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

2022-04-26 Thread Mateo Jean 
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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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Re: [Freesurfer] Pass Code

2022-04-26 Thread fsbuild 
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Sending the info to your email shortly.
- R.​
On Apr 23, 2022, at 23:43, Activeingredient  
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Re: [Freesurfer] pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z

2022-04-26 Thread fsbuild 
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Sending the info to your email shortly.
- R.On Apr 23, 2022, at 20:56, Peng, Shichun  
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Re: [Freesurfer] Request for Pass Code VP_7_2_0

2022-04-26 Thread fsbuild 
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Sending the info to your email shortly.
- R.On Apr 24, 2022, at 03:25, Kevin Wang  
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CautionHello,I recently 
downloaded the archive for the file VP_7_2_0.  Could you please send the 
pass code required to expand the archive?  Thank 
you!Sincerely,Kevin___Freesurfer 
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Re: [Freesurfer] FreeSurfer 7Zip archive passcode

2022-04-26 Thread fsbuild 
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Sending the info to your email shortly.
- R.On Apr 25, 2022, at 04:59, Katharina Hense 
 
wrote:External Email - Use 
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Re: [Freesurfer] recon-all error

2022-04-26 Thread Huang, Yujing 
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 
 On Behalf Of Rebecca Elizabeth Cooper
Sent: Monday, April 25, 2022 7:12 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all error


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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


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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$ 
mri_probedicom --i 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 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_512x256/002/I.001)

Opening 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 as part10

DCM_FILEOPENFAILED

   20092 DCM failed to open file: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.

Re: [Freesurfer] Cortical depth at each cortical voxel

2022-04-26 Thread Aganj, Iman 
Hi Panos,

Please see my responses interleaved.

Best,
Iman


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fotiadis, Panagiotis
Sent: Monday, April 25, 2022 10:48 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cortical depth at each cortical voxel

Hi Iman,

Apologies for the follow up! I had a couple questions concerning the software:


  1.  Concerning the MLI_thickness.m function: I used a binary mask of the 
cortical ribbon (= I) as its first input and L (where L = 
makeLineSegments(round(.2*size(I,1)) ) as the second input (similarly to the 
suggestion in EXAMPLE.m file). I tried different radii as well for the 
makeLineSegments function and the thickness results are highly linear to each 
other. Do those inputs seem reasonable in this case (i.e., for real 3D MRI 
scans), in your opinion?

In makeLineSegments, you may want to use a radius that is a few voxels larger 
than the maximum thickness that you expect (voxels being the unit of the 
measured thickness).


  1.  Concerning the cortical depth calculation for each voxel: Unless I'm 
mistaken, the (cortical depth = Thickness/2 - SkeletonDistance) equation would 
give me the cortical depth of each voxel from the closest surface layer, right? 
 So for instance, if my voxel of interest were "above" the skeleton (i.e., the 
middle layer of the cortical ribbon), then the above equation would give out 
its distance from the surface layer that is also above the skeleton, whereas if 
my voxel were "below" the skeleton, then the aforementioned equation would give 
its distance from the surface layer that is also below the skeleton, right?



That is correct.


Would there be, however, a way to compute the cortical depth of each cortical 
voxel from the outer surface layer of the cortical ribbon? I believe that would 
be distance t1(v) mentioned in the equations and text in p. 3199 of your paper, 
but I unfortunately wasn't able to pinpoint that variable in the scripts. Is 
that variable hard-coded in the scripts, or would you recommend that I follow a 
different approach to calculate that (for instance set up a conditional 
argument where I use cortical depth = Thickness/2 - SkeletonDistance if the 
voxel is above the skeleton layer, and cortical depth = Thickness/2 + 
SkeletonDistance if the voxel is below the skeleton layer)?


t1(v) is the oneSidedThickness_partial variable in the MLI_thickness function. 
The algorithm, however, works pretty locally and cannot really distinguish 
between the inner and outer surfaces of the cortical ribbon. So, In order to 
use t1(v) for your purpose (or your other suggested approach), you would need a 
label for each voxel that says which surface the voxel is closer to. If you 
have masks for the subcortical areas (e.g. the white-matter mask) and the 
beyond-pial area (~(GM | WM)), you could create such a label by comparing the 
distance transform maps created from the two masks (by Matlab's bwdist 
function). In fact, the distance transform from the latter mask might just give 
you the cortical depth that you are looking for.


Thank you again very much for your time and help!

Best,
Panos

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Aganj, Iman 
mailto:iag...@mgh.harvard.edu>>
Date: Thursday, April 21, 2022 at 1:02 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [External] Re: [Freesurfer] Cortical depth at each cortical voxel
Of course! Please let me know if you have any questions about the toolbox.

Best,
Iman

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Fotiadis, Panagiotis
Sent: Thursday, April 21, 2022 12:32 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Cortical depth at each cortical voxel

Hi Iman,

That is extremely helpful, thank you very much (also the paper is a great read)!

Best,
Panos


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Aganj, Iman 
mailto:iag...@mgh.harvard.edu>>
Date: Thursday, April 21, 2022 at 12:06 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [External] Re: [Freesurfer] Cortical depth at each cortical voxel
Hi Panos,

You can do such a volumetric analysis using this toolbox:

Code:  https://www.nitrc.org/projects/thickness
Paper:  https://onlinelibrary.wiley.com/doi/epdf/10.1002/hbm.20740

You can apply the MLI_thickness function to the gray matter (soft or binary) 
mask, which returns the layer thickness at each voxel (Thickness) and the 
distance of each voxel to the center of the layer (SkeletonDistance). Cortical 
depth would then be SkeletonDistance at the given voxel subtracted from half of 
Thickness (at th

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

2022-04-26 Thread 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:


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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] Request for 7Zip Archive passcode

2022-04-26 Thread Logan Tate 
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Hi, I made a prior request but believe the passcode was sent to someone who
posted under my request, and not myself.

I just need a passcode to archive the zip folder for file
FS_7_2_0_Ubuntu_18_04_06.ova.7z

Sorry for the spam! Thank you.
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Re: [Freesurfer] Beta values (resubmitting)

2022-04-26 Thread 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:


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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] Mri Convert Bruker MGRE files dicom to nii error

2022-04-26 Thread Huang, Yujing 
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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Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

2022-04-26 Thread Zhener Zhang 
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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[Freesurfer] Resampling of surface-based bivariate data

2022-04-26 Thread Burke Rosen 
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] Beta values (resubmitting)

2022-04-26 Thread Laura Willers de Souza 
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).
[cid:67fd98ba-4655-445d-bdc7-fd5bbb6e6bb2]

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).

[cid:part1.KvgY07aY.UPvnt0iC@mgh.harvard.edu]

  *   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?
 *   Thus the glm equation for the 1st cluster would be:
 *   1st group  cortical thickness = 2.64 - 0.12X + n
 *   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] recon-all error

2022-04-26 Thread Rebecca Elizabeth Cooper 
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 
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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Rebecca Elizabeth
> Cooper
> *Sent:* Monday, April 25, 2022 7:12 PM
> *To:* Freesurfer support list 
> *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: Image removed by sender.] Downloads.zip
> **[image:
> Image removed by sender.]*
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Huang, Yujing
> *Sent:* Tuesday, 26 April 2022 8:34 AM
> *To:* Freesurfer support list 
> *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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Huang, Yujing
> *Sent:* Saturday, April 23, 2022 1:50 PM
> *To:* 'Freesurfer support list' 
> *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/17Ga0Xp3SP-CwTjSyxKsZeuTrgi6PpoirdFYSw1C92Ho9dbRuQ2edmCex8QhiTy5y5Cs23DSgVQ3raixqX1CCAYc4jqqGEkMfifaT9qn5lZY0V5u49HuYtMSpfl3ALWhlVVEGRw-1lrEgUfxwjlLaCNKPi7mXrXnTamJDmd-gI6fHx5x9Hrs8kLDNyuPywIbEhb6ACqCM2iigyvCET3XPFsV6d7P519XoIKBFdwsR3RMW1qL-HOfyjuuVJcT9UDNwz4ZvD0QoKk3kXMIvmIbsRA5AGmVIyS9ONlsG5HyGRdXx5OtiA8CPUEIa2-TnspNu1ppPe8sf09ihQa19o9-hAg/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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
> coope...@student.unimelb.edu.au 
> *Sent:* Saturday, April 23, 2022 2:44 AM
> *To:* 'Freesurfer support list' 
> *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$
> mri_probedicom --i
> /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
>
>
>
> ERROR:
> /data/netapp01/work/ENIGMA

Re: [Freesurfer] meanings of trac-all outputs

2022-04-26 Thread Zeng, Qi 
External Email - Use Caution

Hi Freesurfer experts,

Follow up on the last question and correct me if I am wrong, the difference
between dlabel/diff/lowb_brain_mask.nii.gz and dmri/nodif_brain_mask.nii.gz
is that:
> the dlabel/diff/lowb_brain_mask.nii.gz is generated from "bet" (brain
extraction)
> and dmri/nodif_brain_mask.nii is derived from aparc+aseg_mask.nii.gz
which contains T1 information.
Because in fsl, nodif_brain_mask is named for "bet binary brain mask".

Best,
Qi

Best,
Qi

On Fri, Apr 22, 2022 at 3:25 PM Zeng, Qi  wrote:

> Hi experts,
>
> Just want to check if dmri/dwi.nii.gz is the 4D dwi volumes after
> correction for B0 inhomogeneities, eddy current, and head motion? and
> dmri/nodif_brain_mask.nii.gz is the 3D ROI mask for the whole brain? and
> dmri/bvals and dmri/bvecs are rotated bvals and rotated bvecs?
> Thank you!
>
> Best,
> Qi
>


-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
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