send all the 
terminal output


On 3/21/2022 5:02 PM, Isabelle Deschamps wrote:

*External Email - Use Caution *

I did try tkregisterfv, but I get the following error:

cannot find
/Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/surf/lh.white

[MacBook-Pro-4:~] Isa% tkregisterfv --fstal --s S0010_FS

According to the tutorial, if I leave the –surfs out, the command
should work but it does not.

I also tried running it with the –surf I get the same error.

I have only ran the following commands so far:

foreach i ("S0010" "S0028" "S0039" "S0057" "S0074" "S0081" "S0096"
"S0120" "S0131" "S0139" "S0146" "S0152" "S0163" "S0168" "S0171"
"S0179" "S0205" "S0250" "S0262" "S0263" "S0272" "S0299" "S0300"
"S0313" "S0328" "S0363" "S0372" "S0375" "S0378" "S0391" "S0409"
"S0418" "S0419" "S0432" "S0442" "S0448" "S0451" "S0471" "S0481"
"S0493" "S0504" "S0509" "S0524" "S0525" "S0528" "S0537" "S0544"
"S0557" "S0589" "S0601" "S0650" "S0669" "S0676" "S0682" "S0715"
"S0727" "S0738" "S0741" "S0747" "S0762" "S0768" "S0770" "S0800"
"S0809" "S0837" "S0839" "S0861" "S0888" "S0896" "S0933" "S0949"
"S0955" "S0982" "S0988" "S1031" "S1058" "S1082" "S1088" "S1091"
"S1128" "S1133")

recon-all -i
/Volumes/CopyPaste/fMRI/fMRI/Freesurfer/"$i".anat.nii.gz -subjid
"$i"_FS

end

I wanted to verify the registration at this point, but I can.

Thank you for your help,

isabelle

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

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>on behalf of
Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
*Date: *Thursday, March 17, 2022 at 22:51
*To: *freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Tkregister2 not opening GUI

*CAUTION:* This email originated from outside of Georgian College.
Do not click links or open attachments unless you recognize the
sender and know the content is safe.

Can you try tkregisterfv ? The old tk tools are not supported any
more. tkregisterfv uses freeview

On 3/17/2022 6:03 AM, Nathan Kindred (PGR) wrote:

*External Email - Use Caution *

Hi Isabelle,

It’s been a couple of years since I ran FreeSurfer on a Mac,
but I also have had this issue before and it was due to the
macOS. I don’t know if anything has changed recently but if
not then the only solution would be to try to install an older
macOS that 

Re: [Freesurfer] slice timing for multiband fMRI

[Douglas N. Greve]

You can give mkanalysis-sess the slice order with -stc as you would with 
an ordinary non-accellerated scan. Then give it the number of slice 
groups with -ngroups nSliceGroups
I don't quite remember what nSliceGroups means, but I think it means the 
number of simultaneously acquired slices.

On 3/28/2022 3:21 AM, Laura Doll wrote:
>  External Email - Use Caution
>
> Hi everyone,
>
> We are currently piloting an fMRI measurement with multiband sequence on a 3T 
> Siemens scanner to increase resolution, but I don't know how to do the slice 
> timing correction:
> I assume, that I have to use a slicedelay file instead of the usual 
> up/down/even/odd/siemens flags? But how do I know which slices were excited 
> simultaneously?
>
> Our multiband acceleration factor is 2, if I got our MRI physicist correctly, 
> GRAPPA acceleration is also 2, and we are using a TR of 2s.
> More details of the sequence are in the attached pdf (which is unfortunately 
> in German).
>
> Looking forward to any suggestions.
>
> Best,
> Laura
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Questions regarding ROI creation for SPM based on FreeSurfer parcellation

[Douglas N. Greve]

I would probably just use the 1st option.

On 3/30/2022 5:20 AM, Falko Mecklenbrauck wrote:


External Email - Use Caution

Dear FreeSurfer-Experts,

I’m in need of your experience to help me with a decision in my 
current project:


I want to use certain areas, that were identified by structural graph 
theoretical analyses based on the FreeSurfer parcellation and DTI 
data, as Regions of interest in SPM. We already have a script that 
helps with the transfer and creation of ROIs however it is still 
unclear what’s the best way to create the ROIs. Here are a few of my 
ideas and pros and cons regarding these:


1. Parcel the MNI T1 standard brain used in SPM with FreeSurfer and 
create the ROIs from the identified regions from that
PRO: direct use of the standard space, that is later used in SPM’s 
group level analysis
CON: SPM tends to be peculiar in giving information about their 
standard template, so I am unsure if the one I found in the 
spm12-folder is the correct one to use


2. Extract the ROIs of each participant individually and then use SPM 
to normalize and averaging/summing these

PRO: Ending up in same space as the SPM analysis
CON: identified regions are (at the moment) not individually 
identified, although they could be; normalization is difficult with 
just ROIs
ALTERNATIVE: use FreeSurfer not on individual “raw” T1 images but on 
already normalized T1 images and then do the ROIs individually per 
participant.


Probably, I am also forgetting another possibility.
I am looking forward to hearing your ideas and comments.
Thank you very much in advance,
Best wishes,
Falko


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] mri_vol2vol anatomical to functional

[Douglas N. Greve]

Have you visually verified that the registration is correct (only work 
with LTAs) using tkregisterfv ?
How are you viewing the combined anatomical/functional in pics? If you 
just load the functional without a registration file, then that is not 
right.


On 3/29/2022 11:28 AM, Manenti, Giorgio wrote:


External Email - Use Caution

I'm not sure I understand what you are saying or what the problem is.

Can you provide the actual command line you are using, all the terminal

output, and a picture that shows what the problem is?

Hi Douglas,

thank you for your time; I am trying to get the ribbon at functional 
space resolution (I need it to extract the white matter from my ROIs)


Here I am copying the 2 commands (one using .reg file, the second 
using .lta) I am using, and the terminal terminal outputs. Attached 
you will also find 3 screenshots from freeview with 1) original ribbon 
2) ribbon transformed in functional space using the .reg file and 3) 
ribbon transformed using the .lta file.


(Please Note:  I am using Matlab to integrate this analysis in the 
general pipeline, so the command are started by the s=system() function;)


%%REG

s=system(['mri_vol2vol --reg 'regpath ' --mov 'inputvol ' --targ 
'funcTemp ' --o 'outputvol ]);


regio_read_register: loading lta

Matrix fromregfile:

0.99982  -0.01069 -0.01533  -0.11505;

0.01423  -0.09676 0.99521  -0.84297;

0.01212   0.99525 0.09659  -5.72961;

0.0   0.0 0.0   1.0;

movvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz

targvol 
FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii


outvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon_func.mgz

regfile FSfast_struc/all_sub/f02_Sess03/bold/register.dof6.lta

invert 0

tal 0

talres 2

regheader 0

noresample 0

interp trilinear(1)

precision float(3)

Gdiag_no -1

Synth 0

SynthSeed 1649422337

Final tkRAS-to-tkRASMatrixis:

0.99982  -0.01069 -0.01533  -0.11505;

0.01423  -0.09676 0.99521  -0.84297;

0.01212   0.99525 0.09659  -5.72961;

0.0   0.0 0.0   1.0;

Vox2Vox Matrixis:

2.01888  -0.03096 0.02351   23.93213;

0.02447   0.19504 -2.18955   197.85437;

-0.02873  -2.00955 -0.21287   240.49161;

0.0   0.0 0.0   1.0;

Resampling

Output registrationmatrixisidentity

mri_vol2vol done

%%LTA

s=system(['mri_vol2vol --lta 'ltapath ' --mov 'inputvol ' --targ 
'funcTemp ' --o 'outputvol ]);


Matrix fromLTA:

0.99983  -0.01069 -0.01533  -0.11505;

0.01423  -0.09676 0.99521  -0.84293;

0.01212   0.99525 0.09659  -5.72960;

0.0   0.0 0.0   1.0;

Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz 
FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii


INFO: src volume infodiffersfromtheonestoredinlta.getsmodifiednow.

volume geometry:

extent  : (256, 256, 256)

voxel   : ( 1., 1.,  1.)

x_(ras) : (-1., -0., -0.)

y_(ras) : ( 0.,  0., -1.)

z_(ras) : (-0.,  1.,  0.)

c_(ras) : ( 0.2540,  9.2232,  8.1562)

file    : Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz

volume geometry:

extent  : (104, 104, 69)

voxel   : ( 2.0192, 2.0192,  2.2000)

x_(ras) : (-0.9995, -0.0137,  0.0296)

y_(ras) : ( 0.0126, -0.9991, -0.0397)

z_(ras) : ( 0.0301, -0.0393,  0.9988)

c_(ras) : ( 1.5530, 16.4346, 14.9788)

file    : bold/template.nii.gz

INFO: dst volume infodiffersfromtheonestoredinlta.getsmodifiednow.

volume geometry:

extent  : (104, 104, 69)

voxel   : ( 2.0192,  2.0192,  2.2000)

x_(ras) : (-0.9995, -0.0137,  0.0296)

y_(ras) : ( 0.0126, -0.9991, -0.0397)

z_(ras) : ( 0.0301, -0.0393,  0.9988)

c_(ras) : ( 1.5530, 16.4345, 14.9788)

file    : 
FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii


volume geometry:

extent  : (256, 256, 256)

voxel   : ( 1.,  1.,  1.)

x_(ras) : (-1., -0., -0.)

y_(ras) : ( 0.,  0., -1.)

z_(ras) : (-0.,  1.,  0.)

c_(ras) : ( 0.2540, 9.2232,  8.1562)

file    : Anatomy_Processed/hum_15496.long.long002/mri/orig.mgz

movvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz

targvol 
FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii


outvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon_func.mgz

regfile FSfast_struc/all_sub/f02_Sess03/bold/register.dof6.lta

invert 0

tal 0

talres 2

regheader 0

noresample 0

interp trilinear(1)

precision float(3)

Gdiag_no -1

Synth 0

SynthSeed 1649445621

Final tkRAS-to-tkRASMatrixis:

0.99828   0.04446 -0.03809   2.43217;

0.03729   0.01869 0.99913   9.13850;

-0.04513   0.99884 -0.01700   12.13850;

0.0   0.0 0.0   1.0;

Vox2Vox Matrixis:

2.01577  -0.07692 -0.09781   28.12225;

-0.09113  -0.03433 -2.19744   198.19705;

-0.07530  -2.01747 0.04112   244.54424;

0.0   0.0 0.0   1.0;

Resampling

Output registrationmatrixisidentity

mri_vol2vol done

Many thanks again,

Best

Giorgio

Re: [Freesurfer] lh.white surface co-registration

[Douglas N. Greve]

On 3/28/2022 2:39 PM, Salar Dini, Elaheh wrote:


External Email - Use Caution

Thanks Douglas. I have read the freesurfer official page on surface 
co-registration, but I still can't grasp where the .lta file comes 
from in case of surface co-registration. I suspect that you can't use 
the same lta file that you used for vol2vol. Is that correct? Where 
can I obtain the .lta file from then?



Yes, same as vol2vol. Use bbregister to get the lta



Also, on another note, may I ask if I have a correct understanding of 
lh.thickness file? My understanding is that this specific file doesn't 
have any specific defined coordinate attached to it? It's just the 
cortical thickness information at each point? Or am I wrong and there 
are x,y,z coordinates signature for each spatial point? If the latter 
is correct, is there a way to change those coordinates to the new ones 
as well?


It is just the thickness values at each point. They xyz is implicitly 
associated with the point.



I appreciate your time and help as always.

Ela





_

From: Douglas N. Greve 
<https://secure-web.cisco.com/17OodPYghcF8xu13apLQJnrZwMndsOUlTSuCjvDDt6SgCol09_qAW93OBD8HhMdCRhhl9p3tXHLgU2kayTTIUhKR1JcVQGDbPeMz4uamfAxgqeI6wwHMmztdYPBAnZVlCy19Ekdtc1uQTH2Zrh2xlvBp5Ejm9RGSsgKycmLAtNrclE4ZHJbgajxmX7UsoHXpw08LO8oc-p-jPUBlFXdrQTeD7k8AaHvTpPlXra_Qt4TnhPl94xaInD02P105E3LmdwPQYDQNgdSYeSuL5aBcf0HIpq7BfG6v1Gzvaj5018URU_q5gNLDINGhPaC4IH17u/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Douglas%2BN.%2BGreve%2522>


Sent: Thu, 17 Mar 2022 19:45:36 -0700 
<https://secure-web.cisco.com/1ozBajFUF0nJ2pFTI06qybqYM32BhDzC3THPssslmlxgusNPpxFyKmufcX1ZMtVPm9pZCXFXxxivy-l2hUWZjVubKSr9UW8itjLKn-flYrxlH_fwsBYieTW_rsGangYku1jYmUXjNJ9dasDXI9V1zY9HvjYjNkryfSYj-pNd3oOIPL41GlzjNQHoBbwjb1hsDxKt8kAJzJlliWuxZHeeA9bsH2GLbks2fxliJrSNDw7sdwLv7cTLdV07tZT3iVSyONdhelYhpnWzHVbkrHfx4LzOzw0bhSuY1PXbj8RlE_zbutry9CA0lkP7bKdUr3Zr-/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20220317>


To: elaheh.salad...@yale.edu



If you have an LTA file, you can run
mris_apply_reg --lta lh.white your.lta lh.white.newcoords


*From:* Salar Dini, Elaheh
*Sent:* Wednesday, March 16, 2022 4:15 PM
*To:* Freesurfer support list 
*Subject:* lh.white surface co-registration
Dear Freesurfer experts,

Is there a way to move lh.white of a subject to a new coordinate? 
Something quite similar as volumetric co-registration but for 
surfaces. To be exact, I have moved a subject's brainmask.mgz, 
orig.mgz, aparc+aseg.mgz, and T1 mgz to a new coordinate using 
mri_coreg and subsequently vol2vol, but the surfaces are still in the 
original coordinate and doesn't match the volumes. Is there a way to 
move the surface files to the new coordinate?


OS: Centos 7, Freesurfer version: 7.2.0

Thank you for your time and help.
Kindly,
Ela






___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] repeated measures ANOVA 2x2 covariate

[Douglas N. Greve]

See https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis

On 3/28/2022 3:18 AM, Agurne Sampedro Calvete wrote:


External Email - Use Caution

Dear Douglas,

Do you mean calculate a type of change score (e.g. time2 minus time1) 
and then compare the differences between the two groups? How can I 
calculate the difference between the two time points?

Thank you very much.

Best regards,

Agurne





El dom, 27 mar 2022 a las 23:07, Douglas N. Greve 
() escribió:


Probably the easiest thing to do since you have only two time
points is to compute the difference between the two, then just do
a simple group analysis where you include the covariates that you
want.

On 3/23/2022 10:00 AM, Agurne Sampedro Calvete wrote:


External Email - Use Caution

Dear FreeSurfer experts,

I am doing a repeated measures ANOVA 2x2 (2 groups and 2 time
points) and I would like to include in the analysis a covariate
that is constant over the 2 times (e.g., baseline medication).
I would like to see a "group x time x covariate" interaction.

What should the design look like? I know that without covariate
the design is as follows:


GroupDescriptorFile 1

Class Subject1

Class Subject2

Variables    Tp1vsTp2.Group1   Tp1vsTp2.Grroup2

Input  Subject1_time1  Subject1
1 0

Input  Subject1_time2  Subject1 -1 0

Input   Subject2_time1  Subject2 0 1

Input  Subject2_time2  Subject02  0 -1

Design matrix:

1 0 1 0

1 0 -1 0

0 1 0 1

0 1 0 -1


Contrasts (.mtx files):
Tp1vsTp2.Group1        0 0 1 0
Tp1vsTp2.Group2        0 0 0 -1
Interaction (timexgroup) 0 0 1 -1


However, I do not know how I could include the interaction with
that covariate.

Thank you very much in advance.

Kind regards,

Agurne



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
<https://secure-web.cisco.com/1IuqXuXyJX5KD8JRY0t7329bqQKarO63jDbBFnaSqMtBNof0r4rJhamzR-1IFC7L5NF9QypcA0qEPLfHMAmIWZbY1k8L4vMUR2MX0VjfRsmyr4s5EJ_TT5ylipKF30Ro4H9Vgi-4F7Az2PUIeaX_C6lkIllxCGn4xH-FKcg8XGGTGhRNvVe2W_xHtet8hsbkegWqc2bynGCsRCmANRBiMOUlHLNhwYz77WVlgOic_d_uiVBtBGYTWppr8yOmjGxA0G0SVESVmxkIrOYLs1PQxdHRxXPjb6FrtimwGaF23cx8Go4F7YaCxeuMWNdB8NT-U/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

<https://secure-web.cisco.com/1IuqXuXyJX5KD8JRY0t7329bqQKarO63jDbBFnaSqMtBNof0r4rJhamzR-1IFC7L5NF9QypcA0qEPLfHMAmIWZbY1k8L4vMUR2MX0VjfRsmyr4s5EJ_TT5ylipKF30Ro4H9Vgi-4F7Az2PUIeaX_C6lkIllxCGn4xH-FKcg8XGGTGhRNvVe2W_xHtet8hsbkegWqc2bynGCsRCmANRBiMOUlHLNhwYz77WVlgOic_d_uiVBtBGYTWppr8yOmjGxA0G0SVESVmxkIrOYLs1PQxdHRxXPjb6FrtimwGaF23cx8Go4F7YaCxeuMWNdB8NT-U/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
The information in this e-mail is intended only for the person to
whom it is addressed.  If you believe this e-mail was sent to you
in error and the e-mail contains patient information, please
contact the Mass General Brigham Compliance HelpLine at
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://www.massgeneralbrigham.org/complianceline

<https://secure-web.cisco.com/1x9B7YpCjD7VW1WOl4gdYgjWJaMAl6ZcCMJGhmN5gUtZ0YXG8Enkx51L_R3G0cJ693F_fG5lCRkt4sxeDiV13uqWwSBBh_dyzortnZiOS9drMMD_P-Au8qnLxyoMxq9TJmuajNMhlryO_xv-wNYC3iu1BLBD_kEsGxWrGA6-N6mF7A1nSHgnXIJgR2v-cmbpxUGY4MuhbsMa5U7WRmtPxHAdsunuA3KeCPkQmFjsE_jrbOB8wtLJtpozQAH_7EkqvXtPEwEQEBzflVC67XgqyMHWtSJPj3uY5ZyoKkIqjzXAhaXAKRtC7hi6nJ5Jq2vbw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
<*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://www.massgeneralbrigham.org/complianceline

<https://secure-web.cisco.com/1x9B7YpCjD7VW1WOl4gdYgjWJaMAl6ZcCMJGhmN5gUtZ0YXG8Enkx51L_R3G0cJ693F_fG5lCRkt4sxeDiV13uqWwSBBh_dyzortnZiOS9drMMD_P-Au8qnLxyoMxq9TJmuajNMhlryO_xv-wNYC3iu1BLBD_kEsGxWrGA6-N6mF7A1nSHgnXIJgR2v-cmbpxUGY4MuhbsMa5U7WRmtPxHAdsunuA3KeCPkQmFjsE_jrbOB8wtLJtpozQAH_7EkqvXtPEwEQEBzflVC67XgqyMHWtSJPj3uY5ZyoKkIqjzXAhaXAKRtC7hi6nJ5Jq2vbw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>>
.
Please note that this e-mail is not secure (encrypted).  If you do
not wish to continue communication over unencrypted e-mail, please
notify the

Re: [Freesurfer] Beta values

[Douglas N. Greve]

Can you send the fsgd file?

On 4/1/2022 3:28 PM, Laura Willers de Souza wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm extracting beta values ​​from some analyzes and I would like to 
know if I'm extracting and interpreting these values ​​correctly.


To extract the beta values ​​I used this command:
mri_segstats --seg 
lh.cortisol_CSF.glmdir/cortisol_CSF_slope/perm.th20.neg.sig.ocn.mgh 
--i lh.cortisol_CSF.glmdir/beta.mgh --excludeid 0 --avgwf 
lh.cortisol_CSF.beta.clusters.dat


The model consists of 1 group and 1 covariate.
I used the contrasts for intercept and slope.
The beta values ​​extraction file contains 2 lines (image below).

  * Would the first line be the beta value for the intercept and the
second line for the slope?
  * Thus the glm equation for the 1st cluster would be:   cortical
thickness = 2.57 - 0.12X + n


Is this correct?

Thanks in advance!

*Laura Willers de Souza *

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Medial prefrontal cortex

[Douglas N. Greve]

Have you looked in the destrieux atlas? It is the a2009s annot.

On 4/1/2022 10:28 AM, Patricia Schwery wrote:


External Email - Use Caution

Hi there,


I would like to know if someone could tell me how i can measure the 
medial prefrontal cortex (mPFC) with freesurfer as i see it is 
displayed within the superior frontal but i would need only the mPFC.



I thank you so much for your help.


Patricia


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] transitioning from tkmedit to freeview

[Douglas N. Greve]

Note also that  you can use tkmeditfv to run freeview with tkmedit-like 
options (and more).


On 3/30/2022 8:00 PM, Wang, Ruopeng wrote:

Hi Victor,

On Mar 30, 2022, at 4:30 PM, Zeng, Victor (BIDMC - Keshavan - 
Psychiatry)  wrote:


External Email - Use Caution

Hi,

My lab has been using tkmedit, although it is deprecated, for pial 
edits. We resist transitioning towards freeview due to changed 
functionality, which I understand because freeview is used for more 
than just pial edits but - Are there any tools that can I am not 
aware of that makes freeview similar to tkmedit?


 1. the main thing is the removal of keyboard shortcuts. Being able
to press ctrl-G to turn on/off segmentation rapidly, and ctrl-1/2
to turn on/off the T1.mgz rapidly makes quality checking a lot
faster rather than having to manually click on the volume you
want to turn off.

In freeview you can use Alt+V to turn on/off a volume and Alt+C to 
cycle through volumes. You will find all the available functions with 
short cuts under “Layer” menu.


 2.  likewise, being able to press x/y/z to easily switch between
views (sagittal, axial etc)



This can be achieved with Alt + x/y/z. All the available short cuts 
can be found under “View” menu.


 3. tkmedit in my lab was configured so that right click replaced
voxel intensity to zero, and wheel click replaced voxel intensity
to voxel intensity of the T1.mgz (essentially restoring the
original voxel intensity). Can you configure the options so that
it readily does that (I understand that instead of right click it
would probably be left click now)

There is an option under Tools -> Preferences -> Special Settings -> 
Edit to allow right click to erase a voxel.


Best,
Ruopeng




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] GLM analysis - volume and surface area

[Douglas N. Greve]

Hi, sorry for the late response. No, there is nothing else you have to 
do. Using perm is a really good idea with volume and area, so glad to 
hear that is what you are doing.

best
doug


On 3/10/2022 8:21 AM, Laura Willers de Souza wrote:


External Email - Use Caution

Of course!

To do GLM for volume and surface area analysis, is there any change in 
commands in relation tocortical thickness analysis? Like some 
more command, or some other detail that must be changed (besides, 
of course, the flag that specifies the measure to be analyzed) - 
I'm already using permutation in the correction of multiple comparisons.


Many thanks!

--

On 3/09/2022 15:20 PM, Douglas N. Greve wrote:

Can you just ask the question again so I don't have to sort it out myself?


---

On 2/22/2022 9:15 AM, Laura Willers de Souza wrote:

Thanks so much for the explanation!

There is something different in the analysis of volume and surface 
area in relation to the analysis of cortical thickness? Like some more 
command, or some other detail that must be changed (besides, of 
course, the flag that specifies the measure to be analyzed) - I'm 
already using permutation in the correction of multiple comparisons.




--

On 2/21/2022 15:20 PM, Douglas N. Greve wrote:

Yes, it is. It is confusing when you talk about area and volume 
sincethese are not point measures like thickness (ie, what is the 
volume orarea of a vertex?). The area of a vertex is computed as the 
mean of theadjacent triangles of the vertex. The volume is the mean of 
theneighboring truncated tetrahedra. When you run mris_preproc, it 
willapply a jacobian correction (like VBM). Otherwise, it operates the 
sameas if you had a thickness value at the vertex, ie, same GLM, etc. 
Makesure to use permutation for correction of multiple comparisons.


-

On 2/21/2022 12:13 PM, Laura Willers de Souza wrote:

Hello FreeSurfer Developers,

I would like to know if it is correct to perform volume and
surfacearea analysis using freesurfer's GLM!?

In several mailing list questions I have already seen instructions
forperforming these types of analysis. But I understand that
freesurferdoes vertex-wise analysis in the 2D surface space. So,
it is not clearto me how it is possible to evaluate a 3D
measurement, as volume, witha 2D method!?

I've also read that surface area analysis via vertex-wise
analysisdoesn't make much sense. The best would be to do ROI-based
analysis.Can you explain that to me?

Thanks in advance!

Att,

*Laura Willers de Souza *

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] WM error near the right putamen

[Douglas N. Greve]

This is actually a bug in version 7.[012]. This area is probably not 
valid anyway. We'll have a fix in 7.3


On 3/21/2022 7:31 PM, Gabor Perlaki wrote:


External Email - Use Caution

Dear all,

fswiki suggests that " There are regions where the surfaces are not 
intended to be accurate that you should be aware of: Areas around the 
hippocampus and amygdala. "


I also found inaccuracy of the WM surface near the putamen and 
accumbens regions. WM surface goes into the putamen (please see the 
attached picture). Do I need to fix this error or is it normal? Are 
the thickness of ctx-rh-medialorbitofrontal and the volume of right 
putamen valid in this case?

Thank you in advance,
Gabor


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] lh.pial and rh.pial is 0Kb, I cannot open them by using freesurfer

[Douglas N. Greve]

On 3/24/2022 4:49 PM, Muhammed Görünen wrote:


External Email - Use Caution

Hi,

I run recon-all process for a subject's T1 data. At the end, the pial 
files are 0Kb and I cannot open them from python.
Did it end with an error? Did you run out of space? What version of FS? 
Can you send the recon-all.log file?
What would be the problem here? Also, is there any difference between 
pial file and pial.T1 file? I will be happy if you can answer.

The ?h.pial should be a symbolic link to ?h.pial.T1


Best,
--Muhammed

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] [External] Re: [External] Re: classes for GLM analysis

[Douglas N. Greve]

it does not suprise me that 2014 is not working as that is pretty old. 
I've been using 2018 and that seems to work.


On 3/24/2022 9:31 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


External Email - Use Caution

It is seemingly working in matlab R2021b rather than matlab R2014a. 
Can you confirm this? Otherwise that should be noted in the wiki


Get Outlook for iOS 
<https://secure-web.cisco.com/1qkaPGnEUesscFizw2LPsI4p5jrKjbVVDRinN3KloptB7-u42_llA31m49Ufr_8Clot1-MtBqsFxcEfgWntv3Xxct-AzZoSOiP0ZCcpqxJgJIZshsNB0FNW2KvKglGGKpPSH5xz-sZ_IicnTlZm3kN5YtOsX7TkYCsoY7pREyQYwC5YkV327GXxRAggHHpVOJXY1_xqDa_4ZMygOVqFhEfKqQROsL-mQmUUMj0RbMgk-u8weU3TZ4Q0UlLfAH7Ukpwj7x8ucKzh-QcMS9atfGFlKeRcgg749P_jcVOPKLVJyZk6sEnKn_k2vj6-aHa3iS/https%3A%2F%2Faka.ms%2Fo0ukef>


*From:* Zeng,Victor (BIDMC - Keshavan - Psychiatry) 


*Sent:* Wednesday, March 16, 2022 5:52:54 PM
*To:* Freesurfer support list 
*Subject:* Re: [External] Re: [Freesurfer] [External] Re: classes for 
GLM analysis
Sorry for the different approach - but I just propensity matched 
people for now so I don't have to deal with so many confounding 
variables. Now I am trying to do multiple correction, with 
mriglmfit-sim not working because of high FWHM (you can ignore my 
other email about that...). So therefore, I am trying palm, and come 
up with this error:


Running PALM alpha119 using MATLAB 8.3.0.532 (R2014a) with the 
following options:
-i 
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisMGH/Replication/rh.pial_lgi.NCBT1_.10.mgh
-m 
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisGLM/Replication/rh.pial_lgi.NCBT1_.10.glmdir/mask.mgh

-d design.mat
-t design.con
-logp
-n 1000
-C 1.958920
-o fsp
-twotail
-s 
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white 
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white.avg.area.mgh

Found FSL in /usr/share/fsl/5.0
Found FreeSurfer in /usr/local/freesurfer/dev7
Found SPM in /home/gamma/spm8
Loading surface 1/1: 
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white
Reading input 1/1: 
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisMGH/Replication/rh.pial_lgi.NCBT1_.10.mgh

Reading design matrix and contrasts.
Elapsed time parsing inputs: ~ 7.22525 seconds.
Number of possible permutations is 9.7768e+204.
Generating 1000 shufflings (permutations only).
Building null distribution.
0.1% [Design 1/1, Contrast 1/1, Shuffling 1/1000, Modality 1/1]
/bin/sh: line 1: 14553 Illegal instruction     matlab -display iconic 
< run_palm.m

error: cannot find expected palm output "fsp_clustere_tstat_fwep.mgz"


This is with Freesurfer dev 20211206. Thanks and sorry for so many 
questions lately

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

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


*Sent:* Wednesday, March 16, 2022 6:09 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* [External] Re: [Freesurfer] [External] Re: classes for GLM 
analysis

Can't tell without the fsgd file

On 3/7/2022 8:30 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


External Email - Use Caution

Just to double check the numbers - I seem to have been getting into 
an error in how many columns in the FSGD it is expecting.


I have 9 different sites, 4 different patient groups, and M/F -> 72 
classes.
I also am covarying for four different factors, so the contrast 
matrix I am making is 72*(4+1) long. Since I want to regress out the 
four factors completely, only the first 72 numbers in 360 contrast 
matters. My FSGD file has 4 columns e.g like


Input GP0001 NCBostonM 60 12000 -0.01 -0.02

It says ERROR: gdfReadV1: Input line 1, subjid = GP0001
Found 4 variables, expected. 10

Where is this 10 coming from?


Get Outlook for iOS 
<https://secure-web.cisco.com/1CmpY6foykm2rgWGgaYrcRzr0P1qxgDx48OEn8PvE6j99IOUxv9ZDpni6l_fwdI0OnVsStgqydtrgGvRxD4iZJCyTKZa8Dw1KUY3OONMPI3cE7Qi1l_KELRl8n24hVPEEhocKMhRUg_1t85ggKzUKEZVAOIz7yPHUVLLZfk39UNS0PrEnMBJfo8A8Np9KAmjpIlyC9joWFe0HLW07DCyeto9M92KBQUpVEzQgHjceUKhsqMkGslqpLpjBUqM27_qtOLXWiFNOjeMJAJGG0Y8htddsdMi5sJj7xe3NOfGAHj9CoVwCN-4CWO9uzpjm0hSj/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F17NelGJ6sesfwsPcUOcH7NLCIl8poWbpnFKSkRs_Tip5fMdIWsq5voGkTtGHzn1xIw9teACerNPVmg1UDC86aygtsYvxBGSc9QJKdZxMm3Y3dOV1lpERz-8vKc-W35SxGCTR7slBrlWoSLntQcxVoI5N_W36lxBKe00LuMnuLFccVkMttfaKkDki2gEKr8rEZfBAP4oLIvzypnlk5I1Xvxx0pH9IvNr3Jhcz2dIr3phyRLDzKH1xF2zITaP2GCEjdSzIMvOq7JGNJG1jnPXQseKuq2b3dOWmyQa-nctRxcywiYYaHXfKoduT5XAwSGGo-wLjxNlMJmdBY1XoH2zdiyw%2Fhttps%2A3A%2A2F%2A2Faka.ms%2A2Fo0ukef__%3BJSUlJQ%21%21CvMGjuU%21vnOXunRQmCxtLIcEPxW_nYbG9yY7BIv3V7k4X1XUzyiTt2WwyEMm6bntnIqPAS9-nTX0Jg%24>


*From:* Zeng,Victor (BIDMC - Keshava

Re: [Freesurfer] Question about calculation of pial area in DKatlas

[Douglas N. Greve]

On 3/24/2022 2:53 AM, Dongyue Zhou wrote:


External Email - Use Caution

Dear FreeSurfer experts:
 I want to calculate mean pial surface area in DKatlas in individual 
space.And I know the function read_annotation.m in $FREESURFER_HOME/matlab for 
loading this atlas.
And if I can load sub/surf/?h.area.pial as the area in each vertice and 
calculate mean pial area by dividing sum PSA of all vertices in one ROI by the 
number of vertices in this ROI?

That should work

But why my result is not the same as result in sub/stats/?h.aparc.stats ?  Does 
the column named surface area represent mean PSA in each ROI?
The value in aparc.stats is the total, not the mean. I'm not sure why 
you would want the mean.




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] mri_vol2vol anatomical to functional

[Douglas N. Greve]

I'm not sure I understand what you are saying or what the problem is. 
Can you provide the actual command line you are using, all the terminal 
output, and a picture that shows what the problem is?

On 3/23/2022 2:46 PM, Manenti, Giorgio wrote:
>  External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I am getting problems to transform my xh.ribbon.mgh from anatomical 
> 256x256x256 to functional 104x104x69 space.
>
> When converting the ribbon via “ mri_vol2vol —reg REGfile —mov INPUT —targ 
> funcTEMPLATE —o OUTPUT “ and checking via freeview, i am getting the right 
> functional space dimensions but the INPUT and OUTPUT .mgz are never 
> overlapping. Why am i getting this misplacement ? Is this problem due to the 
> register file i provide or maybe it is just a visualisation error (perhaps 
> freeview is not the best way to check the conversion).
>
> I tried to change REGfile by providing the 1) init.register.dof6.dat and 2) 
> register.dof6.lta (changing “—reg with —lta”). I am getting an almost perfect 
> merge when using the .lta file but still the two volumes are misaligned.
> I tried mri_label2vol as well, but as expected i got worse results.
>
> To provide a minimum more detail, after recon-all i process the anatomy with 
> the longitudinal recon. At that point i use the longitudinal anatomy to 
> register the functional data, which i process by 1) mk-template 2) topup & 
> applytopup.
>
> Many thanks in advance
> Warm regards
>
> Giorgio
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] mri_segment_hypothalamic_subunits error: Illegal instruction 4

[Douglas N. Greve]

You're command line is incomplete (it needs more than just --s). Run it 
with --help and/or visit the wiki page


On 3/23/2022 2:40 PM, Alice Tao wrote:


External Email - Use Caution

Thank you so much for the response! Unfortunately, that is the full 
command line and output:


$ mri_segment_hypothalamic_subunits --s
Illegal instruction: 4

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias 
Gonzalez, Juan E. 

*Sent:* Wednesday, March 23, 2022 10:51 AM
*To:* Freesurfer support list 
*Subject:* [EXTERNAL] Re: [Freesurfer] 
mri_segment_hypothalamic_subunits error: Illegal instruction 4

Dear Alice,

Can you please send us your full command line and output?

Cheers,

/E


Juan Eugenio Iglesias
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* http://www.jeiglesias.com 
 




On Mar 23, 2022, at 10:41, Alice Tao  wrote:

External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to use the mri_segment_hypothalamic_subunits tool on 
subjects that have been analyzed with recon-all as described on the 
wiki page (*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/HypothalamicSubunits 
), 
but I received the following error when I run the 
mri_segment_hypothalamic_subunits command 
(mri_segment_hypothalamic_subunits--s):


  Illegal instruction: 4

Does anyone have any suggestions on how to trouble-shoot this 
problem? recon-all does not seem to have any issues.


1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
2) Platform: macOS Monterey, version 12.2.1

Thank you!
Alice
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message 

Re: [Freesurfer] repeated measures ANOVA 2x2 covariate

[Douglas N. Greve]

Probably the easiest thing to do since you have only two time points is 
to compute the difference between the two, then just do a simple group 
analysis where you include the covariates that you want.


On 3/23/2022 10:00 AM, Agurne Sampedro Calvete wrote:


External Email - Use Caution

Dear FreeSurfer experts,

I am doing a repeated measures ANOVA 2x2 (2 groups and 2 time points) 
and I would like to include in the analysis a covariate that is 
constant over the 2 times (e.g., baseline medication).

I would like to see a "group x time x covariate" interaction.

What should the design look like? I know that without covariate the 
design is as follows:


GroupDescriptorFile 1

Class Subject1

Class Subject2

Variables    Tp1vsTp2.Group1   Tp1vsTp2.Grroup2

Input   Subject1_time1  Subject1 1 0

Input   Subject1_time2  Subject1 -1    0

Input   Subject2_time1  Subject2 0 1

Input   Subject2_time2  Subject02  0 -1

Design matrix:

1 0 1 0

1 0 -1 0

0 1 0 1

0 1 0 -1


Contrasts (.mtx files):
Tp1vsTp2.Group1        0 0 1 0
Tp1vsTp2.Group2        0 0 0 -1
Interaction (timexgroup) 0 0 1 -1


However, I do not know how I could include the interaction with that 
covariate.


Thank you very much in advance.

Kind regards,

Agurne



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] qdec analysis error

[Douglas N. Greve]

Sorry, we are not supporting qdec anymore. You will need to use the 
command-line stream


On 3/23/2022 8:02 AM, David wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I have a problem. Can you help me

freesurfer version : 6.0.0

Load qdec when I run qdec.table.dat, the data is loaded correctly, but 
when I design, I choose discrete and continuous factors for analysis

The error log is as follows
：

Input table: /media/root/Backup_Plus2/new/RECON/qdec/qdec5.table.dat
Subj#, SubjID, Data...
    1 bd1 d Male 15.00 8.00
    2 bd2 d Female 19.00 13.00
    3 bd3 d Male 25.00 9.00
    4 bd4 d Male 17.00 12.00
    5 bd5 d Male 16.00 10.00
    6 bd6 m Female 22.00 12.00
    7 bd7 d Male 17.00 11.00
    8 bd8 d Female 19.00 13.00
    9 bd9 m Female 26.00 7.00
   10 bd10 m Male 53.00 15.00
   11 bd11 m Female 56.00 4.00
   12 bd12 d Female 21.00 14.00
   13 bd13 m Female 19.00 12.00
   14 bd14 m Female 32.00 15.00
   15 bd15 d Male 21.00 9.00
   16 bd16 d Male 16.00 10.00
   17 bd17 d Male 15.00 11.00
   18 bd18 d Female 32.00 10.00
   19 bd19 d Female 20.00 15.00
   20 bd20 d Female 17.00 11.00
   21 bd22 m Male 22.00 11.00
   22 bd23 m Female 28.00 6.00
   23 bd24 d Male 26.00 11.00
   24 bd25 m Female 24.00 9.00
   25 bd26 m Female 30.00 6.00
   26 bd27 m Female 20.00 12.00
   27 bd28 d Female 28.00 16.00
   28 bd29 m Female 18.00 12.00
   29 bd30 d Male 21.00 15.00
   30 bd31 d Female 30.00 16.00
   31 bd32 d Male 18.00 11.00
   32 bd33 d Female 16.00 10.00
   33 bd34 d Male 21.00 11.00
   34 bd35 d Female 15.00 10.00
   35 bd36 d Female 16.00 10.00
   36 bd37 d Male 19.00 14.00
   37 bd39 d Male 16.00 10.00
   38 bd40 m Female 20.00 14.00
   39 bd41 m Female 21.00 15.00
   40 bd42 d Male 23.00 9.00
   41 bd43 m Male 27.00 9.00
   42 bd44 d Female 15.00 8.00
   43 bd45 m Male 19.00 9.00
   44 bd46 d Female 16.00 11.00
   45 bd47 m Female 23.00 15.00
   46 bd48 m Male 18.00 13.00
   47 bd49 d Female 22.00 15.00
   48 bd50 d Female 17.00 11.00
   49 bd51 d Male 17.00 10.00
   50 bd52 d Male 27.00 15.00
   51 bd53 m Male 16.00 9.00
   52 bd54 d Male 18.00 12.00
   53 bd55 d Female 18.00 11.00
   54 bd56 m Female 16.00 10.00
   55 bd57 d Male 16.00 9.00
   56 bd58 m Male 22.00 9.00
   57 bd59 m Male 16.00 8.00
   58 bd60 d Male 16.00 9.00
   59 bd61 m Female 18.00 10.00
   60 bd62 d Female 15.00 9.00
   61 hc1 h Male 52.00 7.00
   62 hc2 h Female 24.00 10.00
   63 hc3 h Male 45.00 7.00
   64 hc4 h Female 18.00 13.00
   65 hc5 h Female 19.00 10.00
   66 hc6 h Female 17.00 12.00
   67 hc7 h Female 19.00 7.00
   68 hc8 h Male 48.00 5.00
   69 hc9 h Female 53.00 6.00
   70 hc10 h Female 52.00 15.00
   71 hc11 h Female 19.00 12.00
   72 hc12 h Female 18.00 12.00
   73 hc13 h Female 20.00 12.00
   74 hc14 h Female 18.00 12.00
   75 hc15 h Female 19.00 13.00
   76 hc16 h Female 18.00 11.00
   77 hc17 h Female 19.00 12.00
   78 hc18 h Female 19.00 12.00
   79 hc19 h Female 19.00 12.00
   80 hc20 h Female 19.00 12.00
   81 hc21 h Female 18.00 12.00
   82 hc22 h Female 18.00 12.00
   83 hc23 h Female 18.00 11.00
   84 hc24 h Female 18.00 12.00
   85 hc25 h Female 18.00 12.00
   86 hc26 h Female 18.00 11.00
   87 hc27 h Female 18.00 12.00
   88 hc28 h Female 18.00 12.00
   89 hc29 h Female 18.00 11.00
   90 hc30 h Male 20.00 12.00
   91 hc31 h Female 29.00 17.00
   92 hc32 h Female 16.00 10.00
   93 hc33 h Female 17.00 10.00
   94 hc34 h Female 26.00 14.00
   95 hc35 h Female 24.00 17.00
   96 hc36 h Female 22.00 17.00
   97 hc37 h Male 25.00 17.00
   98 hc38 h Male 24.00 17.00
   99 hc39 h Male 25.00 17.00
1  groups  discrete 3
    1  d
    2  m
    3  h
2  gender  discrete 2
    1  Male
    2  Female
3  age  continuous 0
4  edu  continuous 0
    Continuous Factors: Mean: StdDev:
    --- - ---
    age    22.293 9.015
    edu    11.374 2.827

Number of subjects:   99
Number of factors:    4 (2 discrete, 2 continuous)
Number of classes:    6
Number of regressors: 18

Data table loading completed successfully.
SUBJECTS_DIR 

Re: [Freesurfer] Negative eTIV

[Douglas N. Greve]

Check the talairach registration (talairch.xfm). It must be badly messed up

On 3/23/2022 4:47 AM, lqcheng2017 wrote:


External Email - Use Caution

Dear experts,

I extracted the eTIV using the mri_segstats, but it showed negative 
value. How could I solve this problem?


Thank you very much.


cmdline mri_segstats --subject Gelb --etiv-only
UseRobust  0
atlas_icv (eTIV) = -2105 mm^3    (det: -925.465454 )


Best,
Luqi


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Freesurfer mri_convert

[Douglas N. Greve]

please send the command line, log file, version of FS, etc

On 3/22/2022 11:59 AM, Zoe O'Brien-Moran wrote:


External Email - Use Caution

Dear FS Experts

I am having continued issues with the mri_normalize function on MPRAGE 
data


I get an error message:
3d normalization pass 1 of 2
error: No such file or directory
error: MRInormFindControlPoints: could not find enough control points
error: No such file or directory
error: MRInormFindControlPoints failed

Can you advise on any reason this may be happening?

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Tkregister2 not opening GUI

[Douglas N. Greve]

Does /Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/surf/lh.white 
exist and do you have permission to read it? If yes to both, then try 
running it with --debug as the first option, then send all the terminal 
output



On 3/21/2022 5:02 PM, Isabelle Deschamps wrote:


External Email - Use Caution

I did try tkregisterfv, but I get the following error:

cannot find 
/Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/surf/lh.white


[MacBook-Pro-4:~] Isa% tkregisterfv --fstal --s S0010_FS

According to the tutorial, if I leave the –surfs out, the command 
should work but it does not.


I also tried running it with the –surf I get the same error.

I have only ran the following commands so far:

foreach i ("S0010" "S0028" "S0039" "S0057" "S0074" "S0081" "S0096" 
"S0120" "S0131" "S0139" "S0146" "S0152" "S0163" "S0168" "S0171" 
"S0179" "S0205" "S0250" "S0262" "S0263" "S0272" "S0299" "S0300" 
"S0313" "S0328" "S0363" "S0372" "S0375" "S0378" "S0391" "S0409" 
"S0418" "S0419" "S0432" "S0442" "S0448" "S0451" "S0471" "S0481" 
"S0493" "S0504" "S0509" "S0524" "S0525" "S0528" "S0537" "S0544" 
"S0557" "S0589" "S0601" "S0650" "S0669" "S0676" "S0682" "S0715" 
"S0727" "S0738" "S0741" "S0747" "S0762" "S0768" "S0770" "S0800" 
"S0809" "S0837" "S0839" "S0861" "S0888" "S0896" "S0933" "S0949" 
"S0955" "S0982" "S0988" "S1031" "S1058" "S1082" "S1088" "S1091" 
"S1128" "S1133")


recon-all -i /Volumes/CopyPaste/fMRI/fMRI/Freesurfer/"$i".anat.nii.gz 
-subjid "$i"_FS


end

I wanted to verify the registration at this point, but I can.

Thank you for your help,

isabelle

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


*Date: *Thursday, March 17, 2022 at 22:51
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] Tkregister2 not opening GUI

*CAUTION:* This email originated from outside of Georgian College. Do 
not click links or open attachments unless you recognize the sender 
and know the content is safe.


Can you try tkregisterfv ? The old tk tools are not supported any 
more. tkregisterfv uses freeview


On 3/17/2022 6:03 AM, Nathan Kindred (PGR) wrote:

*External Email - Use Caution *

Hi Isabelle,

It’s been a couple of years since I ran FreeSurfer on a Mac, but I
also have had this issue before and it was due to the macOS. I
don’t know if anything has changed recently but if not then the
only solution would be to try to install an older macOS that will
support 32bit apps.

Best,

Nathan

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

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Isabelle Deschamps 
<mailto:isabelle.descha...@georgiancollege.ca>
*Date: *Wednesday, 16 March 2022 at 19:20
*To: *freesurfer@nmr.mgh.harvard.edu

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *[Freesurfer] FW: Tkregister2 not opening GUI

⚠ External sender. Take care when opening links or attachments. Do
not provide your login details.

*External Email - Use Caution *

Good afternoon,

I am following up on my question regarding the GUI for TKregister2
and TKregister2_Cmld not opening.

Is there another way to open the GUI?

Thank you kindly for your help,

isabelle

*From: *Isabelle Deschamps 
<mailto:isabelle.descha...@georgiancollege.ca>
*Date: *Thursday, March 10, 2022 at 14:52
*To: *freesurfer@nmr.mgh.harvard.edu

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Tkregister2 not opening GUI

Good afternoon,

I am trying to verify the registration and for some reason the GUI
is not opening.

I am using a Macbook Pro running macOS Montery with a 2.4 Gz
Quad-Core Intel Core i5

I have Freesurfer version: maOS-7.2.0

I do not get an error when I run TKregister2 or TKregister_cmld

This is the output that I get without the GUI opening

No target volume specified, assuming FreeSurfer orig volume.

targetvolume orig

movable volume (null)

reg file(null)

LoadVol0

ZeroCRAS1

7.2.0

Re: [Freesurfer] Permission denied error from -localGI

[Douglas N. Greve]

What version of FS are you running?

On 3/20/2022 8:47 PM, Billah, Tashrif wrote:
It does not exist and cannot be created in a shared cluster. Is there 
a way to define a different folder for 
/scratch/tp24093955057547375.load_mgh.m.mgh?


===
Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800

Do you have permission to /scratch? Does it exist?

===
Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800

Hi all,

We are trying to run recon-all with -localGI but running into an unknown
permission denied error:

$ recon-all -s sub-1001 -localGI

```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
 exit
=


< M A T L A B (R) >
Copyright 1984-2017 The MathWorks, Inc.
R2017a (9.2.0.556344) 64-bit (glnxa64)
March 27, 2017


>> reading filled volume...
/bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied


ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for 
reading

ERROR: loading
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 as MGH
Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022

```

Our MATLAB environment is properly setup and we regularly run other
FreeSurfer-MATLAB commands. So I do not think that is causing the issue.

Best,
Tashrif

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] vertexwise correlation between the two maps and atlases in volume (MNI) to surface

[Douglas N. Greve]

On 3/17/2022 4:41 PM, std...@virgilio.it wrote:


External Email - Use Caution

Hi list,

a) I have two maps, one's of rs-fMRI functional connectivity (by 
FS-FAST) and one's of receptor density (from a PET-Atlas). Both the 
maps are in surface space. How can I measure the vertexwise 
correlation between the two maps?


You can use the per-vertex option (--pvr) in mri_glmfit. Search through 
the mail archives to find how to use it



b) How can I move some atlases in volume (MNI) to surface?
I have tried to use:

mri_vol2surf --src ATLAS_vol.nii --regheader fsaverage --projfrac 0.5 
--hemi lh --out ATLAS_surface.nii


but the results are inconsistent.

Probably easiest to just run recon-all on the MNI152 volume, then map it 
to that output



Thanks


Stefano


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Turning Significant Cluster (sig.cluster.summary or sig.mgh) into binary .nii ROI

[Douglas N. Greve]

Are you trying to create a volume-based binary mask or a surface-based 
mask? From the commands below, it looks like surface (but why would you 
need it to be in nii?). In the surface case, you can just

mri_binarize --i ocn.mgh --match clusterno --o clusterno.mask.nii
where "ocn" is the ocn file created by mri_glmfit-sim and clusterno is 
the number of the cluster



On 3/16/2022 3:00 PM, Emily Popa wrote:


External Email - Use Caution

Hello, I am just following up on my previous question. To put it more 
shortly (I apologize for making the question so long before), I am 
just searching for a way to convert a significant cluster from a group 
analysis into a binary .nii mask so I can use the mask (after some 
registration steps) to perform ASL analysis in that specific ROI for 
the same subjects (in FSL).


Best,

Emily S. Popa, M.S.

Staff Research Associate II, Neuroimaging

Pacific Brain Health Center | Pacific Neuroscience Institute 
Foundation | Providence Saint John’s Health Center


1301 20^th  St. #250 Santa Monica, CA. 90404

(408) 750-7971 (M)

cid3519*image001.jpg@01D7EC78.96AA1AC0 
cid3519*image002.jpg@01D7EC78.96AA1AC0 
cid3519*image003.jpg@01D7EC78.96AA1AC0 
cid3519*image004.jpg@01D7EC78.96AA1AC0 
cid3519*image005.jpg@01D7EC78.96AA1AC0 



*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Emily Popa 


*Date: *Thursday, March 10, 2022 at 2:31 PM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *[Freesurfer] Turning Significant Cluster 
(sig.cluster.summary or sig.mgh) into binary .nii ROI


*External Email - Use Caution *

Hello,

I have been struggling to figure out a way to get the significant 
results of a freesurfer group analysis (just one significant cluster) 
from either the sig.cluster.summary or sig.mgh file into a binarized 
ROI in .nii format. I used mri_glmfit to perform the cortical 
thickness analysis on sMRI data and found the significant cluster only 
in the left hemisphere. I tried to follow some instructions I found on 
the FreeSurfer site, however, at the first step/line below 
(mri_volsynth) the –delta-crsf input was referred to on the site as 
the vertex number, but on the –help documentation, it was specified 
that this input should be: col row slice frame : 0-based. Looking at 
the cluster summary file, for the significant cluster there is a 
maximum vertex, but I am not sure if this is the vertex number I 
should be using.


mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness 
--pdf delta --delta-crsf 5 9 5 1 --o delta.sm00.mgh


mris_fwhm --smooth-only --subject fsaverage --hemi lh --i 
delta.sm00.mgh --niters 10 --o delta.sm10.mgh


mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh

When trying the first line above for mri_volsynth, I get this error: 
Segmentation fault: 11 (so I think my input 

Re: [Freesurfer] Tkregister2 not opening GUI

[Douglas N. Greve]

Can you try tkregisterfv ? The old tk tools are not supported any more. 
tkregisterfv uses freeview


On 3/17/2022 6:03 AM, Nathan Kindred (PGR) wrote:


External Email - Use Caution

Hi Isabelle,

It’s been a couple of years since I ran FreeSurfer on a Mac, but I 
also have had this issue before and it was due to the macOS. I don’t 
know if anything has changed recently but if not then the only 
solution would be to try to install an older macOS that will support 
32bit apps.


Best,

Nathan

*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Isabelle 
Deschamps 

*Date: *Wednesday, 16 March 2022 at 19:20
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *[Freesurfer] FW: Tkregister2 not opening GUI

⚠External sender. Take care when opening links or attachments. Do not 
provide your login details.


*External Email - Use Caution *

Good afternoon,

I am following up on my question regarding the GUI for TKregister2 and 
TKregister2_Cmld not opening.


Is there another way to open the GUI?

Thank you kindly for your help,

isabelle

*From: *Isabelle Deschamps 
*Date: *Thursday, March 10, 2022 at 14:52
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Tkregister2 not opening GUI

Good afternoon,

I am trying to verify the registration and for some reason the GUI is 
not opening.


I am using a Macbook Pro running macOS Montery with a 2.4 Gz Quad-Core 
Intel Core i5


I have Freesurfer version: maOS-7.2.0

I do not get an error when I run TKregister2 or TKregister_cmld

This is the output that I get without the GUI opening

No target volume specified, assuming FreeSurfer orig volume.

targetvolume orig

movable volume (null)

reg file(null)

LoadVol0

ZeroCRAS1

7.2.0

Diagnostic Level -1

% % % % % % % % avi2talxfm

talairach.xfm -

1.008570.02020-0.00990-0.12365;

-0.017891.032510.24795-28.10577;

0.02556-0.306601.209133.54973;

0.00.00.01.0;

INFO: loading target 
/Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/mri/orig.mgz


Zeroing CRAS of target

new xfm -

1.008570.02020-0.009901.93629;

-0.017891.032510.24795-11.46406;

0.02556-0.306601.20913-50.28331;

0.00.00.01.0;

-

Ttarg: 

-1.00.00.0128.0;

-0.00.01.0-128.0;

0.0-1.00.0128.0;

0.00.00.01.0;

INFO: loading movable 
/Applications/freesurfer/7.2.0/average/mni305.cor.mgz


Tmov: 

-1.00.00.0128.0;

0.00.01.0-128.0;

0.0-1.00.0128.0;

0.00.00.01.0;

mkheaderreg = 0, float2int = 0

 Input registration matrix 

1.008570.02020-0.009901.93629;

-0.017891.032510.24795-11.46406;

0.02556-0.306601.20913-50.28331;

0.00.00.01.0;

Determinant 1.33659

subject = S0010_FS

RegMat ---

1.008570.02020-0.009901.93629;

-0.017891.032510.24795-11.46406;

0.02556-0.306601.20913-50.28331;

0.00.00.01.0;

UnZeroing CRAS for fstal output xfm

Any help would be greatly appreciated.

Isabelle


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] lh.white surface co-registration

[Douglas N. Greve]

If you have an LTA file, you can run
mris_apply_reg --lta lh.white your.lta lh.white.newcoords

On 3/16/2022 4:15 PM, Salar Dini, Elaheh wrote:


External Email - Use Caution

Dear Freesurfer experts,

Is there a way to move lh.white of a subject to a new coordinate? 
Something quite similar as volumetric co-registration but for 
surfaces. To be exact, I have moved a subject's brainmask.mgz, 
orig.mgz, aparc+aseg.mgz, and T1 mgz to a new coordinate using 
mri_coreg and subsequently vol2vol, but the surfaces are still in the 
original coordinate and doesn't match the volumes. Is there a way to 
move the surface files to the new coordinate?


OS: Centos 7, Freesurfer version: 7.2.0

Thank you for your time and help.
Kindly,
Ela






___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all errors after mri_pretess

[Douglas N. Greve]

The log might not be capturing all the standard error output. Run this 
and send the output.log

recon-all -debug -s neo289e -segmentation -fill |& tee output.log


On 3/11/2022 3:19 PM, Alexopoulos, Dimitrios wrote:


External Email - Use Caution

Yes it fails every time at the same spot.  The log is attached.

Jim

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Douglas N. Greve

*Sent:* Wednesday, March 09, 2022 12:24 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] recon-all errors after mri_pretess

** External Email - Caution **

Does this fail every time like this? It looks like it just abruptly 
stopped. Does anything print out to standard error?


On 3/4/2022 11:18 AM, Alexopoulos, Dimitrios wrote:

*External Email - Use Caution *

Hi, we’re running FS 7.2 ‘recon-all -all’ on a subject and are
getting errors on our cluster (CentOS 8)

The attached recon-all.log file is attached for details. The last
several lines of the file are below. Any comments as to why its
failing? Jim.

pass   1 (--):   0 found -   0 modified |    TOTAL:   0

pass   1 (-+):   0 found -   0 modified |    TOTAL:   0

Total Number of Modified Voxels = 631 (out of 421942: 0.149547)

binarizing input wm segmentation...

Ambiguous edge configurations...

mri_pretess done

@#@FSTIME  2022:03:03:12:51:58 mri_pretess N 4 e 3.84 S 0.01 U
3.70 P 96% M 56636 F 1 R 2214 W 0 c 330 w 325 I 8801 O 646 L 3.37
3.47 3.45

@#@FSLOADPOST 2022:03:03:12:52:02 mri_pretess N 4 3.37 3.47 3.45

#

#@# Fill Thu Mar  3 12:52:02 CST 2022



The materials in this message are private and may contain
Protected Healthcare Information or other information of a
sensitive nature. If you are not the intended recipient, be
advised that any unauthorized use, disclosure, copying or the
taking of any action in reliance on the contents of this
information is strictly prohibited. If you have received this
email in error, please immediately notify the sender via telephone
or return mail.



___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
<https://secure-web.cisco.com/1U2oI2UH3WrHae73NsZciWTLqbJB1Fqz0LQPco2AO3nHqmwBPM4kk2juJuDEkRiI5XhUW6sPZDJ5kmTH-87tQCqn1UkUHNmbFbE72zuguqrBuWfDrhyQiDx3n-Fq03yROj_yGp9vxuthpnY9EjZbfgimtgzguuWVvyFaLYl_sbKoFdd5vQOXodhv4FqrH6xsd2ktUxhgNbS9sxqy4xkLBZDetkd7sMY_0wIcTHdGY1XZtiTzfa47Vq2S9Dnq94kuitpgpWBT_oaJlxacudHCCt7bq9Su0WROufKXwlNOxuqGn1bGAxeKWBGCd3Ln0RzZZXvD0PXkLY9buHydWLA71TQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>



The materials in this message are private and may contain Protected 
Healthcare Information or other information of a sensitive nature. If 
you are not the intended recipient, be advised that any unauthorized 
use, disclosure, copying or the taking of any action in reliance on 
the contents of this information is strictly prohibited. If you have 
received this email in error, please immediately notify the sender via 
telephone or return mail.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Using vol2surf to fsaverage.

[Douglas N. Greve]

Yes, just specify --regheader subjectname instead of a --reg

On 3/11/2022 9:34 AM, Jacoby, John wrote:

Hi all,

Usually when I want to map volume data to the fsaverage surface, I use 
mri_vol2surf with a registration that transforms the volume into the 
space of the subject's orig.mgz and with --trgsubject set to 
'fsaverage'. Currently, I have some volumes that have already been 
transformed to the subjects' orig.mgz space that I want to bring to 
the fsaverage surface. Can I still just give mri_vol2surf the same 
registration that I used to transform this volume in the first place, 
or will this try to re-apply that registration and end up in the wrong 
space? If that's incorrect, what's the best way to go about doing this?


Thank you!

Best,
John

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] FWHM errors for mri_glmfit-sim for lgi?

[Douglas N. Greve]

Yes, oftentimes. You should not smooth the LGI. Also, I would strongly 
suggest that you use permutation instead of mcz sim. For perm, the fwhm 
won't matter.


On 3/10/2022 3:26 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


External Email - Use Caution

I receive FWHM values much larger than what 
average/mult-comp-cor/fsaverage/rh/cortex has (around ~50) w/ LGI, but 
normal when looking at GM thickness. Is this expected?


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] how to load flat surface in freeview

[Douglas N. Greve]

What happens if you run
freeview -f 
/home/francesca/freesurfer/subjects/sub01_mprage/surf/lh.inflated



On 3/10/2022 7:32 AM, Francesca Strappini wrote:


External Email - Use Caution

Dear Freesurfer experts,

I'm trying to load the flat surface that I created with this command line:

mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d

I tried loading the patch inside freeview but I got this error message:
[francesca@GIOVE surf]$ tksurferfv sub01_mprage lh inflated
freeview -f 
/home/francesca/freesurfer/subjects/sub01_mprage/surf/lh.inflated:curvature=/home/francesca/freesurfer/subjects/sub01_mprage/surf/lh.curv 
-viewport 3d
ASSERTION FAILED: 
/home/rd521/space_freesurfer/build/docker_centos8/trunk/rd521-7.2.0/utils/mrisurf_metricProperties.cpp:4248 
mris->dist_nsize == 0
ASSERTION FAILED: 
/home/rd521/space_freesurfer/build/docker_centos8/trunk/rd521-7.2.0/utils/mrisurf_metricProperties.cpp:4248 
mris->dist_nsize == 0

Errore di accesso al segmento di memoria (creato file core)

And I tried to run this command line but nothing happened:
[francesca@GIOVE surf]$freeview -f lh.inflated:patch=lh.full.flat.patch.3d

Thank you,
Francesca



--
Francesca Strappini, Ph.D.
Psychology Department
Sapienza University of Rome
Via dei Marsi 78, Rome 00185 Italy
Tel.: +39 392 151 4029
E-mail: francesca.strapp...@uniroma1.it 



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Atlas of primary motor and auditory cortex

[Douglas N. Greve]

On 3/9/2022 2:15 PM, Jingyi Wang wrote:


External Email - Use Caution

Hello Freesurfer experts,

I ran the recon-all command and got all the .label files for the 
segmentations of the cortical areas. However, I have some questions 
about the label for primary motor and auditory cortex.


  * I found two types of labels associated with the primary motor
cortex: lh.L_M1.label and lh.BA4a_exvivo.label. Are they both
valid, and the lh.BA4a_exvivo.label segmentations are finer
parcellation than the other one?


I think they came from different techniques, so it's up to you


  * What's the primary auditory cortex .label file?

We don't have an A1 label as a label file. You can use the transverse 
temporal in the aparc.annot (heschl's gyrus)

Thanks in advance!

Jingyi Wang
Postdoctoral Scholar
LEAP Neuro Lab
Psychological & Brain Sciences
University of California, Santa Barbara


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] complete unfinished steps of recon all

[Douglas N. Greve]

Yea, not so easy. You need to see how far it got and then use the 
appropriate flags. The most time consuming step is the volume labeling. 
See if aseg.presurf.mgz exists. If it does, then you can skip that with 
-autorecon2-noaseg -autorecon3. If subject/mri/transforms.m3z and 
norm.mgz exist but not aseg.presurf.mgz, then you could run with 
-autorecon2-noaseg -autorecon3 -careg



On 3/8/2022 3:05 PM, Hossein Rahimzadeh wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

Due to the fact that the freesurfer runs for a long time, the computer 
is turned off several times during the run due to electricity 
fluctuations. How to complete unfinished steps of recon-all.
I tried to continue the analysis with the command "recon-all -make all 
-s subject, but" I got the following error:

ERROR: -make is no longer supported
1)freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
2)linux ubuntu 20.04
3)two recon-all.log of two subjects have attached
Best regards,
Hossein Rahimzadeh Biomedical Engineering, MSc. Shahid Beheshti 
University of Medical Sciences, Tehran, Iran.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] [External] Re: classes for GLM analysis

[Douglas N. Greve]

Can't tell without the fsgd file

On 3/7/2022 8:30 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


External Email - Use Caution

Just to double check the numbers - I seem to have been getting into an 
error in how many columns in the FSGD it is expecting.


I have 9 different sites, 4 different patient groups, and M/F -> 72 
classes.
I also am covarying for four different factors, so the contrast matrix 
I am making is 72*(4+1) long. Since I want to regress out the four 
factors completely, only the first 72 numbers in 360 contrast matters. 
My FSGD file has 4 columns e.g like


Input GP0001 NCBostonM 60 12000 -0.01 -0.02

It says ERROR: gdfReadV1: Input line 1, subjid = GP0001
Found 4 variables, expected. 10

Where is this 10 coming from?


Get Outlook for iOS 
<https://secure-web.cisco.com/17NelGJ6sesfwsPcUOcH7NLCIl8poWbpnFKSkRs_Tip5fMdIWsq5voGkTtGHzn1xIw9teACerNPVmg1UDC86aygtsYvxBGSc9QJKdZxMm3Y3dOV1lpERz-8vKc-W35SxGCTR7slBrlWoSLntQcxVoI5N_W36lxBKe00LuMnuLFccVkMttfaKkDki2gEKr8rEZfBAP4oLIvzypnlk5I1Xvxx0pH9IvNr3Jhcz2dIr3phyRLDzKH1xF2zITaP2GCEjdSzIMvOq7JGNJG1jnPXQseKuq2b3dOWmyQa-nctRxcywiYYaHXfKoduT5XAwSGGo-wLjxNlMJmdBY1XoH2zdiyw/https%3A%2F%2Faka.ms%2Fo0ukef>


*From:* Zeng,Victor (BIDMC - Keshavan - Psychiatry) 


*Sent:* Monday, February 21, 2022 5:50:46 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [External] Re: [Freesurfer] classes for GLM analysis
Do you have a Freesurfer page I can read up on those hybrid ways just 
to see whether that could be an option?


Also, although its a binary, you would recommend against have sex be a 
continuous measurement like age, due to the design of how the 
contrasts are determined? I.e continuous measurements aren't treated 
like integers


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

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


*Sent:* Sunday, February 13, 2022 12:24 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* [External] Re: [Freesurfer] classes for GLM analysis
It is probably not going to work very well if you have some classes 
that only have one member. You can eliminate members of classes that 
only have a few members. If you really need to have those cases, there 
are hybrid ways to analyze the data (but you can't use an FSGD at that 
point)


On 2/6/2022 10:41 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


External Email - Use Caution

Hi all,

I am doing an analysis and generating the FSGD. I understand sex and 
race are classes in this context, but something I was also hoping to 
regress out is the effects of scanner/sequences. We have a large 
participant size, so we have around 10+ scanner/sequences, which 
makes for a large amount of classes combinations, with some having 
just 1 (if not zero) fitting into a class.


Would you proceed with this nonetheless? If not, should 
scanner/sequence be something that we consider? Should we find some 
other way to adjust site (I don't think we can z-score...). Or can we 
consider site/scanner as a continuous variable


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://secure-web.cisco.com/17qN5bDkuaeK781Lqatoj7wq00PaGKTEtcEQvhi_FMPstmuXqCbw1qu_o6m09Gx4i6uzhknWy3SdQKE8Kb42oK-aio4Z9BzzYUaW_YPZQxDITHj-XRutpm12FBHGiBhhjS4fGEam49ZyUl-0RuilU7txRjrKBOCCcsMxELYwLBlBvM23K9AWEX11Fji5iPijRXtSy4HuznIM_2nykUGok-ydbPxoYKFMVlxMuIWIzRXLiFzltn0SRH5tVQCCenBq1ij3h-gtSrMR9kxsTnFh47IjilDG3VyDbP-ABFnjzWd-65nT6_0-J2yvS26iWhf2IVujw-_cA2300rli3E8W6jg/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21CvMGjuU%21oWSHsHxjED1I9do4R5UyRdbrrRZ0JwASmA6lT5nMBEMbU4m_jfTGWrhBU-2K4sn01nxIwg%24>



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communic

Re: [Freesurfer] Cutting the Full Surface

[Douglas N. Greve]

In FreeView
Click on the brain with scissors icon ("Cut"), select your points, then 
"Cut Closed Line",
   make sure the cusror is in the patch, then hit "Fill Uncut Area", 
then save as a patch



On 3/7/2022 12:03 PM, Francesca Strappini wrote:


External Email - Use Caution

Dear FreeSurfer experts,

I'm trying to cut and flatten the full surface. I understand that 
tksurfer is deprecated and on my PC does not work properly. Is there 
an alternative way to perform the cuts?


Thank you,
Francesca



--
Francesca Strappini, Ph.D.
Psychology Department
Sapienza University of Rome
Via dei Marsi 78, Rome 00185 Italy
Tel.: +39 392 151 4029
E-mail: francesca.strapp...@uniroma1.it 



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all errors after mri_pretess

[Douglas N. Greve]

Does this fail every time like this? It looks like it just abruptly 
stopped. Does anything print out to standard error?


On 3/4/2022 11:18 AM, Alexopoulos, Dimitrios wrote:


External Email - Use Caution

Hi, we’re running FS 7.2 ‘recon-all -all’ on a subject and are getting 
errors on our cluster (CentOS 8)


The attached recon-all.log file is attached for details. The last 
several lines of the file are below. Any comments as to why its 
failing? Jim.


pass   1 (--):   0 found -   0 modified |    TOTAL:   0

pass   1 (-+):   0 found -   0 modified |    TOTAL:   0

Total Number of Modified Voxels = 631 (out of 421942: 0.149547)

binarizing input wm segmentation...

Ambiguous edge configurations...

mri_pretess done

@#@FSTIME  2022:03:03:12:51:58 mri_pretess N 4 e 3.84 S 0.01 U 3.70 P 
96% M 56636 F 1 R 2214 W 0 c 330 w 325 I 8801 O 646 L 3.37 3.47 3.45


@#@FSLOADPOST 2022:03:03:12:52:02 mri_pretess N 4 3.37 3.47 3.45

#

#@# Fill Thu Mar  3 12:52:02 CST 2022



The materials in this message are private and may contain Protected 
Healthcare Information or other information of a sensitive nature. If 
you are not the intended recipient, be advised that any unauthorized 
use, disclosure, copying or the taking of any action in reliance on 
the contents of this information is strictly prohibited. If you have 
received this email in error, please immediately notify the sender via 
telephone or return mail.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Using T1 FLAWS in recon-all

[Douglas N. Greve]

never heard of FLAWS. My good search says that it is WM and CSF 
suppression, so it probably won't work.


On 3/4/2022 6:10 AM, Mathilde Pichon wrote:


External Email - Use Caution

Hello,

I know T1 MPRAGE is the prefered format to perform a recon-all 
segmentation.

But some of my patients' data only have FLAWS images and no MPRAGE images.
So is it possible to perform a recon-all with FLAWS images ?

Regards,

Mathilde

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] ERROR: Flag -sveres unrecognized

[Douglas N. Greve]

What version are you trying to run? selxavg-sess has been depricated for 
years. Try selxavg3-sess


On 3/3/2022 10:59 AM, CALLACHAND Muntasir wrote:


External Email - Use Caution

Hi,

I have a problem when i try to run the function selxavg-sess 
 
with the optional arguments -sveres. This message occur :


ERROR: Flag -sveres unrecognized

Do you know what i can do to fix this?

Best,
Muntasir CALLACHAND

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Error: inputs cannot have multiple frames

[Douglas N. Greve]

It means that you have two frames in the 001.mgz file. Sometimes this 
happens with multiecho mprages. If this  is the case, you can convert 
your input to a single frame with

mri_concat --rms file.mgz --o file.rms.mgz
Then use file.rms.mgz as the input to recon-all

On 3/3/2022 12:04 AM, HYE JUNG YOUN wrote:


External Email - Use Caution

Dear Freesurfer developers,

I realised some of my recon-alls been processed with the following error:

ERROR: input(s) cannot have multiple frames! 
/Users/mac_01/Desktop/1155_401/mri/orig/001.mgz has 2 frames


(I have attached the recon-all.log)

I checked the mri info and I think the problem is the dimensions which 
is 256 x 256 x 211 x 2.


I’ll attach the original commands I used with mri info in txt file in 
case it would help you to see where I went wrong.


If anyone has been through this problem or if you know what I can do 
to fix this, please let me know.


Best,

H


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] bbregister dependencies recon-all

[Douglas N. Greve]

You pretty much have to run it through to the end. You can try using 
mri_coreg (this is the first step of bbregister). It does not need 
anything but two images and will  run in  a few min.

On 3/3/2022 5:24 AM, Guillem París wrote:
>  External Email - Use Caution
>
> Hello,
>
> I'm trying to run a Boundary-based registration by using bbregister. In
> the documentation, it is specified that the anatomical image has to be
> previously analysed in FreeSurfer. I assume that means to run the
> "recon-all" pipeline.
>
> Now, are all the stages of "recon-all -all" needed to perform this
> registration? Since I am time-constrained, I would like to run as few
> stages as possible, so I can use bbregister.
>
> If it matters, I'm trying to register a DWI to the same subject's T1-w.
>
> Thank you!
>
> Guillem
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] GLM analysis - volume and surface area

[Douglas N. Greve]

Can you just ask the question again so I don't have to sort it out myself?

On 3/2/2022 3:30 PM, Laura Willers de Souza wrote:


External Email - Use Caution

Sorry about that!

I'm resending with previous emails.

The first message below is the one you didn't know how to respond to 
because you didn't have the previous e-mails.


---

On 2/22/2022 9:15 AM, Laura Willers de Souza wrote:

Thanks so much for the explanation!

There is something different in the analysis of volume and surface 
area in relation to the analysis of cortical thickness? Like some more 
command, or some other detail that must be changed (besides, of 
course, the flag that specifies the measure to be analyzed) - I'm 
already using permutation in the correction of multiple comparisons.




--

On 2/21/2022 15:20 PM, Douglas N. Greve wrote:

Yes, it is. It is confusing when you talk about area and volume 
sincethese are not point measures like thickness (ie, what is the 
volume orarea of a vertex?). The area of a vertex is computed as the 
mean of theadjacent triangles of the vertex. The volume is the mean of 
theneighboring truncated tetrahedra. When you run mris_preproc, it 
willapply a jacobian correction (like VBM). Otherwise, it operates the 
sameas if you had a thickness value at the vertex, ie, same GLM, etc. 
Makesure to use permutation for correction of multiple comparisons.


-

On 2/21/2022 12:13 PM, Laura Willers de Souza wrote:

Hello FreeSurfer Developers,

I would like to know if it is correct to perform volume and
surfacearea analysis using freesurfer's GLM!?

In several mailing list questions I have already seen instructions
forperforming these types of analysis. But I understand that
freesurferdoes vertex-wise analysis in the 2D surface space. So,
it is not clearto me how it is possible to evaluate a 3D
measurement, as volume, witha 2D method!?

I've also read that surface area analysis via vertex-wise
analysisdoesn't make much sense. The best would be to do ROI-based
analysis.Can you explain that to me?

Thanks in advance!

Best,

Laura.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Permission denied error from -localGI

[Douglas N. Greve]

Do you have permission to /scratch? Does it exist?

On 3/2/2022 9:50 AM, Billah, Tashrif wrote:

Hi all,

We are trying to run recon-all with -localGI but running into an 
unknown permission denied error:


$ recon-all -s sub-1001 -localGI

```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); 
exit

=


< M A T L A B (R) >
Copyright 1984-2017 The MathWorks, Inc.
R2017a (9.2.0.556344) 64-bit (glnxa64)
March 27, 2017


>> reading filled volume...
/bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied


ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for 
reading
ERROR: loading 
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz 
as MGH

Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file 
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!



recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022

```

Our MATLAB environment is properly setup and we regularly run other 
FreeSurfer-MATLAB commands. So I do not think that is causing the issue.


Best,
Tashrif

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[Douglas N. Greve]

The problem is that your design matrix is badly scaled. The eTIV values 
are much larger than the group membership (value=1). Try subtracting the 
mean of the eTIV and dividing by the stddev to normalize it.



On 2/25/2022 8:07 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Thank you for your response. I uploaded the .mgh, .fsgd, and .mtx 
files that I used to run the mri_glmfit command. I can upload 
the recon-all outputs of the individual samples as well, if needed. 
The files are uploaded in google drive, please access them via the 
link below.


*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://drive.google.com/drive/folders/1QNzMxJdmc7Bo1KGlh9OC9f7DVzZ9ej2k?usp=sharing 
<https://secure-web.cisco.com/1dyd7-xjzX4Lq_6TpVFINCBx2OzGb31QOy2b8WE4RlFK-rQW7JTWTbadgXYRKAnzQhyfbYr9ZYTmLKlwKzSSQ4tMlXDsMkhJgQ181lHtFxzXgb_Dry1feAP8aKFqOXA1x-F4FuNAsaU8BolN83rf62nnKC8adsct_OhZVZYRMXe1RciKtM0FCMjooYYAmkUm3qRc7PDz8BtLyoRaBXtfZE5nsVlYanmwZSr2cbx0n4upHQjEdEUkJRoX-4GMRt5qLHTNxfJ1mrN8SJ3vMTeBuBdNo8CCqaFKBm3Lb0rAycL-Ir-ihasFHFqKxRhpfCxVCNtXsrjGigkWr7ym9LaK0nw/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F1QNzMxJdmc7Bo1KGlh9OC9f7DVzZ9ej2k%3Fusp%3Dsharing>


Thank you in advance,
Hyunwoo Jeong.



2022년 2월 26일 (토) 오전 8:16, Douglas N. Greve 
님이 작성:


Can you upload the data to me somewhere? I'd need the input volume
and the fsgd and any contrasts

On 2/21/2022 10:24 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Thank you for your suggestion. Unfortunately, the same problem
occurred when I ran the command with --no-pcc. Folders and files
with the same names were created. and the following error message
(identical to the previous one) appeared.

error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break

/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596

Do you have any other suggestions? I appreciate your help so far.

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 10:18, 정현우 님이
작성:

Hi Dr. Greve,

Thank you for your suggestion. Unfortunately, the same
problem occurred when I ran the command with --no-pcc.
Folders and files with the same names were created. and the
following error message (identical to the previous one) appeared.

error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break

/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596

Do you have any other suggestions? I appreciate your help so far.

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 1:41, Douglas N. Greve
님이 작성:

It looks like it is failing when computing the partial
correlation coef. Try  running it with --no-pcc

On 2/16/2022 10:53 AM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Yes, it seems like the output folder and some output
files were created.

After running the mri_glmfit,
'three_group_comparison.area.lh.glmdir' folder was
created. In the glmdir folder,
'three_group_comparison.area' folder was created, and
the following files were also created: beta.mgh,
dof.dat, eres.mgh, fwhm.dat, mask.mgh, mri_glmfit.log,
rstd.mgh, rvar.mgh, sar1.mgh, surface, and Xg.dat.

In the 'three_group_comparison.area' folder, the
following files were created: C.dat, F.mgh, gamma.mgh,
maxvox.dat, sig.mgh, and z.mgh.

Do you have any idea what could have been the problem?

Thanks,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve
님이 작성:

Did it create the output folder and some output
files? I noticed that there is a "error: No such
file or directory" error 

On 2/14/2022 8:46 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Thank you for your reply. I attached the fsgd file,
mtx file and the Xg.dat file below.

Hyunwoo Jeong

2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve
님이 작성:

can you send your fsgd file and the Xg.dat file?

On 2/14/2022 1:21 AM, 정현우 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compare cortical surface
area among three groups while controlling for
estimated total intracranial volume (eTIV), as
described on the Surface Based Group Analysis
  

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[Douglas N. Greve]

Can you upload the data to me somewhere? I'd need the input volume and 
the fsgd and any contrasts


On 2/21/2022 10:24 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Thank you for your suggestion. Unfortunately, the same problem 
occurred when I ran the command with --no-pcc. Folders and files with 
the same names were created. and the following error message 
(identical to the previous one) appeared.


error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break 
/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596


Do you have any other suggestions? I appreciate your help so far.

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 10:18, 정현우 님이 작성:

Hi Dr. Greve,

Thank you for your suggestion. Unfortunately, the same problem
occurred when I ran the command with --no-pcc. Folders and files
with the same names were created. and the following error message
(identical to the previous one) appeared.

error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break

/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596

Do you have any other suggestions? I appreciate your help so far.

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 1:41, Douglas N. Greve
님이 작성:

It looks like it is failing when computing the partial
correlation coef. Try  running it with --no-pcc

On 2/16/2022 10:53 AM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Yes, it seems like the output folder and some output files
were created.

After running the mri_glmfit,
'three_group_comparison.area.lh.glmdir' folder was created.
In the glmdir folder, 'three_group_comparison.area' folder
was created, and the following files were also created:
beta.mgh, dof.dat, eres.mgh, fwhm.dat, mask.mgh,
mri_glmfit.log, rstd.mgh, rvar.mgh, sar1.mgh, surface, and
Xg.dat.

In the 'three_group_comparison.area' folder, the following
files were created: C.dat, F.mgh, gamma.mgh, maxvox.dat,
sig.mgh, and z.mgh.

Do you have any idea what could have been the problem?

Thanks,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve
님이 작성:

Did it create the output folder and some output files? I
noticed that there is a "error: No such file or
directory" error 

On 2/14/2022 8:46 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Thank you for your reply. I attached the fsgd file, mtx
file and the Xg.dat file below.

Hyunwoo Jeong

2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve
님이 작성:

can you send your fsgd file and the Xg.dat file?

On 2/14/2022 1:21 AM, 정현우 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compare cortical surface area
among three groups while controlling for estimated
total intracranial volume (eTIV), as described on
the Surface Based Group Analysis tutorial
(*MailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be*

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0

<https://secure-web.cisco.com/1A0QSPCwnovVVVsFNKDP8OXxiBFqZ78jELzRvCgQt7us3rKayy2caTMVKC0nI4ildx0WJqzN5lLz1i-T5FHTbnyaiJAYj3f4mSQ4YHgEnKgBthfsubdAmofQmb_wxbJARZK70-yJh-Q-zB-SO-qUOdB5mSbQ71p0R-muUphnBpsvIZSn12rCp8u9iFutHnHZiR2SHvMYZrtWgA2qG1HwIVF7eXEz_S43Y9x_BasmQivW7O0E14rKYKn2Hc6i1PPi-krEJ-p90KuI4uEnOqU2T3HEQaZ4yicZdxZVpeFkSkL2Taw7LCrmTuBUijdwzR0I8MhzyhVIWFnyo-WUBgBXiig/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0>).


I ran the following command:

mri_glmfit --y
three_group_comparison.area.lh.10.mgh --fsgd
three_group_comparison.area.fsgd dods --C
three_group_comparison.area.mtx --surf fsaverage lh
--cortex --glmdir
three_group_comparison.area.lh.glmdir --eres-save

Then I got the following error:

gdfRead(): reading three_group_comparison.area.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will
NOT be done.
Continuous Variable Means (all subjects)
0 eTIV 1.53351e+06 139455
Class Size and Means of each Continuous Variable
1 0 42 1566070.5417
2 1 34 1515147.1360
3 2 15 1483959.5000
INFO: gd2mtx_method is dods

Re: [Freesurfer] Using mri_transform with output of bbregister

[Douglas N. Greve]

This is a bit tricky as you need a volume as a template that has the 
dimensions/resolution you want. One fast and dirty way to do it is to 
upsample the orig to 0.5mm, eg
mri_convert --upsample 2 orig.mgz orig.us2.mgz
You can then run
mri_vol2vol --mov T2.nii.gz --lta reg.lta --targ orig.us2.mgz --o t2.us2.mgz
It might complain that the output volume in the lta file does not match 
the target volume; if this causes it to fail, I can give you a work-around

On 2/25/2022 12:23 PM, Tisdall, Dylan wrote:
>  External Email - Use Caution
>
> Hi all,
>
> Thanks again for all the help so far with getting my data registered and 
> surfaces extracted. I have one further issue that I'm hoping to get help with.
>
> I've used bbregister to align my T2 scan with the surfaces from my T1 scan. 
> However, the output is resampled down to 1mm iso and a 256^3 volume; I'd like 
> to keep the native 0.8 mm resolution and FOV if possible (acknowledging, of 
> course, there's actually some blurring in the interpolation, but just for the 
> sake of nominal consistency).
>
> I tried to work around this by applying the .lta output by bbregister to my 
> T2 scan (with the goal of eventually using the --out-like flag to specify the 
> sampling resolution, but not doing that yet):
>
> mri_transform T2_SPACE.nii.gz T2_SPACE_transform.lta T2_SPACE_warped.nii.gz
>
> However, when I load the resulting output volume (T2_SPACE_warped.nii.gz) in 
> freeview, it has swapped axes. Strangely, this isn't the case with the output 
> volume generated by bbregister... it's well-aligned with the surfaces. 
> Similarly, if I load the T2_SPACE.nii.gz into freeview, and apply 
> T2_SPACE_transform.lta as part of the load command, the volume is 
> well-aligned.
>
> So what's different about how mri_transform applies that .lta file, compared 
> to bbregister and freeview?
>
> Is there a way to just get bbregister to resample my T2 scan with the 
> original resolution and FOV, so I can avoid applying mri_transform 
> altogether? I don't see an --out-like option for bbregister, but is there a 
> different flag?
>
>
> Thanks again,
> Dylan
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Neverending mris_fix_topology

[Douglas N. Greve]

You can't tell from the image whether the wm in cerebellum or dura is 
attached. you need to look at the wm.mgz volume to see. You can load the 
?h.orig.nofix as well. In the terminal output of recon-all/topofix, it 
should give a vertex number of the topodefect. Go to that vertex n the 
nofix surface. That should get you close to the problem.


On 2/25/2022 3:25 PM, Peled, Noam wrote:


It’s running quite a long time, with this repeating message:

“

This often happens because cerebellum or dura has not been removed 
from wm.mgz.


This may cause recon-all to run very slowly or crash.

if so, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview


“

I think the cerebellum and the dura seem to be ok:

Any ideas?

Thanks!

Noam

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Peled, Noam

*Sent:* Thursday, February 24, 2022 1:18 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] Neverending mris_fix_topology

Thanks Bruce, I’m going to try that now.

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Fischl, Bruce

*Sent:* Thursday, February 24, 2022 1:05 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] Neverending mris_fix_topology

Hi Noam

Have you tried running it without -parallel? It looks like it is 
waiting for some other PID to finish


Bruce

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Peled, Noam

*Sent:* Thursday, February 24, 2022 12:36 PM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] Neverending mris_fix_topology

Dear group,

I’m trying to run recon-all 
(freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551) on my 
Martinos’ desktop.


I killed it after waiting quite a of time for the mris_fix_topology to 
be completed:


Waiting for PID 225967 of (225964 225967) to complete...

What can I do to be able to process this subject?

I attached the recon-all log. You can also find all the logs here:

/autofs/space/mmvtclin_001/thibault/1/users/npeled/subjects/UN07/scripts

Thanks!

Noam


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Douglas N. Greve]

yes, it does

On 2/25/2022 5:14 PM, Jennifer Bramen wrote:


External Email - Use Caution

Hi Doug

I want to confirm that the signal any region flagged as cortex is 
restricted to gray matter. If that is the case, then I finally have 
what I need. Thank you.


Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & 
Foundation | Providence Saint John's Health Center

1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: * on behalf of "Douglas 
N. Greve" 

*Reply-To: *Freesurfer support list 
*Date: *Friday, February 25, 2022 at 10:25 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

Are you doing an ROI analysis or a voxel-wise analysis? If an ROI 
analysis, then use mri_gtmpvc (with or without PVC). This will give 
you GM, WM, and CSF ROIs. Or do you mean you want a single average 
across all GM?


On 2/24/2022 1:15 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

I would like to measure uptake exclusively in gray matter. What
would you recommend to accomplish this?

In my previous message, I was wondering if adding a gray matter
mask would be a potential way to restrict the analysis to gray
matter. Thanks!

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute &
Foundation | Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Tuesday, February 22, 2022 at 3:00 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based
analysis

I don't understand. What mask?

On 2/22/2022 8:55 AM, Jennifer Bramen wrote:

*External Email - Use Caution *

If I only want to extract intensity from gray matter, do I
need to add an additional mask?

Thanks!

Jennifer

Get Outlook for iOS

<https://secure-web.cisco.com/1L8X_xbSuY_t_ihVbCVT-VrYnrnVaUkpY43uE0_YCYKJhAviIYu8oxZ5PPt-xMtue1nKBFFsIIdc4KBLgKFCEwa74gpigVENV1GyuIW9GZY7CdyW1O-DI9kzTj0IqZfoGPgj6xImBezDDXVXDYk72vjK3VGgjUz9iLXe0ZpQBziIaJ_lOjni1eZ5hbGxBsHdweSgAAcH3WrreH39jB3E5W_oCbiM_eemv-N1wxKjATTFgYLmBFmxGUK3F_I7myhQ2giptsjKDwBlg67W0Te63GAUl8h6wI9xpMnF5vpkiBB50ky4Fc1twBGrvBs8O3yh8Jw9cAIYSm4G0yFmFVx77AA/https%3A%2F%2Faka.ms%2Fo0ukef>



*From:* freesurfer-boun...@nmr.mgh.harvard.edu
    
    <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
*Sent:* Monday, February 21, 2022 7:13:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] PetSurfer: subcortical
volume-based analysis

The GTM gives you values for each ROI regardless of whether it
is GM, WM, or CSF. They will probably give you similar
answers, but the GTM will be more robust.

On 2/21/2022 8:48 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

Thanks! Yes, I already mapped my PET to anatomical space
using mri_vol2vol and glmdir/aux/bbpet2anat.lta.

RE: selection of mgx instead of gtm: I am analyzing
amyloid PET data and I believe it is recommended to
extract gray matter localized PET data. Is that what I am
doing by using the mgx image?

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience
Institute & Foundation | Providence Saint John's Health
Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

        *From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf
of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list

<mailto:freesur

Re: [Freesurfer] Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames!

[Douglas N. Greve]

I'm not sure what question you are asking

On 2/25/2022 1:17 PM, Knut J Bjuland wrote:


External Email - Use Caution

DearFreesurferexperts,


IgetthiserrorwhenIamrunning FreeSurfer.


Checkingfor(invalid)multi-frameinputs...
ERROR:input(s)cannothavemultipleframes!
/home/knutjb/subjects/test/mri/orig/001.mgzhas4frames
Ifthisisamulti-frameMEMPRAGEimage,
usemri_concat--rmstocombineechoframes.


Ithasat1_sag_mpragesequence,anditalsogivethis waning

filesarenotfoundtobedifferentandcannotbesorted.


Inaddition,Igettheseerrorswhenimportingusingrecon-all-ifile-all-stest


INFO:Found770filesin//20210224_151919/5_t1_sag_mprage
INFO:ScanningforSeriesNumber5
ScanningDirectory
INFO:found768filesinseries
INFO:loadingseriesheaderinfo.


WhenIamrunningmri_concat--rmsIamabletorunrecon-all-all.


Yoursincerely,

KnutJørgenBjuland



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Douglas N. Greve]

Are you doing an ROI analysis or a voxel-wise analysis? If an ROI 
analysis, then use mri_gtmpvc (with or without PVC). This will give you 
GM, WM, and CSF ROIs. Or do you mean you want a single average across 
all GM?


On 2/24/2022 1:15 PM, Jennifer Bramen wrote:


External Email - Use Caution

I would like to measure uptake exclusively in gray matter. What would 
you recommend to accomplish this?


In my previous message, I was wondering if adding a gray matter mask 
would be a potential way to restrict the analysis to gray matter. Thanks!


Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & 
Foundation | Providence Saint John's Health Center

1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: * on behalf of "Douglas 
N. Greve" 

*Reply-To: *Freesurfer support list 
*Date: *Tuesday, February 22, 2022 at 3:00 PM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

I don't understand. What mask?

On 2/22/2022 8:55 AM, Jennifer Bramen wrote:

*External Email - Use Caution *

If I only want to extract intensity from gray matter, do I need to
add an additional mask?

Thanks!

Jennifer

Get Outlook for iOS

<https://secure-web.cisco.com/1L8X_xbSuY_t_ihVbCVT-VrYnrnVaUkpY43uE0_YCYKJhAviIYu8oxZ5PPt-xMtue1nKBFFsIIdc4KBLgKFCEwa74gpigVENV1GyuIW9GZY7CdyW1O-DI9kzTj0IqZfoGPgj6xImBezDDXVXDYk72vjK3VGgjUz9iLXe0ZpQBziIaJ_lOjni1eZ5hbGxBsHdweSgAAcH3WrreH39jB3E5W_oCbiM_eemv-N1wxKjATTFgYLmBFmxGUK3F_I7myhQ2giptsjKDwBlg67W0Te63GAUl8h6wI9xpMnF5vpkiBB50ky4Fc1twBGrvBs8O3yh8Jw9cAIYSm4G0yFmFVx77AA/https%3A%2F%2Faka.ms%2Fo0ukef>



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

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
*Sent:* Monday, February 21, 2022 7:13:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] PetSurfer: subcortical volume-based
analysis

The GTM gives you values for each ROI regardless of whether it is
GM, WM, or CSF. They will probably give you similar answers, but
the GTM will be more robust.

On 2/21/2022 8:48 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

Thanks! Yes, I already mapped my PET to anatomical space using
mri_vol2vol and glmdir/aux/bbpet2anat.lta.

RE: selection of mgx instead of gtm: I am analyzing amyloid
PET data and I believe it is recommended to extract gray
matter localized PET data. Is that what I am doing by using
the mgx image?

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute &
Foundation | Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Monday, February 21, 2022 at 2:02 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] PetSurfer: subcortical
volume-based analysis

You need to first map your pet to the anatomical space using
mri_vol2vol and the registration glmdir/aux/bbpet2anat.lta
BTW, why are you computing the ROI anlaysis from the mgx data
instead of using the output from the gtm? Note that you cannot
use the white matter values that come from  mgx.

On 2/21/2022 12:57 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

I am trying to extract mean intensity in my PET data for
every ROI. Doug said to run mri_segstats passing the PET
with --i and using --seg to spec the segmentation.*I would
like to confirm that I am using this properly.*

mri_segstats --i
$PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz --seg
$SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel
lh --sum $PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg

where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz
is the PET data regi

Re: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter

[Douglas N. Greve]

Hi Jee Won and Priyanka,

I created a bit of a hack that I'd like y'all to test out. Go to 
https://gate.nmr.mgh.harvard.edu/safelinks/greve/ (user guest, pwd 
collab) and download dngtester and ventfix (you may need to chmod a+x 
both of them). Run ventfix with --help to see how to run it. I've run it 
on a bunch of cases, and it seems to work, but I'd like to see how it 
runs on your data before I fully incorporate it into FS.

doug



On 1/10/2022 8:49 AM, Kang, Jee Won wrote:
>  External Email - Use Caution
>
> Hello all,
>
> Apologies for the delay in response!
>
> For the applications in my group's work, we are looking at ventricular 
> volume, as well as white matter volume. To that degree, we are interested in 
> whether there are any processing steps earlier in the pipeline that we can 
> implement just to minimize the manual editing required - just anecdotally, 
> there have been cases where lateral ventricle volume increases over 5% after 
> making manual edits, and I was unable to identify if there was a common 
> element to the subjects with ventricle problems.
>
> Thank you for your work on this! We really appreciate it.
>
> Thank you,
> Jee Won
> 
>
>
> Message: 2
> Date: Tue, 4 Jan 2022 22:11:53 +
> From: "Nadar, Priyanka (NIH/CC/OCRTME) [F]" 
> Subject: Re: [Freesurfer] [EXTERNAL] Re: Ventricle segmentation issue
>  - ventricle mislabeled as white matter
> To: Freesurfer support list 
> Message-ID:
>  
> 
>
> Content-Type: text/plain; charset="us-ascii"
>
>  External Email - Use Caution
>
> I am not part of Jee Won's team: just generally interested. For my work, I am 
> looking at ventricular volume and so it would be good to not have to manually 
> correct a large number of my scans.
> 
> From: Douglas N. Greve 
> Sent: Tuesday, January 4, 2022 1:19 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: [EXTERNAL] Re: [Freesurfer] Ventricle segmentation issue - ventricle 
> mislabeled as white matter
>
>
> CAUTION: This email originated from outside of the organization. Do not click 
> links or open attachments unless you recognize the sender and are confident 
> the content is safe.
>
>
> Hi Jee Won and Priyanka, there are several things going on here. First, the 
> original aseg (aseg.presurf.mgz) has these areas labeled as nothing (0); they 
> show up as WM in aseg.mgz and aparc+aseg.mgz. Obviously, it would be good to 
> have them properly labeled, but is this critical to your applications? Eg, 
> are you looking at ventricular volume?
>
> On 12/21/2021 9:19 AM, Kang, Jee Won wrote:
>
>  External Email - Use Caution
>
> Hello all,
>
>
> I found a very common error in our data while I was correcting recons. The 
> lateral ventricles (usually the horns) are being misclassified as white 
> matter in aseg.mgz. This happened in around 1/3 of our 108 subjects.
>
>
> We were able to fix this issue by manually filling in the ventricles in 
> aseg.presurf.mgz and re-running Freesurfer with the command autorecon2-noaseg 
> -autorecon3, but this is obviously quite a labor-intensive fix for a 
> substantial portion of our data. This was also the only way to fix the 
> segmentation - filling in the mislabeled areas as 255 in the wm.mgz did not 
> fix the problem. I'm not sure why Freesurfer is having issues here, as the 
> areas it is mislabeling have very distinct intensity boundaries - the T1 
> intensity is usually between 20 and 45 in the areas that are being 
> mislabeled. I've attached a screenshot of a subject's aseg.presurf.mgz who 
> had this ventricle segmentation issue, and you can see that a large portion 
> of the right ventricle has just not been segmented properly; the intensity of 
> the area in the aseg.presurf.mgz and wm.mgz volumes is just 0, and it was 41 
> (R cerebral white matter) in aseg.mgz.
>
>
> Would you be able to provide some insight into why this might have been 
> happening, and what we could do in the future to prevent such extensive 
> manual editing in the future? I can also say that this data was processed 
> with a T2 image as well, and supplying that flag didn't help with the 
> segmentation issue.
>
>
> Thank you,
>
> Jee Won
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://secure-web.cisco.com/1ZGRySYd-5iOMX55uEC_0An1dt-wqdEh2tYIkVApSE6ZYz5vgCOhjM3YCIEraQI_yeq-f2LVImXeqaaoq02BGetl2OuNR0310S0nQ-icV2Z6kJOU_eMoItd70EyNI3_bFVlchyLjila_nbuiyQ_JMj09HBn9XgmDiOuoC28CQMUEG25sb2-CgIy3mNn_1jTIhKRD7g5lDXMIKgIOJqf0WN

Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics

[Douglas N. Greve]

To use the commands I mentioned. You must have a single voxel volume 
(dim = 1 1 1). You might be able to make something from you map with 
something like

mri_mask -bb 0 VOI.mgz VOI.mgz VOI.masked.mgz
# Get the dimension of this volume with
mri_info --dim VOI.masked.mgz
# Now create a single voxel with
mri_convert -ds DSX DSY DSZ VOI.masked.mgz singlevoxel.mgz
Where DSX DXY DSZ are the dimenions from mri_info above
Check the dimension of the singlevoxel.mgz to make sure it is 1 1 1
Then load it in freeview over the anatomical to make sure it is in the 
right place


On 2/22/2022 10:49 PM, Brown, Alexander wrote:


External Email - Use Caution

Hello,

The output of mri_info --dim VOI.mgz is 344 344 344 1.

VOI.mgz is a mask of the MRS "voxel". "Voxel" is a slightly misleading 
term in this context, as the MRS "voxel" is the small rectangular 
volume from which the MRS data is acquired. I basically have a 
rectangular ROI mask (VOI.mgz) that has been registered to orig.mgz, 
and would like to extract the tissue composition of the mask 
(VOI.mgz). Sorry for the poor prior descriptions.


Thanks,
Alex



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


*Sent:* Tuesday, February 22, 2022 5:20:45 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] how to register single-voxel spectroscopy 
VOI to Freesufer-processed brain and extract tissue composition 
statistics

What is the size of your VOI.mgz? Ie, if you run
mri_info --dim VOI.mgz
It should be 1 1 1, meaning that it is a single voxel


On 2/22/2022 3:27 PM, Brown, Alexander wrote:


External Email - Use Caution

Hi Dr. Greve,

I ran the mri_compute_volume_fractions command and have attached the 
terminal output. The output files generated (i.e, cortex.mgz) are the 
partial volume segmentations for the whole brain. There were no 
output files that segmented the VOI mask (VOI.mgz). Maybe I didn't 
specify the input correctly? I inititally recieved errors saying the 
--regheader flag needs 2 arguments, so I used --regheader  



Now that the tissue maps are generated, Another option I considered 
is using mri_segstats to extract tissue composition stats from the 
VOI by using the mri_compute_volume_fractions output volumes (i.e. 
cortex.mgz) as the segmentation input files and using the VOI.mgz as 
a mask. However, I am not sure how to address calculating the partial 
volumes using mri_segstats in coordination with the VOI.mgz mask.


Thanks again for all the help.


Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

*Sent:* Monday, February 21, 2022 9:21 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] how to register single-voxel spectroscopy 
VOI to Freesufer-processed brain and extract tissue composition 
statistics
If you already have the VOI that is aligned to the mprage via the 
geometry in the volume header, then you can use 
mri_compute_volume_fractions to compute the composition; specify 
--regheader subject. To be clear, this assumes that the VOI is a 
single voxel in a "volume" (eg, nii or mgz) and when you run

freeview orig.mgz VOI.mgz
you see the VOI in the right place on the orig.mgz. When these 
conditions are met, mri_compute_volume_fractions will give you what 
you want. One last thing is that volume_fractions will give you 
another single-voxel "volume" as output. There are several ways to 
get the value out, the easiest is probably matlab, something like

a = MRIread('singlevoxvol.mgz');
a.vol % will give you the value

On 2/21/2022 6:57 PM, Brown, Alexander wrote:


External Email - Use Caution

Yes, it is MRS.

Attached is a screenshot showing a mask of the svs VOI overlaid on 
the structural. This is from Gannet MRS software that uses SPM12 to 
register and segment the VOI. I have the generated VOI.nii mask from 
the Gannet output - maybe I could use the mask as the registration 
input for Freesurfer?


Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of D

Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness

[Douglas N. Greve]

Hi Asim, I ran into some issues on my test. I think the software is 
doing what it is supposed to do, but I think there is something wrong 
with the underlying permutation method when using PVRs. This will take a 
while for me to figure out. In the  meantime, you can try using the more 
conventional mcz correction. If the cluster p-value is very strong, then 
the liberalness of the method might not matter.


On 2/22/2022 5:32 PM, Dhungana, Asim wrote:
Thank you! I ran the development version of the mri_glmfit-sim command 
on my data, and it did not crash and seems to give reasonable outputs 
(smaller clusters disappear after correction). Whenever your tests are 
done, it will be good to know if they confirm that everything is working.


Best,
Asim

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


*Sent:* Monday, February 21, 2022 6:29 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while 
regressing out cortical thickness
I just updated the code to accept PVRs. I'm not sure what I have to do 
to test it; I guess I need to run the null test like I did for the 
non-PVR version. This will take a while. In the mean time, can you 
download the development version and just try it on your data to see 
if it crashes or gives results that don't seem to make sense? You'll 
have to wait until the development version is updated (probably tomorrow).



On 2/17/2022 5:22 PM, Dhungana, Asim wrote:
Hello Doug, just following up on my questions below on how/if I can 
correct for multiple comparisons with PVR. Thanks again.


Best,
Asim

*From:* Dhungana, Asim  
<mailto:adhung...@mgh.harvard.edu>

*Sent:* Monday, February 14, 2022 11:45 AM
*To:* Freesurfer support list  
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while 
regressing out cortical thickness
OK, I see. How would you recommend correcting for multiple 
comparisons if the perm option does not work with PVR?


Also, are you saying that I should only use the glm.osgm.lh/eres.mgh 
file as a pvr argument? Does this look correct:


mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr glm.osgm.lh/eres.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

Best,
Asim

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

*Sent:* Sunday, February 13, 2022 5:29 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while 
regressing out cortical thickness

Re: long run  time. Sorry, permutation will not work with PVR.
Re: mean thickness. Use the eres.mgh from you osgm analysis instead 
of the raw thickness map (lh.thickness.fwhm10.mgh)


On 2/8/2022 4:12 PM, Dhungana, Asim wrote:

Dear Freesurfer experts,

I am trying to run a GLM analysis comparing the difference in the 
cortical CBF maps between two groups, but I would like to regress 
out cortical thickness. I read through a post with a similar 
question 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html 
<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html>), 
but I am still a little confused and want to confirm the steps of my 
analysis below:


---

1. Compile/smooth CBF data on surface for all subjects.
mris_preproc
--hemi lh \
--projfrac 0.5 \
--target fsaverage \
--o lh.cbf.00.mgh \
--iv subj1/cbf.mgz  subj1/register_pasl.dat \
--iv subj2/cbf.mgz  subj2/register_pasl.dat \
... until subjN

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.cbf.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.cbf.fwhm10.mgh

2. Compile/smooth thickness data on surface for all subjects.
mris_preproc \
--fsgd cbf.fsgd \
--target fsaverage \
--hemi lh \
--meas thickness \
--out lh.thickness.00.mgh

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.thickness.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.thickness.fwhm10.mgh

3. GLM fit of CBF maps, including thickness as a regressor.
mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

4. Multiple comparisons correction
mri_glmfit-sim \
--glmdir lh.cbf.fwhm10.glmdir \
--perm 1000 1.3 abs \
--cwp 0.05 \
--2spaces \
--bg 35

---

I am currently having issues with Step 4; it has been over an hour, 

Re: [Freesurfer] Annotation File to ROI Volume Estimate

[Douglas N. Greve]

I see it in the help:
   -b
    tabular output



On 2/24/2022 12:23 PM, Jacoby, John wrote:

Hi Doug, thanks for the pointer. That was exactly what I was looking for.

When I copied the command from recon-all.log, it used a -b flag. I 
can't find documentation for this flag either in the --help or on the 
wiki. Could you elaborate on what it does? Thank you!


Best,
John

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Dividing surface overlays

[Douglas N. Greve]

You can also look in pctsurfcon. This compute the percent gray/white 
contrast. It does so on the T1w, but you could look inside the script to 
see how it does it and adapt to your situation.


On 2/23/2022 3:26 PM, Adam Martersteck wrote:


External Email - Use Caution

Hi Dylan,

Give this a try:
fscalc gm_lh.nii.gz div wm_lh.nii.gz --o gmwmratio_lh.nii.gz

On Wed, Feb 23, 2022 at 12:24 PM Tisdall, Dylan 
 wrote:


      External Email - Use Caution

Hi all,

I've generated two surface overlays, using mri_vol2surf with
positive and negative projfrac to get a GM and WM samples
(gm_lh.nii.gz and wm_lh.nii.gz). I'd now like to take the
vertex-wise ratio of these two overlays, and make a new one
(gmwmratio_lh.nii.gz). I've tried doing this as:

fslmaths gm_lh.nii.gz -div wm_lh.nii.gz gmwmratio_lh.nii.gz

but the result is:

Image Exception: #22 :: Failed to read volume gm_lh.nii.gz
Error : Error: Nonsensical ROI for gm_lh.nii.gz

Is there another tool I can use to compute this ratio? Is there a
better workflow than making two surfaces and dividing?


Thanks,
Dylan



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics

[Douglas N. Greve]

What is the size of your VOI.mgz? Ie, if you run
mri_info --dim VOI.mgz
It should be 1 1 1, meaning that it is a single voxel


On 2/22/2022 3:27 PM, Brown, Alexander wrote:


External Email - Use Caution

Hi Dr. Greve,

I ran the mri_compute_volume_fractions command and have attached the 
terminal output. The output files generated (i.e, cortex.mgz) are the 
partial volume segmentations for the whole brain. There were no output 
files that segmented the VOI mask (VOI.mgz). Maybe I didn't specify 
the input correctly? I inititally recieved errors saying the 
--regheader flag needs 2 arguments, so I used --regheader  



Now that the tissue maps are generated, Another option I considered is 
using mri_segstats to extract tissue composition stats from the VOI by 
using the mri_compute_volume_fractions output volumes (i.e. 
cortex.mgz) as the segmentation input files and using the VOI.mgz as a 
mask. However, I am not sure how to address calculating the partial 
volumes using mri_segstats in coordination with the VOI.mgz mask.


Thanks again for all the help.


Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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


*Sent:* Monday, February 21, 2022 9:21 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] how to register single-voxel spectroscopy 
VOI to Freesufer-processed brain and extract tissue composition 
statistics
If you already have the VOI that is aligned to the mprage via the 
geometry in the volume header, then you can use 
mri_compute_volume_fractions to compute the composition; specify 
--regheader subject. To be clear, this assumes that the VOI is a 
single voxel in a "volume" (eg, nii or mgz) and when you run

freeview orig.mgz VOI.mgz
you see the VOI in the right place on the orig.mgz. When these 
conditions are met, mri_compute_volume_fractions will give you what 
you want. One last thing is that volume_fractions will give you 
another single-voxel "volume" as output. There are several ways to get 
the value out, the easiest is probably matlab, something like

a = MRIread('singlevoxvol.mgz');
a.vol % will give you the value

On 2/21/2022 6:57 PM, Brown, Alexander wrote:


External Email - Use Caution

Yes, it is MRS.

Attached is a screenshot showing a mask of the svs VOI overlaid on 
the structural. This is from Gannet MRS software that uses SPM12 to 
register and segment the VOI. I have the generated VOI.nii mask from 
the Gannet output - maybe I could use the mask as the registration 
input for Freesurfer?


Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

*Sent:* Monday, February 21, 2022 5:25 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] how to register single-voxel spectroscopy 
VOI to Freesufer-processed brain and extract tissue composition 
statistics
WARNING: This message has originated from an External Source. This 
may be a phishing expedition that can result in unauthorized access 
to our IT System. Please use proper judgment and caution when opening 
attachments, clicking links, or responding to this email.

I don't know what an svs is. Is it like MRS?

On 2/21/2022 5:51 PM, Brown, Alexander wrote:


External Email - Use Caution

Hello,

I have been asked to provide tissue composition stats (%GM,%WM,%CSF) 
for an SVS VOI. How can I register the svs file to the 
Freesurfer-processed brain and extract these values?


Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://secure-web.cisco.com/1e96LBxkUv68RHs1pnQwkmKj0-gaAFawVHvt27a_9svFF4RLXdp8KyQwXNUy36ellLTeVEmcDilRCRCMVwdL_zeBpbbDLtDO_sJmqKF5tm4eIeGT-8hC6hGCzHNv45EyZeEZ42mvwrVyzO8P_xLIttODh6NN3h6X027goG67ASOy6Upo-kKCIx2pPYblDw17MPO-YcBkzXNy8iUnU8xX6wIL9ganVrOrNfkvqx8ylF3JsGNWqOTyMxULXHCI_wy8jfj2dPH-GHO9TWzP

Re: [Freesurfer] Annotation File to ROI Volume Estimate

[Douglas N. Greve]

You don't need to go that far. You can run mris_annotoical_stats. Look 
in recon-all.log to find the command line used to create the 
?h.aparc.annot and just change the annot and output file


On 2/22/2022 10:02 AM, Jacoby, John wrote:

Hi all,

We were sent a FreeSurfer annotation file that denotes some ROIs we're 
interested in. What's the proper way to map this annotation to the 
cortical ribbon volume and get an estimate of that volume for each 
ROI? I've already registered the annotations to the subject from 
fsaverage space using mri_surf2surf. I'm thinking something like:


mri_label2vol --annot {registered_annotation_file} --temp 
{$SUBJECT/mri/orig.mgz} --o {output_volume_segmentation_file} 
--subject {$SUBJECT} --hemi {lh,rh} --identity --proj frac 0 1 0.01


And then run mri_segstats on the output_volume_segmentation_file

This seems to do what I need, but I want to confirm that I'm not 
missing import details. I'm also not entirely sure what the 'delta' 
parameter of the --proj flag is doing. I gather that it's some kind of 
step size, but will it have a big impact on the resulting ribbon volume?


Thanks for any help!

Best,
John

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Subject ID error with bbregister

[Douglas N. Greve]

Try just adding a line at the end of the lta file like
subject 126346

On 2/22/2022 9:45 AM, Tisdall, Dylan wrote:
>  External Email - Use Caution
>
> Hi Doug and Matt,
>
> I'm pretty confident my $SUBJECTS_DIR is correct, its the same one I used for 
> recon-all on this subject and the files seem to be in the right place; wee 
> below:
>
> [mtisdall@ftdc-gpu01 126346]$ echo $SUBJECTS_DIR
> /home/mtisdall/Research/7TAnalysis/subjects
>
> [mtisdall@ftdc-gpu01 126346]$ ls $SUBJECTS_DIR/126346
> label  mri  scripts  stats  surf  tmp  touch  trash
>
>
> I don't see a blank subject line in the lta file. I tried to make the initial 
> transform manually in Freeview by just loading the two volumes, using 
> `Transform Volume` until they were close, and then saving the resulting 
> transform. I then re-loaded my 7T data, using the option in FreeView to apply 
> the transform on load, and it looks right. See the file contents below:
>
> [mtisdall@scisub 126346]$ cat 7Tto3Tinit.lta
> type  = 1 # LINEAR_RAS_TO_RAS
> nxforms   = 1
> mean  = 0. 0. 0.
> sigma = 1.
> 1 4 4
> 9.961947798728943e-01 8.715574443340302e-02 4.656613983300417e-10 
> -1.702789425849915e+00
> -8.682409673929214e-02 9.924039244651794e-01 -8.715574443340302e-02 
> -7.269048690795898e+00
> -7.596124429255724e-03 8.682409673929214e-02 9.961947798728943e-01 
> 1.319813346862793e+01
> 0.000e+00 0.000e+00 0.000e+00 
> 1.000e+00
> src volume info
> valid = 1  # volume info valid
> filename = /home/mtisdall/Research/7TAnalysis/126346/niis/3T_MPRAGE.nii
> volume = 208 240 256
> voxelsize = 1.000e+00 1.000e+00 1.000e+00
> xras   = 1.000e+00 0.000e+00 0.000e+00
> yras   = 0.000e+00 1.000e+00 0.000e+00
> zras   = 0.000e+00 0.000e+00 1.000e+00
> cras   = 5.000e-01 1.455932617187500e+01 -1.323728942871094e+01
> dst volume info
> valid = 1  # volume info valid
> filename = /home/mtisdall/Research/7TAnalysis/126346/niis/3T_MPRAGE.nii
> volume = 208 240 256
> voxelsize = 1.000e+00 1.000e+00 1.000e+00
> xras   = 1.000e+00 0.000e+00 0.000e+00
> yras   = 0.000e+00 1.000e+00 0.000e+00
> zras   = 0.000e+00 0.000e+00 1.000e+00
> cras   = 5.000e-01 1.455932617187500e+01 -1.323728942871094e+01
> fscale 0.10
>
>
> Note that, when I move the --s flag to the end of the command line, it runs 
> slightly further, but ultimately fails searching for `subject-unknown` within 
> my subjects directory:
>
> [mtisdall@scisub 126346]$ bbregister --mov mgz/7T_MEMPRAGE.mgz --init-reg 
> 7Tto3Tinit.lta --reg 7Tto3T.lta --o 7TMEMPRAGE_warped.mgz --t1 --s 126346
> ...
> Loading mov
> error: 
> mghRead(/home/mtisdall/Research/7TAnalysis/subjects/subject-unknown/mri/orig.mgz,
>  -1): could not open file
>
>
> Any other suggestions on what I'm doing wrong here?
>
>
> Thanks again,
> Dylan
>
>
>
>> Date: Mon, 21 Feb 2022 16:58:22 -0500
>> From: "Douglas N. Greve" 
>> Subject: Re: [Freesurfer] Subject ID error with bbregister
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID: <6f0565c8-c4f3-8289-d41b-0558a1fb6...@mgh.harvard.edu>
>> Content-Type: text/plain; charset=UTF-8; format=flowed
>>
>> Is there a blank subject line in the lta file? If so, it is probably
>> trying to get the subject from there. You can try putting the --s after
>> the --lta
>>
>> On 2/21/2022 3:43 PM, Tisdall, Dylan wrote:
>>>  External Email - Use Caution
>>>
>>> Hi all,
>>>
>>> Quick question on a puzzling error with bbregister version 7.1.1. When I 
>>> run:
>>>
>>> bbregister --s 126346 --mov mgz/7T_MEMPRAGE --init-reg 7Tto3Tinit.lta --reg 
>>> 7Tto3T.lta --o 7TMEMPRAGE_warped.mgz --t1
>>>
>>> I get the error:
>>>
>>> ERROR: must spec a subject id
>>>
>>> which I thought I'd done with the --s flag. What am I missing?
>>>
>>> Even more odd, if I just move the to the end of the command, bbregister 
>>> will run, but eventually fails with:
>>>
>>> error: 
>>> mghRead(/hom/mtisdall/Research/7TAnalysis/subject//subject-unknown/mri/orig.mgz,
>>>  -1): could not open file
>>>
>>> Is there something obvious I'm doing wrong with these two command lines 
>>> that cause these behaviors?
>

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Douglas N. Greve]

I don't understand. What mask?

On 2/22/2022 8:55 AM, Jennifer Bramen wrote:


External Email - Use Caution



If I only want to extract intensity from gray matter, do I need to add 
an additional mask?


Thanks!

Jennifer

Get Outlook for iOS 
<https://secure-web.cisco.com/1L8X_xbSuY_t_ihVbCVT-VrYnrnVaUkpY43uE0_YCYKJhAviIYu8oxZ5PPt-xMtue1nKBFFsIIdc4KBLgKFCEwa74gpigVENV1GyuIW9GZY7CdyW1O-DI9kzTj0IqZfoGPgj6xImBezDDXVXDYk72vjK3VGgjUz9iLXe0ZpQBziIaJ_lOjni1eZ5hbGxBsHdweSgAAcH3WrreH39jB3E5W_oCbiM_eemv-N1wxKjATTFgYLmBFmxGUK3F_I7myhQ2giptsjKDwBlg67W0Te63GAUl8h6wI9xpMnF5vpkiBB50ky4Fc1twBGrvBs8O3yh8Jw9cAIYSm4G0yFmFVx77AA/https%3A%2F%2Faka.ms%2Fo0ukef>


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


*Sent:* Monday, February 21, 2022 7:13:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
The GTM gives you values for each ROI regardless of whether it is GM, 
WM, or CSF. They will probably give you similar answers, but the GTM 
will be more robust.


On 2/21/2022 8:48 PM, Jennifer Bramen wrote:


External Email - Use Caution

Thanks! Yes, I already mapped my PET to anatomical space using 
mri_vol2vol and glmdir/aux/bbpet2anat.lta.


RE: selection of mgx instead of gtm: I am analyzing amyloid PET data 
and I believe it is recommended to extract gray matter localized PET 
data. Is that what I am doing by using the mgx image?


Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & 
Foundation | Providence Saint John's Health Center

1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: * 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas 
N. Greve"  <mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list  
<mailto:freesurfer@nmr.mgh.harvard.edu>

*Date: *Monday, February 21, 2022 at 2:02 PM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>

*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

You need to first map your pet to the anatomical space using 
mri_vol2vol and the registration glmdir/aux/bbpet2anat.lta
BTW, why are you computing the ROI anlaysis from the mgx data instead 
of using the output from the gtm? Note that you cannot use the white 
matter values that come from mgx.


On 2/21/2022 12:57 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

I am trying to extract mean intensity in my PET data for every
ROI. Doug said to run mri_segstats passing the PET with --i and
using --seg to spec the segmentation.*I would like to confirm
that I am using this properly.*

mri_segstats --i
$PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz --seg
$SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel lh --sum
$PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg

where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is the
PET data registered and resampled into the individual’s
T1-weighrd MRI space.

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute &
Foundation | Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Wednesday, February 16, 2022 at 7:30 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based
analysis

If you want to do an ROI analysis using FS-based ROIs, you should
do that at the individual level. Resample the PET to the
anatoimical space, then run mri_segstats passing the PET with --i
and using --seg to spec the segmentation. If you really want to
do it in MNI305 space, then it is the same thing just using the
MNI305-based (2mm) segmentation

On 2/14/2022 6:11 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

Dear Freesurfer Developers

I am doing an ROI--based amyloid PET scan analysis. I have
completed all of the steps from the PetSurfer wiki. I now
have the preprocessed, averaged, resampled, smoothed PET data
in MNI305 space whic

Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)

[Douglas N. Greve]

No, not really. If you get the data to me, I'll take a look if I can. 
Make sure to send specific information about vertices that you are 
having problems with so I don't have to go looking for it.


On 2/21/2022 6:29 PM, Edan Daniel wrote:


External Email - Use Caution

Hi Doug,
It is something we do *a lot* of, thus we hoped we'd be able to find a 
way to make the recon-wm implement our edits without additional manual 
edits, like we used to do with v6.
Do you have any idea what could have caused this change in 
stubbornness in v7, or how would it be best to try to overcome this?
We can try using the samseg stream as Bruce has kindly suggested, but 
we hoped to find a way to make our standard fs pipeline work with v7.


Many thanks!!!
Edan @ PrincetonBrainDevLab

On Mon, Feb 21, 2022 at 5:04 PM Douglas N. Greve 
 wrote:


If this is not something you have to do a lot of, you can put a
repositioning point. See the release notes.

On 2/21/2022 1:10 PM, Fischl, Bruce wrote:


Hi Edan

Control points might be helpful in both cases, but you are right
it is more often the case when the wm is too dark. Another thing
you can try is using expert options for mri_segment to constrain
the intensity ranges of wm/gm. Or you could try using the samseg
stream (someone else will have to help you with this, but it
might well do better for your acquisitions)

Cheers

Bruce

*From:* Edan Daniel 
<mailto:ed...@princeton.edu>
*Sent:* Monday, February 21, 2022 11:14 AM
*To:* Fischl, Bruce 
<mailto:bfis...@mgh.harvard.edu>
*Cc:* Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in
white matter segmentation (7.1.1, 7.2.0)

*External Email - Use Caution *

Thanks Bruce!

This looks like a helpful solution for the places where the wm is
not identified- we will definitely try it!

We have one other type of issue which is more prevalent, that I
was not sure if control points will be able to help with (we have
not worked with control points before so sorry if this is a
misinformed question)

The main issue we're facing is that the final segmentation we get
is too aggressive, that is, in many places too *many* voxels are
categorized as wm and thus we have lower ability to characterize
properties of the gray matter in the occipital cortex. What we
usually do is clean the wm segmentation to make it less bulky,
but now these edits are not being incorporated in the final
segmentation. We are very confused by this because this type of
edits were easily incorporated in v6, but not with v7.

From my understanding- the control points would be helpful in the
opposite case- where not enough voxels are recognized as wm (such
as in the rightmost part of the attached image)- but not much in
the rest of the image where we can see that the magenta borders
(x.orig.nofix) are 'tighter' around the wm when compared to the
borders after running through recon -wm (teal, x.white.preaparc).

Is there a way to leverage the control points for this cause, or
is there something else we can try to make the recon -wm less
stubborn and accept our manual edits?

For reference, the full command we run is as follows:

recon-all -autorecon2-wm -autorecon3 -subjid '
freesurferfoldername ' -cc-crs ' num2str(corpus_point)

Attaching another image - please let me know if the
visibility here is better or if you'd like to see a different
visualization.

Many thanks

Edan @ PrincetonBrainDevLab

On Fri, Feb 18, 2022 at 9:53 AM Fischl, Bruce
 wrote:

Hi Edan

It’s hard for me to see what’s going on in those images. What
is the intensity of the white matter in the middle of the
occipital strands in the brain.mgz and the
brain.finalsurfs.mgz? If it is significantly lower than 110
you probably want some control points in the occipital lobe.

Cheers
Bruce

*From:* Edan Daniel 
*Sent:* Friday, February 18, 2022 12:15 AM
*To:* Freesurfer support list
; Fischl, Bruce

*Subject:* Re: [Freesurfer] autorecon2-wm not reflecting
edits in white matter segmentation (7.1.1, 7.2.0)

*External Email - Use Caution *

Hi Bruce!

We are focusing on the occipital lobe where the white matter
boundary is often too far into the gray matter, and we need
those voxels to record visual signals.

Attaching a few images for reference - notice how much
'thicker' the wm segmentation is in the white.preaparc vs the
lh.orig.nofix. wm edits of this sort were accepted when we
were using the same pipeline with v6 (separate datasets), but
now with v7 our edits

Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics

[Douglas N. Greve]

If you already have the VOI that is aligned to the mprage via the 
geometry in the volume header, then you can use 
mri_compute_volume_fractions to compute the composition; specify 
--regheader subject. To be clear, this assumes that the VOI is a single 
voxel in a "volume" (eg, nii or mgz) and when you run

freeview orig.mgz VOI.mgz
you see the VOI in the right place on the orig.mgz. When these 
conditions are met, mri_compute_volume_fractions will give you what you 
want. One last thing is that volume_fractions will give you another 
single-voxel "volume" as output. There are several ways to get the value 
out, the easiest is probably matlab, something like

a = MRIread('singlevoxvol.mgz');
a.vol % will give you the value

On 2/21/2022 6:57 PM, Brown, Alexander wrote:


External Email - Use Caution

Yes, it is MRS.

Attached is a screenshot showing a mask of the svs VOI overlaid on the 
structural. This is from Gannet MRS software that uses SPM12 to 
register and segment the VOI. I have the generated VOI.nii mask from 
the Gannet output - maybe I could use the mask as the registration 
input for Freesurfer?


Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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


*Sent:* Monday, February 21, 2022 5:25 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] how to register single-voxel spectroscopy 
VOI to Freesufer-processed brain and extract tissue composition 
statistics
WARNING: This message has originated from an External Source. This may 
be a phishing expedition that can result in unauthorized access to our 
IT System. Please use proper judgment and caution when opening 
attachments, clicking links, or responding to this email.

I don't know what an svs is. Is it like MRS?

On 2/21/2022 5:51 PM, Brown, Alexander wrote:


External Email - Use Caution

Hello,

I have been asked to provide tissue composition stats (%GM,%WM,%CSF) 
for an SVS VOI. How can I register the svs file to the 
Freesurfer-processed brain and extract these values?


Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://secure-web.cisco.com/1SZ_ZwxUHUoHqP332XFGWKlV1rBGVZpWfjoGbMwovH8RMj2XdDYrM9GgfKAiqt0TrmkE3Gwe0p6N2B-5ZMPuLVZPJXyW0NKljySOhcBqh9dOUag4g2j3zWx5OSaGYVqNRqpWcQ42YvXBRMppsZDyLzqBQ81UYPC_sooTdOYpHFKKb0XXVAHa7OFCexOXG_2VMsjR-B_RlbEy-a8Eog3lcJSSB-mGFDIN8GzE92BZShp4UQHnygF8s7SK9jO7EgXqWIQbb1H5LGnm-TO4arAF8nUF_stbNshv42dAMfwZziQIKRoi36_H65-ZZVLJe5Z-mQrn57AEHzksDP0bz7gLlhA/https%3A%2F%2Fnam02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Caabgk8%2540mail.missouri.edu%257Cb780495e7cc04454891108d9f591850c%257Ce3fefdbef7e9401ba51a355e01b05a89%257C0%257C0%257C637810827623402419%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DS6AoUqej6ir9sOSfR7h%252Bx0phctkv0%252BTzwCB7XwS2Tww%253D%26reserved%3D0>



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] [External] Re: classes for GLM analysis

[Douglas N. Greve]

On 2/21/2022 6:50 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


External Email - Use Caution

Do you have a Freesurfer page I can read up on those hybrid ways just 
to see whether that could be an option?

No, this is a general statistics question, not something FS-specific.


Also, although its a binary, you would recommend against have sex be a 
continuous measurement like age, due to the design of how the 
contrasts are determined? I.e continuous measurements aren't treated 
like integers
It is not  that. It is that when you say that M=1 and F=2, you are 
expecting F to be twice that of M (or half). This usually does not make 
sense.


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

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


*Sent:* Sunday, February 13, 2022 12:24 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* [External] Re: [Freesurfer] classes for GLM analysis
It is probably not going to work very well if you have some classes 
that only have one member. You can eliminate members of classes that 
only have a few members. If you really need to have those cases, there 
are hybrid ways to analyze the data (but you can't use an FSGD at that 
point)


On 2/6/2022 10:41 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


External Email - Use Caution

Hi all,

I am doing an analysis and generating the FSGD. I understand sex and 
race are classes in this context, but something I was also hoping to 
regress out is the effects of scanner/sequences. We have a large 
participant size, so we have around 10+ scanner/sequences, which 
makes for a large amount of classes combinations, with some having 
just 1 (if not zero) fitting into a class.


Would you proceed with this nonetheless? If not, should 
scanner/sequence be something that we consider? Should we find some 
other way to adjust site (I don't think we can z-score...). Or can we 
consider site/scanner as a continuous variable


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://secure-web.cisco.com/1e58fbAB8bqm7NyMtK8bHh7_ADs4rJ1eJVjFa6RmNOqRvv5vg65kchIzr15LWl7zHaU-d2Q-sk_kxMV3GrldfYKVX5nxsInjHqrZW5hXBohWIbe9tDyDc8fVZUJ_v1KTsJLUnQP04g79MxnlFuKNxknOo-IqbpEzNKBQao0B2ALpLzqZON9xwp1VX53Bc4yDM--1gAyd6ocwWVK7WpTGxyHY3x7zXw_Vd5o2M5RHxlrL-8Q5CcJLyFT9V2-J6GASLNz0kNV16joDe-ehG7a5_cnxuKyq5RIgWDIUsENquGg2IrEYV6H0ZFo2qnNVk9drS/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21CvMGjuU%21oWSHsHxjED1I9do4R5UyRdbrrRZ0JwASmA6lT5nMBEMbU4m_jfTGWrhBU-2K4sn01nxIwg%24>



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Douglas N. Greve]

The GTM gives you values for each ROI regardless of whether it is GM, 
WM, or CSF. They will probably give you similar answers, but the GTM 
will be more robust.


On 2/21/2022 8:48 PM, Jennifer Bramen wrote:


External Email - Use Caution

Thanks! Yes, I already mapped my PET to anatomical space using 
mri_vol2vol and glmdir/aux/bbpet2anat.lta.


RE: selection of mgx instead of gtm: I am analyzing amyloid PET data 
and I believe it is recommended to extract gray matter localized PET 
data. Is that what I am doing by using the mgx image?


Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & 
Foundation | Providence Saint John's Health Center

1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: * on behalf of "Douglas 
N. Greve" 

*Reply-To: *Freesurfer support list 
*Date: *Monday, February 21, 2022 at 2:02 PM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

You need to first map your pet to the anatomical space using 
mri_vol2vol and the registration glmdir/aux/bbpet2anat.lta
BTW, why are you computing the ROI anlaysis from the mgx data instead 
of using the output from the gtm? Note that you cannot use the white 
matter values that come from  mgx.


On 2/21/2022 12:57 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

I am trying to extract mean intensity in my PET data for every
ROI. Doug said to run mri_segstats passing the PET with --i and
using --seg to spec the segmentation.*I would like to confirm that
I am using this properly.*

mri_segstats --i
$PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz --seg
$SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel lh --sum
$PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg

where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is the
PET data registered and resampled into the individual’s T1-weighrd
MRI space.

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute &
Foundation | Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Wednesday, February 16, 2022 at 7:30 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based
analysis

If you want to do an ROI analysis using FS-based ROIs, you should
do that at the individual level. Resample the PET to the
anatoimical space, then run mri_segstats passing the PET with --i
and using --seg to spec the segmentation. If you really want to do
it in MNI305 space, then it is the same thing just using the
MNI305-based (2mm) segmentation

On 2/14/2022 6:11 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

Dear Freesurfer Developers

I am doing an ROI--based amyloid PET scan analysis. I have
completed all of the steps from the PetSurfer wiki. I now have
the preprocessed, averaged, resampled, smoothed PET data in
MNI305 space which is constrained to the subcortical gray
matter mask.

*How do I extract mean intensity within all of the subcortical
ROI?*

Thank you!

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute &
Foundation | Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069




___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
<https://secure-web.cisco.com/1pHRKHdySejszKCsrs9a5H_HhNUL-CC5YeU4Cl_81vNtgCRYphxx1lXfNUS28oh3w1R-TndgZ47wOf2XFHWg3dBsYow738wDFOOYfSwGLuBCjeJ-FaIOQPsyai7IAeZ1dOxsmP6GuyW5j2bVWEFjAU09qZ4M9zHUa2XyfmlPf4piiqQbo3Ayz3gL78M-vcSa8d1BpjLa9zF3PA4aHAuzSSyumGTLdIAY-5_L_6XgNw7iEG5NYmI7TPk5Phat5eGYdipePAy6m0hB1ibRYO0p1h0wvZVeul211fN1oB8Pwq1PTrPMjeCu

Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness

[Douglas N. Greve]

I just updated the code to accept PVRs. I'm not sure what I have to do 
to test it; I guess I need to run the null test like I did for the 
non-PVR version. This will take a while. In the mean time, can you 
download the development version and just try it on your data to see if 
it crashes or gives results that don't seem to make sense? You'll have 
to wait until the development version is updated (probably tomorrow).



On 2/17/2022 5:22 PM, Dhungana, Asim wrote:
Hello Doug, just following up on my questions below on how/if I can 
correct for multiple comparisons with PVR. Thanks again.


Best,
Asim

*From:* Dhungana, Asim 
*Sent:* Monday, February 14, 2022 11:45 AM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while 
regressing out cortical thickness
OK, I see. How would you recommend correcting for multiple comparisons 
if the perm option does not work with PVR?


Also, are you saying that I should only use the glm.osgm.lh/eres.mgh 
file as a pvr argument? Does this look correct:


mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr glm.osgm.lh/eres.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

Best,
Asim

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


*Sent:* Sunday, February 13, 2022 5:29 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while 
regressing out cortical thickness

Re: long run  time. Sorry, permutation will not work with PVR.
Re: mean thickness. Use the eres.mgh from you osgm analysis instead of 
the raw thickness map (lh.thickness.fwhm10.mgh)


On 2/8/2022 4:12 PM, Dhungana, Asim wrote:

Dear Freesurfer experts,

I am trying to run a GLM analysis comparing the difference in the 
cortical CBF maps between two groups, but I would like to regress out 
cortical thickness. I read through a post with a similar question 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html 
<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html>), 
but I am still a little confused and want to confirm the steps of my 
analysis below:


---

1. Compile/smooth CBF data on surface for all subjects.
mris_preproc
--hemi lh \
--projfrac 0.5 \
--target fsaverage \
--o lh.cbf.00.mgh \
--iv subj1/cbf.mgz  subj1/register_pasl.dat \
--iv subj2/cbf.mgz  subj2/register_pasl.dat \
... until subjN

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.cbf.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.cbf.fwhm10.mgh

2. Compile/smooth thickness data on surface for all subjects.
mris_preproc \
--fsgd cbf.fsgd \
--target fsaverage \
--hemi lh \
--meas thickness \
--out lh.thickness.00.mgh

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.thickness.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.thickness.fwhm10.mgh

3. GLM fit of CBF maps, including thickness as a regressor.
mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

4. Multiple comparisons correction
mri_glmfit-sim \
--glmdir lh.cbf.fwhm10.glmdir \
--perm 1000 1.3 abs \
--cwp 0.05 \
--2spaces \
--bg 35

---

I am currently having issues with Step 4; it has been over an hour, 
and it seems that the command will not finish executing. It is also 
not outputting any error messages. Whenever I run this analysis using 
the same parameters but without regressing out thickness, this step 
takes under five minutes on my machine and returns appropriate 
results. It seems like I must be doing something wrong, but I'm not 
sure. Please let me know if there is anything that you would 
change/add above.


Also, I noticed that you recommended regressing out the overall mean 
thickness (which you can obtain through mri_glmfit --surf fsaverage 
lh --osgm --y lh.thickness.fwhm10.mgh --o glm.osgm.lh --eres-save). 
Is glm.osgm.lh the mean stratified by class or the overall mean? If I 
were to include this in my GLM fit, would this be the correct command:


mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh glm.osgm.lh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

Thank you for taking a look at this, let me know if you need any 
other information.


Best,
Asim Dhungana

​Freesurfer version: 
freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
<http

Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics

[Douglas N. Greve]

I don't know what an svs is. Is it like MRS?

On 2/21/2022 5:51 PM, Brown, Alexander wrote:


External Email - Use Caution

Hello,

I have been asked to provide tissue composition stats (%GM,%WM,%CSF) 
for an SVS VOI. How can I register the svs file to the 
Freesurfer-processed brain and extract these values?


Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Contrasts 3 groups 4 covariates

[Douglas N. Greve]

On 2/19/2022 6:10 PM, fernanda rohrsetzer wrote:


External Email - Use Caution

Hi guys,
I'm a beginner in Freesurfer and I want to perform an analysis of the 
difference between 3 groups in cortical thickness,volume and area 
having age, mean thickness and etiv as covariate.
my design matrix for 3 groups comparison as "1 -1 0 0 0 0 0 0 0 0 0 0 
0 0 0 (LR-HR)

1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 (LR-MDD)
0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 (HR-MDD)

If possible, I would like to know how my contrasts change when I wish 
to test the change in thickness with age, after removing the group 
effects.

It is just move the non-zero values in the contrast to the age columns, like
0 0 0    1 -1 0    0 0 0 0 0 0 0 0 0
Another question I have is how can I create contrasts to control etiv 
between groups, like 2x2 comparison.

I don't understand.
btw, you should normalize your covariates (ie, remove the mean, divide 
by the sqrt(sum(squares)))

I'm sorry if I was not clear...
thanks
Fernanda  
  
my FSGD file is

GroupDescriptorFile 1 Title MyStudy
Class LR
Class HR
Class MDD
Variables age meanThick totalarea eTIV Input Sub001 LR 14.3 1350519.71 
1954527.71 1552459.71 Input Sub002 MDD 15.7 1558515.86 1689767.98 
1809809.87



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] GLM analysis - volume and surface area

[Douglas N. Greve]

Yes, it is. It is confusing when you talk about area and volume since 
these are not point measures like thickness (ie, what is the volume or 
area of a vertex?). The area of a vertex is computed as the mean of the 
adjacent triangles of the vertex. The volume is the mean of the 
neighboring truncated tetrahedra. When you run mris_preproc, it will 
apply a jacobian correction (like VBM). Otherwise, it operates the same 
as if you had a thickness value at the vertex, ie, same GLM, etc. Make 
sure to use permutation for correction of multiple comparisons.


On 2/21/2022 12:13 PM, Laura Willers de Souza wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I would like to know if it is correct to perform volume and surface 
area analysis using freesurfer's GLM!?


In several mailing list questions I have already seen instructions for 
performing these types of analysis. But I understand that freesurfer 
does vertex-wise analysis in the 2D surface space. So, it is not clear 
to me how it is possible to evaluate a 3D measurement, as volume, with 
a 2D method!?


I've also read that surface area analysis via vertex-wise analysis 
doesn't make much sense. The best would be to do ROI-based analysis. 
Can you explain that to me?


Thanks in advance!

*Laura Willers de Souza *

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] vertex indices in EPI space - mri_surf2vol registration issues

[Douglas N. Greve]

you are right! Just fixed it.
thanks


On 2/18/2022 2:15 PM, Gomez, Daniel wrote:
> There is a minor bug/typo in mri_surf2vol that was leading to registration 
> issues if the "--fillribbon" flag is used, like in my case.
>
> https://github.com/freesurfer/freesurfer/blob/dev/mri_surf2vol/mri_surf2vol.cpp#L373
> The call to   MRIcopyHeader(OutVol,VtxVol); has to happen after the closing 
> of the if/else statement, otherwise the if branch (fillribbon) won't be 
> covered and the output vtxvol file will have a wrong header.
>
> Regards,
> Daniel
>
> "Gomez, Daniel"  writes:
>
>> Dear FS users,
>>
>> I’m trying to get surface indices from surfaces generated with recon-all 
>> into a
>> volume in native functional/EPI space. I’m using mri_surf2vol for that, 
>> though
>> if there is a better alternative solution, I’m happy to take it.
>>
>> My issue is that the output index volume (vtxvol) I get from mri_surf2vol 
>> does not seem to ever be properly aligned/registered with the target space.
>>
>> Here's the command I run (I'm interesting in vtxvol.nii.gz)
>>
>> mri_surf2vol  --reg anat2epi.dat  --hemi lh --vtxvol vtxvol.nii.gz 
>> --fillribbon --outvol foo.nii.gz --template epi.nii.gz --mkmask
>>
>> Upon further investigation, I learn I can’t get the projection to work 
>> properly even if I try projecting the surface onto the native anatomical 
>> space. As in:
>>
>> mri_surf2vol  --hemi lh --vtxvol vtxvol.nii.gz --fillribbon --outvol 
>> foo.nii.gz --template ../mri/orig.mgz --mkmask --identity sub-01
>>
>> Given the output vtxvol doesn't even have the same dimensions as the 
>> template specified in the command line, it makes me think I’m doing 
>> something wrong:
>>
>>> nib-ls vtxvol.nii.gz ../mri/orig.mgz
>> vtxvol.nii.gz   float32 [320, 320, 320] 1.00x1.00x1.00   sform
>> ../mri/orig.mgz  uint8  [320, 320, 320] 0.75x0.75x0.75
>>
>> What is the proper way to get vertex indices in EPI space?
>>
>> Thank you,
>>
>> Daniel
>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] vertex indices in EPI space - mri_surf2vol registration issues

[Douglas N. Greve]

You can use something like
mris_apply_reg --lta lh.white reg.lta lh.white.reg
The direction of reg.lta does not matter -- it will figure out the right 
direction based on the geometry info


On 2/16/2022 12:20 PM, Gomez, Daniel wrote:
> Dear FS users,
>
> I’m trying to get surface indices from surfaces generated with recon-all into 
> a volume in native functional/EPI space. I’m using mri_surf2vol for that, 
> though if there is a better alternative solution, I’m happy to take it.
>
> My issue is that the output index volume (vtxvol) I get from mri_surf2vol 
> does not seem to ever be properly aligned/registered with the target space.
>
> Here's the command I run (I'm interesting in vtxvol.nii.gz)
>
> mri_surf2vol  --reg anat2epi.dat  --hemi lh --vtxvol vtxvol.nii.gz 
> --fillribbon --outvol foo.nii.gz --template epi.nii.gz --mkmask
>
> Upon further investigation, I learn I can’t get the projection to work 
> properly even if I try projecting the surface onto the native anatomical 
> space. As in:
>
> mri_surf2vol  --hemi lh --vtxvol vtxvol.nii.gz --fillribbon --outvol 
> foo.nii.gz --template ../mri/orig.mgz --mkmask --identity sub-01
>
> Given the output vtxvol doesn't even have the same dimensions as the template 
> specified in the command line, it makes me think I’m doing something wrong:
>
>> nib-ls vtxvol.nii.gz ../mri/orig.mgz
> vtxvol.nii.gz   float32 [320, 320, 320] 1.00x1.00x1.00   sform
> ../mri/orig.mgz  uint8  [320, 320, 320] 0.75x0.75x0.75
>
> What is the proper way to get vertex indices in EPI space?
>
> Thank you,
>
> Daniel
>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Confusing Permissions Error

[Douglas N. Greve]

Did the perms to that file change during the run?

On 2/17/2022 10:36 AM, Jacoby, John wrote:

Hi all,

I have a recon that looks like it ran (almost) to completion, but then 
threw a permissions error in the stdout and directed me to the log. I 
can't determine what the issue might have been. I've attached the .log 
file as well as .error and .done files. I'll also paste the end of the 
stdout below because for some reason the permissions error was not 
captured by the log file. I appreciate any insight anyone can give.


Best,
John

end of stdout:

tee: 
/autofs/vast/bandlab/studies/kyoto_preliminary/data/derivatives/freesurfer/sub-LALM61_ses-LALM61/scripts/recon-all.log: 
Permission denied

setting seed for random number generator to 1234
total integrated curvature = 26.759*4pi (336.266) --> -26 handles
ICI = 173.9, FI = 1548.0, variation=24893.111
writing Gaussian curvature to ./rh.white.preaparc.K...done.
writing mean curvature to ./rh.white.preaparc.H...done.
@#@FSTIME  2022:02:17:09:34:06 mris_curvature N 4 e 1.41 S 0.03 U 1.30 
P 94% M 157860 F 0 R 20801 W 0 c 20 w 53 I 0 O 2176 L 1.29 1.25 1.20

@#@FSLOADPOST 2022:02:17:09:34:07 mris_curvature N 4 1.29 1.25 1.20
Linux erso.nmr.mgh.harvard.edu 4.18.0-365.el8.x86_64 #1 SMP Thu Feb 10 
16:11:23 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux


tee: 
/autofs/vast/bandlab/studies/kyoto_preliminary/data/derivatives/freesurfer/sub-LALM61_ses-LALM61/scripts/recon-all.log: 
Permission denied
recon-all -s sub-LALM61_ses-LALM61 exited with ERRORS at Thu Feb 17 
09:34:08 EST 2022
tee: 
/autofs/vast/bandlab/studies/kyoto_preliminary/data/derivatives/freesurfer/sub-LALM61_ses-LALM61/scripts/recon-all.log: 
Permission denied


tee: 
/autofs/vast/bandlab/studies/kyoto_preliminary/data/derivatives/freesurfer/sub-LALM61_ses-LALM61/scripts/recon-all.log: 
Permission denied
For more details, see the log file 
/autofs/vast/bandlab/studies/kyoto_preliminary/data/derivatives/freesurfer/sub-LALM61_ses-LALM61/scripts/recon-all.log
To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
BugReporting - Free Surfer Wiki 

top. Bug Reporting. Submitting a request for help . When submitting a 
request for help with your problems please be aware that the 
developers will try and repeat your ...

surfer.nmr.mgh.harvard.edu



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)

[Douglas N. Greve]

 is very stubborn and we were
not able to overcome this. Methods like manually editing
the wm surface worked well with v6 and do not work now
with v7. We have also tried editing the filled.mgz with
v7.2 following the new tutorial, and that did not work
either.

Is there any way we can overcome this stubbornness?


Many thanks!

Edan @ Princeton BrainDevLab

On Thu, Feb 17, 2022 at 6:07 PM Douglas N. Greve
 wrote:

The edits you are making only change the initial surface;
the surface placement then refines the placement.
Sometimes the surface placement can be quite stubborn. If
this is the case, the ?h.orig.nofix and  ?h.orig will
reflect your edits (nofix exactly; ?h.orig to some
extent). Also check the the white.preaparc is where the
problem starts.

When you say that v6 did better, do you mean on this same
data or on different data? The surface placement has not
changed that much since v6.

On 2/14/2022 12:50 PM, Edan Daniel wrote:

*External Email - Use Caution *

We have been having issues with recreating the final
surfaces after editing the white matter segmentation,
which used to work smoothly in version 6.
After running a subject through recon-all (version
7.1.1 *without* the parallel flag) and then editing
the white matter, we run the following command (w v7.1.1):

recon-all -autorecon2-wm -autorecon3 -subjid '
freesurferfoldername ' -cc-crs ' num2str(corpus_point)

The ribbon file and surfaces do update *very slightly*
but it’s largely ignoring our (sometimes large) edits.
This pipeline worked well for us in version 6- do you
have any idea what might be going on?

Would love to hear your thoughts about this.

Many thanks!!

Edan, Braindevlab@Princeton

___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

*MailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
<https://secure-web.cisco.com/1BhcjfvnDAXHKeDR6R-iodPMLY3xi6xzTIkDcLTzdfO3AL026S0Y3nNiwNsk_Rhlx_6JzCATRItAPsiC_YL1qTPC76JQ1MNnw3UFSezKkrQcBMfyG1DRPHx23o0SxD83e-UdoqRq6N_xTPo7NheFjY7DCWEVDO0VG4JQcj_B6gRwgTjcEusrZjCc7AIQLTBCPjUGmV7iAA6k3S4pAbv0fOyoEPiRWC2ZgYRUgdQU37hKnQcsQQh0NXPeMNjg9XNO503u9KpbREhWN6C_FpIcwAg0QwUJZtmVUfCQCbYUiXIzPMh5ccArQBCnw4ESKv_GujZUYT0Xdb3SffsHy_AhtuA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

<https://secure-web.cisco.com/1BhcjfvnDAXHKeDR6R-iodPMLY3xi6xzTIkDcLTzdfO3AL026S0Y3nNiwNsk_Rhlx_6JzCATRItAPsiC_YL1qTPC76JQ1MNnw3UFSezKkrQcBMfyG1DRPHx23o0SxD83e-UdoqRq6N_xTPo7NheFjY7DCWEVDO0VG4JQcj_B6gRwgTjcEusrZjCc7AIQLTBCPjUGmV7iAA6k3S4pAbv0fOyoEPiRWC2ZgYRUgdQU37hKnQcsQQh0NXPeMNjg9XNO503u9KpbREhWN6C_FpIcwAg0QwUJZtmVUfCQCbYUiXIzPMh5ccArQBCnw4ESKv_GujZUYT0Xdb3SffsHy_AhtuA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

<https://secure-web.cisco.com/12WGi9fwMNRKoc7g0UsFngq4QzxkPkp8uUBbbPuKzCH_q-TezGLWNd9gLzSp5bA5xyVBH4b49Ud7EB5J4_56yDSUeCG8y4c9zwEkJDUAc0Twj6u13EwndIb9BDN6wtlLMFHjG8bvBBhNl4Eku3J-b3JAibe2gc0BJQdXG3SDNjvzjTedpGREZ5R1OxhDqNatpoOWUkC7c7gNubVq8xP8-ifLLMnnaz-Y8YMsLkKNy6MZTu8U3DuMberr-t84pfbtBdl4XlvA_HRz0s2rMYnsl2DHweu8kDVysoXaKUBeUYf9RBeRHtRniA7Bv98iG7P9a/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Douglas N. Greve]

You need to first map your pet to the anatomical space using mri_vol2vol 
and the registration glmdir/aux/bbpet2anat.lta
BTW, why are you computing the ROI anlaysis from the mgx data instead of 
using the output from the gtm? Note that you cannot use the white matter 
values that come from  mgx.


On 2/21/2022 12:57 PM, Jennifer Bramen wrote:


External Email - Use Caution

I am trying to extract mean intensity in my PET data for every ROI. 
Doug said to run mri_segstats passing the PET with --i and using --seg 
to spec the segmentation.*I would like to confirm that I am using this 
properly.*


mri_segstats --i $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz 
--seg $SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel lh 
--sum $PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg


where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is the PET 
data registered and resampled into the individual’s T1-weighrd MRI space.


Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & 
Foundation | Providence Saint John's Health Center

1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: * on behalf of "Douglas 
N. Greve" 

*Reply-To: *Freesurfer support list 
*Date: *Wednesday, February 16, 2022 at 7:30 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

If you want to do an ROI analysis using FS-based ROIs, you should do 
that at the individual level. Resample the PET to the anatoimical 
space, then run mri_segstats passing the PET with --i and using --seg 
to spec the segmentation. If you really want to do it in MNI305 space, 
then it is the same thing just using the MNI305-based (2mm) segmentation


On 2/14/2022 6:11 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

Dear Freesurfer Developers

I am doing an ROI--based amyloid PET scan analysis. I have
completed all of the steps from the PetSurfer wiki. I now have the
preprocessed, averaged, resampled, smoothed PET data in MNI305
space which is constrained to the subcortical gray matter mask.

*How do I extract mean intensity within all of the subcortical ROI?*

Thank you!

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute &
Foundation | Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069



___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
<https://secure-web.cisco.com/1pHRKHdySejszKCsrs9a5H_HhNUL-CC5YeU4Cl_81vNtgCRYphxx1lXfNUS28oh3w1R-TndgZ47wOf2XFHWg3dBsYow738wDFOOYfSwGLuBCjeJ-FaIOQPsyai7IAeZ1dOxsmP6GuyW5j2bVWEFjAU09qZ4M9zHUa2XyfmlPf4piiqQbo3Ayz3gL78M-vcSa8d1BpjLa9zF3PA4aHAuzSSyumGTLdIAY-5_L_6XgNw7iEG5NYmI7TPk5Phat5eGYdipePAy6m0hB1ibRYO0p1h0wvZVeul211fN1oB8Pwq1PTrPMjeCu2cTqbID6R2Q-DwaPaMHuhE_4IcMArFhh63A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer