[Freesurfer] Unable to read in images from Freeview command window

2023-07-31 Thread Rachel Wagner 
External Email - Use Caution

Hello,

I am looking to cortically project onto a pial surface and am trying to use the 
following code in the freeview GUI to do so:

[FreeView] -v 004/mri/wm.mgz:colormap=jet 004/mri/brainmask.mgz -f 
004/surf/lh.pial:edgecolor=blue 004/surf/lh.white:edgecolor=red
error: mghRead(/home/developer/freesurfer/004/mri/wm.mgz, -1): could not open 
file
MRIread failed: Unable to read from /home/developer/freesurfer/004/mri/wm.mgz


I don’t know how to resolve this, any guidance would be greatly appreciated.

Thank you,
Rachel Wagner
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[Freesurfer] Code not working

2023-07-31 Thread Rachel Wagner 
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Hello all,

I’m getting an error as follows:

developer@developer-VirtualBox:~/freesurfer$ setenv SUBJECTS_DIR 
$FREESURFER_HOME/subjects

Command 'setenv' not found, did you mean:

  command 'getenv' from snap getenv (0.3.1)

See 'snap info ' for additional versions.

developer@developer-VirtualBox:~/freesurfer$



Is something not installed? These functions were working previously.

Thanks,
Rachel
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[Freesurfer] Command not found

2023-07-30 Thread Rachel Wagner 
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Hello all,

I have not used freesurfer in a couple of months, and have returned to create a 
new cortical projection image. I’m having an issue with my commands, they don’t 
seem to be recognized anymore and I’m not sure why:

developer@developer-VirtualBox:~/freesurfer$ freeview

Command 'freeview' not found, did you mean:

  command 'treeview' from deb treeview

Try: sudo apt install 



Is there any way to resolve this?
Thanks,
Rachel Wagner
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[Freesurfer] (no subject)

2023-03-30 Thread Rachel Wagner 
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Please unsubscribe me
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[Freesurfer] Ubuntu compatibility

2023-02-03 Thread Rachel Wagner 
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Hello,

I am trying to use mri_easyreg on Ubuntu 18 and realize I need to upgrade to 
freesurfer 7.3.2 to use this function.

I am encountering issues downloading 7.3.2. Are the two compatible? Is there a 
link for setup I should follow?

Thanks,
Rachel
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[Freesurfer] Directory not set properly?

2023-02-03 Thread Rachel Wagner 
External Email - Use Caution

Hello,

I am trying to run recon-all on my data and am encountering the following issue:

developer@developer-VirtualBox:~/freesurfer$ recon-all -subject 3T00300 -i 
/usr/home/developer/desktop/TIWI.nii -T2 
/usr/home/developer/desktop/T2_Flair.nii -T2pial -all
ERROR: cannot find /usr/home/developer/desktop/TIWI.nii
Linux developer-VirtualBox 5.4.0-137-generic #154~18.04.1-Ubuntu SMP Tue Jan 10 
16:58:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 3T00300 exited with ERRORS at Fri Feb  3 10:49:02 EST 2023

For more details, see the log file
To report a problem, see 
http://secure-web.cisco.com/1bRGI0GFgxZrKH_-NM5aKbo8jy3AYVqO8EQuizksRFT_koqn81PU2cr1DkXQyRINIPyeSWIKIyYPcoqr8kupKx4tBCb2HSe7fD9ve-vdnYa-QrIqr1k_OXMaLh0N6bcBTxtV2lLTCivFswp6W1h6FsQidLmojE3OLS2GBmLBZOF-sUsKTvJ1RhjmYXGGlOWRazCA_tRoFg_Tb1AqqsRigcBORUAx3Vu58Y0ZnuO_iR9nC7CSIks7lT2uxruqzDv-DvHvWiIFDe-I_RCMVVFJSmzLFKTkiHNx6WEcVs17okJNyj5sNVboDUvLakOmQnm3HGpsbVZedgB5-kPvzkr9XNg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

developer@developer-VirtualBox:~/freesurfer$ recon-all -subject 3T00300 -i 
sample-001.mgz
ERROR: cannot find sample-001.mgz
Linux developer-VirtualBox 5.4.0-137-generic #154~18.04.1-Ubuntu SMP Tue Jan 10 
16:58:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 3T00300 exited with ERRORS at Fri Feb  3 10:52:53 EST 2023

For more details, see the log file
To report a problem, see 
http://secure-web.cisco.com/1bRGI0GFgxZrKH_-NM5aKbo8jy3AYVqO8EQuizksRFT_koqn81PU2cr1DkXQyRINIPyeSWIKIyYPcoqr8kupKx4tBCb2HSe7fD9ve-vdnYa-QrIqr1k_OXMaLh0N6bcBTxtV2lLTCivFswp6W1h6FsQidLmojE3OLS2GBmLBZOF-sUsKTvJ1RhjmYXGGlOWRazCA_tRoFg_Tb1AqqsRigcBORUAx3Vu58Y0ZnuO_iR9nC7CSIks7lT2uxruqzDv-DvHvWiIFDe-I_RCMVVFJSmzLFKTkiHNx6WEcVs17okJNyj5sNVboDUvLakOmQnm3HGpsbVZedgB5-kPvzkr9XNg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

developer@developer-VirtualBox:~/freesurfer$


Is it that my path is not set correctly?

Thank you!
Rachel Wagner
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Re: [Freesurfer] Unsupported Datatype

2022-11-16 Thread Rachel Wagner 
External Email - Use Caution

I see, thank you!

Do you know of a way I can convert it to a file type that is supported? Or what 
an alternative file type might be?

Thank you again!
Rachel

From: Huang, Yujing<mailto:yhuan...@mgh.harvard.edu>
Sent: November 16, 2022 10:29 AM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Unsupported Datatype

Hi Rachel,

It appears that your nifti has RGB datatype (128). Freesurfer doesn’t support 
that yet.

Best,

Yujing

From: Huang, Yujing
Sent: Wednesday, November 16, 2022 7:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: RE: Unsupported Datatype

Hi Rachel,

Can you provide the version of Freesurfer that you are running?

Thanks.

Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rachel Wagner
Sent: Tuesday, November 15, 2022 11:23 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Unsupported Datatype


External Email - Use Caution
Hello, I’m getting the following error, not sure how to resolve!

developer@developer-VirtualBox:~$ mri_convert 
dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii 
dicom-series-005-t2_swi_tra_p2_3mm_Mag.mgz
mri_convert dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii 
dicom-series-005-t2_swi_tra_p2_3mm_Mag.mgz
reading from dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii...
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
error: No such file or directory
error: niiRead(): unsupported datatype 128 (with scl_slope = 0) in 
/home/developer/dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii


Thanks!
Rachel Wagner

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[Freesurfer] Unsupported Datatype

2022-11-15 Thread Rachel Wagner 
External Email - Use Caution

Hello, I’m getting the following error, not sure how to resolve!

developer@developer-VirtualBox:~$ mri_convert 
dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii 
dicom-series-005-t2_swi_tra_p2_3mm_Mag.mgz
mri_convert dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii 
dicom-series-005-t2_swi_tra_p2_3mm_Mag.mgz
reading from dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii...
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
error: No such file or directory
error: niiRead(): unsupported datatype 128 (with scl_slope = 0) in 
/home/developer/dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii


Thanks!
Rachel Wagner
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[Freesurfer] Image Edits

2022-07-15 Thread Rachel Wagner 
External Email - Use Caution

Hello all!

I hope you are all keeping well. I was wondering if there was a way to save 
images from freeview that are higher quality than png?

In addition, is there a way to set the color bar scale from 0 to 1 and 
hopefully at 10 internals 0, 0.1, 0.2, 0.3...1?  Even when selecting the ‘fixed 
axis’ option, it seems to automatically adjust.

Thanks!
Rachel Wagner
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[Freesurfer] mri_vol2surf error

2022-07-11 Thread Rachel Wagner 
External Email - Use Caution

Hello everyone,

I am trying to display my lesion map I created in Matlab on a cortical surface, 
and am getting the following error:

developer@developer-VirtualBox:~$ mri_vol2surf --mov 
rReslice_Combined_roi_meanRD.nii --mni152reg --trgsubject fsaverage --hemi lhrh 
--out lh_spm.mgh --projfrac-max 0 1 .1
srcvol = rReslice_Combined_roi_meanRD.nii
srcreg = /usr/local/freesurfer/7.2.0/average/mni152.register.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lhrh
trgsubject = fsaverage
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 1
INFO: float2int code = 0
Done loading volume
INFO: This REGISTER_DAT transform is valid only for volumes between  COR types 
with c_(r,a,s) = 0.
Input reg is register.dat
 original matrix ---
0.99753  -0.00732   0.01760   0.95709;
-0.01296  -0.00926   0.99706  -17.81596;
-0.01460  -1.00094   0.00244  -18.54964;
0.0   0.0   0.0   1.0;
 original matrix ---
Reading surface /usr/home//fsaverage/surf/lhrh.white
error: No such file or directory
error: MRISread(/usr/home//fsaverage/surf/lhrh.white): could not open file
error: No such file or directory
error: mri_vol2surf: could not read surface /usr/home//fsaverage/surf/lhrh.white


Could anyone help me fix this? I am very new to this software and need to have 
this results ready for my supervisor if possible!

Thank you,
Rachel
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Re: [Freesurfer] FW: How to project SPM image

2022-07-11 Thread Rachel Wagner 
External Email - Use Caution

Please disregard previous email! I was able to run recon-all on the MNI 
template and named it template_RW.nii

I have run the following code:
mri_vol2surf --src rReslice_Combined_roi_meanRD.nii --regheader template_RW.nii 
--projfrac 0.5 --hemi lh --out /home/developer/template

And am getting this error:
srcvol = rReslice_Combined_roi_meanRD.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /home/developer/template/template_RW.nii/mri/orig.mgz as target 
reference.
error: mghRead(/home/developer/template/template_RW.nii/mri/orig.mgz, -1): 
could not open file

Am I setting the registration incorrectly?

Thank you again!
Rachel

From: Douglas N. Greve<mailto:dgr...@mgh.harvard.edu>
Sent: July 10, 2022 6:11 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FW: How to project SPM image

First, what is rReslice_Combined_roi_meanRD.nii? How was it created? If that is 
you lesion map, then it is  not the right input to BBR. I can't remember, but 
if the AAL is in the MNI152 space, then it will be easier to just run recon-all 
on the MNI152 ( or whatever the atnatomical reference is for the AAL). You can 
then just run mri_vol2surf using --regheader and  skip BBR. You may have to 
play with some of the options (eg, projection fraction)


On 7/5/2022 2:08 PM, Rachel Wagner wrote:

External Email - Use Caution
Hello Dr. Greve,

I hope this finds you well! I am currently working on displaying my SPM overlay 
on a 3D brain volume in FreeSurfer (email below). Dr. Fischl mentioned you may 
know the command line to do so – I hope this isn’t a bother, I know you must be 
quite busy – totally understood if you don’t have the time.

So far, I have the following:
bbregister --mov rReslice_Combined_roi_meanRD.nii --bold \ inflated -overlay 
--s  fsaverage \ --init-rr --lta register.lta

I am hoping to smooth out the surface and change the coloring to ultimately 
export a heatmap image from FreeSurfer that looks something like 
this.<https://secure-web.cisco.com/1oOMXS4Xcve-ZJ8PxylSUuZevRGR5aotHueMxgJxcMGkXSkjJ6wTsTr4oavOgdzgC__DuhBfa2YoeXPPAkWNDkDveceWCqonnMePOe7RO8-EzKOCNiY55G6RP0RxIqcSzGoy5xrThG11tzNHAx4J2oOvo_ESpDm-Xy5SRds7mHaMi14AVwz97DtG6A7__AhYWMzxD1DhY1be4RuervQ_3GhIJP9U47Jlyf-6BJDot29n-DzmhaePM1AHaWepGK-h2DLlNNr5gjpR4VuJMYqBEkqYBtAH7eWX7f2lcu_279ka4M5ClsgZa3q8hqXJMfnAB0nP3mVb7RfWqryW2ibpstA/https%3A%2F%2Fwww.researchgate.net%2Ffigure%2FDecreased-functional-connectivity-from-Wernickes-area-homologue-in-children-born-VPT_fig3_329809185>

Would you have any suggestions for how I should alter my code?

Thank you very much in advance – no problem again if you don’t have the time!


Kind Regards,
Rachel Wagner


From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: July 5, 2022 9:34 AM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image

Hi Rachel

I’ll leave bbreg command lines to others (Doug?), but in general you don’t want 
to base the registration on the inflated since it doesn’t have a meaningful 
location within the volume. I would use the standard bbreg command, then use 
mri_vol2surf to paint what you want onto the surface. Once it is on any surface 
for a subject you should be able to display it on any other surface for that 
same subject (and same hemisphere).
Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 On Behalf Of Rachel Wagner
Sent: Tuesday, July 5, 2022 12:17 AM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thank you, that would work very well! I’m trying this code without success, am 
I missing a component to display on an inflated surface?

bbregister --mov rReslice_Combined_roi_meanRD.nii --bold \ inflated -overlay 
--s  fsaverage \ --init-rr --lta register.lta

From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: July 4, 2022 3:45 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image

Well you can display it on inflated surfaces instead of white ones, which will 
remove most of the folds. Then you can smooth the surface overlay however you 
like (the colors on the surface) in freeview

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rachel Wagner
Sent: Monday, July 4, 2022 3:27 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] FW: How to project SPM image

2022-07-11 Thread Rachel Wagner 
External Email - Use Caution

To create rReslice_Combined_roi_meanRD.nii, I extracted ROIs from the AAL atlas 
to code the lesion map by frequency.

Could I use fsaverage for the anatomical reference?

So far, I have:
mri_vol2surf --src rReslice_Combined_roi_meanRD.nii --out 
rReslice_Combined_roi_meanRD_surf.nii --hemi lhrh --out_type nii --regheader 
/usr/home/register.dat

Which seems to pull the incorrect registration file. Do I need to recreate the 
registration file with MNI?

Thank you very much – I admit I’m not well versed with coding, trying to learn!


From: Douglas N. Greve<mailto:dgr...@mgh.harvard.edu>
Sent: July 10, 2022 6:11 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FW: How to project SPM image

First, what is rReslice_Combined_roi_meanRD.nii? How was it created? If that is 
you lesion map, then it is  not the right input to BBR. I can't remember, but 
if the AAL is in the MNI152 space, then it will be easier to just run recon-all 
on the MNI152 ( or whatever the atnatomical reference is for the AAL). You can 
then just run mri_vol2surf using --regheader and  skip BBR. You may have to 
play with some of the options (eg, projection fraction)


On 7/5/2022 2:08 PM, Rachel Wagner wrote:

External Email - Use Caution
Hello Dr. Greve,

I hope this finds you well! I am currently working on displaying my SPM overlay 
on a 3D brain volume in FreeSurfer (email below). Dr. Fischl mentioned you may 
know the command line to do so – I hope this isn’t a bother, I know you must be 
quite busy – totally understood if you don’t have the time.

So far, I have the following:
bbregister --mov rReslice_Combined_roi_meanRD.nii --bold \ inflated -overlay 
--s  fsaverage \ --init-rr --lta register.lta

I am hoping to smooth out the surface and change the coloring to ultimately 
export a heatmap image from FreeSurfer that looks something like 
this.<https://secure-web.cisco.com/1oOMXS4Xcve-ZJ8PxylSUuZevRGR5aotHueMxgJxcMGkXSkjJ6wTsTr4oavOgdzgC__DuhBfa2YoeXPPAkWNDkDveceWCqonnMePOe7RO8-EzKOCNiY55G6RP0RxIqcSzGoy5xrThG11tzNHAx4J2oOvo_ESpDm-Xy5SRds7mHaMi14AVwz97DtG6A7__AhYWMzxD1DhY1be4RuervQ_3GhIJP9U47Jlyf-6BJDot29n-DzmhaePM1AHaWepGK-h2DLlNNr5gjpR4VuJMYqBEkqYBtAH7eWX7f2lcu_279ka4M5ClsgZa3q8hqXJMfnAB0nP3mVb7RfWqryW2ibpstA/https%3A%2F%2Fwww.researchgate.net%2Ffigure%2FDecreased-functional-connectivity-from-Wernickes-area-homologue-in-children-born-VPT_fig3_329809185>

Would you have any suggestions for how I should alter my code?

Thank you very much in advance – no problem again if you don’t have the time!


Kind Regards,
Rachel Wagner


From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: July 5, 2022 9:34 AM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image

Hi Rachel

I’ll leave bbreg command lines to others (Doug?), but in general you don’t want 
to base the registration on the inflated since it doesn’t have a meaningful 
location within the volume. I would use the standard bbreg command, then use 
mri_vol2surf to paint what you want onto the surface. Once it is on any surface 
for a subject you should be able to display it on any other surface for that 
same subject (and same hemisphere).
Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 On Behalf Of Rachel Wagner
Sent: Tuesday, July 5, 2022 12:17 AM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thank you, that would work very well! I’m trying this code without success, am 
I missing a component to display on an inflated surface?

bbregister --mov rReslice_Combined_roi_meanRD.nii --bold \ inflated -overlay 
--s  fsaverage \ --init-rr --lta register.lta

From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: July 4, 2022 3:45 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image

Well you can display it on inflated surfaces instead of white ones, which will 
remove most of the folds. Then you can smooth the surface overlay however you 
like (the colors on the surface) in freeview

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rachel Wagner
Sent: Monday, July 4, 2022 3:27 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thank you, noted!

I think I am on the right track, but I’d like to smooth the surface out 
(particularly the coloring and the sulci, which are quite deep) considerably – 
is there any way for me to do that?

Re: [Freesurfer] Tksurfer Error

2022-07-10 Thread Rachel Wagner 
External Email - Use Caution

Thanks very much Dr. Greve!

Just had another question for you, if you have the time!

I am currently working on displaying my SPM overlay on a 3D brain volume, using 
bbregister, and am getting this: 
https://secure-web.cisco.com/1Y47t3gF3E5zpTqY7OR_RkIvNSeef_CHIYkO-YK-6vd1D17vS9NYSCvba3g_O1eFjmtS6mpdDGb0QX667fxWA9VEo7WyiA4Q1LYPYp5VqCjvhAio-qTT-szuNc4McV8R7RxOw2cP2ozw8-zxrvxOLgpvEDnL23EIzAV1_cOop2q6RqCebdyBWs_5M52SuQ-Y1olfanVQtz3tNleTdujH_C8p_QBWk6_dz7EcaP0M-dGXIJ0O9dWrLiUnUFksz5xC--oEI9xgcsNah-JjbxPzeRFJJpbFWjE_M9nv8yEf4F6dZ8HiHUEjCME0XDSf3iPf9sBMkaLHDil9Q8rRS5pNrK5WMKa0ZQMFzIAknIpLC3rA/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD%2Fview%3Fusp%3Ddrivesdk

I am hoping to smooth out the surface, so it is more continuous, and change the 
coloring of the brain. Are there options to do so?

Kind Regards,
Rachel




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

Sent: Sunday, July 10, 2022, 4:09 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tksurfer Error

tksurfer is depracated. Try using tksurferfv instead

On 6/29/2022 4:33 PM, Rachel Wagner wrote:

External Email - Use Caution
Hello,

I am attempting to paint my spm functional data onto freesurfer’s anatomical 
image.

I ran this code: tksurfer bert lh inflated -overlay updated.img -overlay-reg 
register.dat

And got this error:

Tcl_Init failed: Can't find a usable init.tcl in the following directories:
/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4



This probably means that Tcl wasn't installed properly.

Tk_Init failed: invalid command name "tcl_findLibrary"
Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories:
./library
./tix8.1
./library
./tix8.1
/usr/pubsw/packages/tcltktixblt/current/lib/tix8.1


How can I fix this error?

Thanks,
Rachel



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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://secure-web.cisco.com/18uFsKV3T7bqI7k7n51PEj3Ai3lAoopZ_xXXCkLfme24lyxewgHcgnxoXD0FCQM1PZ-vM4ryzcP41h7fTbiwmAKXp7Kyrkk3-YoE04-h4TcI_2NkupiXtIx5UDa7w5m8FwGfvGl9SwcSl839YOL12UTK4eup8PDiP96ZmO8hKFI3VmY5Twh8cv0JPUk4hfIikzoIxDOuQDpJG6ww9SNG77f3QBUM27qof9HiUeI9BXWHJpGPBQILzkp9RP-rDqKVxDfbqWgK9Ucs6p4eR0tjLWo7VA_utdANSrj-pCDLUk3Qp8m68HWJlx5mfo4ZkR_Q7DIhdKa7FLbL0LOwjVT9xFd2i5lGCt7rQ6DqZYXkGGj4/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer


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The information in this e-mail is intended only for the person to whom it is 
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[Freesurfer] Cortical Projection

2022-07-08 Thread Rachel Wagner 
External Email - Use Caution

Hello all,

I am currently working on displaying my SPM overlay on a 3D brain volume, using 
bbregister, and am getting this: 
https://secure-web.cisco.com/1V05qEsg4uCsadH5DrWJGv9HH1_bizH0ESv2KX7f4dPKwalObCjmyYti7MbcQF5yREgot9Xsbdl21CBIAQL5Y65xH-oa8mM4DODGY7burr48zeKefCRRkDUrq-WGrtXMOCDhgHKnxo60Eqx8msz17eI2tbu_3AmMCNZfok4c7kIQiDL6HtPVNvlhSYs5_uFdJDn1rgRtKBr8viyvMVOxskFI5xH32NQLR71OHaVoplEcNXDd0meSt1u1KNFHYWSXp83ecj5ZWQHBJRplnoRiF9dBL_SfU7tFxlJVwLpkZ7jVxo9vbN4Dk1zyGDpyt0WtN1IQ5O9NzFVw7h77ceu7poCvAPHQRxyRAUxQRkMBP_Cc/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD%2Fview%3Fusp%3Ddrivesdk

I am hoping to smooth out the surface so it is more continuous and change the 
coloring of the brain. Are there options to do so?

Thank you very much in advance!

___
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] Export Image

2022-07-07 Thread Rachel Wagner 
External Email - Use Caution

Hello everyone, this is probably a silly question, but how can I export images 
from freeview? I don’t see an export option!
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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 project SPM image

2022-07-06 Thread Rachel Wagner 
External Email - Use Caution

Thank you very much Bruce, I will give that a try and see if I can ask about 
the command lines!

From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: July 5, 2022 9:34 AM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image

Hi Rachel

I’ll leave bbreg command lines to others (Doug?), but in general you don’t want 
to base the registration on the inflated since it doesn’t have a meaningful 
location within the volume. I would use the standard bbreg command, then use 
mri_vol2surf to paint what you want onto the surface. Once it is on any surface 
for a subject you should be able to display it on any other surface for that 
same subject (and same hemisphere).
Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rachel Wagner
Sent: Tuesday, July 5, 2022 12:17 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thank you, that would work very well! I’m trying this code without success, am 
I missing a component to display on an inflated surface?

bbregister --mov rReslice_Combined_roi_meanRD.nii --bold \ inflated -overlay 
--s  fsaverage \ --init-rr --lta register.lta

From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: July 4, 2022 3:45 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image

Well you can display it on inflated surfaces instead of white ones, which will 
remove most of the folds. Then you can smooth the surface overlay however you 
like (the colors on the surface) in freeview

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rachel Wagner
Sent: Monday, July 4, 2022 3:27 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thank you, noted!

I think I am on the right track, but I’d like to smooth the surface out 
(particularly the coloring and the sulci, which are quite deep) considerably – 
is there any way for me to do that?

From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: July 3, 2022 7:44 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image

I see, and what’s wrong with the screen shot you have? (and “Bruce” is fine).

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rachel Wagner
Sent: Sunday, July 3, 2022 7:41 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Hi Dr. Fischl,

My apologies, I don’t have much of a background in software generally!

For the SPM image, I used the AAL atlas to label lesioned brain regions and 
colored by frequency to generate the heatmap. Image dimensions: 1x1x1, Image 
Size [91 109 91], Pixel Dimensions [2 2 2], Bits Per Pixel: 32. I will map onto 
fsaverage!

I’m hoping to display it as a heatmap on an average surface, to look something 
like this: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be | Decreased functional connectivity from 
Wernicke's area homologue in... | Download Scientific Diagram 
(researchgate.net)<https://secure-web.cisco.com/1oOMXS4Xcve-ZJ8PxylSUuZevRGR5aotHueMxgJxcMGkXSkjJ6wTsTr4oavOgdzgC__DuhBfa2YoeXPPAkWNDkDveceWCqonnMePOe7RO8-EzKOCNiY55G6RP0RxIqcSzGoy5xrThG11tzNHAx4J2oOvo_ESpDm-Xy5SRds7mHaMi14AVwz97DtG6A7__AhYWMzxD1DhY1be4RuervQ_3GhIJP9U47Jlyf-6BJDot29n-DzmhaePM1AHaWepGK-h2DLlNNr5gjpR4VuJMYqBEkqYBtAH7eWX7f2lcu_279ka4M5ClsgZa3q8hqXJMfnAB0nP3mVb7RfWqryW2ibpstA/https%3A%2F%2Fwww.researchgate.net%2Ffigure%2FDecreased-functional-connectivity-from-Wernickes-area-homologue-in-children-born-VPT_fig3_329809185>

This is a screenshot of what I currently have within FreeSurfer: MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 
https://secure-web.cisco.com/1ooS-r-4oGHlyeFKwoHAT8TeYO1EfFdqNXuupuF2g2w_BV1upskV1XlGkYmcg3-P40ozqq7Ox1x1TvlWm9nW7QDCSCMt67OFME_Eua8LeSqKM22GlkfER-EupC1PoCGoaepbFyKJqrRQcXJoS3hr1dUGnR-jst1k148TpTpcXrLMFkJNjAwG5u68Gyx4uGBuuQpPhpwinSEyYbkMp5V9CTKsMQs9K9xw9ofwlqVMJJ0pMXzoE5_bqaa_Y5xqviRfPhRLmaFwuLxrmZja1hMNyo5WJJFM6ma6FPV61exqI_ZlktE4dAYETqIRTkAg6oFPCSRzRonIUriccquPVkP9BBUvQJmqJddhhOQykn3AyVK0/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD%2Fview%3Fusp%3Dsharing<https://secure-web.cisco.com/117

Re: [Freesurfer] How to project SPM image

2022-07-04 Thread Rachel Wagner 
External Email - Use Caution

Thank you, that would work very well! I’m trying this code without success, am 
I missing a component to display on an inflated surface?

bbregister --mov rReslice_Combined_roi_meanRD.nii --bold \ inflated -overlay 
--s  fsaverage \ --init-rr --lta register.lta

From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: July 4, 2022 3:45 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image

Well you can display it on inflated surfaces instead of white ones, which will 
remove most of the folds. Then you can smooth the surface overlay however you 
like (the colors on the surface) in freeview

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rachel Wagner
Sent: Monday, July 4, 2022 3:27 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thank you, noted!

I think I am on the right track, but I’d like to smooth the surface out 
(particularly the coloring and the sulci, which are quite deep) considerably – 
is there any way for me to do that?

From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: July 3, 2022 7:44 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image

I see, and what’s wrong with the screen shot you have? (and “Bruce” is fine).

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rachel Wagner
Sent: Sunday, July 3, 2022 7:41 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Hi Dr. Fischl,

My apologies, I don’t have much of a background in software generally!

For the SPM image, I used the AAL atlas to label lesioned brain regions and 
colored by frequency to generate the heatmap. Image dimensions: 1x1x1, Image 
Size [91 109 91], Pixel Dimensions [2 2 2], Bits Per Pixel: 32. I will map onto 
fsaverage!

I’m hoping to display it as a heatmap on an average surface, to look something 
like this: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be | Decreased functional connectivity from 
Wernicke's area homologue in... | Download Scientific Diagram 
(researchgate.net)<https://secure-web.cisco.com/1oOMXS4Xcve-ZJ8PxylSUuZevRGR5aotHueMxgJxcMGkXSkjJ6wTsTr4oavOgdzgC__DuhBfa2YoeXPPAkWNDkDveceWCqonnMePOe7RO8-EzKOCNiY55G6RP0RxIqcSzGoy5xrThG11tzNHAx4J2oOvo_ESpDm-Xy5SRds7mHaMi14AVwz97DtG6A7__AhYWMzxD1DhY1be4RuervQ_3GhIJP9U47Jlyf-6BJDot29n-DzmhaePM1AHaWepGK-h2DLlNNr5gjpR4VuJMYqBEkqYBtAH7eWX7f2lcu_279ka4M5ClsgZa3q8hqXJMfnAB0nP3mVb7RfWqryW2ibpstA/https%3A%2F%2Fwww.researchgate.net%2Ffigure%2FDecreased-functional-connectivity-from-Wernickes-area-homologue-in-children-born-VPT_fig3_329809185>

This is a screenshot of what I currently have within FreeSurfer: MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 
https://secure-web.cisco.com/1x9o8bxkk43qmiWQ2TZujpnjUHXaryQQ2Df4xQliCpOLAWdcyM3Yk1e05TwAMsWC6Ak5C4lQKr_Z7v8rJtn0RkilCCuR6GyFYXOtqlvJBf6rlhhTdbZe4NRZhPuu37fkdRBD11rmnQNnvmGISAKj3CcsQTTIFjc7jwqJ2qQG4PoDbzbC66GPggmQbm2nJddpH7NSDPpgwmuVIxnG8BLaSfbYXfTTvuzFBrOZIgAJcCds8EXTPrAnVddjnepj8E1eNyrZowDLGYvCoU1u0KyxihOYOPWsUkAg8Cpzb13Snkybje9ll9O1IDkReNw0mesPESxe8VNGJT80Odjz-b4fe5Q/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD%2Fview%3Fusp%3Dsharing<https://secure-web.cisco.com/117ePUqDOWTzA8pswn-Mibsr2qBEZIMKV-Yd9P886w1Gz_L53sraXddp6xh_K6otFd1qp6tl3kHUNUk5TqYrNzizCdMJEp5zKR4XRSMj-pTdv0Us9VNWBasmYcsRRwLCrbr56qNZWBqSCMo1n9uuDVn2jwX3TJvflVYJ5eFy_AeuSRsYP4IZpVfIgQa_M_jpxzqEUcOyymM_iHc8lqsaOMkCXyzUnvQHwgy4EzHxKFkCoCHHa5jVAf9Gnol0mf4Yr2C8MosmAo4UiuPBgk6J_IX3DQcx-3NEMfUZdj7TOzoVG7H3Nuaid0CL4spvphW5d5l6r4qJCNk1rNi9tIb_xxQ/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD%2Fview%3Fusp%3Dsharing>

Thank you very much again for your help!
Rachel


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>>
Sent: Sunday, July 3, 2022 6:37:42 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image


Can you give us more details? How did you create the 
rReslice_Combined_roi_meanRD.nii? What resolution is it? And how are you trying 
to display it? On an average surface? Why are you mapping it to bert and not 
fsaverage?



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rachel Wagner
Sent:

Re: [Freesurfer] How to project SPM image

2022-07-04 Thread Rachel Wagner 
External Email - Use Caution

Thank you, noted!

I think I am on the right track, but I’d like to smooth the surface out 
(particularly the coloring and the sulci, which are quite deep) considerably – 
is there any way for me to do that?

From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: July 3, 2022 7:44 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image

I see, and what’s wrong with the screen shot you have? (and “Bruce” is fine).

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rachel Wagner
Sent: Sunday, July 3, 2022 7:41 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Hi Dr. Fischl,

My apologies, I don’t have much of a background in software generally!

For the SPM image, I used the AAL atlas to label lesioned brain regions and 
colored by frequency to generate the heatmap. Image dimensions: 1x1x1, Image 
Size [91 109 91], Pixel Dimensions [2 2 2], Bits Per Pixel: 32. I will map onto 
fsaverage!

I’m hoping to display it as a heatmap on an average surface, to look something 
like this: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be | Decreased functional connectivity from 
Wernicke's area homologue in... | Download Scientific Diagram 
(researchgate.net)<https://secure-web.cisco.com/1oOMXS4Xcve-ZJ8PxylSUuZevRGR5aotHueMxgJxcMGkXSkjJ6wTsTr4oavOgdzgC__DuhBfa2YoeXPPAkWNDkDveceWCqonnMePOe7RO8-EzKOCNiY55G6RP0RxIqcSzGoy5xrThG11tzNHAx4J2oOvo_ESpDm-Xy5SRds7mHaMi14AVwz97DtG6A7__AhYWMzxD1DhY1be4RuervQ_3GhIJP9U47Jlyf-6BJDot29n-DzmhaePM1AHaWepGK-h2DLlNNr5gjpR4VuJMYqBEkqYBtAH7eWX7f2lcu_279ka4M5ClsgZa3q8hqXJMfnAB0nP3mVb7RfWqryW2ibpstA/https%3A%2F%2Fwww.researchgate.net%2Ffigure%2FDecreased-functional-connectivity-from-Wernickes-area-homologue-in-children-born-VPT_fig3_329809185>

This is a screenshot of what I currently have within FreeSurfer: MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 
https://secure-web.cisco.com/1W1qPJh0LIQdhLZew9v66ICIq4AvFY0hvWp5vgpcvBdzUKGZmY54EGMZenEAene3E3PkxgNm-WnN0ULTb_AGcyFw4saW8gnst6T4WViac5p4fpdnnJD8Sv1QBTSGAPEgOYU-sgVpXFSro7OCJZqJtYI15R-7QxNDEUuL0Nc0mwcrUAHyczg5mgfjJuEMovWqMPGnXZM55wsRRI9UBy2A2dEn_MHXazZNOKTPgsXapUrvtr9zOXXji83wyE62F0Myqf7fztA84aBgQBiVF770eJLM4kF-mBD6a7Pt49hcwX6xTZqdOsWpMMp1WLAyozpFnbk_1E4YjHgRskzt1Atuty8UVtCliDjbtsuTCdHuZ1tM/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD%2Fview%3Fusp%3Dsharing<https://secure-web.cisco.com/117ePUqDOWTzA8pswn-Mibsr2qBEZIMKV-Yd9P886w1Gz_L53sraXddp6xh_K6otFd1qp6tl3kHUNUk5TqYrNzizCdMJEp5zKR4XRSMj-pTdv0Us9VNWBasmYcsRRwLCrbr56qNZWBqSCMo1n9uuDVn2jwX3TJvflVYJ5eFy_AeuSRsYP4IZpVfIgQa_M_jpxzqEUcOyymM_iHc8lqsaOMkCXyzUnvQHwgy4EzHxKFkCoCHHa5jVAf9Gnol0mf4Yr2C8MosmAo4UiuPBgk6J_IX3DQcx-3NEMfUZdj7TOzoVG7H3Nuaid0CL4spvphW5d5l6r4qJCNk1rNi9tIb_xxQ/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD%2Fview%3Fusp%3Dsharing>

Thank you very much again for your help!
Rachel


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>>
Sent: Sunday, July 3, 2022 6:37:42 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image


Can you give us more details? How did you create the 
rReslice_Combined_roi_meanRD.nii? What resolution is it? And how are you trying 
to display it? On an average surface? Why are you mapping it to bert and not 
fsaverage?



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rachel Wagner
Sent: Sunday, July 3, 2022 6:26 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image



External Email - Use Caution

Hello Dr. Fischl, thank you for your reply, it is much appreciated.



I am trying to cortically project my spm lesion location/frequency map, 
according to instructions linked here: AnalyzingData/MNE_SPM2Freesurfer - Meg 
Wiki 
(cam.ac.uk)<https://secure-web.cisco.com/1Qq-eLDAcZvkiA1oj8V5IkWowioqEfn5og-amJx-SY4k1in27LFW-IYPjtKPBkz1pSyyypTf849rJVAmyJ-Xzl8hgSfRw_PnCU1IcK9vgJzylh5b5zbo__pkcMlQw3COQCtiD9Sjb3UUrTitRCZHp7K2aER3VxlzHcdNjLpvYNT25_gZPm3q08d1C6zm3oJAaOEzRs2pM7XWXRyfFr4kIvENC6HRC5Rym2tl9beh-v6o3WhIxUvTxUqG9UKik41wBeLCBHAlxXgQSjetU13wcX3LQV4OqWruZLoxxbjFjgttUeagi7QRPA8pJi6cegsKrkFGhnEdEFvpjRnL8d5vHBg/https%3A%2F%2Fimaging.mrc-cbu.cam.ac.uk%2Fmeg%2FAnalyzingData%2FMNE_SPM2Freesurfer>



I have used the following code: bbregister --mov 
rReslice_Combined_roi_meanRD.nii --bold \ --s bert \ --init-rr --lta 
register.lta

Re: [Freesurfer] How to project SPM image

2022-07-03 Thread Rachel Wagner 
External Email - Use Caution

Hi Dr. Fischl,

My apologies, I don’t have much of a background in software generally!

For the SPM image, I used the AAL atlas to label lesioned brain regions and 
colored by frequency to generate the heatmap. Image dimensions: 1x1x1, Image 
Size [91 109 91], Pixel Dimensions [2 2 2], Bits Per Pixel: 32. I will map onto 
fsaverage!

I’m hoping to display it as a heatmap on an average surface, to look something 
like this: | Decreased functional connectivity from Wernicke's area homologue 
in... | Download Scientific Diagram 
(researchgate.net)<https://secure-web.cisco.com/1oOMXS4Xcve-ZJ8PxylSUuZevRGR5aotHueMxgJxcMGkXSkjJ6wTsTr4oavOgdzgC__DuhBfa2YoeXPPAkWNDkDveceWCqonnMePOe7RO8-EzKOCNiY55G6RP0RxIqcSzGoy5xrThG11tzNHAx4J2oOvo_ESpDm-Xy5SRds7mHaMi14AVwz97DtG6A7__AhYWMzxD1DhY1be4RuervQ_3GhIJP9U47Jlyf-6BJDot29n-DzmhaePM1AHaWepGK-h2DLlNNr5gjpR4VuJMYqBEkqYBtAH7eWX7f2lcu_279ka4M5ClsgZa3q8hqXJMfnAB0nP3mVb7RfWqryW2ibpstA/https%3A%2F%2Fwww.researchgate.net%2Ffigure%2FDecreased-functional-connectivity-from-Wernickes-area-homologue-in-children-born-VPT_fig3_329809185>

This is a screenshot of what I currently have within FreeSurfer: 
https://secure-web.cisco.com/117ePUqDOWTzA8pswn-Mibsr2qBEZIMKV-Yd9P886w1Gz_L53sraXddp6xh_K6otFd1qp6tl3kHUNUk5TqYrNzizCdMJEp5zKR4XRSMj-pTdv0Us9VNWBasmYcsRRwLCrbr56qNZWBqSCMo1n9uuDVn2jwX3TJvflVYJ5eFy_AeuSRsYP4IZpVfIgQa_M_jpxzqEUcOyymM_iHc8lqsaOMkCXyzUnvQHwgy4EzHxKFkCoCHHa5jVAf9Gnol0mf4Yr2C8MosmAo4UiuPBgk6J_IX3DQcx-3NEMfUZdj7TOzoVG7H3Nuaid0CL4spvphW5d5l6r4qJCNk1rNi9tIb_xxQ/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD%2Fview%3Fusp%3Dsharing

Thank you very much again for your help!
Rachel


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fischl, Bruce 

Sent: Sunday, July 3, 2022 6:37:42 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to project SPM image


Can you give us more details? How did you create the 
rReslice_Combined_roi_meanRD.nii? What resolution is it? And how are you trying 
to display it? On an average surface? Why are you mapping it to bert and not 
fsaverage?



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rachel Wagner
Sent: Sunday, July 3, 2022 6:26 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to project SPM image



External Email - Use Caution

Hello Dr. Fischl, thank you for your reply, it is much appreciated.



I am trying to cortically project my spm lesion location/frequency map, 
according to instructions linked here: AnalyzingData/MNE_SPM2Freesurfer - Meg 
Wiki 
(cam.ac.uk)<https://secure-web.cisco.com/1Qq-eLDAcZvkiA1oj8V5IkWowioqEfn5og-amJx-SY4k1in27LFW-IYPjtKPBkz1pSyyypTf849rJVAmyJ-Xzl8hgSfRw_PnCU1IcK9vgJzylh5b5zbo__pkcMlQw3COQCtiD9Sjb3UUrTitRCZHp7K2aER3VxlzHcdNjLpvYNT25_gZPm3q08d1C6zm3oJAaOEzRs2pM7XWXRyfFr4kIvENC6HRC5Rym2tl9beh-v6o3WhIxUvTxUqG9UKik41wBeLCBHAlxXgQSjetU13wcX3LQV4OqWruZLoxxbjFjgttUeagi7QRPA8pJi6cegsKrkFGhnEdEFvpjRnL8d5vHBg/https%3A%2F%2Fimaging.mrc-cbu.cam.ac.uk%2Fmeg%2FAnalyzingData%2FMNE_SPM2Freesurfer>



I have used the following code: bbregister --mov 
rReslice_Combined_roi_meanRD.nii --bold \ --s bert \ --init-rr --lta 
register.lta



However, my results still look very grainy. Is there a better way to do this?



Thank you again,

Rachel Wagner









From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: June 30, 2022 9:09 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image



Can you summarize what you are trying to do? What kind of overlay are you 
trying to visualize and what exactly do you mean by a “3D image”?



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rachel Wagner
Sent: Thursday, June 30, 2022 2:48 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image



External Email - Use Caution

Thank you so much for your response – I’m a master’s student and am really 
struggling - I’ve been stuck trying to do this for about 2 weeks now, so the 
help is so appreciated!



My results look very grainy in mricron so my supervisor wants me to keep trying 
in FreeSurfer unfortunately for me.



I uploaded a the brain.mgz volume in freeview, but I’m not sure how to add an 
overlay and project as a 3D image. Would you happen to have any ideas?



Thank you so, so much again,

Rachel Wagner



From: niels.f...@gmx.de<mailto:niels.f...@gmx.de>
Sent: June 30, 2022 2:35 PM
To: 'Freesurfer support list'<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image



You don't often get email from niels.f...@gmx.de<mailto:niels.f...@gmx.de>. 
Learn why this is 
important<https://secure-web.cisco

Re: [Freesurfer] How to project SPM image

2022-07-03 Thread Rachel Wagner 
External Email - Use Caution

Hello Dr. Fischl, thank you for your reply, it is much appreciated.

I am trying to cortically project my spm lesion location/frequency map, 
according to instructions linked here: AnalyzingData/MNE_SPM2Freesurfer - Meg 
Wiki 
(cam.ac.uk)<https://secure-web.cisco.com/1Qq-eLDAcZvkiA1oj8V5IkWowioqEfn5og-amJx-SY4k1in27LFW-IYPjtKPBkz1pSyyypTf849rJVAmyJ-Xzl8hgSfRw_PnCU1IcK9vgJzylh5b5zbo__pkcMlQw3COQCtiD9Sjb3UUrTitRCZHp7K2aER3VxlzHcdNjLpvYNT25_gZPm3q08d1C6zm3oJAaOEzRs2pM7XWXRyfFr4kIvENC6HRC5Rym2tl9beh-v6o3WhIxUvTxUqG9UKik41wBeLCBHAlxXgQSjetU13wcX3LQV4OqWruZLoxxbjFjgttUeagi7QRPA8pJi6cegsKrkFGhnEdEFvpjRnL8d5vHBg/https%3A%2F%2Fimaging.mrc-cbu.cam.ac.uk%2Fmeg%2FAnalyzingData%2FMNE_SPM2Freesurfer>

I have used the following code: bbregister --mov 
rReslice_Combined_roi_meanRD.nii --bold \ --s bert \ --init-rr --lta 
register.lta

However, my results still look very grainy. Is there a better way to do this?

Thank you again,
Rachel Wagner




From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: June 30, 2022 9:09 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image

Can you summarize what you are trying to do? What kind of overlay are you 
trying to visualize and what exactly do you mean by a “3D image”?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rachel Wagner
Sent: Thursday, June 30, 2022 2:48 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thank you so much for your response – I’m a master’s student and am really 
struggling - I’ve been stuck trying to do this for about 2 weeks now, so the 
help is so appreciated!

My results look very grainy in mricron so my supervisor wants me to keep trying 
in FreeSurfer unfortunately for me.

I uploaded a the brain.mgz volume in freeview, but I’m not sure how to add an 
overlay and project as a 3D image. Would you happen to have any ideas?

Thank you so, so much again,
Rachel Wagner

From: niels.f...@gmx.de<mailto:niels.f...@gmx.de>
Sent: June 30, 2022 2:35 PM
To: 'Freesurfer support list'<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image

You don't often get email from niels.f...@gmx.de<mailto:niels.f...@gmx.de>. 
Learn why this is 
important<https://secure-web.cisco.com/1IGyjHfcGxatghbnnU4QrmkjiCFhtGpKgDShLha5LYdEXD8WHfidRqqVti-tRNc_NRrmceKvWCQqvppztwIyjyHoLtCRG8g-_oV0axWfVJBREqBDdqXiWbD3r4lqXwu1ATUnSHzr1Sm0hzwo9fZKMmaip9vMaZ-ziZtyq-o7jLLqcFSCJKMqj--KkVlWH1krwZu6xMc3iky_sPV5EDDuis16g4Bsx9Gtgx_ok2cbVmfCOgmv9kF1iV6S_H9cshZy0_0U2pGRX1vhHUDPzaaKSiDD2oKm3dVcgmx1rmzjlgOP78SWxfDc_SlHhotPQ8vOpc-kxEyf5XH9hCJY2HviLIg/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification>
Sure is, through freeview, however if you already have spm format files, it is 
much easier to use mricron

Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 Im Auftrag von Rachel Wagner
Gesendet: Donnerstag, 30. Juni 2022 18:18
An: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thanks very much, I will absolutely do so! Just so I know – is there not any 
way of generating such figures in Freesurfer?

From: niels.f...@gmx.de<mailto:niels.f...@gmx.de>
Sent: June 30, 2022 4:47 AM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image

You don't often get email from niels.f...@gmx.de<mailto:niels.f...@gmx.de>. 
Learn why this is 
important<https://secure-web.cisco.com/1i1UJeVjwlumrCAM-yAFlTcIKRz-AyoK3nEvXbthMrwntcUHURlFyX0rrFR0wouQHmspA4ZjoxOBIENpbDQzxXHDKpH2XTzH9AVcV2-B4cB0UnhepvutfJUWDgE0-b-jVluP0RVxcQb-6AbvjsVgjiH9THZp_5rNkZbCuvXkXkry7ESkyYXR4FggRrHhNYLoaEY5HgYqZwH5KsROiIvUMmu53rbttVpblAHaQUYBctJJR9xT50C6dDBPznLTYAWAisLm9sL6xcef1unrvAi6o59VwqbVaOLCnJmSHsjZ0sV9dPYEKoTc4lyh75EVhpn0SIbo5FCH1IrROZqKSf0rP1g/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification>

External Email - Use Caution
Rachel,  these figures were likely created with a software called mricron, not 
freesurfer.  Check it out :)

Holen Sie sich Outlook für 
Android<https://secure-web.cisco.com/1XvY3sA4-dRCvGWfgKiNWJHfOTGrrzAnDZB_-8JrFkF7ZCfI9UW5jD-mM3a0HD6u6u-XOhrGWWBIWdw7cY7iSa6VTZTpj5EPSIccAc83wMVuyE_Chh-Y41UAN1BN5hQgeEgwVxgy85ZFxD7a8RVjtO8x6YqLzn7R9EMm2j7-fuhi78CfCs8nGC2FCMTkxO59TfxCqAzZqBqbxZZYQSG8lgqX6_TrMa4UUKSK6XvwvVg2tbqUcsVxSl7jUvScAgBwcwlyfhyTurS387OW-PVJF9KA3zrYsboQDmxhlaGQRAaebLvS6Y_IpKv4NbRNQeNiKP1WYwTYcY_qpo0Wyl9Kxkw/https%3A%2F%2Faka.ms%2FAAb9ysg>



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The information in this e-

Re: [Freesurfer] How to project SPM image

2022-06-30 Thread Rachel Wagner 
External Email - Use Caution

Thank you so much for your response – I’m a master’s student and am really 
struggling - I’ve been stuck trying to do this for about 2 weeks now, so the 
help is so appreciated!

My results look very grainy in mricron so my supervisor wants me to keep trying 
in FreeSurfer unfortunately for me.

I uploaded a the brain.mgz volume in freeview, but I’m not sure how to add an 
overlay and project as a 3D image. Would you happen to have any ideas?

Thank you so, so much again,
Rachel Wagner

From: niels.f...@gmx.de<mailto:niels.f...@gmx.de>
Sent: June 30, 2022 2:35 PM
To: 'Freesurfer support list'<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image

You don't often get email from niels.f...@gmx.de. Learn why this is 
important<https://secure-web.cisco.com/1IGyjHfcGxatghbnnU4QrmkjiCFhtGpKgDShLha5LYdEXD8WHfidRqqVti-tRNc_NRrmceKvWCQqvppztwIyjyHoLtCRG8g-_oV0axWfVJBREqBDdqXiWbD3r4lqXwu1ATUnSHzr1Sm0hzwo9fZKMmaip9vMaZ-ziZtyq-o7jLLqcFSCJKMqj--KkVlWH1krwZu6xMc3iky_sPV5EDDuis16g4Bsx9Gtgx_ok2cbVmfCOgmv9kF1iV6S_H9cshZy0_0U2pGRX1vhHUDPzaaKSiDD2oKm3dVcgmx1rmzjlgOP78SWxfDc_SlHhotPQ8vOpc-kxEyf5XH9hCJY2HviLIg/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification>
Sure is, through freeview, however if you already have spm format files, it is 
much easier to use mricron

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Rachel Wagner
Gesendet: Donnerstag, 30. Juni 2022 18:18
An: Freesurfer support list 
Betreff: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thanks very much, I will absolutely do so! Just so I know – is there not any 
way of generating such figures in Freesurfer?

From: niels.f...@gmx.de<mailto:niels.f...@gmx.de>
Sent: June 30, 2022 4:47 AM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image

You don't often get email from niels.f...@gmx.de<mailto:niels.f...@gmx.de>. 
Learn why this is 
important<https://secure-web.cisco.com/1i1UJeVjwlumrCAM-yAFlTcIKRz-AyoK3nEvXbthMrwntcUHURlFyX0rrFR0wouQHmspA4ZjoxOBIENpbDQzxXHDKpH2XTzH9AVcV2-B4cB0UnhepvutfJUWDgE0-b-jVluP0RVxcQb-6AbvjsVgjiH9THZp_5rNkZbCuvXkXkry7ESkyYXR4FggRrHhNYLoaEY5HgYqZwH5KsROiIvUMmu53rbttVpblAHaQUYBctJJR9xT50C6dDBPznLTYAWAisLm9sL6xcef1unrvAi6o59VwqbVaOLCnJmSHsjZ0sV9dPYEKoTc4lyh75EVhpn0SIbo5FCH1IrROZqKSf0rP1g/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification>

External Email - Use Caution
Rachel,  these figures were likely created with a software called mricron, not 
freesurfer.  Check it out :)

Holen Sie sich Outlook für 
Android<https://secure-web.cisco.com/1XvY3sA4-dRCvGWfgKiNWJHfOTGrrzAnDZB_-8JrFkF7ZCfI9UW5jD-mM3a0HD6u6u-XOhrGWWBIWdw7cY7iSa6VTZTpj5EPSIccAc83wMVuyE_Chh-Y41UAN1BN5hQgeEgwVxgy85ZFxD7a8RVjtO8x6YqLzn7R9EMm2j7-fuhi78CfCs8nGC2FCMTkxO59TfxCqAzZqBqbxZZYQSG8lgqX6_TrMa4UUKSK6XvwvVg2tbqUcsVxSl7jUvScAgBwcwlyfhyTurS387OW-PVJF9KA3zrYsboQDmxhlaGQRAaebLvS6Y_IpKv4NbRNQeNiKP1WYwTYcY_qpo0Wyl9Kxkw/https%3A%2F%2Faka.ms%2FAAb9ysg>


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Re: [Freesurfer] How to project SPM image

2022-06-30 Thread Rachel Wagner 
External Email - Use Caution

Thanks very much, I will absolutely do so! Just so I know – is there not any 
way of generating such figures in Freesurfer?

From: niels.f...@gmx.de
Sent: June 30, 2022 4:47 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to project SPM image

You don't often get email from niels.f...@gmx.de. Learn why this is 
important

External Email - Use Caution
Rachel,  these figures were likely created with a software called mricron, not 
freesurfer.  Check it out :)

Holen Sie sich Outlook für 
Android

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[Freesurfer] How to project SPM image

2022-06-29 Thread Rachel Wagner 
External Email - Use Caution

Hello,

I am trying to project my SPM nii image onto an anatomical image to project 
them onto a cortical surface in Freesurfer, to generate images which look like 
this: Fig. 4: Refining neuroanatomical treatment targets for addiction. | 
Nature 
Medicine<https://secure-web.cisco.com/1mejk3edpL22Nxd2a1vnicVV8HsoH4qBsXKIzfqDBspXAg5pVr7WGexSGzvpRiWk8ceSpVjDMLZ3c4NxMcheYNeI3oPLKCAiKVwNrEye0yox3vKETMmnMIUiLoUv7mhj5GqeFb29eWe-MHdVe2YeOzTWIXhtvZaKL-l8zJmFR6sKFa0u1vPIuY8q0SW0dvaDQY_wnRnfajRp4bw9Df3vHTTwkGYtTiQiYTK55yk3PHky3CLlJ2Gv2wNAXqPN8abr0pUkzJG21z-g7X2quN2TvlfuFTh8yU4nUstoua4zkPO1Jx8NGEU54Z5srWhovYcnGhXjxKA3oZnHQ31KZzxIyTw/https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41591-022-01834-y%2Ffigures%2F4>

Has anyone done this before and would be able to point me towards any resources 
to do so?

Thank you,
Rachel Wagner
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[Freesurfer] Tksurfer Error

2022-06-29 Thread Rachel Wagner 
External Email - Use Caution

Hello,

I am attempting to paint my spm functional data onto freesurfer’s anatomical 
image.

I ran this code: tksurfer bert lh inflated -overlay updated.img -overlay-reg 
register.dat

And got this error:

Tcl_Init failed: Can't find a usable init.tcl in the following directories:
/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4



This probably means that Tcl wasn't installed properly.

Tk_Init failed: invalid command name "tcl_findLibrary"
Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories:
./library
./tix8.1
./library
./tix8.1
/usr/pubsw/packages/tcltktixblt/current/lib/tix8.1


How can I fix this error?

Thanks,
Rachel
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Re: [Freesurfer] Command Not Found

2022-06-28 Thread Rachel Wagner 
External Email - Use Caution

Oh thank you, good catch! I am now encountering the issue below:

developer@developer-VirtualBox:~$ tkregister2 --s home --mov updated.mgz 
--regheader --reg register.dat --surf orig
tkregister_tcl /usr/local/freesurfer/7.2.0/tktools/tkregister2.tcl
surfname set to orig
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume updated.mgz
reg file   register.dat
LoadVol1
ZeroCRAS   0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
ERROR: could not find orig as either mgz or COR
/usr/local/freesurfer/7.2.0/subjects/home/mri/orig

Could this be another typo on my part or should I be using a different path?

Thanks again!
Rachel

From: Wighton, Paul<mailto:pwigh...@mgh.harvard.edu>
Sent: June 28, 2022 4:36 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Command Not Found

You don't often get email from pwigh...@mgh.harvard.edu. Learn why this is 
important<https://secure-web.cisco.com/1jnAu9rZyQoAsHaEXFKNaea_IoqrfNDjTa3fixAdF7c_WZaD8XRsCcN6osTq_CGAreLqRbDx4eZa528eU0R3IlrFdtRmTEhiPM8eWkmKpBzPHCx1MumoGqEPNTLyt9qCEX94kwQgCS6Z1wxx39C4ZoiSu5bP_hiAtdY08XFyA7iBmFcLayc4X_QskxFXP1snp4NASkLp3rXE3mKToDppINnv2nDnG52e091xf29pjQzW46h5-LXZkym2URm3ZRkr2DrY2ksZjAZM2GuLmSn8fm5OrlvNIikiwIUVqjuL-WxawQ6oQRmlHHFoOc50GXYK0/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification>
Hi Rachel,

Are you trying to run tkregister2?  Looks like you forgot the t at the start of 
the command.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Rachel Wagner 

Sent: Tuesday, June 28, 2022 4:29 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Command Not Found


External Email - Use Caution

Hello,



Thank you for your help! I am trying to register my spm image and am getting 
the following error:



developer@developer-VirtualBox:~$ kregister2 --s home --mov updated.mgz 
--regheader --reg register.dat --surf orig

kregister2: command not found





Is my path not set correctly?



Thanks again,

Rachel Wagner

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[Freesurfer] Command Not Found

2022-06-28 Thread Rachel Wagner 
External Email - Use Caution

Hello,

Thank you for your help! I am trying to register my spm image and am getting 
the following error:

developer@developer-VirtualBox:~$ kregister2 --s home --mov updated.mgz 
--regheader --reg register.dat --surf orig
kregister2: command not found


Is my path not set correctly?

Thanks again,
Rachel Wagner
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[Freesurfer] Error Opening File

2022-06-28 Thread Rachel Wagner 
External Email - Use Caution

Hello,

I am getting the following error when trying to convert a file on my desktop:

developer@developer-VirtualBox:~$ mri_convert home/developer/desktop/brain.mgz 
brain.nii
mri_convert home/developer/desktop/brain.mgz brain.nii
reading from home/developer/desktop/brain.mgz...
error: mghRead(home/developer/desktop/brain.mgz, -1): could not open file
developer@developer-VirtualBox:~$

Am I doing something incorrectly?

Thanks!
Rachel
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[Freesurfer] Converting File Type

2022-06-28 Thread Rachel Wagner 
External Email - Use Caution

Hello,

I have an img and an mgz file I would like to convert to a nii file. How can I 
do so?

Thanks!
Rachel
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[Freesurfer] Setting Location?

2022-06-17 Thread Rachel Wagner 
External Email - Use Caution

Hello, I am attempting to convert an image file and am getting the following 
error:

developer@developer-VirtualBox:~$ mri_convert Combined_roi_meanRD.nii 
Combined_roi_meanRD.img
mri_convert Combined_roi_meanRD.nii Combined_roi_meanRD.img
reading from Combined_roi_meanRD.nii...
error: niiRead(): error opening file /home/developer/Combined_roi_meanRD.nii


I believe this is due to the location I have stored it (desktop); how do I set 
the location?

Thank you,
Rachel Wagner
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Re: [Freesurfer] FSL Password

2022-06-15 Thread Rachel Wagner 
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Thank you very much for the help! Upon trying that, I get this:

developer@developer-VirtualBox:~$ cd ~/Downloads
developer@developer-VirtualBox:~/Downloads$ $ sudo  python3  fslinstaller.py
$: command not found
developer@developer-VirtualBox:~/Downloads$ sudo  python3  fslinstaller.py
[sudo] password for developer:

I am strangely again stopped from being able to type anything at all. Is there 
a way to install without having to use admin privileges?

Thanks again,
Rachel

From: fsbuild<mailto:fsbu...@contbay.com>
Sent: June 15, 2022 9:08 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: Rachel Wagner<mailto:rwag...@uwo.ca>
Subject: Re: [Freesurfer] FSL Password

You don't often get email from fsbu...@contbay.com. Learn why this is 
important<https://secure-web.cisco.com/1N3iUzddPi2jIvZ-fdJT6dVvqvdlk8jMWCb5xVRl_di_VT4expPTYsPssDrxvEcB4xjXq9n8p7IX-4J5jrEAylzAnCf0Ad3Ru50cH7kwG7fkzZO0g8u68ZgGYynIJaefYJ7qckr3igecNWZK_GLLJbMRzqLL5UOl9f7SQSGjcx4UphoobLNRZ37eJkHvcmiiGH3xByFI1lJ3dvqWLfqhS4nSV2zsSwXNZOVVvzEZ8sAi2DfQ8uVzwdsqBelOsAKhxwcDobw7Lv7Wc5xRIC1-4Y2uJ3wXXRu0-E09rrcm3BNDaN9kfKdtf4pzEJypWfFW7L1cC2j6vOFPvMVxHEVhDoA/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification>
Try,

$ sudo  python3  fslinstaller.py

… then enter password for developer.  The sudo command will use admin 
privileges which may allow install to occur.

- R.


On Jun 15, 2022, at 20:54, Rachel Wagner  wrote:

External Email - Use Caution

Hello,

I am downloading FSL into ubuntu freesurfer VM, and have gotten the following 
prompt:

developer@developer-VirtualBox:~/Downloads$  python3 fslinstaller.py
--- FSL Installer - Version 3.2.3 ---
[Warning] Some operations of the installer require administative rights,
for example installing into the default folder of /usr/local.
If your account is an 'Administrator' (you have 'sudo' rights)
then you will be prompted for your administrator password
when necessary.
When asked a question, the default answer is given in square brackets.
Hit the Enter key to accept this default answer.
Where would you like the FSL install to be (including the FSL folder name)? 
[/usr/local/fsl]:
Downloading...
Checking FSL package
[OK] File downloaded
Installing FSL software version 6.0.5.2...
We require your password to continue...
password:


When I try to type in the password, I am unable to type at all, for some reason 
I can’t write anything in the terminal. Is there any way for me to troubleshoot?

Thanks very much!
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[Freesurfer] FSL Password

2022-06-15 Thread Rachel Wagner 
External Email - Use Caution

Hello,

I am downloading FSL into ubuntu freesurfer VM, and have gotten the following 
prompt:

developer@developer-VirtualBox:~/Downloads$  python3 fslinstaller.py
--- FSL Installer - Version 3.2.3 ---
[Warning] Some operations of the installer require administative rights,
for example installing into the default folder of /usr/local.
If your account is an 'Administrator' (you have 'sudo' rights)
then you will be prompted for your administrator password
when necessary.
When asked a question, the default answer is given in square brackets.
Hit the Enter key to accept this default answer.
Where would you like the FSL install to be (including the FSL folder name)? 
[/usr/local/fsl]:
Downloading...
Checking FSL package
[OK] File downloaded
Installing FSL software version 6.0.5.2...
We require your password to continue...
password:


When I try to type in the password, I am unable to type at all, for some reason 
I can’t write anything in the terminal. Is there any way for me to troubleshoot?

Thanks very much!
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[Freesurfer] Nii to Img file

2022-06-15 Thread Rachel Wagner 
External Email - Use Caution

Hello,

Thank you for your assistance!

I am trying to convert an nii nifti file to an img file within free surfer. 
I’ve used the mri convert function and did create the img file, but I’m getting 
an error message in SPM when I try to co-register it to another img file.

Is there a particular way I should be converting an nii file?

My only other thought is that potentially I’m not exporting properly. I am 
using ubunu VM on a windows computer, and need to export the two img files from 
ubuntu to my windows files so I can upload them in matlab. Is there a preferred 
way to export files out of the ubuntu VM?

Thanks very much again,
Rachel

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Re: [Freesurfer] SPM to FreeSurfer

2022-06-15 Thread Rachel Wagner 
External Email - Use Caution

Apologies for repeat email – I’m getting the following error message, is there 
something I should add?

developer@developer-VirtualBox:~$ mri_convert i.mgz i.img
mri_convert i.mgz i.img
reading from i.mgz...
error: mghRead(/home/developer/i.mgz, -1): could not open file
developer@developer-VirtualBox:~$

From: Rachel Wagner<mailto:rwag...@uwo.ca>
Sent: June 15, 2022 5:04 PM
To: Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
Subject: SPM to FreeSurfer

Hello,

I am trying to take my SPM images and cortically project them with free surfer 
(SpmPainting - Free Surfer Wiki 
(harvard.edu)<https://secure-web.cisco.com/1T_Lpxp9cC1mW8MHHtVem56Yk4Wt6jHB1_kEXL_UVjWkhtWW5kokRpWuwHmGdye6C0NNpHg7ZADzCWPnd5_7_sU2Y3u6J1-QUHmaJNOZzrS3ig9OuCXhwnb3LYUbElFU8_3dxXYGva1S1NEwrctcFiFdtPgTSJ9hiMx_YH3j__Z4kQKIqD-Q4Ojk86LNUkbR09SF9Nm931fNq1C7Dsv8hNN7P4TMLn2T1qcQbbqYboihhM70a5F4J_iD9xaZdyiPAB9UiTdGTVZtup-RzjNn4iiyNXe712IhsXRsNOf13SImLNRoEeX9zwaS6BOQ8R4hi_cw6ote3pkSLzX317SrnYA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSpmPainting>.
 As it might be quite obvious, I have very little experience using these 
softwares.

I am typing in the suggested code as follows:
developer@developer-VirtualBox:~$ mri_convert 
$SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img
mri_convert /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz 
brain.img
reading from /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz...
error: mghRead(/usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz, 
-1): could not open file
developer@developer-VirtualBox:~$ ^C
developer@developer-VirtualBox:~$

Is there something I am doing incorrectly?

Thank you!
Rachel

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[Freesurfer] SPM to FreeSurfer

2022-06-15 Thread Rachel Wagner 
External Email - Use Caution

Hello,

I am trying to take my SPM images and cortically project them with free surfer 
(SpmPainting - Free Surfer Wiki 
(harvard.edu).
 As it might be quite obvious, I have very little experience using these 
softwares.

I am typing in the suggested code as follows:
developer@developer-VirtualBox:~$ mri_convert 
$SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img
mri_convert /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz 
brain.img
reading from /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz...
error: mghRead(/usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz, 
-1): could not open file
developer@developer-VirtualBox:~$ ^C
developer@developer-VirtualBox:~$

Is there something I am doing incorrectly?

Thank you!
Rachel
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