[Freesurfer] mri_surf2surf results in large area with zero values

[Frauke Beyer]

Dear experts,

I have an issue with mri_surf2surf (i suspect). I have resampled
T1-values to the fsaverage template using mri_vol2surf and a --projfrac
of 0.25 with the default white matter surface. Then I loaded these
values in Matlab using MRIread, inverted them and saved them back into a
file using MRIwrite. In Matlab, there were no suspicious data points
(e.g. the range of R1 values excluded 0, minimum was 0.25). This was
also true when loading the R1values as an overlay in Freeview. Now I
wanted to smooth this image using mri_surf2surf with target and source
subject being identical to fsaverage and fwhm of 10mm. 

exact command was: mri_surf2surf --srcsubject fsaverage --trgsubject
fsaverage --hemi lh --sval
/nobackup/aventurin4/data_fbeyer/flica_myelin/flica_inputs/round2/t1maps/lh.t1map.proj0.25.fsavg_inv.mgh
--tval
/nobackup/aventurin4/data_fbeyer/flica_myelin/flica_inputs/round2/t1maps/lh.t1map.proj0.25.fsavg_inv_smoothed10mm.mgh
--fwhm-trg 10

But now, while it worked fine for some subjects in the 4D file for
others large areas of 0 emerged in the smoothed file. Those were mostly
found in inferior temporal/orbitofrontal lobe.

Does anybody have an idea what could cause this strange behaviour?

Thank you so much for your help,

Frauke


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Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

Thanks for the additional information, Anastasia.
I will look for those files.

What I am after is a list of xyz coordinates for each of the 18 tracts. I see 
masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I'm 
looking for. They have names like
_AS_..nii.gz
where str1 = bbr or flt and
str2 = roi1 or roi2
I can extract the lists of coordinates from them with mri_cor2label although I 
haven't checked these lists to make sure they are actually what we need.

I haven't found documentation on these files nor do I see them in the tutorial 
directories for the three elmo's.
I have bedbpostx running but do not expect it to produce them. I suppose it is 
trac-all -path which will do so but I thought I would ask my questions anyway.


  1.  Are these the files that I'm looking for?
  2.  If so, where can I find documentation?
  3.  What is the shortest path to generate them?

It strikes me that maybe it is the streamlines which best define the tracts 
rather than these volumetric masks. I still do not thoroughly understand where 
in the processing sequence the streamlines get assigned to specific tracts. ??

Thanks - Don


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 9:23 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Hi Don - If the output files described here show up in the end, all is well:



https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX



Best,

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 4:52:57 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Great - thanks.

It's running.

I see several warnings which I presume can be ignored:

hostname: Name or service not known



Best - Don





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 4:24 PM
To: freesurfer 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - See: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html



Best,

a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] newbie trac-all -bedp question



I am getting the following output with error on this command:



trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23



INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0

WARN: Running bedbostx locally - this might take a while

WARN: It is recommended to run this step on a cluster

bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri

/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: 131: 
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected



I apologize for not finding the answer in the list archive.

It's probably there.



I'm running under ubuntu 14.04.



bedpostx_mgh is a shell script which calls for /bin/sh.

On my machine, that is a symlink to /bin/bash

If I change it to be explicitly /bin/bash, it runs a bit further.

Here is the full output:



INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0

WARN: Running bedbostx locally - this might take a while

WARN: It is recommended to run this step on a cluster

bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri

subjectdir is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri

Making bedpostx directory structure

Queuing preprocessing stages

/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")

Queuing parallel processing stage

0 slices processed

/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")

Queuing post processing stage

/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriege

[Freesurfer] DICOM input to recon-all

[Karin Westin]

Hi everybody!

I'm very new to freesurfer and I'm trying to perform a reconstruction using
recon-all. My problem is I don't see how I can access a single file to
input to recon-all. I've run dcmunpack -src 
but the only output I get  is

Found 2 unique series: 4 401
Subject (name of subject)
Date (date of examination)
Time 11
Institution (place of acqusition)
4 3DBRAVO+Gd 3.344 8.724 13 0.9375 ROW 195.312 ./EE975AF8
401 refSAGBRAVO+gd 3.344 8.724 13 0.46875 unknown 195.312 ./EEF3A407


How do I access the actual files of these series?

Best,
Karin
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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 Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] newbie trac-all -bedp question

[Yendiki, Anastasia]

Hi Don - No, dlabel/ contains files that are used in the pathway 
reconstruction, but the output of the reconstruction is saved in dpath/. 
There's a subdirectory in there for each pathway, and it contains a volume 
called path.pd.nii.gz. This is the probability that each voxel belongs to this 
pathway, in the subject's native diffusion space. As TRACULA is a probabilistic 
method, you get a probability associated with each voxel, rather than a set of 
voxel coordinates.


More info (potentially too much info) on TRACULA outputs:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles


Best,

a.y



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Krieger, Donald N. 

Sent: Wednesday, April 11, 2018 8:06:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Thanks for the additional information, Anastasia.

I will look for those files.



What I am after is a list of xyz coordinates for each of the 18 tracts. I see 
masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I’m 
looking for. They have names like

_AS_..nii.gz

where str1 = bbr or flt and

str2 = roi1 or roi2

I can extract the lists of coordinates from them with mri_cor2label although I 
haven’t checked these lists to make sure they are actually what we need.



I haven’t found documentation on these files nor do I see them in the tutorial 
directories for the three elmo’s.

I have bedbpostx running but do not expect it to produce them. I suppose it is 
trac-all -path which will do so but I thought I would ask my questions anyway.



  1.  Are these the files that I’m looking for?
  2.  If so, where can I find documentation?
  3.  What is the shortest path to generate them?



It strikes me that maybe it is the streamlines which best define the tracts 
rather than these volumetric masks. I still do not thoroughly understand where 
in the processing sequence the streamlines get assigned to specific tracts. ??



Thanks - Don





From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 9:23 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - If the output files described here show up in the end, all is well:



https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX



Best,

a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 4:52:57 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Great – thanks.

It’s running.

I see several warnings which I presume can be ignored:

hostname: Name or service not known



Best - Don





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 4:24 PM
To: freesurfer 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - See: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html



Best,

a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] newbie trac-all -bedp question



I am getting the following output with error on this command:



trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23



INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0

WARN: Running bedbostx locally - this might take a while

WARN: It is recommended to run this step on a cluster

bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri

/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: 131: 
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected



I apologize for not finding the answer in the list archive.

It's probably there.



I'm running under ubuntu 14.04.



bedpostx_mgh is a shell script which calls for /bin/sh.

On my machine, that is a symlink to /bin/bash

If I change it to be explicitly /bin/bash, it runs a bit further.

Here is the full output:



INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

Actual FREESURFER_

Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

Great - thanks - that's what I need.
I can use the probability for each pixel as a weight for the neuroelectric 
current count for that pixel to quantify the activity for the tract.

I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 
0.0 - 1.0

Thanks again - best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Hi Don - No, dlabel/ contains files that are used in the pathway 
reconstruction, but the output of the reconstruction is saved in dpath/. 
There's a subdirectory in there for each pathway, and it contains a volume 
called path.pd.nii.gz. This is the probability that each voxel belongs to this 
pathway, in the subject's native diffusion space. As TRACULA is a probabilistic 
method, you get a probability associated with each voxel, rather than a set of 
voxel coordinates.


More info (potentially too much info) on TRACULA outputs:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles



Best,

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 8:06:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Thanks for the additional information, Anastasia.

I will look for those files.



What I am after is a list of xyz coordinates for each of the 18 tracts. I see 
masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I'm 
looking for. They have names like

_AS_..nii.gz

where str1 = bbr or flt and

str2 = roi1 or roi2

I can extract the lists of coordinates from them with mri_cor2label although I 
haven't checked these lists to make sure they are actually what we need.



I haven't found documentation on these files nor do I see them in the tutorial 
directories for the three elmo's.

I have bedbpostx running but do not expect it to produce them. I suppose it is 
trac-all -path which will do so but I thought I would ask my questions anyway.



  1.  Are these the files that I'm looking for?
  2.  If so, where can I find documentation?
  3.  What is the shortest path to generate them?



It strikes me that maybe it is the streamlines which best define the tracts 
rather than these volumetric masks. I still do not thoroughly understand where 
in the processing sequence the streamlines get assigned to specific tracts. ??



Thanks - Don





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 9:23 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - If the output files described here show up in the end, all is well:



https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX



Best,

a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 4:52:57 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Great - thanks.

It's running.

I see several warnings which I presume can be ignored:

hostname: Name or service not known



Best - Don





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 4:24 PM
To: freesurfer 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - See: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html



Best,

a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] newbie trac-all -bedp question



I am getting the following output with error on this command:



trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23



INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0

WARN: Running bedbostx locally - this might take a while

WARN: It is recommended to run this s

Re: [Freesurfer] newbie trac-all -bedp question

[Yendiki, Anastasia]

The volume would have to be normalized to a total sum of 1 for the voxel values 
to represent an actual distribution.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Krieger, Donald N. 

Sent: Wednesday, April 11, 2018 10:43:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Great – thanks – that’s what I need.

I can use the probability for each pixel as a weight for the neuroelectric 
current count for that pixel to quantify the activity for the tract.



I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 
0.0 – 1.0



Thanks again – best – Don



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - No, dlabel/ contains files that are used in the pathway 
reconstruction, but the output of the reconstruction is saved in dpath/. 
There's a subdirectory in there for each pathway, and it contains a volume 
called path.pd.nii.gz. This is the probability that each voxel belongs to this 
pathway, in the subject's native diffusion space. As TRACULA is a probabilistic 
method, you get a probability associated with each voxel, rather than a set of 
voxel coordinates.



More info (potentially too much info) on TRACULA outputs:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles



Best,

a.y





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 8:06:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Thanks for the additional information, Anastasia.

I will look for those files.



What I am after is a list of xyz coordinates for each of the 18 tracts. I see 
masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I’m 
looking for. They have names like

_AS_..nii.gz

where str1 = bbr or flt and

str2 = roi1 or roi2

I can extract the lists of coordinates from them with mri_cor2label although I 
haven’t checked these lists to make sure they are actually what we need.



I haven’t found documentation on these files nor do I see them in the tutorial 
directories for the three elmo’s.

I have bedbpostx running but do not expect it to produce them. I suppose it is 
trac-all -path which will do so but I thought I would ask my questions anyway.



  1.  Are these the files that I’m looking for?
  2.  If so, where can I find documentation?
  3.  What is the shortest path to generate them?



It strikes me that maybe it is the streamlines which best define the tracts 
rather than these volumetric masks. I still do not thoroughly understand where 
in the processing sequence the streamlines get assigned to specific tracts. ??



Thanks - Don





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 9:23 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - If the output files described here show up in the end, all is well:



https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX



Best,

a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 4:52:57 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Great – thanks.

It’s running.

I see several warnings which I presume can be ignored:

hostname: Name or service not known



Best - Don





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 4:24 PM
To: freesurfer 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - See: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html



Best,

a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] newbie trac-all -bedp question



I am getting the following output with error on this command:



trac-all -bedp -s HDFT1001 -i ep2d_diff

[Freesurfer] Canonical HRF shape generated by FSFAST

[Sarah Cole]

Hi Doug,

At the end of my FSFAST analysis, I would like to plot the Canonical HRF
shape generated by FSFAST for my events. I have found this thread:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-July/031902.html

but I am not sure if I understand this line:
"plot(X.runflac(1).flac.ev(2).tirf,
X.runflac(1).flac.ev(2).Xirf)"


Could you please clarify how to plot the Canonical HRF that was generated
by FSFAST?

Thank you,

Sarah
___
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 Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Canonical HRF shape generated by FSFAST

[Sarah Cole]

Just one clarification, this is for first level analysis (individual
subjects).

Thanks

On Wed, Apr 11, 2018 at 9:54 AM, Sarah Cole  wrote:

> Hi Doug,
>
> At the end of my FSFAST analysis, I would like to plot the Canonical HRF
> shape generated by FSFAST for my events. I have found this thread:
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-
> July/031902.html
>
> but I am not sure if I understand this line: "
> plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf)"
>
>
> Could you please clarify how to plot the Canonical HRF that was generated
> by FSFAST?
>
> Thank you,
>
> Sarah
>
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Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

I was thinking that for a single voxel, the total of the values assigned to the 
voxel over all the tracts would have a maximum of 255 and that 255 would 
correspond to a probability of 1.0.
I can see is likely wrong but for sure it's too simple since each voxel could 
contain crossing fibers from several tracts; hence the total probability 
assigned to the voxel over all the tracts might be greater than 1.0.
??

Surely there is some normalization applied to the values assigned to the voxels 
so they fall between 0 and 255.
Does that normalization vary from one subject to the next and perhaps even from 
one tract to the next?
And how is the normalization mapped to probability?

Thanks - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:48 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question


The volume would have to be normalized to a total sum of 1 for the voxel values 
to represent an actual distribution.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 10:43:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Great - thanks - that's what I need.

I can use the probability for each pixel as a weight for the neuroelectric 
current count for that pixel to quantify the activity for the tract.



I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 
0.0 - 1.0



Thanks again - best - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - No, dlabel/ contains files that are used in the pathway 
reconstruction, but the output of the reconstruction is saved in dpath/. 
There's a subdirectory in there for each pathway, and it contains a volume 
called path.pd.nii.gz. This is the probability that each voxel belongs to this 
pathway, in the subject's native diffusion space. As TRACULA is a probabilistic 
method, you get a probability associated with each voxel, rather than a set of 
voxel coordinates.



More info (potentially too much info) on TRACULA outputs:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles



Best,

a.y





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 8:06:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Thanks for the additional information, Anastasia.

I will look for those files.



What I am after is a list of xyz coordinates for each of the 18 tracts. I see 
masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I'm 
looking for. They have names like

_AS_..nii.gz

where str1 = bbr or flt and

str2 = roi1 or roi2

I can extract the lists of coordinates from them with mri_cor2label although I 
haven't checked these lists to make sure they are actually what we need.



I haven't found documentation on these files nor do I see them in the tutorial 
directories for the three elmo's.

I have bedbpostx running but do not expect it to produce them. I suppose it is 
trac-all -path which will do so but I thought I would ask my questions anyway.



  1.  Are these the files that I'm looking for?
  2.  If so, where can I find documentation?
  3.  What is the shortest path to generate them?



It strikes me that maybe it is the streamlines which best define the tracts 
rather than these volumetric masks. I still do not thoroughly understand where 
in the processing sequence the streamlines get assigned to specific tracts. ??



Thanks - Don





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 9:23 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - If the output files described here show up in the end, all is well:



https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX



Best,

a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@up

Re: [Freesurfer] DICOM input to recon-all

[Boyd, Emma]

Hi Karin,


This tutorial will explain how to find your dicom input file: 
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice


Best,

Emma


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Karin Westin 

Sent: Wednesday, April 11, 2018 9:29:37 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] DICOM input to recon-all

Hi everybody!

I'm very new to freesurfer and I'm trying to perform a reconstruction using 
recon-all. My problem is I don't see how I can access a single file to input to 
recon-all. I've run dcmunpack -src 
but the only output I get  is

Found 2 unique series: 4 401
Subject (name of subject)
Date (date of examination)
Time 11
Institution (place of acqusition)
4 3DBRAVO+Gd 3.344 8.724 13 0.9375 ROW 195.312 ./EE975AF8
401 refSAGBRAVO+gd 3.344 8.724 13 0.46875 unknown 195.312 ./EEF3A407


How do I access the actual files of these series?

Best,
Karin
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[Freesurfer] -make all error

[Carissa Nicole Weis]

Hello,

I am running recon-all for several subjects’ 7T data using Freesurfer version 
6.0 and currently trying to ensure appropriate skull stripping and pial/wm 
surface generation. For a few participants that needed some control points 
added and for which I reran them through the –autorecon2-cp option, I was 
unable to open the pial surfaces for review. I’ve seen on some of the other 
posts that you guys recommend running “recon-all –make all” to rebuild the 
files. I’ve tried to run the -make all command but have been running into the 
same error in the “Jacobian white lh” step:

#@# Jacobian white lh Wed Apr 4 12:07:37 CDT 2018
/bigraid-03/LS/Data/7T_fall2017/6315/6315_fs/scripts

mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg 
../surf/lh.jacobian_white

reading surface from ../surf/lh.white.preaparc…
mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn’t match 
../surf/lh.white.preaparc

No such file or directory
mrisReadTriangleFile failed.

No such file or directory
mris_jacobian: could not read target surface ../surf/lh.sphere.reg
No such file or directory

recon-all –s 6315_fs exited with ERRORS at Wed Apr 4 12:07:40 CDT 2018


All of the output in the log file up until this point appears to have finished 
without error. I can now open the surfaces for review, but am wondering what is 
affected by –make all not finishing completely.


Carissa N. Weis, B.S.
Graduate Student
Affective Neuroscience Laboratory
University of Wisconsin-Milwaukee
cnw...@uwm.edu

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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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] newbie trac-all -bedp question

[Yendiki, Anastasia]

This wouldn't work because these 18 tracts do not include all tracts in the 
brain.

On Apr 11, 2018 11:19 AM, "Krieger, Donald N."  wrote:
I was thinking that for a single voxel, the total of the values assigned to the 
voxel over all the tracts would have a maximum of 255 and that 255 would 
correspond to a probability of 1.0.
I can see is likely wrong but for sure it’s too simple since each voxel could 
contain crossing fibers from several tracts; hence the total probability 
assigned to the voxel over all the tracts might be greater than 1.0.
??

Surely there is some normalization applied to the values assigned to the voxels 
so they fall between 0 and 255.
Does that normalization vary from one subject to the next and perhaps even from 
one tract to the next?
And how is the normalization mapped to probability?

Thanks - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:48 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question


The volume would have to be normalized to a total sum of 1 for the voxel values 
to represent an actual distribution.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 10:43:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Great – thanks – that’s what I need.

I can use the probability for each pixel as a weight for the neuroelectric 
current count for that pixel to quantify the activity for the tract.



I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 
0.0 – 1.0



Thanks again – best – Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - No, dlabel/ contains files that are used in the pathway 
reconstruction, but the output of the reconstruction is saved in dpath/. 
There's a subdirectory in there for each pathway, and it contains a volume 
called path.pd.nii.gz. This is the probability that each voxel belongs to this 
pathway, in the subject's native diffusion space. As TRACULA is a probabilistic 
method, you get a probability associated with each voxel, rather than a set of 
voxel coordinates.



More info (potentially too much info) on TRACULA outputs:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles



Best,

a.y





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 8:06:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Thanks for the additional information, Anastasia.

I will look for those files.



What I am after is a list of xyz coordinates for each of the 18 tracts. I see 
masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I’m 
looking for. They have names like

_AS_..nii.gz

where str1 = bbr or flt and

str2 = roi1 or roi2

I can extract the lists of coordinates from them with mri_cor2label although I 
haven’t checked these lists to make sure they are actually what we need.



I haven’t found documentation on these files nor do I see them in the tutorial 
directories for the three elmo’s.

I have bedbpostx running but do not expect it to produce them. I suppose it is 
trac-all -path which will do so but I thought I would ask my questions anyway.



  1.  Are these the files that I’m looking for?
  2.  If so, where can I find documentation?
  3.  What is the shortest path to generate them?



It strikes me that maybe it is the streamlines which best define the tracts 
rather than these volumetric masks. I still do not thoroughly understand where 
in the processing sequence the streamlines get assigned to specific tracts. ??



Thanks - Don





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 9:23 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - If the output files described here show up in the end, all is well:



https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX



Best,

a.y



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

Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

Thanks for getting back, Anastasia.

I'm not suggesting that it should be done differently than it is.

I'm just trying to understand how the voxel values map to probability. That's 
why I described the wrong headed way I was thinking about it ... so you could 
tell me where I'm going wrong.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 11:54 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question

This wouldn't work because these 18 tracts do not include all tracts in the 
brain.

On Apr 11, 2018 11:19 AM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:
I was thinking that for a single voxel, the total of the values assigned to the 
voxel over all the tracts would have a maximum of 255 and that 255 would 
correspond to a probability of 1.0.
I can see is likely wrong but for sure it's too simple since each voxel could 
contain crossing fibers from several tracts; hence the total probability 
assigned to the voxel over all the tracts might be greater than 1.0.
??

Surely there is some normalization applied to the values assigned to the voxels 
so they fall between 0 and 255.
Does that normalization vary from one subject to the next and perhaps even from 
one tract to the next?
And how is the normalization mapped to probability?

Thanks - Don

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:48 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question


The volume would have to be normalized to a total sum of 1 for the voxel values 
to represent an actual distribution.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 10:43:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Great - thanks - that's what I need.

I can use the probability for each pixel as a weight for the neuroelectric 
current count for that pixel to quantify the activity for the tract.



I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 
0.0 - 1.0



Thanks again - best - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - No, dlabel/ contains files that are used in the pathway 
reconstruction, but the output of the reconstruction is saved in dpath/. 
There's a subdirectory in there for each pathway, and it contains a volume 
called path.pd.nii.gz. This is the probability that each voxel belongs to this 
pathway, in the subject's native diffusion space. As TRACULA is a probabilistic 
method, you get a probability associated with each voxel, rather than a set of 
voxel coordinates.



More info (potentially too much info) on TRACULA outputs:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles



Best,

a.y





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 8:06:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Thanks for the additional information, Anastasia.

I will look for those files.



What I am after is a list of xyz coordinates for each of the 18 tracts. I see 
masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I'm 
looking for. They have names like

_AS_..nii.gz

where str1 = bbr or flt and

str2 = roi1 or roi2

I can extract the lists of coordinates from them with mri_cor2label although I 
haven't checked these lists to make sure they are actually what we need.



I haven't found documentation on these files nor do I see them in the tutorial 
directories for the three elmo's.

I have bedbpostx running but do not expect it to produce them. I suppose it is 
trac-all -path which will do so but I thought I would ask my questions anyway.



  1.  Are these the files that I'm looking for?
  2.  If so, where can I find documentation?
  3.  What is the shortest path to generate them?



It strikes me that maybe it is the streamlines which best define the tracts 
rather than these volumetric masks. I still do not thoroughly understand where 
in the processing seq

Re: [Freesurfer] Surface label to volume and then back to surface

[David Beeler]

Hi Doug, thanks for the response!

So it looks like my initial transform from surface label to anatomical volume 
wasn't working because my template.nii.gz and brainmask were in a different 
space than the functional data I was processing. This happened because I was 
taking the raw f.nii.gz, doing some transformations first, and saving it to a 
file called f_reg.nii.gz. I was then trying to run preproc-sess using the -i 
flag to specify this f_reg.nii.gz, but when preproc runs mktemplate-sess it 
still uses f.nii.gz to make the template, regardless of what the -i or -mcin 
flags say. I just added a line in the if($DoTemplate) section of preproc-sess 
to have the option of adding a -funcstem and it worked fine. I have now updated 
my preprocessing to run all the commands individually instead of using 
preproc-sess at all, and I'm probably going to send another message to this 
list later making sure I'm doing that correctly.

Additionally, Re: "I think you could do it with a single call to
mri_label2vol using --regheader and specifying the func template."

This works great! Thanks for the shortcut. I got the surface label direct to 
functional volume transform working with:

mri_vol2vol --regheader --mov $OUTPUTDIR/rh.MT.volume.anat.nii.gz --targ 
$MEANFUNCDIR/meanfunc.nii.gz --o $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz 
--nearest

But I'm still not entirely sure exactly what information is contained in 
regheader (or where I can view this information). The reason I have been using 
regheader instead of register.dof6.lta is that my functional data is aligned to 
the anatomical prior to running preprocessing, and my understanding was that 
using regheader would just downsample (similar to mri_convert) and I wouldn't 
need to specify a registration file. Is this a flawed understanding of 
regheader?

So transforming to functional space seems to be okay now, but transforming back 
to the surface is still not perfect.

I tried
mri_vol2surf --mov $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz --regheader 
$SUBJID --projfrac 0.5 --interp nearest --hemi rh --o 
$OUTPUTDIR/regheadersurface.nii.gz

and also

bbregister --s $SUBJID --reg $OUTPUTDIR/testreg.lta --mov 
$MEANFUNCDIR/meanfunc.nii.gz --init-fsl --bold

mri_vol2surf --mov $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz --reg 
$OUTPUTDIR/testreg.lta --projfrac 0.5 --interp nearest --hemi rh --o 
$OUTPUTDIR/testregsurface.nii.gz

Which both give essentially the same result:
Original Label: http://web.mit.edu/dsbeeler/www/images/MTlabel.png
Back to Surface Overlay: http://web.mit.edu/dsbeeler/www/images/MTpatchy.png
This is actually much better than it was, but is there a way to get rid of the 
patchiness?


Again, thanks for all the useful info!

David

__


Hi David, I've tried to answer your questions below.

doug


On 03/30/2018 01:48 PM, David Beeler wrote:
> Hi all,
> Sorry in advance, this is a bit of an annoying one!
>
> I am trying to use freesurfer's automatically generated MT label as a
> parcel to constrain activity measured during a functional MT
> localizer. I am currently doing my analysis in the volume and I'd like
> to transform the MT surface label into the subject's volume functional
> space (i.e. the same space as the sig.nii.gz for a particular
> contrast), take the voxels in sig.nii.gz that are within the MT label,
> and project them back onto the surface (preferably to be viewed as an
> overlay with freeview). I will eventually run the analysis on the
> surface as well (making this much less roundabout, but I also use
> volume parcels so understanding how to correctly go between the volume
> and surface is important to me).
>
> In my pipeline I start off by running preproc-sess, then I register
> and transform my preprocessed functional data (fmcpr.nii.gz) to the
> subject's anatomical (without upsampling). After doing mkanalysis and
> mkcontrast, I run selxavg on this volume. So the functional data is
> aligned with the anatomical, but still has low res dimensions.
>
> If it's not too much to ask, would it be possible to provide the
> specific commands to do all these transformations properly? I'll
> provide some of the commands I've tried below so you can see where I'm
> going wrong:
>
> First I want to transform the MT label to the functional volume. I've
> tried:
>
> mri_label2vol --subject $SUBJID --label
> $SUBJECTS_DIR/$SUBJID/label/rh.MT.label --o
> $OUTPUTDIR/rh.MT.volume.anat.nii.gz --temp
> $SUBJECTS_DIR/$SUBJID/mri/orig.mgz --identity --fill-ribbon --hemi rh
>
> ...which I would expect to put the label in high resolution anatomical
> volume space (orig.mgz), but it doesn't fill the graymatter ribbon
> nicely at all.
I  would have expected this to work. Can you send a pic? I just ran it
myself, and it seemed to do ok.
>
> I then use mri_vol2vol to transform to functional/sig.nii.gz space (I
> could also just downsample with mri_convert since I've already aligned
> my sig.nii.gz to my anatomical,

Re: [Freesurfer] newbie trac-all -bedp question

[Yendiki, Anastasia]

The probability maps are independent for each tract. Each one just tells you 
how likely this one tract is to go through any given voxel, but it tells you 
nothing about other tracts. Does this make sense?

On Apr 11, 2018 12:00 PM, "Krieger, Donald N."  wrote:
Thanks for getting back, Anastasia.

I’m not suggesting that it should be done differently than it is.

I’m just trying to understand how the voxel values map to probability. That’s 
why I described the wrong headed way I was thinking about it … so you could 
tell me where I’m going wrong.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 11:54 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question

This wouldn't work because these 18 tracts do not include all tracts in the 
brain.

On Apr 11, 2018 11:19 AM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:
I was thinking that for a single voxel, the total of the values assigned to the 
voxel over all the tracts would have a maximum of 255 and that 255 would 
correspond to a probability of 1.0.
I can see is likely wrong but for sure it’s too simple since each voxel could 
contain crossing fibers from several tracts; hence the total probability 
assigned to the voxel over all the tracts might be greater than 1.0.
??

Surely there is some normalization applied to the values assigned to the voxels 
so they fall between 0 and 255.
Does that normalization vary from one subject to the next and perhaps even from 
one tract to the next?
And how is the normalization mapped to probability?

Thanks - Don

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:48 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question


The volume would have to be normalized to a total sum of 1 for the voxel values 
to represent an actual distribution.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 10:43:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Great – thanks – that’s what I need.

I can use the probability for each pixel as a weight for the neuroelectric 
current count for that pixel to quantify the activity for the tract.



I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 
0.0 – 1.0



Thanks again – best – Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - No, dlabel/ contains files that are used in the pathway 
reconstruction, but the output of the reconstruction is saved in dpath/. 
There's a subdirectory in there for each pathway, and it contains a volume 
called path.pd.nii.gz. This is the probability that each voxel belongs to this 
pathway, in the subject's native diffusion space. As TRACULA is a probabilistic 
method, you get a probability associated with each voxel, rather than a set of 
voxel coordinates.



More info (potentially too much info) on TRACULA outputs:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles



Best,

a.y





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 8:06:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Thanks for the additional information, Anastasia.

I will look for those files.



What I am after is a list of xyz coordinates for each of the 18 tracts. I see 
masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I’m 
looking for. They have names like

_AS_..nii.gz

where str1 = bbr or flt and

str2 = roi1 or roi2

I can extract the lists of coordinates from them with mri_cor2label although I 
haven’t checked these lists to make sure they are actually what we need.



I haven’t found documentation on these files nor do I see them in the tutorial 
directories for the three elmo’s.

I have bedbpostx running but do not expect it to produce them. I suppose it is 
trac-all -path which will do so but I thought I would ask my questions anyway.



  1.  Are these the files that I’m looking for?
  2.  If so, whe

Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

Thanks, Anastasia.

I'll think about this and get back if I can't figure it out.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 12:46 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question

The probability maps are independent for each tract. Each one just tells you 
how likely this one tract is to go through any given voxel, but it tells you 
nothing about other tracts. Does this make sense?

On Apr 11, 2018 12:00 PM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:
Thanks for getting back, Anastasia.

I'm not suggesting that it should be done differently than it is.

I'm just trying to understand how the voxel values map to probability. That's 
why I described the wrong headed way I was thinking about it ... so you could 
tell me where I'm going wrong.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 11:54 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question

This wouldn't work because these 18 tracts do not include all tracts in the 
brain.

On Apr 11, 2018 11:19 AM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:
I was thinking that for a single voxel, the total of the values assigned to the 
voxel over all the tracts would have a maximum of 255 and that 255 would 
correspond to a probability of 1.0.
I can see is likely wrong but for sure it's too simple since each voxel could 
contain crossing fibers from several tracts; hence the total probability 
assigned to the voxel over all the tracts might be greater than 1.0.
??

Surely there is some normalization applied to the values assigned to the voxels 
so they fall between 0 and 255.
Does that normalization vary from one subject to the next and perhaps even from 
one tract to the next?
And how is the normalization mapped to probability?

Thanks - Don

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:48 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question


The volume would have to be normalized to a total sum of 1 for the voxel values 
to represent an actual distribution.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 10:43:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Great - thanks - that's what I need.

I can use the probability for each pixel as a weight for the neuroelectric 
current count for that pixel to quantify the activity for the tract.



I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 
0.0 - 1.0



Thanks again - best - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - No, dlabel/ contains files that are used in the pathway 
reconstruction, but the output of the reconstruction is saved in dpath/. 
There's a subdirectory in there for each pathway, and it contains a volume 
called path.pd.nii.gz. This is the probability that each voxel belongs to this 
pathway, in the subject's native diffusion space. As TRACULA is a probabilistic 
method, you get a probability associated with each voxel, rather than a set of 
voxel coordinates.



More info (potentially too much info) on TRACULA outputs:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles



Best,

a.y





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 8:06:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Thanks for the additional information, Anastasia.

I will look for those files.



What I am after is a list of xyz coordinates for each of the 18 tracts. I see 
masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I'm 
looking for. They have names like

_AS_..nii.gz

where str1 = bbr or flt and

str2 = roi1 or roi2

I can extract the lists of coord

[Freesurfer] Subparcellation Problem

[Connor Garris]

Hello,

I'm running into a problem when subparcellating my regions of interest
where after subparcellating there are some sublcusters that are labelled
identically by freesurfer even though they are distinct subclusters. More
specifically, I ran one iteration of mris_divide_parcellation passing it
400mm subclustering size and then ran a second iteration passing it 200mm
(I did this because I want subclusters that are square-ish in shape as
opposed to long bands). On the first iteration there is no problem, the
second iteration however produces the problem I described where distinct
subclusters are considered to be the same by freesurfer. I have attached a
picture of exactly the problem since this explanation is a little
convoluted.
Any help would be greatly appreciated.

Thank you,
-Connor
___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Subparcellation Problem

[Connor Garris]

Also, I'm using Freesurfer 5.3

On Wed, Apr 11, 2018 at 1:50 PM, Connor Garris  wrote:

> Hello,
>
> I'm running into a problem when subparcellating my regions of interest
> where after subparcellating there are some sublcusters that are labelled
> identically by freesurfer even though they are distinct subclusters. More
> specifically, I ran one iteration of mris_divide_parcellation passing it
> 400mm subclustering size and then ran a second iteration passing it 200mm
> (I did this because I want subclusters that are square-ish in shape as
> opposed to long bands). On the first iteration there is no problem, the
> second iteration however produces the problem I described where distinct
> subclusters are considered to be the same by freesurfer. I have attached a
> picture of exactly the problem since this explanation is a little
> convoluted.
> Any help would be greatly appreciated.
>
> Thank you,
> -Connor
>
___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

Hi, Anastasia.

Yes, that makes it simpler.

I can see that each of the path.pd.nii.gz has a voxel entry for the same number 
of voxels. I'm looking at elmo.2008 for which that number is 1,294,336 which I 
presume is the volume of this person's brain as delivered by freesurfer.

Most of those voxels are set to 0.
I presume that means that the probability that the tract passes through that 
voxel is very near 0.0 .
For the forceps major, 7342 voxels have non-zero entries ranging from 1 to 255. 
Most of them are pretty low numbers so the average value for the 7342 non-zero 
voxels is about 16.
For a voxel that has an entry of 1, I presume the probability that the tract 
passes  through that voxel is near zero. For a voxel that has an entry of 127,  
is the probability that the tract passes through it 0.5 ?
And if the entry is 255, is the probability 1.0?

It's that mapping of voxel value to probability that I'm trying to get at. Or 
am I misunderstanding what the voxel value means?

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 12:46 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question

The probability maps are independent for each tract. Each one just tells you 
how likely this one tract is to go through any given voxel, but it tells you 
nothing about other tracts. Does this make sense?

On Apr 11, 2018 12:00 PM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:
Thanks for getting back, Anastasia.

I'm not suggesting that it should be done differently than it is.

I'm just trying to understand how the voxel values map to probability. That's 
why I described the wrong headed way I was thinking about it ... so you could 
tell me where I'm going wrong.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 11:54 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question

This wouldn't work because these 18 tracts do not include all tracts in the 
brain.

On Apr 11, 2018 11:19 AM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:
I was thinking that for a single voxel, the total of the values assigned to the 
voxel over all the tracts would have a maximum of 255 and that 255 would 
correspond to a probability of 1.0.
I can see is likely wrong but for sure it's too simple since each voxel could 
contain crossing fibers from several tracts; hence the total probability 
assigned to the voxel over all the tracts might be greater than 1.0.
??

Surely there is some normalization applied to the values assigned to the voxels 
so they fall between 0 and 255.
Does that normalization vary from one subject to the next and perhaps even from 
one tract to the next?
And how is the normalization mapped to probability?

Thanks - Don

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:48 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question


The volume would have to be normalized to a total sum of 1 for the voxel values 
to represent an actual distribution.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 10:43:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Great - thanks - that's what I need.

I can use the probability for each pixel as a weight for the neuroelectric 
current count for that pixel to quantify the activity for the tract.



I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 
0.0 - 1.0



Thanks again - best - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - No, dlabel/ contains files that are used in the pathway 
reconstruction, but the output of the reconstruction is saved in dpath/. 
There's a subdirectory in there for each pathway, and it contains a volume 
called path.pd.nii.gz. This is the probability that each voxel belongs to this 
pathway, in the subject's native diffusion space. As TRACULA is a probabilistic 
method, you get a probability associated with each voxel, rather than a set of 
vox

Re: [Freesurfer] newbie trac-all -bedp question

[Yendiki, Anastasia]

Hi Don - You would normalize these numbers by their sum, not by their maximum 
(i.e., not by 255).


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Krieger, Donald N. 

Sent: Wednesday, April 11, 2018 1:51:43 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Hi, Anastasia.



Yes, that makes it simpler.



I can see that each of the path.pd.nii.gz has a voxel entry for the same number 
of voxels. I’m looking at elmo.2008 for which that number is 1,294,336 which I 
presume is the volume of this person’s brain as delivered by freesurfer.



Most of those voxels are set to 0.

I presume that means that the probability that the tract passes through that 
voxel is very near 0.0 .

For the forceps major, 7342 voxels have non-zero entries ranging from 1 to 255. 
Most of them are pretty low numbers so the average value for the 7342 non-zero 
voxels is about 16.

For a voxel that has an entry of 1, I presume the probability that the tract 
passes  through that voxel is near zero. For a voxel that has an entry of 127,  
is the probability that the tract passes through it 0.5 ?

And if the entry is 255, is the probability 1.0?



It’s that mapping of voxel value to probability that I’m trying to get at. Or 
am I misunderstanding what the voxel value means?



Best - Don



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 12:46 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question



The probability maps are independent for each tract. Each one just tells you 
how likely this one tract is to go through any given voxel, but it tells you 
nothing about other tracts. Does this make sense?



On Apr 11, 2018 12:00 PM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:

Thanks for getting back, Anastasia.



I’m not suggesting that it should be done differently than it is.



I’m just trying to understand how the voxel values map to probability. That’s 
why I described the wrong headed way I was thinking about it … so you could 
tell me where I’m going wrong.







From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 11:54 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



This wouldn't work because these 18 tracts do not include all tracts in the 
brain.



On Apr 11, 2018 11:19 AM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:

I was thinking that for a single voxel, the total of the values assigned to the 
voxel over all the tracts would have a maximum of 255 and that 255 would 
correspond to a probability of 1.0.

I can see is likely wrong but for sure it’s too simple since each voxel could 
contain crossing fibers from several tracts; hence the total probability 
assigned to the voxel over all the tracts might be greater than 1.0.

??



Surely there is some normalization applied to the values assigned to the voxels 
so they fall between 0 and 255.

Does that normalization vary from one subject to the next and perhaps even from 
one tract to the next?

And how is the normalization mapped to probability?



Thanks - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:48 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



The volume would have to be normalized to a total sum of 1 for the voxel values 
to represent an actual distribution.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 10:43:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Great – thanks – that’s what I need.

I can use the probability for each pixel as a weight for the neuroelectric 
current count for that pixel to quantify the activity for the tract.



I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 
0.0 – 1.0



Thanks again – best – Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - No, dlabel/ contains files that are used in the pathway 

Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

Ok - I have that sum.
For the forceps major, it's 111,685.
If I normalize by that, i.e. divide each voxel value by that, then I certainly 
get something that looks like a probability distribution since the sum of the 
normalized voxel entries over the entire volume is 1.0 as you had said in an 
earlier post.
But the maximum probability for any single voxel is 255/111685, i.e 0.0028.
Is that to be interpreted as the probability that the forceps major passes 
through a voxel with that value?
That is awfully low ... what am I missing?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 1:55 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Hi Don - You would normalize these numbers by their sum, not by their maximum 
(i.e., not by 255).



a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 1:51:43 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Hi, Anastasia.



Yes, that makes it simpler.



I can see that each of the path.pd.nii.gz has a voxel entry for the same number 
of voxels. I'm looking at elmo.2008 for which that number is 1,294,336 which I 
presume is the volume of this person's brain as delivered by freesurfer.



Most of those voxels are set to 0.

I presume that means that the probability that the tract passes through that 
voxel is very near 0.0 .

For the forceps major, 7342 voxels have non-zero entries ranging from 1 to 255. 
Most of them are pretty low numbers so the average value for the 7342 non-zero 
voxels is about 16.

For a voxel that has an entry of 1, I presume the probability that the tract 
passes  through that voxel is near zero. For a voxel that has an entry of 127,  
is the probability that the tract passes through it 0.5 ?

And if the entry is 255, is the probability 1.0?



It's that mapping of voxel value to probability that I'm trying to get at. Or 
am I misunderstanding what the voxel value means?



Best - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 12:46 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



The probability maps are independent for each tract. Each one just tells you 
how likely this one tract is to go through any given voxel, but it tells you 
nothing about other tracts. Does this make sense?



On Apr 11, 2018 12:00 PM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:

Thanks for getting back, Anastasia.



I'm not suggesting that it should be done differently than it is.



I'm just trying to understand how the voxel values map to probability. That's 
why I described the wrong headed way I was thinking about it ... so you could 
tell me where I'm going wrong.







From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 11:54 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



This wouldn't work because these 18 tracts do not include all tracts in the 
brain.



On Apr 11, 2018 11:19 AM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:

I was thinking that for a single voxel, the total of the values assigned to the 
voxel over all the tracts would have a maximum of 255 and that 255 would 
correspond to a probability of 1.0.

I can see is likely wrong but for sure it's too simple since each voxel could 
contain crossing fibers from several tracts; hence the total probability 
assigned to the voxel over all the tracts might be greater than 1.0.

??



Surely there is some normalization applied to the values assigned to the voxels 
so they fall between 0 and 255.

Does that normalization vary from one subject to the next and perhaps even from 
one tract to the next?

And how is the normalization mapped to probability?



Thanks - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:48 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



The volume would have to be normalized to a total sum of 1 for the voxel values 
to represent an actual distribution.



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

Re: [Freesurfer] -make all error

[Dicamillo, Robert]

Hello Carissa,

There have been some changes to the files related to the “—make all” option.  
You can try downloading an updated version of the
 recon-all.makefile from the list of files under,

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos7_x86_64/

and replace the existing one in $FREESURFER_HOME/bin with the downloaded one.

One way to do this from the terminal would be,

… move aside the old recon-all.makefile.OLD ...

$ mv  $FREESURFER_HOME/bin/recon-all.makefile  
$FREESURFER_HOME/bin/recon-all.makefile.OLD

… and if you downloaded the new one into your home directory downloads folder, 
then you would copy it in from
the path, e.g., if saved to $HOME/Downloads,

$ cp  -f  $HOME/Downloads/recon-all.makefile  
$FREESURFER_HOME/bin/recon-all.makefile

… check they files now the same - you should get no output from the diff 
command …

$ diff  $HOME/Downloads/recon-all.makefile  
$FREESURFER_HOME/bin/recon-all.makefile

The try running  your rein-all again.

- rob


On Apr 11, 2018, at 11:53 AM, Carissa Nicole Weis 
mailto:cnw...@uwm.edu>> wrote:

Hello,

I am running recon-all for several subjects’ 7T data using Freesurfer version 
6.0 and currently trying to ensure appropriate skull stripping and pial/wm 
surface generation. For a few participants that needed some control points 
added and for which I reran them through the –autorecon2-cp option, I was 
unable to open the pial surfaces for review. I’ve seen on some of the other 
posts that you guys recommend running “recon-all –make all” to rebuild the 
files. I’ve tried to run the -make all command but have been running into the 
same error in the “Jacobian white lh” step:

#@# Jacobian white lh Wed Apr 4 12:07:37 CDT 2018
/bigraid-03/LS/Data/7T_fall2017/6315/6315_fs/scripts

mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg 
../surf/lh.jacobian_white

reading surface from ../surf/lh.white.preaparc…
mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn’t match 
../surf/lh.white.preaparc

No such file or directory
mrisReadTriangleFile failed.

No such file or directory
mris_jacobian: could not read target surface ../surf/lh.sphere.reg
No such file or directory

recon-all –s 6315_fs exited with ERRORS at Wed Apr 4 12:07:40 CDT 2018


All of the output in the log file up until this point appears to have finished 
without error. I can now open the surfaces for review, but am wondering what is 
affected by –make all not finishing completely.


Carissa N. Weis, B.S.
Graduate Student
Affective Neuroscience Laboratory
University of Wisconsin-Milwaukee
cnw...@uwm.edu

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[Freesurfer] Running matlab-based components of freesurfer on windows 10 linux shell

[Savio Wong]

Hi everyone,

I have installed freesurfer on windows 10 linux shell following this link:

http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/

Recon-all and freeview run perfectly on the system. However, when I tried
to run mkcontrast, I encountered the following error:

An Error has occurred while trying to initialize the MCR.
The error is: Fatal error loading library
/usr/local/freesurfer/MCRv83/bin/glnxa64/libmwmclbase.so
Error: libmwblas.so: cannot enable executable stack as shared object
requires: Invalid argument
Error:mclmcr initialization failed
ERROR running mkcontrast

It seems that the windows 10 linux shell lacks some libraries to run the
matlab:

https://www.mathworks.com/matlabcentral/answers/308911-
can-i-install-matlab-in-bash-on-ubuntu-on-windows

Does anyone have any experience in this error? is there any solution for
that?

Any advice is much appreciated.

best..savio
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Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Hoopes, Andrew]

Hi Anna,

You can download the new mri_normalize from this link - 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_normalize

To get it into your FS installation, first set executable permissions and then 
move it into your $FREESURFER_HOME/bin directory (sudo might be required):

chmod +x /path/to/downloaded/mri_normalize
mv /path/to/downloaded/mri_normalize ${FREESURFER_HOME}/bin/

best
Andrew

From:  on behalf of Anna Daniels 

Reply-To: FS Help 
Date: Monday, April 9, 2018 at 1:10 PM
To: FS Help 
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at 
110, cannot allocate memory)

Hi Bruce,
thank you for the quick reply!
Ubuntu 16.04 LTS 64-bit
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Please let me know how to incorporate the new version into the installation.
Thank you very much and best,
Anna


Hi Anna

no attachments :<

Srishti's issue stemmed from control points outside of the head. The
current (dev) version of mri_normalize detects and removes them. Can you
grab a new version of mri_normalize and see if it fixes your problem? Let
us know your hardware/software environment and we will get it to you

cheers
Bruce


On Fri, 6 Apr 2018, Anna Daniels wrote:

> Hi Bruce, hi Srishti,
>
> I have exactly the same problem with several subjects rerunning recon-all
> and there was sufficient memory available. I also tried out the last command
> directly which resulted in the same error log.
>
> ?mri_normalize 
> -f/home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_edits_transfer/rrer
> uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg
> aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> Attached you can find the input file.
>
> Thank you and best,
> Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE]
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Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Bruce Fischl]

p.s. you probably want to grab a new freeview also, as it lets you jump 
to the voxel coords of each control point so you can see them
On Wed, 11 Apr 
2018, Hoopes, Andrew wrote:




Hi Anna,

 

You can download the new mri_normalize from this link -
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_normalize

 

To get it into your FS installation, first set executable permissions and then 
move it into your
$FREESURFER_HOME/bin directory (sudo might be required):

 

chmod +x /path/to/downloaded/mri_normalize

mv /path/to/downloaded/mri_normalize ${FREESURFER_HOME}/bin/

 

best

Andrew

 

From:  on behalf of Anna Daniels 

Reply-To: FS Help 
Date: Monday, April 9, 2018 at 1:10 PM
To: FS Help 
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at 
110, cannot allocate
memory)

 

Hi Bruce,

thank you for the quick reply!

Ubuntu 16.04 LTS 64-bit

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Please let me know how to incorporate the new version into the installation.

Thank you very much and best,

Anna



Hi Anna

no attachments :<

Srishti's issue stemmed from control points outside of the head. The
current (dev) version of mri_normalize detects and removes them. Can you
grab a new version of mri_normalize and see if it fixes your problem? Let
us know your hardware/software environment and we will get it to you

cheers
Bruce


On Fri, 6 Apr 2018, Anna Daniels wrote:

> Hi Bruce, hi Srishti,
>
> I have exactly the same problem with several subjects rerunning recon-all
> and there was sufficient memory available. I also tried out the last command
> directly which resulted in the same error log.
>
> ?mri_normalize 
-f/home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_edits_transfer/rrer
> uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg
> aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> Attached you can find the input file.
>
> Thank you and best,
> Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE]


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Re: [Freesurfer] Canonical HRF shape generated by FSFAST

[Douglas N. Greve]

X.runflac(1).flac.ev(2).tirf is the time samples (eg, 0 to 30 sec)

X.runflac(1).flac.ev(2).Xirf is the actual HRF

If you are  using the spmhrf, you can look at the matlab function 
fast_spmhrf


On 04/11/2018 10:56 AM, Sarah Cole wrote:
> Just one clarification, this is for first level analysis (individual 
> subjects).
>
> Thanks
>
> On Wed, Apr 11, 2018 at 9:54 AM, Sarah Cole  > wrote:
>
> Hi Doug,
>
> At the end of my FSFAST analysis, I would like to plot the
> Canonical HRF shape generated by FSFAST for my events. I have
> found this thread:
> 
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-July/031902.html
> 
> 
>
> but I am not sure if I understand this line:
> "plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf)"
>
>
> Could you please clarify how to plot the Canonical HRF that was
> generated by FSFAST?
>
> Thank you,
>
> Sarah
>
>
>
>
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Re: [Freesurfer] Surface label to volume and then back to surface

[Douglas N. Greve]

On 04/11/2018 12:44 PM, David Beeler wrote:
> Hi Doug, thanks for the response! So it looks like my initial 
> transform from surface label to anatomical volume wasn't working 
> because my template.nii.gz and brainmask were in a different space 
> than the functional data I was processing. This happened because I was 
> taking the raw f.nii.gz, doing some transformations first, and saving 
> it to a file called f_reg.nii.gz. I was then trying to run 
> preproc-sess using the -i flag to specify this f_reg.nii.gz, but when 
> preproc runs mktemplate-sess it still uses f.nii.gz to make the 
> template, regardless of what the -i or -mcin flags say. I just added a 
> line in the if($DoTemplate) section of preproc-sess to have the option 
> of adding a -funcstem and it worked fine. I have now updated my 
> preprocessing to run all the commands individually instead of using 
> preproc-sess at all, and I'm probably going to send another message to 
> this list later making sure I'm doing that correctly. Additionally, 
> Re: "I think you could do it with a single call to mri_label2vol using 
> --regheader and specifying the func template." This works great! 
> Thanks for the shortcut. I got the surface label direct to functional 
> volume transform working with: mri_vol2vol --regheader --mov 
> $OUTPUTDIR/rh.MT.volume.anat.nii.gz --targ 
> $MEANFUNCDIR/meanfunc.nii.gz --o 
> $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz --nearest But I'm still 
> not entirely sure exactly what information is contained in regheader 
> (or where I can view this information). The reason I have been using 
> regheader instead of register.dof6.lta is that my functional data is 
> aligned to the anatomical prior to running preprocessing, and my 
> understanding was that using regheader would just downsample (similar 
> to mri_convert) and I wouldn't need to specify a registration file. Is 
> this a flawed understanding of regheader?
Regheader assumes that the two volumes "share a RAS space". This is a 
little hard to explain. Each volume has some geometry information in it 
that determines where a voxel is in RAS (right, anterior, superior) 
space. --regheader assumes that the RAS space is the same, so, if the 
RAS for voxel in volume 1 is the samseg as that of a voxel in volume2, 
then they must represent the same place anatomically. If you have 
already resampled your functional data into the 1mm, 256^3 anatomical 
space, then --regheader should work ok
> So transforming to functional space seems to be okay now, but 
> transforming back to the surface is still not perfect. I tried 
> mri_vol2surf --mov $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz 
> --regheader $SUBJID --projfrac 0.5 --interp nearest --hemi rh --o 
> $OUTPUTDIR/regheadersurface.nii.gz and also bbregister --s $SUBJID 
> --reg $OUTPUTDIR/testreg.lta --mov $MEANFUNCDIR/meanfunc.nii.gz 
> --init-fsl --bold mri_vol2surf --mov 
> $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz --reg 
> $OUTPUTDIR/testreg.lta --projfrac 0.5 --interp nearest --hemi rh --o 
> $OUTPUTDIR/testregsurface.nii.gz Which both give essentially the same 
> result: Original Label: 
> http://web.mit.edu/dsbeeler/www/images/MTlabel.png Back to Surface 
> Overlay: http://web.mit.edu/dsbeeler/www/images/MTpatchy.png This is 
> actually much better than it was, but is there a way to get rid of the 
> patchiness?
The patchiness is caused by something else. When you run vol2surf, you 
can try --projfrac-max -.1 1 .1 That should reduce the patchiness. If it 
is still not tolerable, then let me know
> Again, thanks for all the useful info!
> David
> __
> Hi David, I've tried to answer your questions below.
>
> doug
> On 03/30/2018 01:48 PM, David Beeler wrote:
> > Hi all,
> > Sorry in advance, this is a bit of an annoying one!
> >
> > I am trying to use freesurfer's automatically generated MT label as a 
> > parcel to constrain activity measured during a functional MT 
> > localizer. I am currently doing my analysis in the volume and I'd like 
> > to transform the MT surface label into the subject's volume functional 
> > space (i.e. the same space as the sig.nii.gz for a particular 
> > contrast), take the voxels in sig.nii.gz that are within the MT label, 
> > and project them back onto the surface (preferably to be viewed as an 
> > overlay with freeview). I will eventually run the analysis on the 
> > surface as well (making this much less roundabout, but I also use 
> > volume parcels so understanding how to correctly go between the volume 
> > and surface is important to me).
> >
> > In my pipeline I start off by running preproc-sess, then I register 
> > and transform my preprocessed functional data (fmcpr.nii.gz) to the 
> > subject's anatomical (without upsampling). After doing mkanalysis and 
> > mkcontrast, I run selxavg on this volume. So the functional data is 
> > aligned with the anatomical, but still has low res dimensions.
> >
> > If it's not too much to ask, would i

Re: [Freesurfer] Running matlab-based components of freesurfer on windows 10 linux shell

[Douglas N. Greve]

The fsfast commands require matlab or octave. I'm not sure how that will 
work in the linux shell in windows


On 04/11/2018 03:50 PM, Savio Wong wrote:
> Hi everyone,
>
> I have installed freesurfer on windows 10 linux shell following this link:
>
> http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/
>  
>
>
> Recon-all and freeview run perfectly on the system. However, when I 
> tried to run mkcontrast, I encountered the following error:
>
> An Error has occurred while trying to initialize the MCR.
> The error is: Fatal error loading library 
> /usr/local/freesurfer/MCRv83/bin/glnxa64/libmwmclbase.so Error: 
> libmwblas.so: cannot enable executable stack as shared object 
> requires: Invalid argument
> Error:mclmcr initialization failed
> ERROR running mkcontrast
>
> It seems that the windows 10 linux shell lacks some libraries to run 
> the matlab:
>
> https://www.mathworks.com/matlabcentral/answers/308911-can-i-install-matlab-in-bash-on-ubuntu-on-windows
>  
> 
>  
>
>
> Does anyone have any experience in this error? is there any solution 
> for that?
>
> Any advice is much appreciated.
>
> best..savio
>
>
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Re: [Freesurfer] mri_surf2surf results in large area with zero values

[Douglas N. Greve]

can you send your command line and terminal output?


On 04/11/2018 05:41 AM, Frauke Beyer wrote:
> Dear experts,
>
> I have an issue with mri_surf2surf (i suspect). I have resampled
> T1-values to the fsaverage template using mri_vol2surf and a --projfrac
> of 0.25 with the default white matter surface. Then I loaded these
> values in Matlab using MRIread, inverted them and saved them back into a
> file using MRIwrite. In Matlab, there were no suspicious data points
> (e.g. the range of R1 values excluded 0, minimum was 0.25). This was
> also true when loading the R1values as an overlay in Freeview. Now I
> wanted to smooth this image using mri_surf2surf with target and source
> subject being identical to fsaverage and fwhm of 10mm.
>
> exact command was: mri_surf2surf --srcsubject fsaverage --trgsubject
> fsaverage --hemi lh --sval
> /nobackup/aventurin4/data_fbeyer/flica_myelin/flica_inputs/round2/t1maps/lh.t1map.proj0.25.fsavg_inv.mgh
> --tval
> /nobackup/aventurin4/data_fbeyer/flica_myelin/flica_inputs/round2/t1maps/lh.t1map.proj0.25.fsavg_inv_smoothed10mm.mgh
> --fwhm-trg 10
>
> But now, while it worked fine for some subjects in the 4D file for
> others large areas of 0 emerged in the smoothed file. Those were mostly
> found in inferior temporal/orbitofrontal lobe.
>
> Does anybody have an idea what could cause this strange behaviour?
>
> Thank you so much for your help,
>
> Frauke
>
>
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Re: [Freesurfer] Creating average surface for fMRI subjects and extracting cortical thickness

[Douglas N. Greve]

Are you doing this inside or outside of FSFAST? If outside you would 
register your fmri to the anatomical with bbregister, then use 
mri_vol2surf to map it to the surface, then surf2surf to map it to 
fsaverage, then smooth, then mri_glmfit to test for a differnece between 
groups, then mri_glmfit-sim to get clusters. One of the cluster outputs 
will be "ocn" file. This is a segmentation-like surface structure. To 
get the mean thickness in each cluster, you would run mris_preproc to 
get a stack of thickness maps in fsaverage space, then run something like


mri_segstats --i lh.thickness.stack.mgh --seg ocn.mgh --exlucdeid 0 
--avgwf cluster.thickness.stack.dat


cluster.thickness.stack.dat will have a row for each subject and a 
column for each cluster



On 04/10/2018 12:06 PM, Arsenije Subotic wrote:
>
> Dear experts,
>
>
> I would like to create an average surface template of fMRI activation 
> for two groups, and then determine areas of low cerebrovascular 
> reactivity in my disease group, create a ROI, and extract the cortical 
> thickness in this region and see how it compares to a control group by 
> translating this ROI onto the control surface template. Do you have 
> any tips or suggestions on how this workflow should be done?
>
>
> I've currently been able to create an average surface for both groups, 
> and I know how to create labels using tksurfer and to extract cortical 
> thickness using mri_anatomical_stats. Is it possible however to create 
> an ROI by only considering areas of low CVR/low activation in my 
> disease group and calculating cortical thickness for this area, and 
> then visualize it somehow and then translate this label onto the 
> control group and doing the same?
>
>
> I know it's a lot of questions, but going through the tutorial 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_tktools)
>  
> it seems that I wasn't able to find exactly what I'm looking for.
>
>
> Thank you for your help,
>
> Arsenije
>
>
>
>
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Re: [Freesurfer] newbie trac-all -bedp question

[Yendiki, Anastasia]

It would answer the question "if I were a voxel of the forceps major, how 
likely would I be to be in any particular location?"


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Krieger, Donald N. 

Sent: Wednesday, April 11, 2018 2:10:50 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Ok – I have that sum.

For the forceps major, it’s 111,685.

If I normalize by that, i.e. divide each voxel value by that, then I certainly 
get something that looks like a probability distribution since the sum of the 
normalized voxel entries over the entire volume is 1.0 as you had said in an 
earlier post.

But the maximum probability for any single voxel is 255/111685, i.e 0.0028.

Is that to be interpreted as the probability that the forceps major passes 
through a voxel with that value?

That is awfully low … what am I missing?



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 1:55 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - You would normalize these numbers by their sum, not by their maximum 
(i.e., not by 255).



a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 1:51:43 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi, Anastasia.



Yes, that makes it simpler.



I can see that each of the path.pd.nii.gz has a voxel entry for the same number 
of voxels. I’m looking at elmo.2008 for which that number is 1,294,336 which I 
presume is the volume of this person’s brain as delivered by freesurfer.



Most of those voxels are set to 0.

I presume that means that the probability that the tract passes through that 
voxel is very near 0.0 .

For the forceps major, 7342 voxels have non-zero entries ranging from 1 to 255. 
Most of them are pretty low numbers so the average value for the 7342 non-zero 
voxels is about 16.

For a voxel that has an entry of 1, I presume the probability that the tract 
passes  through that voxel is near zero. For a voxel that has an entry of 127,  
is the probability that the tract passes through it 0.5 ?

And if the entry is 255, is the probability 1.0?



It’s that mapping of voxel value to probability that I’m trying to get at. Or 
am I misunderstanding what the voxel value means?



Best - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 12:46 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



The probability maps are independent for each tract. Each one just tells you 
how likely this one tract is to go through any given voxel, but it tells you 
nothing about other tracts. Does this make sense?



On Apr 11, 2018 12:00 PM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:

Thanks for getting back, Anastasia.



I’m not suggesting that it should be done differently than it is.



I’m just trying to understand how the voxel values map to probability. That’s 
why I described the wrong headed way I was thinking about it … so you could 
tell me where I’m going wrong.







From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 11:54 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



This wouldn't work because these 18 tracts do not include all tracts in the 
brain.



On Apr 11, 2018 11:19 AM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:

I was thinking that for a single voxel, the total of the values assigned to the 
voxel over all the tracts would have a maximum of 255 and that 255 would 
correspond to a probability of 1.0.

I can see is likely wrong but for sure it’s too simple since each voxel could 
contain crossing fibers from several tracts; hence the total probability 
assigned to the voxel over all the tracts might be greater than 1.0.

??



Surely there is some normalization applied to the values assigned to the voxels 
so they fall between 0 and 255.

Does that normalization vary from one subject to the next and perhaps even from 
one tract to the next?

And how is the normalization mapped to probability?



Thanks - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, A

[Freesurfer] -qcache in recon-all commnd

[Alexopoulos, Dimitrios]

Is it recommended to use the -qcache flag in the basic recon-all -all command? 
What does it do and what are the advantage of using it?

Jim


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Re: [Freesurfer] Surface label to volume and then back to surface

[David Beeler]

Hi Doug, thanks for the explanation! Also --projfrac-max -.1 1 .1 is a big 
improvement, I think it should be good for my purposes. Feeling good about this 
now!

Cheers,
DB
___

On 04/11/2018 12:44 PM, David Beeler wrote:

> Hi Doug, thanks for the response! So it looks like my initial 
> transform from surface label to anatomical volume wasn't working 
> because my template.nii.gz and brainmask were in a different space 
> than the functional data I was processing. This happened because I was 
> taking the raw f.nii.gz, doing some transformations first, and saving 
> it to a file called f_reg.nii.gz. I was then trying to run 
> preproc-sess using the -i flag to specify this f_reg.nii.gz, but when 
> preproc runs mktemplate-sess it still uses f.nii.gz to make the 
> template, regardless of what the -i or -mcin flags say. I just added a 
> line in the if($DoTemplate) section of preproc-sess to have the option 
> of adding a -funcstem and it worked fine. I have now updated my 
> preprocessing to run all the commands individually instead of using 
> preproc-sess at all, and I'm probably going to send another message to 
> this list later making sure I'm doing that correctly. Additionally, 
> Re: "I think you could do it with a single call to mri_label2vol using 
> --regheader and specifying the func template." This works great! 
> Thanks for the shortcut. I got the surface label direct to functional 
> volume transform working with: mri_vol2vol --regheader --mov 
> $OUTPUTDIR/rh.MT.volume.anat.nii.gz --targ 
> $MEANFUNCDIR/meanfunc.nii.gz --o 
> $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz --nearest But I'm still 
> not entirely sure exactly what information is contained in regheader 
> (or where I can view this information). The reason I have been using 
> regheader instead of register.dof6.lta is that my functional data is 
> aligned to the anatomical prior to running preprocessing, and my 
> understanding was that using regheader would just downsample (similar 
> to mri_convert) and I wouldn't need to specify a registration file. Is 
> this a flawed understanding of regheader?

Regheader assumes that the two volumes "share a RAS space". This is a 
little hard to explain. Each volume has some geometry information in it 
that determines where a voxel is in RAS (right, anterior, superior) 
space. --regheader assumes that the RAS space is the same, so, if the 
RAS for voxel in volume 1 is the samseg as that of a voxel in volume2, 
then they must represent the same place anatomically. If you have 
already resampled your functional data into the 1mm, 256^3 anatomical 
space, then --regheader should work ok

> So transforming to functional space seems to be okay now, but 
> transforming back to the surface is still not perfect. I tried 
> mri_vol2surf --mov $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz 
> --regheader $SUBJID --projfrac 0.5 --interp nearest --hemi rh --o 
> $OUTPUTDIR/regheadersurface.nii.gz and also bbregister --s $SUBJID 
> --reg $OUTPUTDIR/testreg.lta --mov $MEANFUNCDIR/meanfunc.nii.gz 
> --init-fsl --bold mri_vol2surf --mov 
> $OUTPUTDIR/rh.MT.volume.func-regheader.nii.gz --reg 
> $OUTPUTDIR/testreg.lta --projfrac 0.5 --interp nearest --hemi rh --o 
> $OUTPUTDIR/testregsurface.nii.gz Which both give essentially the same 
> result: Original Label: 
> http://web.mit.edu/dsbeeler/www/images/MTlabel.png Back to Surface 
> Overlay: http://web.mit.edu/dsbeeler/www/images/MTpatchy.png This is 
> actually much better than it was, but is there a way to get rid of the 
> patchiness?

The patchiness is caused by something else. When you run vol2surf, you 
can try --projfrac-max -.1 1 .1 That should reduce the patchiness. If it 
is still not tolerable, then let me know

> Again, thanks for all the useful info!
> David
> __
> Hi David, I've tried to answer your questions below.
>
> doug
> On 03/30/2018 01:48 PM, David Beeler wrote:
> > Hi all,
> > Sorry in advance, this is a bit of an annoying one!
> >
> > I am trying to use freesurfer's automatically generated MT label as a 
> > parcel to constrain activity measured during a functional MT 
> > localizer. I am currently doing my analysis in the volume and I'd like 
> > to transform the MT surface label into the subject's volume functional 
> > space (i.e. the same space as the sig.nii.gz for a particular 
> > contrast), take the voxels in sig.nii.gz that are within the MT label, 
> > and project them back onto the surface (preferably to be viewed as an 
> > overlay with freeview). I will eventually run the analysis on the 
> > surface as well (making this much less roundabout, but I also use 
> > volume parcels so understanding how to correctly go between the volume 
> > and surface is important to me).
> >
> > In my pipeline I start off by running preproc-sess, then I register 
> > and transform my preprocessed functional data (fmcpr.nii.gz) to the 
> > subject's anatomical (without upsampl

Re: [Freesurfer] -qcache in recon-all commnd

[Douglas Greve]

It is not. -qcache is a preprocessing step prior to doing group analysis 
with QDEC. If you use it, you should only do so after you have finished 
all the individual analysis (eg, manual edits)



On 4/11/18 10:02 PM, Alexopoulos, Dimitrios wrote:
Is it recommended to use the -qcache flag in the basic recon-all -all 
command? What does it do and what are the advantage of using it?


Jim



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




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