Re: [Freesurfer] [External] Re: Converting .label coordinates to MNI

[Berger, Joel]

External Email - Use Caution

Thanks so much for the quick and clear reply Bruce. I'll look into doing that.


Cheers,

Joel


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

Sent: 27 September 2019 12:52:47
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] Converting .label coordinates to MNI

Hi Joel

I believe they are stored in "tkreg ras" by default. In any case,
mri_label2label should let you map them to pretty much any space you
like.

cheers
Bruce
On Fri, 27 Sep 2019, Berger, Joel wrote:

>
> External Email - Use Caution
>
> Hi friendly Freesurfers,
>
>
> I have seen this question asked, but can't find the answer. When exporting a
> label from tksurfer for a particular ROI for a subject, the coordinates in
> the .label document don't match up with any of the coordinates I can view in
> tksurfer. Is there a way/formula to convert these easily, ideally into MNI
> coordinates?
>
>
> I tried loading the label into Matlab with freesurfer_read_label.m
> converting to Talairach with freesurfer_label2tal.m and then also converting
> those coordinates using tal2mni.m, but the Talairach or the MNI
> coordinates do not match with the Talairach/MNI coordinates shown for the
> corresponding vertices in tksurfer.
>
>
> Thank you,
>
> Joel
>
>
>
> 
> Notice: This UI Health Care e-mail (including attachments) is covered by the
> Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended
> only for the use of the individual or entity to which it is addressed, and
> may contain information that is privileged, confidential, and exempt from
> disclosure under applicable law. If you are not the intended recipient, any
> dissemination, distribution or copying of this communication is strictly
> prohibited. If you have received this communication in error, please notify
> the sender immediately and delete or destroy all copies of the original
> message and attachments thereto. Email sent to or from UI Health Care may be
> retained as required by law or regulation. Thank you.
>
> 
>
>



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[Freesurfer] mri_surf2vol -lost cluster

[Albrecht, Daniel S.]

Hello everyone,

I've been using mri_vol2surf to move some activation data in MNI space to the 
fsaverage surface with the following command:

mri_vol2surf --mov MNIvol.nii --projfrac-max 0 1 0.1 --hemi rh --o rh.out.mgz 
--mni152reg

This works well, but I'm losing a small temporal gyrus cluster that sits close 
to pial surface. I was assuming this was due to the proximity to the pial 
surface and resampling, but are there any other options or flags I could use to 
get this to project successfully?

Thanks very much,

Dan
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Re: [Freesurfer] Converting .label coordinates to MNI

[Bruce Fischl]

Hi Joel

I believe they are stored in "tkreg ras" by default. In any case, 
mri_label2label should let you map them to pretty much any space you 
like.


cheers
Bruce
On Fri, 27 Sep 2019, Berger, Joel wrote:



External Email - Use Caution

Hi friendly Freesurfers,


I have seen this question asked, but can't find the answer. When exporting a
label from tksurfer for a particular ROI for a subject, the coordinates in
the .label document don't match up with any of the coordinates I can view in
tksurfer. Is there a way/formula to convert these easily, ideally into MNI
coordinates?


I tried loading the label into Matlab with freesurfer_read_label.m
converting to Talairach with freesurfer_label2tal.m and then also converting
those coordinates using tal2mni.m, but the Talairach or the MNI
coordinates do not match with the Talairach/MNI coordinates shown for the
corresponding vertices in tksurfer.


Thank you,

Joel




Notice: This UI Health Care e-mail (including attachments) is covered by the
Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended
only for the use of the individual or entity to which it is addressed, and
may contain information that is privileged, confidential, and exempt from
disclosure under applicable law. If you are not the intended recipient, any
dissemination, distribution or copying of this communication is strictly
prohibited. If you have received this communication in error, please notify
the sender immediately and delete or destroy all copies of the original
message and attachments thereto. Email sent to or from UI Health Care may be
retained as required by law or regulation. Thank you.



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[Freesurfer] Converting .label coordinates to MNI

[Berger, Joel]

External Email - Use Caution

Hi friendly Freesurfers,


I have seen this question asked, but can't find the answer. When exporting a 
label from tksurfer for a particular ROI for a subject, the coordinates in the 
.label document don't match up with any of the coordinates I can view in 
tksurfer. Is there a way/formula to convert these easily, ideally into MNI 
coordinates?


I tried loading the label into Matlab with freesurfer_read_label.m converting 
to Talairach with freesurfer_label2tal.m and then also converting those 
coordinates using tal2mni.m, but the Talairach or the MNI coordinates do not 
match with the Talairach/MNI coordinates shown for the corresponding vertices 
in tksurfer.


Thank you,

Joel



Notice: This UI Health Care e-mail (including attachments) is covered by the 
Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only 
for the use of the individual or entity to which it is addressed, and may 
contain information that is privileged, confidential, and exempt from 
disclosure under applicable law. If you are not the intended recipient, any 
dissemination, distribution or copying of this communication is strictly 
prohibited. If you have received this communication in error, please notify the 
sender immediately and delete or destroy all copies of the original message and 
attachments thereto. Email sent to or from UI Health Care may be retained as 
required by law or regulation. Thank you.

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Re: [Freesurfer] TRACULA - input Nifti instead of DICOM?

[Yendiki, Anastasia]

Nifti files don't store that info. You'd have to get the gradient table and 
b-values either from the dicom header or from the scanner.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Daniel Callow 

Sent: Friday, September 27, 2019 11:32 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA - input Nifti instead of DICOM?


External Email - Use Caution

Gotcha. I was wondering if it would be possible to extract the bvecs and bval 
files directly from the Nifti file, however, it seems like based on the 
documentation that this is not possible and I will have to specify the bvals 
and bvecs and make sure they are formatted correctly for TRACULA.

Thanks for the reply!
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com
443-254-6298


On Fri, Sep 27, 2019 at 11:26 AM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Yes. Please check out the instructions in the tutorial on how to specify your 
input DWIs and let us know if you have any questions:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Daniel Callow mailto:ddcc2...@gmail.com>>
Sent: Friday, September 27, 2019 10:31:19 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] TRACULA - input Nifti instead of DICOM?


External Email - Use Caution

Hello I was given a dataset already in Nifti format that I would like to run 
Tracula on. Is it possible to input Nifti files in the config file instead of 
DICOMs? How would this work?

Best,
Daniel Callow
--
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com
443-254-6298
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Re: [Freesurfer] TRACULA - input Nifti instead of DICOM?

[Daniel Callow]

External Email - Use Caution

Gotcha. I was wondering if it would be possible to extract the bvecs and
bval files directly from the Nifti file, however, it seems like based on
the documentation that this is not possible and I will have to specify the
bvals and bvecs and make sure they are formatted correctly for TRACULA.

Thanks for the reply!
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


On Fri, Sep 27, 2019 at 11:26 AM Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> Yes. Please check out the instructions in the tutorial on how to specify
> your input DWIs and let us know if you have any questions:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow <
> ddcc2...@gmail.com>
> *Sent:* Friday, September 27, 2019 10:31:19 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] TRACULA - input Nifti instead of DICOM?
>
>
> External Email - Use Caution
>
> Hello I was given a dataset already in Nifti format that I would like to
> run Tracula on. Is it possible to input Nifti files in the config file
> instead of DICOMs? How would this work?
>
> Best,
> Daniel Callow
> --
> *Daniel Callow*
> *PhD Student, Neuroscience and Cognitive Science*
> Exercise for Brain Health Lab
> University of Maryland, College Park
> *ddcc2...@gmail.com *
> 443-254-6298
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] TRACULA - input Nifti instead of DICOM?

[Yendiki, Anastasia]

Yes. Please check out the instructions in the tutorial on how to specify your 
input DWIs and let us know if you have any questions:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Daniel Callow 

Sent: Friday, September 27, 2019 10:31:19 AM
To: Freesurfer support list 
Subject: [Freesurfer] TRACULA - input Nifti instead of DICOM?


External Email - Use Caution

Hello I was given a dataset already in Nifti format that I would like to run 
Tracula on. Is it possible to input Nifti files in the config file instead of 
DICOMs? How would this work?

Best,
Daniel Callow
--
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com
443-254-6298
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[Freesurfer] What's the difference between FSFAST and SPM in the 1-st level GLM?

[Zhi Li]

External Email - Use Caution

Dear Freesurfer experts,

May I ask what's the difference between FSFAST and SPM in the 1st level
GLM? Now I use fsfast to pre-process my task-based imaging data, then model
the data with FSFAST and SPM respectively. I expected to get very similar
results from FSFAST and SPM in the whole brain volume-based analysis.
Although there is some overlap between FSFAST and SPM on the whole brain
activation, however, there is a lot of difference. Activation in some
regions based on SPM was not found in that based on FSFAST. Please see
below for my mkanalysis information:

mkanalysis-sess \
  -fsd Num -mni305 2 -fwhm 8 \
  -event-related  -paradigm Num.par -nconditions 18 \
  -spmhrf 0 -TR 2 -refeventdur 16 -nskip 0 -polyfit 0 \
  -hpf 128 -mcextreg \
  -analysis Num.sm08.mni305  -per-run -force

Any suggestions?

In addition, I am not clear if I convert the volume data from FSFAST to SPM
in a right way. I replace the mask of subcortical mask with the whole brain
mask. Then I convert the pre-processed data from mni305 to mni152 and model
it with SPM. However, there is a lot of loss in the prefrontal and
subcortical regions. Seems like the whole brain data shrinkage in SPM
(please see attached figure).

Looking forward to your kind reply.

Thanks and best,

Li Zhi
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[Freesurfer] TRACULA - input Nifti instead of DICOM?

[Daniel Callow]

External Email - Use Caution

Hello I was given a dataset already in Nifti format that I would like to
run Tracula on. Is it possible to input Nifti files in the config file
instead of DICOMs? How would this work?

Best,
Daniel Callow
-- 
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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Re: [Freesurfer] Which files do I need to mri_deface to anonymized a subject?

[Bruce Fischl]

Hi Tim

you probably also want to do the files in the orig dir (like 
orig/001.mgz).


cheers
Bruce
On Fri, 27 Sep 2019, Tim Schäfer wrote:


   External Email - Use Caution

Dear FS experts,

I want to upload neuroimaging data pre-processed by FreeSurfer's recon-all 
pipeline to a consortium server, and they require all data to be anonymized.

I found mri_deface [1] and wondered which files I would have to apply it to, 
and whether there are any other things I should be aware of.

So far, my plan is to use mri_deface to replace, for each subject, the 
following files in mri/:

* orig.mgz
* orig_nu.mgz
* T1.mgz
* rawavg.mgz

It would also be an option to upload only a subset of all the files produced by 
FreeSurfer, but I do not know which files to exclude and include, so if you 
have suggestions for this, it would also be very welcome. I will also look at 
some public datasets to see how they did it.

[1] https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] Error during processing data. mris_make_surfaces malloc: *** error for object 0x2431900024317: pointer being freed was not allocated.

[Bruce Fischl]

ok, we'll see if we can replicate it.
On Fri, 27 Sep 2019, Троицкий Антон 
Александрович wrote:




External Email - Use Caution

Dear Bruce,

I don't’ know exactly what happened during the processing. 
I have 8 Gb of RAM of my Mac. When the freesurfer is working there is
approximately 2 Gb free RAM. 

Unfortunately, I don’t know how to check the working of RAM and was there a
memory overflow or memory leaking. 

It will be great If you could check my data. I want to mention that the same
problem was with other data of the same patient. I have uploaded the patient
data on my google drive account. So here you can download 
ithttps://drive.google.com/file/d/1Rx2HG2ZXTTphrYDMRwguOljz9T4K7av1/view?usp=
sharing. The error appeared for data for 2019-07-22. But the same problem
appeared for data for 2019-09-04. 

mris_fix_topology(5832,0x7fffc83843c0) malloc: *** error for object
0x7fcf88f2ca50: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
0 defective edges
Abort
Darwin mac-2ap023-2.fccho-moscow.ru 16.7.0 Darwin Kernel Version 16.7.0: Thu
Jan 11 22:59:40 PST 2018; root:xnu-3789.73.8~1/RELEASE_X86_64 x86_64
recon-all -s 2019-09-03_3DBrainView_T1_FSSD_2019-09-26_13-11 exited with
ERRORS at Thu Sep 26 17:43:07 MSK 2019
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


I saw the system requirements for the freesurfer and there was a mention
about 8 RAM. Is it a necessary amount of memory only for freesurfer or for
PC station?

Best regards,
Anton Troitskii.


Are you running out of memory on the machine? If not, and you upload the ent
ire subject dir we will see if we can replicate and fix this problem.
cheers
Bruce
On Tue, 24 Sep 2019, Троицкий Антон Александрович wrote:
External Email - Use Caution
Hello FreeSurfer Developers,

during the processing of patient data an error occurred. I don’t clearly 
understand a reason for this error. Technical description of this error is


mris_make_surfaces(10174,0x7fffbf9553c0) malloc: *** error for object 
0x2431900024317: pointer being freed was not allocated

*** set a breakpoint in malloc_error_break to debug
000: dt: 0., sse=991989.1, rms=2.913
021: dt: 0.5000, sse=841468.7, rms=1.605 (44.916%)
022: dt: 0.5000, sse=803776.9, rms=1.267 (21.055%)
rms = 1.24, time step reduction 1 of 3 to 0.250...
023: dt: 0.5000, sse=793308.4, rms=1.242 (1.982%)
Abort

My suggestion is that the error associated with memory allocation and its 
reading.


Is there any suggestion about why it happened and how can I prevent it in th
e 
future?


Also, I've attached the recon-all.log in case it's of any use.

1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0
2) Platform: macOS Sierra 10.12.6
3) uname -a: Darwin mac-2ap023-2.fccho-moscow.ru 16.7.0 Darwin Kernel Versio
n 
16.7.0: Thu Jan 11 22:59:40 PST 2018; root:xnu-3789.73.8~1/RELEASE_X86_64 x8

6_64
4) recon-all.log: see attached



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Re: [Freesurfer] Error during processing. mris_make_surfaces(10174, 0x7fffbf9553c0) malloc: *** error for object 0x2431900024317: pointer being freed was not allocated/

[Bruce Fischl]

Hi,

if you upload this entire subject to our ftp site we will take a look

cheers
Bruce
On 
Fri, 27 Sep 2019, Троицкий Антон Александрович wrote:




External Email - Use Caution

Hello FreeSurfer Developers,

during the processing of patient data an error occurred. I don’t clearly
understand a reason for this error. Technical description of this error is 

mris_fix_topology(5832,0x7fffc83843c0) malloc: *** error for object
0x7fcf88f2ca50: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
0 defective edges
Abort
Darwin mac-2ap023-2.fccho-moscow.ru 16.7.0 Darwin Kernel Version 16.7.0: Thu
Jan 11 22:59:40 PST 2018; root:xnu-3789.73.8~1/RELEASE_X86_64 x86_64

 

recon-all -s 2019-09-03_3DBrainView_T1_FSSD_2019-09-26_13-11 exited with
ERRORS at Thu Sep 26 17:43:07 MSK 2019

 

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

My assumption is that the error associated with memory allocation and its
reading. 

Is there any suggestion about why it happened and how can I prevent it in
the future?

Also, I've attached the recon-all.log in case it's of any use.

1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0
2) Platform: macOS Sierra 10.12.6
3) uname -a: Darwin mac-2ap023-2.fccho-moscow.ru 16.7.0 Darwin Kernel
Version 16.7.0: Thu Jan 11 22:59:40 PST 2018;
root:xnu-3789.73.8~1/RELEASE_X86_64 x86_64
4) recon-all.log: see attached


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[Freesurfer] Add email to post in mailing list

[Paula Reyero Lobo]

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prl.saheli...@gmail.com
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[Freesurfer] Which files do I need to mri_deface to anonymized a subject?

[Tim Schäfer]

External Email - Use Caution

Dear FS experts,

I want to upload neuroimaging data pre-processed by FreeSurfer's recon-all 
pipeline to a consortium server, and they require all data to be anonymized.

I found mri_deface [1] and wondered which files I would have to apply it to, 
and whether there are any other things I should be aware of.

So far, my plan is to use mri_deface to replace, for each subject, the 
following files in mri/:

* orig.mgz
* orig_nu.mgz
* T1.mgz
* rawavg.mgz

It would also be an option to upload only a subset of all the files produced by 
FreeSurfer, but I do not know which files to exclude and include, so if you 
have suggestions for this, it would also be very welcome. I will also look at 
some public datasets to see how they did it.

[1] https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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