Re: [Freesurfer] recon-all error

[cooperr1]

External Email - Use Caution

Dear Yujing,

 

I had the same problem with Dcm2niix, but I can open and extract them with 
dcm2nii. I’m not sure what that means!

 

Best,

Rebecca

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: Thursday, 28 April 2022 2:26 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all error

 

Hi Rebecca,

 

I was able to access and download the data. But they don’t look like dicom 
files. They don’t have the prefix ‘DICM’ in them. Dcm2niix that I mentioned 
before doesn’t recognize them either.

 

Best,

 

Yujing

 

 

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Rebecca 
Elizabeth Cooper
Sent: Tuesday, April 26, 2022 5:59 PM
To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: Re: [Freesurfer] recon-all error

 

External Email - Use Caution

Dear Yujing,

 

My apologies! Hopefully you can access this now.

 

Kind regards,

Rebecca

 

On Tue, Apr 26, 2022 at 11:29 PM Huang, Yujing mailto:yhuan...@mgh.harvard.edu> > wrote:

Hi Rebecca,

 

Thanks for sending the file. But it doesn’t seem that I have the permission to 
access it.

 

Yujing 

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Rebecca 
Elizabeth Cooper
Sent: Monday, April 25, 2022 7:12 PM
To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: Re: [Freesurfer] recon-all error

 

External Email - Use Caution

Dear Yujing,

 

Thank you kindly for your support. Please see attached.

 

Kind regards,

Rebecca

 

  Downloads.zip

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Huang, Yujing
Sent: Tuesday, 26 April 2022 8:34 AM
To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: Re: [Freesurfer] recon-all error

 

Hi Rebecca,

 

We would like to understand why those dicom files are not recognized by 
Freesurfer. If it is possible, can you provide us some of those dicom files to 
debug?

 

Thanks.

 

Yujing

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Huang, Yujing
Sent: Saturday, April 23, 2022 1:50 PM
To: 'Freesurfer support list' mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: Re: [Freesurfer] recon-all error

 

Hi Rebecca, 

 

Thank you for the information. 

 

I'm wondering if you would like to try converting those dicom using dcm2niix to 
.nii, and then feed .nii to recon-all pipeline. 

 

You can download dcm2niix here:

 

 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/12H2e8xCjrEi-wbb98756SfSMuEwEOb12bspDfWR5MA902FANozPWRbUXsyyL6gN9KEwHx6CuWYNCXonjEXr5aFAfX4Z006TCkWCN7_kN-Bjv4ICPa40hXz9vS2F6d2E_ioG7bqYAPbNvCaZSeJk0JFgxvlcdKvEAx-0cOry-Kpdvt353hndbN7tEkUP5i4Uz7INcDb-OIfQoShj0XmsIhvxzso9Mn_NE2Prbo9kL5JqJoATNSdkUJRceDyGRyu6yzSASHxlWOpixCofpkrEvy03AEtdN4sow1neidzbMCklPa4BDrej7-nKzW3GK_8-dXibJfTbfRkdMm1ayRQ13NQ/https%3A%2F%2Fgithub.com%2Frordenlab%2Fdcm2niix

 

I use the following command to do conversion: dcm2niix -o  -f 
"%s_%p" 

 

Please note that  needs to be specified as last parameter.  '-f <>' 
specifies output file name format - "%s_%p" will have series no + protocol as 
prefix. 

 

Hope these helps.

 

Best,

 

Yujing

 

 


  _  


From: freesurfer-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of 
coope...@student.unimelb.edu.au   
mailto:coope...@student.unimelb.edu.au> >
Sent: Saturday, April 23, 2022 2:44 AM
To: 'Freesurfer support list' 

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

[Zhener Zhang]

External Email - Use Caution

Found it. Thank you very much!


Thanks,
ZZ


On Apr 26, 2022, 12:28 -0700, Zhener Zhang , wrote:
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

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[Freesurfer] help - unzip Ubuntu ova password

[Dan Lerner]

External Email - Use Caution

Hi,

Setting up the Ubuntu vm provided by FreeSurfer. I'm emailing for the password 
as per the instructions.

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

[Fischl, Bruce]

Right, I meant flatten the matrix into a vector/vertex, do the cross-subject 
mapping, then reshape it back to a matrix

-Original Message-
From: Greve, Douglas N.,Ph.D.  
Sent: Wednesday, April 27, 2022 12:24 PM
To: Fischl, Bruce ; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Resampling of surface-based bivariate data

You'd have do both the rows and the cols.

On 4/27/2022 11:44 AM, Fischl, Bruce wrote:
> Why not just flatten it and save it as a .mgz? Then I think it should be 
> straightforward
>
> -Original Message-
> From: Greve, Douglas N.,Ph.D. 
> Sent: Wednesday, April 27, 2022 10:42 AM
> To: freesurfer@nmr.mgh.harvard.edu; Fischl, Bruce 
> Subject: Re: [Freesurfer] Resampling of surface-based bivariate data
>
> 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


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Re: [Freesurfer] recon-all error

[Huang, Yujing]

Hi Rebecca,

I was able to access and download the data. But they don’t look like dicom 
files. They don’t have the prefix ‘DICM’ in them. Dcm2niix that I mentioned 
before doesn’t recognize them either.

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rebecca Elizabeth Cooper
Sent: Tuesday, April 26, 2022 5:59 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all error


External Email - Use Caution
Dear Yujing,

My apologies! Hopefully you can access this now.

Kind regards,
Rebecca

On Tue, Apr 26, 2022 at 11:29 PM Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
Hi Rebecca,

Thanks for sending the file. But it doesn’t seem that I have the permission to 
access it.

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rebecca Elizabeth Cooper
Sent: Monday, April 25, 2022 7:12 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all error


External Email - Use Caution
Dear Yujing,

Thank you kindly for your support. Please see attached.

Kind regards,
Rebecca
[Image removed by sender.] 
Downloads.zip[Image
 removed by sender.]

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Tuesday, 26 April 2022 8:34 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all error

Hi Rebecca,

We would like to understand why those dicom files are not recognized by 
Freesurfer. If it is possible, can you provide us some of those dicom files to 
debug?

Thanks.

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Saturday, April 23, 2022 1:50 PM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all error

Hi Rebecca,

Thank you for the information.

I'm wondering if you would like to try converting those dicom using dcm2niix to 
.nii, and then feed .nii to recon-all pipeline.

You can download dcm2niix here:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://github.com/rordenlab/dcm2niix

I use the following command to do conversion: dcm2niix -o  -f 
"%s_%p" 

Please note that  needs to be specified as last parameter.  '-f <>' 
specifies output file name format - "%s_%p" will have series no + protocol as 
prefix.

Hope these helps.

Best,

Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 
coope...@student.unimelb.edu.au 
mailto:coope...@student.unimelb.edu.au>>
Sent: Saturday, April 23, 2022 2:44 AM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all error


External Email - Use Caution

Hi Yujing,



I guess not. This is the output:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 
mri_probedicom --i 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem



Entering IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256)



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem



I also ran straight to the dicom files themselves, with the same response:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 

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

[Douglas N. Greve]

You'd have do both the rows and the cols.

On 4/27/2022 11:44 AM, Fischl, Bruce wrote:
> Why not just flatten it and save it as a .mgz? Then I think it should be 
> straightforward
>
> -Original Message-
> From: Greve, Douglas N.,Ph.D. 
> Sent: Wednesday, April 27, 2022 10:42 AM
> To: freesurfer@nmr.mgh.harvard.edu; Fischl, Bruce 
> Subject: Re: [Freesurfer] Resampling of surface-based bivariate data
>
> 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

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Re: [Freesurfer] [EXTERNAL] Re: pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z

[Peng, Shichun]

External Email - Use Caution

For some reasons I haven’t received the email yet.
Could you please send the pass code to me again?

Thanks,
Shichun

From: fsbuild [mailto:fsbu...@contbay.com]
Sent: Tuesday, April 26, 2022 8:39 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Peng, Shichun 
Subject: [EXTERNAL] Re: [Freesurfer] pass code for 
FS_7_2_0_Ubuntu_18_04_06.ova.7z


External Email. Do not click links or open attachments unless you trust the 
sender and content. Report suspicious emails using Report Phishing button or 
forward email to ph...@northwell.edu

Sending the info to your email shortly..

- R.


On Apr 23, 2022, at 20:56, Peng, Shichun 
mailto:sp...@northwell.edu>> wrote:

External Email - Use Caution
Could you please send me the pass code to unzip the file?

Thanks,
Shichun
The information contained in this electronic e-mail transmission and any 
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Re: [Freesurfer] Resampling of surface-based bivariate data

[Fischl, Bruce]

Why not just flatten it and save it as a .mgz? Then I think it should be 
straightforward 

-Original Message-
From: Greve, Douglas N.,Ph.D.  
Sent: Wednesday, April 27, 2022 10:42 AM
To: freesurfer@nmr.mgh.harvard.edu; Fischl, Bruce 
Subject: Re: [Freesurfer] Resampling of surface-based bivariate data

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


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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

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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




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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
>
>
>
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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



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Re: [Freesurfer] (no subject)

[Fischl, Bruce]

Just give freeview the path to whatever volume or surface you want to visualize

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jabeur Mouna
Sent: Wednesday, April 27, 2022 5:45 AM
To: Freesurfer support list 
Subject: [Freesurfer] (no subject)


External Email - Use Caution
Hello,

How can i import an image.nii from a folder different from  
/usr/local/freesurfer/7.2.0/subjects to visualise it with freeview ?

Please!
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[Freesurfer] Permission denied error from -localGI

[Billah, Tashrif]

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
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Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error

[Huang, Yujing]

I’m assuming you didn’t source .bashrc after editing it.

You can actually set it on the command line before submitting mri_convert. So, 
the setting only affect that window. You can use echo $FS_LOAD_DWI to verify 
the setting.

Here is an example for csh:

>echo $FS_LOAD_DWI
FS_LOAD_DWI: Undefined variable.
>setenv FS_LOAD_DWI 0
>echo $FS_LOAD_DWI
0
>mri_convert …

I’m hoping it will solve your problem by setting the environment variable.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mateo Jean
Sent: Wednesday, April 27, 2022 8:16 AM
To: freesurfer 
Subject: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error


External Email - Use Caution
Thank you for your answer.

Even though I don't need the DTI values, I can't avoid this message :

"ERROR: the number of frames * number of slices does not equal the number of 
dicom files."

I'm not very familiar with Ubuntu too so I might have made a mistake :


I try to set the environnement variable  ‘export FS_LOAD_DWI = 0’ in bash (I 
use the command $cd then $nano .bashrc and write after
export FS_LICENSE=/home/jeanmri/license.txt
export FREESURFER_HOME=/home/jeanmri/freesurfer/7.2.0
the line export FS_LOAD_DWI = 0)

Then I open with nano the FreeSurferEnv.csh and add  setenv FS_LOAD_DWI 0  at 
the end but when I use mri_convert on my bruker dicom files, the same error 
reappeared.

Did I miss something ?


Best Regards,


 Mateo


De: "Huang, Yujing" mailto:yhuan...@mgh.harvard.edu>>
À: "freesurfer" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Envoyé: Mardi 26 Avril 2022 21:22:28
Objet: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error

Hi Mateo,

It looks like mri_convert terminated prematurely when you tried to convert 
those 512 dicom files.

Those error messages are printed when mri_convert wasn’t able to retrieve DTI 
information from dicom. If you don’t need the DTI values, you can ignore those 
error messages.

Also, looking at the codes, I think if you set environment variable FS_LOAD_DWI 
to 0 before running mri_convert, it should finish convert all 512 dicom files. 
To set the environment variable, you do ‘export FS_LOAD_DWI = 0’ in bash, and 
‘setenv FS_LOAD_DWI 0’ in csh.

Can you give it a try?

Thanks.

Yujing


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Mateo Jean
Sent: Tuesday, April 26, 2022 7:51 AM
To: freesurfer 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error


External Email - Use Caution
Hello FreeSurfer Developers

I hope i don't spam, if anyone has a clue...


I need to convert 512 dicom files from Bruker into .nii . I firstly add .dcm to 
my Bruker multi gradient echo phase files then enter the following command :
mri_convert MRIm001.dcm phaseMGE.nii

Here is the first message :

reading from MRIm001.dcm...
Starting DICOMRead2()
dcmfile = 
/mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2/MRIm001.dcm
dcmdir = 
/mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2
ERROR: don't know how to get DWI parameters from --Bruker BioSpin MRI GmbH --
ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
DICOM File: 
/mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2/MRIm001.dcm
break 
/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/DICOMRead.cpp:4930
Ref Series No = 4
Found 514 files, checking for dicoms
ERROR: don't know how to get DWI parameters from --Bruker BioSpin MRI GmbH --
ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
DICOM File: 
/mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2/MRIm001.dcm
break 
/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/DICOMRead.cpp:4930
ERROR: don't know how to get DWI parameters from --Bruker BioSpin MRI GmbH --
ERROR: GetDICOMInfo(): dcmGetDWIParams() 1

Then 508 error messages like the three last lines appear.
It ends with :

First Sorting
Computing Slice Direction
Vs: 0 0 1
Vs: 0 0 1
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 8
nslices = 63
ndcmfiles = 508
ERROR: the number of frames * number of slices does
not equal the number of dicom files.

I did a test with only 448 files (I just copy-paste the first 448 files = 7 TE 
* 64 slices) and I obtained the same error messages but the nifti files are 
created and seem usable (quick test with Fiji). Here are the last lines :

First Sorting
Computing Slice Direction
Vs: 0 0 1
Vs: 0 0 1
Second Sorting
IsDWI = 1, IsPhilipsDWI = 0
Counting frames
nframes = 7
nslices = 64
ndcmfiles = 448
INFO: rescale not needed
PE Dir = COL (dicom read)
Loading pixel data
TR=50.00, TE=3.10, TI=0.00, flip angle=15.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to phaseMGR.nii...
Saving bvals and bvecs

I'm 

[Freesurfer] Opening for PhD position based in Tours (Loire Valley, France)

[briend]

External Email - Use Caution

Dear colleagues,

The INSERM-U1253 & University of Tours research unit based in Tours 
(Loire Valley, France) invites applications for a PhD position to begin 
in the Fall of 2022 on the reward and interoceptive systems in autism.

The main objective of the current PhD proposal is to identify impaired 
social processing in autism and AD across the last two dimensions. To do 
that, first, this project will explore the neural activity of the reward 
system in these patients via functional magnetic resonance imaging. 
Then, we will probe the deficit of interoception present in these 
disorders. This sensory modality will also be examined in relation to 
social processes, within an innovative device of immersive reality (the 
CAVE: computer automatic virtual environments).
Applicants should hold a Master's degree (or equivalent) in one of the 
following disciplines: computational or cognitive neuroscience, computer 
science, mathematics, physics, cognitive science or related.

Prior experience in the field of computational neuroscience and/or 
neuroimaging are of advantage. Sound knowledge of statistics and 
programming are essential. The candidate’s main missions will be to 
program, run and analyze behavioral and neuroimaging tests with 
individual with autism and healthy controls, involving interoceptive 
tasks and cognitive tests.
A good command of written and spoken English is requested of all 
applicants. Knowledge of French language is beneficial.

Prospective candidates should also contact directly Frederic Briend 
(frederic.bri...@univ-tours.fr) and/or Marianne Latinus 
(marianne.lati...@univ-tours.fr) by June 2, 2022. Please include the 
following documents in your application (as a single PDF-file): Cover 
letter, curriculum vitae, at least one recommendation letter. The 
position should start in October 2022.

Frederic Briend

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Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error

[Mateo Jean]

External Email - Use Caution

Thank you for your answer. 

Even though I don't need the DTI values, I can't avoid this message : 





"ERROR: the number of frames * number of slices does not equal the number of 
dicom files." 




I'm not very familiar with Ubuntu too so I might have made a mistake : 




I try to set the environnement variable ‘ export FS_LOAD_DWI = 0 ’ in bash (I 
use the command $cd then $nano .bashrc and write after 

export FS_LICENSE=/home/jeanmri/license.txt 

export FREESURFER_HOME=/home/jeanmri/freesurfer/7.2.0 

the line export FS_LOAD_DWI = 0 ) 

Then I open with nano the FreeSurferEnv.csh and add setenv FS_LOAD_DWI 0 at the 
end but when I use mri_convert on my bruker dicom files, the same error 
reappeared. 

Did I miss something ? 

Best Regards, 

Mateo 


De: "Huang, Yujing"  
À: "freesurfer"  
Envoyé: Mardi 26 Avril 2022 21:22:28 
Objet: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error 



Hi Mateo, 



It looks like mri_convert terminated prematurely when you tried to convert 
those 512 dicom files. 



Those error messages are printed when mri_convert wasn’t able to retrieve DTI 
information from dicom. If you don’t need the DTI values, you can ignore those 
error messages. 



Also, looking at the codes, I think if you set environment variable FS_LOAD_DWI 
to 0 before running mri_convert, it should finish convert all 512 dicom files. 
To set the environment variable, you do ‘export FS_LOAD_DWI = 0’ in bash, and 
‘setenv FS_LOAD_DWI 0’ in csh. 



Can you give it a try? 



Thanks. 



Yujing 






From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mateo Jean 
Sent: Tuesday, April 26, 2022 7:51 AM 
To: freesurfer  
Subject: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error 




External Email - Use Caution 


Hello FreeSurfer Developers 





I hope i don't spam, if anyone has a clue... 








I need to convert 512 dicom files from Bruker into .nii . I firstly add .dcm to 
my Bruker multi gradient echo phase files then enter the following command : 


mri_convert MRIm001.dcm phaseMGE.nii 





Here is the first message : 





reading from MRIm001.dcm... 


Starting DICOMRead2() 


dcmfile = 
/mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2/MRIm001.dcm
 


dcmdir = 
/mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2 


ERROR: don't know how to get DWI parameters from --Bruker BioSpin MRI GmbH -- 


ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 


DICOM File: 
/mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2/MRIm001.dcm
 


break 
/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/DICOMRead.cpp:4930
 


Ref Series No = 4 


Found 514 files, checking for dicoms 


ERROR: don't know how to get DWI parameters from --Bruker BioSpin MRI GmbH -- 


ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 


DICOM File: 
/mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2/MRIm001.dcm
 


break 
/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/DICOMRead.cpp:4930
 


ERROR: don't know how to get DWI parameters from --Bruker BioSpin MRI GmbH -- 


ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 





Then 508 error messages like the three last lines appear. 


It ends with : 





First Sorting 


Computing Slice Direction 


Vs: 0 0 1 


Vs: 0 0 1 


Second Sorting 


IsDWI = 0, IsPhilipsDWI = 0 


Counting frames 


nframes = 8 


nslices = 63 


ndcmfiles = 508 


ERROR: the number of frames * number of slices does 


not equal the number of dicom files. 





I did a test with only 448 files (I just copy-paste the first 448 files = 7 TE 
* 64 slices) and I obtained the same error messages but the nifti files are 
created and seem usable (quick test with Fiji). Here are the last lines : 





First Sorting 


Computing Slice Direction 


Vs: 0 0 1 


Vs: 0 0 1 


Second Sorting 


IsDWI = 1, IsPhilipsDWI = 0 


Counting frames 


nframes = 7 


nslices = 64 


ndcmfiles = 448 


INFO: rescale not needed 


PE Dir = COL (dicom read) 


Loading pixel data 


TR=50.00, TE=3.10, TI=0.00, flip angle=15.00 


i_ras = (-1, -0, 0) 


j_ras = (-0, -1, 0) 


k_ras = (-0, -0, 1) 


writing to phaseMGR.nii... 


Saving bvals and bvecs 





I'm pretty new with mri convert and I don't understand why it stops converting 
to nii with 512 files (8 TE) but not 448 files for Brucker files. 





Best Regards, 





Mateo 








Version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b 

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Hello,

How can i import an image.nii from a folder different from
/usr/local/freesurfer/7.2.0/subjects
to visualise it with freeview ?

Please!
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