[Freesurfer] Probabilistic atlas illustration

[Julian Jäckle]

Dear all

In the paper "A computational atlas of the hippocampal formation using *ex
vivo*, ultra-high resolution MRI" (DOI:10.1016/j.neuroimage.2015.04.042

 ;2015)
you have two illustrations Fig4&6 showing the probabilistic atlas and mesh
deformation. Can I create such an image myself using freeview /tkmedit? If
so could you explain to me how to do it?

I've attached an example image

Thanks a lot

Julian
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Re: [Freesurfer] REPOST: Two stage model question

[Clara Kühn]

Hi Martin,

thanks for your reply. From your email I understand that looking at the rate of 
change between time points is more useful than spc if I want to look at only 2 
time points at a time.

I have a pre training scan, a post training scan (approximately 3 weeks apart 
with a training intervention in between scans) and a follow up scan after 3 
weeks of no intervention for either group.
Therefore I could compare the rate of change in thickness and area from pre 
scan to post scan between the training group and the control group. Similarly, 
I could check if the rates differ between the groups when looking at post scan 
and follow up. And that I could do with the longitudinal two stage model, right?

Could you explain what you mean with "node at the intervention time" with 
regards to LMEs? Also I'm not sure what you mean with piecewise. I've tried to 
follow the LME tutorial once before. Do you mean that I should only try the 
linear version of the model? How would I do this piecewise?


Thanks for your help!
Clara



- Ursprüngliche Mail -
Von: "mreuter" 
An: "Freesurfer support list" 
Gesendet: Freitag, 21. April 2017 22:09:14
Betreff: Re: [Freesurfer] REPOST: Two stage model question

Hi Clara, 

the SPC (or any percent change) could be problematic, as the base value (either 
the volume at the baseline timepoint, or the average volume) will change 
depending wich interval you look at. You could check if the rate (mm/time_unit) 
or mm^3/time_unit is changing.

I am not sure how your study is setup, so I cannot really recommend anything 
here (e.g. when did the intervention happen exactly). 

Generally I would recommend a piecewise linear model with node at the 
intervention time in LME (mixed effects). 

Best, Martin

> On 21 Apr 2017, at 17:15, Clara Kühn  wrote:
> 
> 
> 
> Dear FreeSurfer experts,
> 
> I have a longitudinal design with 3 groups and 3 time points. For one group 
> the intervention did not work so for now I would like to look at 2 groups 
> only. Can I do this with the Longitudinal Two Stage Model by looking at the 
> spc from tp1 to tp2 and then looking at the spc from tp2 to tp3?
> 
> Are there statistical reasons that forbid this procedure of comparing the 
> change across time between groups?
> 
> Thanks for your help!
> Clara
> 
> -- 
> Clara Kühn, Phd Student
> 
> Max-Planck-Institute for Human Cognitive and Brain Science
> Department of Neuropsychology
> Stephanstrasse 1A
> 04103 Leipzig, Germany
> 
> Phone: +49 341 - 9940 2271
> Fax: +49 341 - 9940 2260
> Web: www.cbs.mpg.de
> E-Mail: cku...@cbs.mpg.de
> 
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> 


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[Freesurfer] Mri_segstats on longitudinal data (NVoxels)

[Ferdi van de Kamp]

Hi all,

My question is twofold

using an user specified ROI in MNI512-space I ask Freesurfer to create
tables for both cross-sectionally& longitudinally processed data.

Mri_segstats performed over both cross-sectional data folders and
longitudinal data folders


However, when inspecting the data, the NVoxels for all time points in the
longitudinal data are equal, while in the cross-sectional they differ (and
are generally larger). Is this to be expected?

In addition to NVoxels and mean intensity, our lab would like to use other
measures such as thickness, does anyone know the correct function to call
for that information?



Right now the pipeline look like this:

Step1 standardised labels from volumes

This step is focused on the ROIs, not the subjects, is submitted as a
single job

Uses *mri_vol2vol *and *mri_cor2label*.

Step 2 Create personalised labels, volumes & tables
This is the part that is submit to the cluster for each subject (separate
for cross-sectional and longitudinal). It uses *mri_label2label*,
*mri_label2vol
*and *mri_segstats*.


Thanks!

Ferdi van de Kamp
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[Freesurfer] White matter volume of a costumized Gyrus

[Josue Luiz Dalboni Da Rocha]

Dear Freesurfer team,


I am working with calculated volumes of a gyrus (a costumized label).

I currently use mris_anatomical_stats to calculate the volumes of my gyrus (in 
label format).

According to the freesurfer tutorial (as I understood), one of the stats 
outputted from mris_anatomical_stats is the volume of the gray matter 
surrounding the white/gray matter border (a surface) specified by the inputted 
label.

We are actually interested in the white matter volume (instead of gray matter 
volume) inside this ROI (a gyrus in our case) specified by the label.

I didn't find yet a command in freesurfer from where I can extract the white 
matter volume of a gyrus from a costumized label.

Could someone advise me?


Best regards,

Josue
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[Freesurfer] illustration of a nifti volume on fsaverage

[james pardon]

Dear All,

Apologies in advance for the naive question. Could you please  let me know
what is the best way of transferring a nifti overlay volume to fsaverage,
solely for illustration purposes? I think I should start by registering
with fsaverage volume and then overlay with Freeview, but I'm not sure what
tools from Freesurfer I should use for 1) between subject volume
registration (nifti volume to fsaverage volume) 2) fsaverage volume to
fsaverage surface.

Thank you,
James
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Re: [Freesurfer] Multicenter studies

[Laura Ferrero Montes]

  Thank you for the information. I just want to be sure if I have  
understood it properly.
  If I had two groups and two sites, my design matrix would be like:

GroupDescriptorFile 1
Class PatientsGroup1
Class PatientsGroup2
Class ControlsGroup1
Class ControlsGroup2

  If I want to test for the effect of group, contrast matrix would be:
  0.5 -0.5 0.5 -0.5

  If I want to test for the effect of site, contrast matrix would be:
  0.5 0.5 -0.5 -0.5

  Finally, in case of interaction test, how contrast matrix would be?





Douglas N Greve  escribió:

> You should make sure to have a balanced design (ie, approx the same pats
> and cons at each site). Then include site as a regressor, ie, if you had
> two groups and two sites, you would have four regressors.  You could
> then test for the effect of group, the effect of site, and the
> interaction. If there is an interaction, then it is hard to interpret
> the differences between groups.
>



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Re: [Freesurfer] White matter volume of a costumized Gyrus

[Bruce Fischl]

Hi Josue

how would you define the borders of the white matter of the gyrus? I guess 
you could use the wmparc stuff and just count voxels based on a distance 
constraint


cheers
Bruce


On Tue, 9 
May 2017, Josue Luiz Dalboni Da Rocha wrote:




Dear Freesurfer team,


I am working with calculated volumes of a gyrus (a costumized label).

I currently use mris_anatomical_stats to calculate the volumes of my gyrus
(in label format).

According to the freesurfer tutorial (as I understood), one of the stats
outputted from mris_anatomical_stats is the volume of the gray matter
surrounding the white/gray matter border (a surface) specified by the
inputted label.

We are actually interested in the white matter volume (instead of gray
matter volume) inside this ROI (a gyrus in our case) specified by the label.

I didn't find yet a command in freesurfer from where I can extract the white
matter volume of a gyrus from a costumized label.

Could someone advise me?


Best regards,

Josue


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Re: [Freesurfer] illustration of a nifti volume on fsaverage

[Bruce Fischl]

if the nifti volume is from an individual subject that has been run through 
recon-all (e.g. an fmri map):


1. Use bbregister to register the fmri to the recon surfaces
2. Use mri_volsurf to sample the fmri data onto the surface
3. Use mri_surf2surf to map from the individual to fsaverage

cheers
Bruce


On Tue, 9 May 2017, james pardon wrote:


Dear All,
Apologies in advance for the naive question. Could you please  let me know
what is the best way of transferring a nifti overlay volume to fsaverage,
solely for illustration purposes? I think I should start by registering with
fsaverage volume and then overlay with Freeview, but I'm not sure what tools
from Freesurfer I should use for 1) between subject volume registration
(nifti volume to fsaverage volume) 2) fsaverage volume to fsaverage surface.

Thank you,
James

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Re: [Freesurfer] illustration of a nifti volume on fsaverage

[james pardon]

Thank you Bruce. What if the nifti volume has not been processed at all in
Freesurfer? My only aim is to illustrate an overlay on FSAVERAGE, with the
obvious caveat of skipping surface construction for this nifti.

Thanks,
James

On Tue, May 9, 2017 at 2:42 PM, Bruce Fischl 
wrote:

> if the nifti volume is from an individual subject that has been run
> through recon-all (e.g. an fmri map):
>
> 1. Use bbregister to register the fmri to the recon surfaces
> 2. Use mri_volsurf to sample the fmri data onto the surface
> 3. Use mri_surf2surf to map from the individual to fsaverage
>
> cheers
> Bruce
>
>
>
> On Tue, 9 May 2017, james pardon wrote:
>
> Dear All,
>> Apologies in advance for the naive question. Could you please  let me know
>> what is the best way of transferring a nifti overlay volume to fsaverage,
>> solely for illustration purposes? I think I should start by registering
>> with
>> fsaverage volume and then overlay with Freeview, but I'm not sure what
>> tools
>> from Freesurfer I should use for 1) between subject volume registration
>> (nifti volume to fsaverage volume) 2) fsaverage volume to fsaverage
>> surface.
>>
>> Thank you,
>> James
>>
>>
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> 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.
>
>
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Re: [Freesurfer] White matter volume of a costumized Gyrus

[Douglas Greve]

You will need to create an annotation with your label in it. This might 
be tricky to do depending on what you want. The easy way is to run 
mris_label2annot with only your label, then run mri_aparc2aseg to 
generate something like the wmparc.mgz (look in the recon-all.log file 
for the command line that generated wmparc.mgz but specify your annot 
with --annot). View the label to make sure it is what you want, then run 
mri_segstats.



On 5/9/17 7:23 AM, Josue Luiz Dalboni Da Rocha wrote:


Dear Freesurfer team,


I am working with calculated volumes of a gyrus (a costumized label).

I currently use mris_anatomical_stats to calculate the volumes of my 
gyrus (in label format).


According to the freesurfer tutorial (as I understood), one of the 
stats outputted from mris_anatomical_stats is the volume of the gray 
matter surrounding the white/gray matter border (a surface) specified 
by the inputted label.


We are actually interested in the white matter volume (instead of gray 
matter volume) inside this ROI (a gyrus in our case) specified by the 
label.


I didn't find yet a command in freesurfer from where I can extract the 
white matter volume of a gyrus from a costumized label.


Could someone advise me?


Best regards,

Josue



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Re: [Freesurfer] illustration of a nifti volume on fsaverage

[Douglas Greve]

You can use mri_coreg to register the volume to fsaverage, then use the 
registration when running freeview or tksurfer



On 5/9/17 10:19 AM, james pardon wrote:
Thank you Bruce. What if the nifti volume has not been processed at 
all in Freesurfer? My only aim is to illustrate an overlay on 
FSAVERAGE, with the obvious caveat of skipping surface construction 
for this nifti.


Thanks,
James

On Tue, May 9, 2017 at 2:42 PM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:


if the nifti volume is from an individual subject that has been
run through recon-all (e.g. an fmri map):

1. Use bbregister to register the fmri to the recon surfaces
2. Use mri_volsurf to sample the fmri data onto the surface
3. Use mri_surf2surf to map from the individual to fsaverage

cheers
Bruce



On Tue, 9 May 2017, james pardon wrote:

Dear All,
Apologies in advance for the naive question. Could you please
 let me know
what is the best way of transferring a nifti overlay volume to
fsaverage,
solely for illustration purposes? I think I should start by
registering with
fsaverage volume and then overlay with Freeview, but I'm not
sure what tools
from Freesurfer I should use for 1) between subject volume
registration
(nifti volume to fsaverage volume) 2) fsaverage volume to
fsaverage surface.

Thank you,
James


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 . If the e-mail was sent
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Re: [Freesurfer] Mri_segstats on longitudinal data (NVoxels)

[Douglas Greve]

Sorry, I'm not sure what you are trying to do. Can you send command lines?



On 5/9/17 6:42 AM, Ferdi van de Kamp wrote:


Hi all,

My question is twofold

using an user specified ROI in MNI512-space I ask Freesurfer to create 
tables for both cross-sectionally& longitudinally processed data.


Mri_segstats performed over both cross-sectional data folders and 
longitudinal data folders



However, when inspecting the data, the NVoxels for all time points in 
the longitudinal data are equal, while in the cross-sectional they 
differ (and are generally larger). Is this to be expected?


In addition to NVoxels and mean intensity, our lab would like to use 
other measures such as thickness, does anyone know the correct 
function to call for that information?


Right now the pipeline look like this:

Step1 standardised labels from volumes

This step is focused on the ROIs, not the subjects, is submitted as a 
single job


Uses /mri_vol2vol /and /mri_cor2label/.

Step 2 Create personalised labels, volumes & tables

This is the part that is submit to the cluster for each subject 
(separate for cross-sectional and longitudinal). It uses 
/mri_label2label/, /mri_label2vol /and /mri_segstats/.



Thanks!

Ferdi van de Kamp


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Re: [Freesurfer] Multicenter studies

[Douglas Greve]

For the interaction it would be

0.5 -0.5 -0.5 0.5


On 5/9/17 8:32 AM, Laura Ferrero Montes wrote:
>
>Thank you for the information. I just want to be sure if I have
> understood it properly.
>If I had two groups and two sites, my design matrix would be like:
>
> GroupDescriptorFile 1
> Class PatientsGroup1
> Class PatientsGroup2
> Class ControlsGroup1
> Class ControlsGroup2
>
>If I want to test for the effect of group, contrast matrix would be:
>0.5 -0.5 0.5 -0.5
>
>If I want to test for the effect of site, contrast matrix would be:
>0.5 0.5 -0.5 -0.5
>
>Finally, in case of interaction test, how contrast matrix would be?
>
>
>
>
>
> Douglas N Greve  escribió:
>
>> You should make sure to have a balanced design (ie, approx the same pats
>> and cons at each site). Then include site as a regressor, ie, if you had
>> two groups and two sites, you would have four regressors.  You could
>> then test for the effect of group, the effect of site, and the
>> interaction. If there is an interaction, then it is hard to interpret
>> the differences between groups.
>>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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Re: [Freesurfer] illustration of a nifti volume on fsaverage

[Bruce Fischl]

Hi James

if it is registered to MNI space I guess you could do vol2surf directly 
on fsaverage, but it won't be very accurate and will for sure miss things


cheers
Bruce
On 
Tue, 9 May 2017, james pardon wrote:



Thank you Bruce. What if the nifti volume has not been processed at all in
Freesurfer? My only aim is to illustrate an overlay on FSAVERAGE, with the
obvious caveat of skipping surface construction for this nifti. 
Thanks,
James

On Tue, May 9, 2017 at 2:42 PM, Bruce Fischl 
wrote:
  if the nifti volume is from an individual subject that has been
  run through recon-all (e.g. an fmri map):

  1. Use bbregister to register the fmri to the recon surfaces
  2. Use mri_volsurf to sample the fmri data onto the surface
  3. Use mri_surf2surf to map from the individual to fsaverage

  cheers
  Bruce


  On Tue, 9 May 2017, james pardon wrote:

Dear All,
Apologies in advance for the naive question. Could
you please  let me know
what is the best way of transferring a nifti overlay
volume to fsaverage,
solely for illustration purposes? I think I should
start by registering with
fsaverage volume and then overlay with Freeview, but
I'm not sure what tools
from Freesurfer I should use for 1) between subject
volume registration
(nifti volume to fsaverage volume) 2) fsaverage
volume to fsaverage surface.

Thank you,
James


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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
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[Freesurfer] mri_convert : pix vs no pix ?

[Shane Schofield]

Dear Doug,I am trying to flip some PET images so that they are in the same 
orientation as the T1.I came across this post 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29281.htmlCan you 
explain what what it means to change the pixel data? Should I use pix or 
without pix? For context I am working with PET data (in img/hdr formats) that 
seemed to have been flipped L/R somehow. 
Thank you.


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Re: [Freesurfer] mri_convert : pix vs no pix ?

[Douglas N Greve]

When the pixel  data are flipped, you are actually changing the way that 
the data are stored on disk (while keeping the direction info in the 
header constant).


On 05/09/2017 12:52 PM, Shane Schofield wrote:
> Dear Doug,
> I am trying to flip some PET images so that they are in the same 
> orientation as the T1.
> I came across this post 
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29281.html
> Can you explain what what it means to change the pixel data? Should I 
> use pix or without pix? For context I am working with PET data (in 
> img/hdr formats) that seemed to have been flipped L/R somehow.
> Thank you.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Obtaining surface normal vector from plial surfaceRAS coordinate

[Jerry Jeyachandra]

Hi Bruce,

Thanks for the response. I've run the operation and have examined the output. 
From my understanding the file contains both a vertex list (XYZ) and a face 
list containing (V1,V2,V3...). Is the XYZ of the vertex list the actual 
surfaceRAS coordinates of the surface as viewed on FreeViewer? If so I can 
compute face normals simply by matching up the 3 vertices encapsulating the 
given surface coordinate and computing the face normal vector, correct?

Thanks again

Jerry


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

Sent: May 8, 2017 4:40:17 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Obtaining surface normal vector from plial surfaceRAS 
coordinate

Hi Jerry

mris_convert -n lh.pial lh.pial.normals.asc

should create a list of surface normals in ascii format

cheers
Bruce
On Mon, 8 May 2017,
Jerry
Jeyachandra wrote:

>
> Hi list,
>
> I’d like to extract the surface normal at a location specified in surfaceRAS
> coordinates after performing segmentation. I know there are methods to
> extract all vertices and faces then compute face normals from there, but I’m
> not familiar with methods to relate these to specified coordinates.
>
> Thanks
>
> Jerry Jeyachandra
>
>
>
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Re: [Freesurfer] mri_convert : pix vs no pix ?

[Shane Schofield]

Sorry, I don't quite understand yet.. Would the header be important as I am not 
using img / hdr ? Under what sort of circumstances would pix be favourable? I 
am using .nii after executing mri_convert to go from img/hdr to nii. I note 
that pix is used in other older threads too. 

On Tuesday, May 9, 2017 5:58 PM, Douglas N Greve 
 wrote:
 

 When the pixel  data are flipped, you are actually changing the way that 
the data are stored on disk (while keeping the direction info in the 
header constant).


On 05/09/2017 12:52 PM, Shane Schofield wrote:
> Dear Doug,
> I am trying to flip some PET images so that they are in the same 
> orientation as the T1.
> I came across this post 
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29281.html
> Can you explain what what it means to change the pixel data? Should I 
> use pix or without pix? For context I am working with PET data (in 
> img/hdr formats) that seemed to have been flipped L/R somehow.
> Thank you.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mri_convert : pix vs no pix ?

[Douglas N Greve]

When freesurfer reads in an img/hdr file, it makes assumptions about the 
how the data are oriented, so, implicitly, you are using orientation 
info. If you do not have a .mat file, then you can't change the header, 
so you have to change the pixels


On 05/09/2017 01:45 PM, Shane Schofield wrote:
> Sorry, I don't quite understand yet.. Would the header be important as 
> I am not using img / hdr ? Under what sort of circumstances would pix 
> be favourable? I am using .nii after executing mri_convert to go from 
> img/hdr to nii. I note that pix is used in other older threads too.
>
>
> On Tuesday, May 9, 2017 5:58 PM, Douglas N Greve 
>  wrote:
>
>
> When the pixel  data are flipped, you are actually changing the way that
> the data are stored on disk (while keeping the direction info in the
> header constant).
>
>
> On 05/09/2017 12:52 PM, Shane Schofield wrote:
> > Dear Doug,
> > I am trying to flip some PET images so that they are in the same
> > orientation as the T1.
> > I came across this post
> > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29281.html
> > Can you explain what what it means to change the pixel data? Should I
> > use pix or without pix? For context I am working with PET data (in
> > img/hdr formats) that seemed to have been flipped L/R somehow.
> > Thank you.
>
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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.
>
>
>
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Maps showing correlations between structural measures

[Martin Juneja]

Dear Dr. Greve,

I created two stacks: one with volume and the other with LGI using mris
commands as following:

mris_preproc --fsgd CV_LGI.fsgd --target fsaverage --hemi lh --meas volume
--out Corr_CV_LGI/lh.vol.mgh
mris_preproc --fsgd CV_LGI.fsgd --target fsaverage --hemi lh --meas
pial_lgi --out Corr_CV_LGI/lh.LGI.mgh

Then I smoothed the data using:

mri_surf2surf --hemi lh --s fsaverage --sval Corr_CV_LGI/lh.vol.mgh --fwhm
10 --cortex --tval Corr_CV_LGI/lh.vol.10.mgh
mri_surf2surf --hemi lh --s fsaverage --sval Corr_CV_LGI/lh.LGI.mgh --fwhm
10 --cortex --tval Corr_CV_LGI/lh.LGI.10.mgh

Finally I ran glmfit command as following:

mri_glmfit --y Corr_CV_LGI/lh.vol.10.mgh --fsgd CV_LGI.fsgd dods --C
Corr-VL-cor.mtx --surf fsaverage lh --cortex --glmdir
Corr_CV_LGI/lh.VL.glmdir --pvr Corr_CV_LGI/lh.LGI.10.mgh

My fsgd file looks like this:
GroupDescriptorFile 1
Class Male
Class Female
Variables Age
InputX001 Male 36
Input X003 Male 29
Input X004 Male 39
etc.

and my contrast file (Corr-VL-cor.mtx) is: 0 0.5 0.5 0 1 (I am interested
in regressing out the effect of age and gender).

These steps do not give me any error but somehow (i) I do not get pcc.mgh
(partial correlation between volume and LGI measures) file and (ii) sig.mgh
file also does not seem correct.

Could you please help me in figuring out the error or where I am doing
wrong?

Thanks.






On Fri, Apr 28, 2017 at 3:19 PM, Douglas N Greve 
wrote:

> To use the PVR, you need to create a stack of the measures that you want
> to use (eg, lGI). This will be the same size as the stack you want to
> correlate with. Eg, if you use mris_preproc to create a thickness stack,
> you would use the same command to create the lGI stack. Create your FSGD
> file as normal, but when you create your contrast file, make sure to add
> a column to handle the per-vertex regressor. Eg, if you have two groups,
> then you would create a contrast [0 0 1] to test for the effect of the
> PVR. When you run mri_glmfit, just add --pvr lgi.mgz
>
>
>
> On 04/27/2017 06:13 PM, Martin Juneja wrote:
> > Hi Dr. Greve,
> >
> > I did not find --help option very helpful here and also I could not
> > find much help from the previous FreeSurfer posts. Could you please
> > share more details here e.g. how to set up fsgd and contrast file and
> > how to run mri_glmfit command here (e.g. what inputs should be
> > provided here?).
> >
> > I am basically interested in correlating volume and gyrification
> > regressing out the effect of age and gender. I already have
> > lh.pial_lgi and lh.volume files saved in 'surf' directory of each
> subject.
> >
> > Thanks.
> >
> > On Thu, Apr 27, 2017 at 8:42 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > You have to use the --pvr option to mri_glmfit. Run it with --help to
> > get more info and write back if you still have questions
> >
> >
> > On 04/26/2017 08:33 PM, Martin Juneja wrote:
> > > Hello FreeSurfer experts,
> > >
> > > I came across a paper:
> > >
> > http://www.sciencedirect.com/science/article/pii/S0166432815001837
> > 
> > > where correlation maps between volume and gyrification are
> reported.
> > >
> > > I am familiar with GLM in FreeSurfer i.e. correlating behavioral
> > > measures with volume and gyrification but I was wondering how to
> > > correlate structure measures with each other e.g. volume and
> > gyrification.
> > >
> > > I would really appreciate any help.
> > >
> > > Thanks.
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > 
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > 
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> 

Re: [Freesurfer] Obtaining surface normal vector from plial surfaceRAS coordinate

[Bruce Fischl]

when you specify -n it write out surface normals instead of surface 
locations. Or you can use Doug's method


cheers
Bruce
On Tue, 9 May 2017, Jerry 
Jeyachandra wrote:




Hi Bruce,

Thanks for the response. I've run the operation and have examined the
output. From my understanding the file contains both a vertex list (XYZ) and
a face list containing (V1,V2,V3...). Is the XYZ of the vertex list the
actual surfaceRAS coordinates of the surface as viewed on FreeViewer? If so
I can compute face normals simply by matching up the 3 vertices
encapsulating the given surface coordinate and computing the face normal
vector, correct?

Thanks again

Jerry


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

Sent: May 8, 2017 4:40:17 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Obtaining surface normal vector from plial
surfaceRAS coordinate  
Hi Jerry

mris_convert -n lh.pial lh.pial.normals.asc

should create a list of surface normals in ascii format

cheers
Bruce
On Mon, 8 May 2017,
Jerry
Jeyachandra wrote:

>
> Hi list,
>
> I’d like to extract the surface normal at a location specified in
surfaceRAS
> coordinates after performing segmentation. I know there are methods to
> extract all vertices and faces then compute face normals from there, but
I’m
> not familiar with methods to relate these to specified coordinates.
>
> Thanks
>
> Jerry Jeyachandra
>
>
>

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Re: [Freesurfer] recon-all freezes while CORRECTING DEFECT 60

[Bruce Fischl]

Hi Daniel

you can load the ?h.defect_labels as an overlay on either the 
inflated.nofix or orig.nofix surface and use it to find the location of 
that defect. Usually this means something big is wrong - it should be 
obvious looking at the inflated.nofix I would think. If you can't find it, 
upload the subject to our ftp site and I'll take a look

Bruce



On Tue, 9 May 2017, Weisholtz, Daniel S.,M.D. wrote:


Hello Freesurfer Developers,
I am trying to run recon-all -all and the procedure is freezing while trying
to correct what appears to be a large defect (vertices=36706). The source T1
image is not great quality due to rippling artifact, but I have inspected
brainmask.mgz, wm.mgz, and aseg.mgz and I cannot identify a large defect.
The dura was not completely removed, and I tried improving this by using
various watershed thresholds as well as using gcut. I also tried manually
removing the remaining dura, but none of this was helpful.  I also tried
using -T2FLAIR, but this did not seem helpful either. 

I am attaching the recon-all.log. This does not include the edits I made to
brainmask.mgz. That was done on a separate attempt. This does include the
-T2FLAIR, as you can see in the recon-all.log file.

1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
2) Platform: OS X Yosemite 10.10.5
3) recon-all.log attached


I very much appreciate any assistance you can provide. Happy to send any of
the data if it would be helpful.

Sincerely,
Dan Weisholtz

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[Freesurfer] Volume comparison between groups and QDEC

[John Anderson]

Dear Dr Doug,
I have two groups of subjects (80 patients and 40 controls). I analyzed the 
data using Freesurfer v6.0.
I want to study the difference between the groups in "precentral gyrus volume". 
After "recon-all" I built Qdec table and I used Qdec to compute the comparison 
by including eTIV a covariate. After correcting the results using Monte Carlo 
simulation or adjusting for FDR I found no difference between the groups in 
volume neither in surface area.

I adjusted the precentral gyrus volume values for eTIV using the commands:

mri_label_volume -eTIV $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm 1948 
$SUBJECTS_DIR/${i}/mri/wmparc.mgz 2017
mri_label_volume -eTIV $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm 1948 
$SUBJECTS_DIR/${i}/mri/wmparc.mgz 2024

I extracted the adjusted volume values to SPSS then I ran box plots comparison 
between the groups and I found difference at (P<0.0001)
Why Qdec doesn't show the difference between the groups although the p value is 
very small. What I am doing wrong in Qdec? Is it wrong to include eTIV a 
covariate?

Thank you for any advice
John___
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Re: [Freesurfer] TRACULA tract reconstruction

[Yendiki, Anastasia]

Hi Joelle - From your trac-all.log file it looks like you're not running the 
official 6.0 release but a beta version:

build-stamp.txt: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae

This does not include the TRACULA updates that were included in the final 6.0 
version. Please download 6.0.

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joëlle Ismay Rosanne Van 
Der Molen [joelle.vandermo...@etu.unige.ch]
Sent: Wednesday, May 03, 2017 7:39 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA tract reconstruction


Hi Anastasia,


I added a screenshot of what I get when I run that command.


Thanks again!


Joëlle



De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Yendiki, Anastasia 

Envoyé : samedi 29 avril 2017 02:15
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstruction

Hi Joelle - The last command in the trac-all.log file (mri_probedicom) works 
fine for me, when I run it on your dicoms. So there must be something else 
after that command that causes the error. What do you see when you run "ls 
/Users/joelle/Documents/Tracula_new/tmp/5047_3_3T.long.5047_3T_base/dmri"?

Thanks!

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joëlle Ismay Rosanne Van 
Der Molen [joelle.vandermo...@etu.unige.ch]
Sent: Tuesday, April 25, 2017 4:54 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA tract reconstruction


Of course, here it is. Thank you for taking a look at it!


Best,

Joëlle


De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Yendiki, Anastasia 

Envoyé : mardi 25 avril 2017 10:25
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstruction

Hi Joëlle - I can't come up with a config file without knowing the locations of 
your files. If you send me the trac-all.log, I can figure out at what step it 
fails.

Best,
a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joëlle Ismay Rosanne Van 
Der Molen [joelle.vandermo...@etu.unige.ch]
Sent: Tuesday, April 25, 2017 4:15 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA tract reconstruction


Hi Anastasia,


I still can't seem to make it run when I don't specify the gradient tables, so 
I think I'm probably doing something wrong in the configuration of the dmrirc 
file... Would you mind sending me the dmrirc file you would use to run this 
subject?


Best,


Joëlle




De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Yendiki, Anastasia 

Envoyé : mercredi 12 avril 2017 19:35
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstruction

Hi Joelle – I tested one of your dicoms and the gradient table that mri_convert 
reads from it works just fine. So you can just pass your dicoms to TRACULA and 
it’ll do the rest. No need for you to specify the gradient tables.

Best,
a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Joëlle Ismay Rosanne Van Der Molen 
mailto:joelle.vandermo...@etu.unige.ch>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, March 31, 2017 at 7:44 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA tract reconstruction


​Hi Anastasia,


I sent the links for the dicom files to you and just want to make sure - did 
you receive them?


Best,


Joëlle


De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 de la part de Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>>
Envoyé : jeudi 30 mars 2017 15:20
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstruction

Hi Joëlle - Can you please send the filedrop upload to me too? Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Joëlle Ismay Rosanne Van Der Molen 
[joelle.vandermo...@etu.unige.ch]
Sent: Thursday, March 30, 2017 7:27 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA tract reconstruction


​Hi Barbara,


Thank you for the tip, I managed to anonymize my dicom images. I uploaded them 
on filedrop. ​

The scanner used for the acquisition is a Siemens Prisma 3 Tesla.


Best,

Joëlle


De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 de la part de Barbara Krei

Re: [Freesurfer] TRACULA tracts corrections

[Yendiki, Anastasia]

Hi Joelle - See my previous email, you should download the 6.0 version. In this 
version TRACULA will attempt to detect which tracts require reinitialization, 
so hopefully you'll see an improvement in this.

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joëlle Ismay Rosanne Van 
Der Molen [joelle.vandermo...@etu.unige.ch]
Sent: Thursday, May 04, 2017 8:20 AM
To: Freesurfer support list
Subject: [Freesurfer] TRACULA tracts corrections


Hi Anastasia & Freesurfer experts,


I've been going through the different processing steps of the longitudinal 
TRACULA stream and as some tracts needed to be rerun, I set up my dmrirc file 
as recommended (subjlist limited to the subject to correct; pathlist limited to 
the path(s) to rerun; npcts corresponding to the tract to rerun; set reinit = 
1) and then ran this file with the -prior flag, followed by the -path flag.


However, surprisingly, it looks as if all the tracts are being reconstructed 
again, not only the one that is specified under pathlist... At least, that is 
the impression I get when looking at the new merged_avg33_mni_bbr.mgz file, and 
at the trac-all.log file.


This brings me to my 2 questions:

1) Is there a way to check that TRACULA reinitializes and reconstructs only the 
desired tracts?

2) If indeed all tracts were reinitialized and rerun, how can I fix that? I 
suspect I'm then doing something wrong in the configuration of the dmrirc file, 
but I cannot seem to find out what.


I added the dmrirc file and the trac-all.log file; I would greatly appreciate 
it if you could help me out.


Additional info: freesurfer version is 6.0, operating system is OS X Yosemite 
10.10.5. Let me know if you need any other information or files.


Best,


Joëlle

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Re: [Freesurfer] TRACULA exports white matter tract labels without DTI data

[Yendiki, Anastasia]

Hi Yong - If you do not have diffusion data, you won't be able to map your 
subjects' white matter tracts. In a T1 scan there is no contrast between white 
matter tracts that would allow you to segment them, as white matter looks 
uniform. All you could do is transform some generic labels from an atlas to 
your subjects.

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yong Li 
[yongl...@gmail.com]
Sent: Friday, May 05, 2017 5:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA exports white matter tract labels without DTI data

Dear Anastasia,
Dear Bruce,

As a newbie in using freesurfer, I would like to ask for help to output white 
matter tract labels of each subject without DTI data. This topic was briefly 
discussed last April by Holleran, Laurena 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg46459.html), 
but I don't find how to do it. To be specific, I would like using TRACULA 'to 
mapping the tracts from the atlas onto the individual subject' as suggested by 
Bruce in his reply to Laurena.

Other questions are:
How to view the extracted white matter tract labels in the individual space? 
freeview or trackvis or other viewers?

Could TRACULA deal with DTI data in Nifti format? If not, is there a way to 
reliably convert DTI data from Nifti to DICOM (*.dcm)?

Hope I make myself clear. Thank you very much in advance!

Best regards,

Yong
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Re: [Freesurfer] Color LUT help

[Yendiki, Anastasia]

Hi Stephanie - The arcuate fasciculus is reconstructed when you run TRACULA on 
your diffusion data, but it is not an ROI. Please refer to the tutorial for how 
to run TRACULA and how to visualize the tracts:

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

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Stephanie Otto 
[so...@nevada.unr.edu]
Sent: Sunday, May 07, 2017 11:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Color LUT help

Hello,

I am running some DTI analyses and can't seem to find the Color LUT number for 
the arcuate fasciculus.  Is there a number assigned for this ROI or another way 
to identify it?

Thank you,

--
Stephanie Otto
Graduate Student, Cognitive and Brain Sciences Program
Department of Psychology, MSS 414
University of Nevada, Reno
so...@nevada.unr.edu
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